Molecular Diagnostics Lab

Acrodysostosis 1, with or without hormone resistance

Gene: PRKAR1A
Protein: protein kinase, cyclic adenosine monophosphate (cAMP)-dependent, regulatory type I, alpha

Clinical Characteristics

• short stature
• severe brachydactyly with short metatarsals, metacarpals and phalanges
• cone-shaped epiphyses
• nasal and maxillary hypoplasia
• decreased vertebral interpedicular distance
• advanced bone age
• resistance to one or more hormones – can include parathyroid hormone, thyroid-stimulating hormone, growth hormone-releasing hormone, gonadotropins
• normal development or mild developmental disability; unknown if developmental disability can be moderate or severe
• clinical overlap with Albright's hereditary osteodystrophy (pseudohypoparathyroidism)

Inheritance Pattern: Autosomal dominant

What Can Be Learned From This Test

Testing is performed by sequencing the entire coding region of the PRKAR1A gene. This will detect point mutations, small deletions and small insertions. It will not detect a partial or whole gene deletion or duplication.

Sample Requirements

Draw one or two 4cc tubes of blood in EDTA/ purple top tube (minimum of 1-2 cc for infants)

Turnaround time: 10-14 business days

CPT Codes and Cost

Additional Information

• OMIM entries

MCT8 - Specific Thyroid Hormone Cell Transporter Deficiency

Gene: SLC16A2 (commonly called MCT8)
Protein: Monocarboxylate transporter 8

Clinical Characteristics

• severe intellectual disability
• hypotonia
• high T3 and low reverse T3 without clinical signs of hypothyroidism
• low muscle mass
• generalized muscle weakness
• progressive spastic quadriplegia
• dystonic or athetoid movements
• paroxysmal kinesigenic dyskinesias
• joint contractures
• dysarthric or absent speech
• delayed myelination
• seizures in approximately 25 percent of cases

Inheritance Pattern: X-linked

What Can Be Learned From This Test

Testing is performed by sequencing the entire coding region of the MCT8 gene. This will detect point mutations, small deletions and small insertions. It will not detect a partial or whole gene deletion or duplication.

MCT8 is the only gene known to be associated with Allan-Herndon-Dudley syndrome. Differential diagnoses include Pelizaeus-Merzbacher disease and MECP2 duplication syndrome, both of which are available for clinical testing in our lab. This test will only detect mutations in MCT8.

Sample Requirements

Draw one or two 4cc tubes of blood in EDTA/purple top tube (minimum of 1-2cc for infants)

Turnaround time: 10-14 business days

CPT Codes and Cost

Additional Information

• GeneReview
• OMIM entries

Gene: APOL1
Protein: Apolipoprotein L-1

Clinical Characteristics

APOL1 variants are associated with increased susceptibility to focal segmental glomerulosclerosis (FSGS4; OMIM 612551) when two risk alleles are present.

Focal segmental glomerulosclerosis is clinically associated with:

• proteinuria
• nephrotic syndrome
• progressive loss of renal function leading to end-stage renal disease

Individuals of African descent are at a greater risk to develop chronic kidney disease than individuals of European descent. Studies have shown that specific variants in APOL1 confer nearly all of this increased risk. These variants, classified as G1 and G2 are prevalent in African Americans, and have not been identified in European Americans.

APOL1 variants are also associated with increased risk of hypertension-attributed end stage renal disease, sickle cell-associated kidney disease, and shortened graft survival of kidney transplants based on the donor genotype.

Inheritance Pattern: Autosomal recessive

What Can Be Learned From This Test

Identification of two risk alleles in one individual is associated with an increased susceptibility to focal segmental glomerulosclerosis and other types of kidney disease.

Some studies indicate that donor kidneys harboring two APOL1 risk variants failed more rapidly after transplantation than those kidneys with zero or one risk variant).

Testing is performed by bi-directional sequencing of exon 6 of APOL1 (NM_145343.2). This test will determine the presence or absence of the G1 and G2 alleles.

Sample Requirements

Draw one 4cc tube of blood in EDTA/purple top tube (minimum of 1-2cc for infants).

Turnaround time: 10-14 business days

CPT Codes and Cost

Additional Information

• OMIM
  

Gene: LMNB1
Protein: lamin-B1

Clinical Characteristics

• slowly progressive neurologic disorder
• onset in fourth or fifth decade of life
• symmetric demyelination of the central nervous system
• phenotype similar to chronic progressive multiple sclerosis
• lack of astrogliosis and preservation of oligodendria (in contrast to multiple sclerosis)
• autonomic dysfunction
  (typically precedes neurological symptoms)
  • orthostatic hypotension
  • abnormal bowel and bladder regulation
  • impotence in males
  • decreased sweating
• loss of fine motor skills
• progressive spasticity
• nystagmus
• ataxia

Inheritance pattern: Autosomal dominant

What Can Be Learned From This Test

Adult onset autosomal dominant leukodystrophy (ADLD) is caused by a duplication of the LMNB1 gene. One family has been reported in which a large deletion upstream of the LMNB1 gene resulted in ADLD due to overexpression of the lamin-B1 protein. Testing is offered in tiers and can be performed either sequentially or simultaneously. Testing is performed by quantitative multiplex PCR to look for a duplication of LMNB1 or the upstream deletion. Fluorescent primers are used to amplify select exons of the LMNB1 gene or the relevant upstream region, along with several reference genes. The quantity of each PCR product is determined by measuring the intensity of the fluorescence. Copy number is calculated based on the normalized ratio of the targeted regions to each of the reference genes for the patient and controls.

These tests will detect duplications of LMNB1 or the upstream deletion. They will not detect point mutations or smaller deletions or insertions. LMNB1 is the only gene known to be associated with adult onset autosomal dominant leukodystrophy (ADLD). To date (July 2016), no sequence variants  of the LMNB1 gene have been identified in association with ADLD.

A negative test does not rule out a genetic cause of a neurologic disorder. There are many other genes associated with different types of neurologic disorders and leukodystrophies. Testing for some of the genes associated with leukodystrophies of childhood onset is available in our lab and can be performed if clinically indicated.

Sample Requirements

Draw one or two 4-cc tubes of blood in EDTA/purple-top tube (minimum of 1-2 cc for infants).

Turn-around time: 10-14 business days

CPT Codes and Cost

Tier 1: Gene Duplication

• Code: 81479
• Cost: $350

Tier 2: Upstream Deletion Testing

• Code: 81479
• Cost: $450

Known Variant Testing

• Code: 81479
• Cost: $350

Additional Information

• United Leukodystrophy Foundation
• OMIM entries
• GeneReviews

Gene: ACTL6A; ARID1A; ARID1B; ARID2; DPF2; PHF6; SMARCA2; SMARCA4; SMARCB1; SMARCE1; SOX11

Clinical Characteristics

The BAF complex related disorders are caused by gene variants in one of the various subunits of the BAF complex, a chromatin-remodeling complex BRG1-Associated Factor. These overlapping phenotypic disorders have been associated with de novo variants causing syndromic intellectual disability such as Coffin-Siris syndrome (CSS), and Nicolaides-Baraitser syndrome (NCBRS).

Inheritance pattern: autosomal dominant, X-linked

What Can Be Learned From This Test

Testing is performed by next generation sequencing of 11 genes associated with these disorders, followed by analysis software alignment to the reference sequences.

A negative test result does not rule out a diagnosis of a BAF-related disorder. Other genes are known to be associated with some of these conditions, and this test will only detect gene variants in the genes listed above. Copy number changes will not be detected through this assay.

Sample Requirements

• Infants/Children: one purple top (EDTA) tube > 2ml
• Adults: one purple top (EDTA) tube > 3ml
• DNA previously isolated may be accepted; requires minimum of 5 micrograms DNA in TE buffer. DNA from FFPE (formalin fixed paraffin embedded) samples will not be accepted.
• Complete the NGS Sample Submission form

Turnaround time: 12-16 weeks

CPT Codes and Cost

Additional Information

• Gene List (PDF)

Gene: TAZ (also known as G4.5)
Protein: tafazzin

Clinical Characteristics

• affects males
• cardiomyopathy
• neutropenia
• growth delay
• 3-Methylglutaconic aciduria
• muscle weakness and fatigue
• cardiolipin deficiency

Inheritance pattern: X-linked

What Can Be Learned From This Test

Testing is performed by sequencing of the entire coding region of the TAZ gene. This will detect point mutations, small deletions and small insertions. For females, the assay will not detect a partial or whole gene deletion. For males, a partial or whole gene deletion may appear as failure to amplify a region of the gene.

TAZ is the only gene known to be associated with Barth syndrome. Mutations will be detected by this assay in greater than 99 percent of individuals who fit the clinical description of Barth syndrome.

Sample Requirements

Draw one or two 4-cc tubes of blood in EDTA/purple-top tube (minimum of 1-2 cc for infants).

Turnaround time: 10 -14 business days

CPT Codes and Cost

Additional Information

• About Barth syndrome from the Barth Syndrome Foundation
• OMIM entries

Choreoathetosis, congenital hypothyroidism and neonatal respiratory distress

Gene: NKX2-1
Protein: homeobox protein Nkx-2.1

Clinical Characteristics

Benign hereditary chorea

• childhood onset chorea, usually before age 5 years
• delayed motor development
• dysarthria and gait abnormalities may occur
• no dementia (in contrast to Huntington’s disease)
• little or no progression beyond second decade of life

Choreoathetosis, congenital hypothyroidism, and neonatal respiratory distress

• also known as brain-lung-thyroid syndrome
• onset at birth
• involuntary movements
• neonatal respiratory distress and risk for recurrent respiratory infections
• congenital hypothyroidism
• global developmental delay
• hypotonia, ataxia and dysarthria may occur

Both show variable expressivity between, and within, families

Inheritance pattern: Autosomal dominant

What Can Be Learned From This Test

Testing is performed by sequencing the entire coding region of NKX2-1. This will detect point mutations, small deletions and small insertions. If mutations are detected via sequencing, copy number analysis will be performed to detect a whole or partial gene deletion, since deletions of the entire NKX2-1 gene have been reported in affected individuals.

NKX2-1 is the only gene known to be associated with these specific disorders. However, a negative test result does not rule out a genetic cause of early onset chorea or congenital hypothyroidism. There are other genes associated with other types of movement disorders, as well as other hypothyroid disorders.

Sample Requirements

Draw one or two 4-cc tubes of blood in EDTA/purple-top tube (minimum of 1-2 cc for infants).

Turnaround time: 10-14 business days

CPT Codes and Cost

Additional Information

• OMIM entries

CASR-related disorders of calcium homeostasis

Gene: CASR
Protein: calcium-sensing receptor

Clinical Characteristics

Familial Hypocalciuric Hypercalcemia Type I (FHH)

• Caused by inactivating mutations:
  • heterozygous mutation
  • mutation causes mild to moderate impairment of CASR function
• Mild to moderate hypercalcemia with relative hypocalciuria
• Normal serum parathyroid (PTH) levels
• May have hypermagnesemia and urine calcium/creatinine clearance ratio below 0.01
• Typically asymptomatic
• Individuals with moderate disease may have:
  • chondrocalcinosis
  • gallstones
  • kidney stones
  • pancreatitis
  • fatigue and weakness
  • polydipsia/polyuria

Neonatal Severe Hyperparathyroidism (NSHPT)

• Caused by inactivating mutations:
  • compound heterozygous or homozygous mutations
  • heterozygous mutations with a dominant negative effect (rare)
• Presents within first 6 months of life
• Severe symptomatic hypercalcemia with relative hypocalciuria
• Multi-glandular parathyroid hyperplasia
• Bone demineralization resulting in rib cage deformities, rachitic changes, and multiple fractures
• Failure to thrive, hypotonia, lethargy
• Severe neurodevelopmental defects if left untreated 

Autosomal Dominant Hypocalcemia (ADH)/ Familial Isolated Hypoparathyroidism (FIH)

• Caused by activating mutations (gain of function)
• Wide clinical spectrum
• May present with neonatal or childhood seizures secondary to fever and infection
• Hypocalcemia and hypercalciuria
• Normal to mildly elevated phosphate levels
• Low to normal parathyroid levels
• Increased risk for renal complications such as nephrocalcinosis, kidney stones, or impaired renal function

Bartter Syndrome, Type V

• Caused by more severe activating mutations (gain of function)
• Hypocalcemia and hypercalciuria
• Renal salt wasting
• Hypokalemic metabolic alkalosis
• Elevated renin and aldosterone levels with low blood pressure

Inheritance Pattern

• Autosomal dominant for FHH, ADH, FIH, Bartter syndrome Type V
• Autosomal recessive for NSHPT
• Rarely autosomal dominant for NSHPT

What Can Be Learned From This Test

Testing is performed by sequencing the entire coding region of the CASR gene. This will detect point mutations, small deletions and small insertions. It will not detect a partial or whole gene deletion or duplication.

A negative test result does not rule out a diagnosis of a calcium homeostasis disorder. Other genes are known to be associated with some of these conditions, and this test will only detect mutations in CASR.

Sample Requirements

Draw one or two 4cc tubes of blood in EDTA/purple top tube (minimum of 1-2 cc for infants)

Turnaround time: 10 -14 business days

CPT Codes and Cost

Additional Information

• OMIM entries

Clinical characteristics

• Polyhydramnios in prenatal period

• Cardiac abnormalities

  • pulmonic stenosis and other valve dysplasias
  • septal defects
  • hypertrophic cardiomyopathy
  • rhythm disturbances

• Distinctive craniofacial appearance

  • high forehead, bitemporal narrowing, hypoplastic supraorbital ridges
  • wide-set and down-slanting eyes, epicanthal folds, ptosis
  • short nose with depressed bridge and upturned nares
  • low-set posteriorly rotated ears with earlobe creases
  • deep philtrum, cupid's bow lip, high-arched palate, micrognathia

• Cutaneous abnormalities

  • Skin: dry skin, keratosis pilaris, palmoplantar hyperkeratosis, multiple palmar creases.
  • Hair: sparse curly hair, absent eyelashes and eyebrows.
  • Nails: dystrophic and/or fast growing.

• Neurologic Involvement

  • cognitive delay ranging from mild to severe
  • hypotonia and developmental delay
  • may include seizures, abnormal EEG or structural brain abnormalities

• Growth Delay

  • postnatal short stature
  • failure to thrive with contributory gastrointestinal and feeding issues
  • head circumference remains within normal range resulting in relative macrocephaly

Inheritance pattern: Autosomal dominant; all reported cases have been sporadic

What Can Be Learned From This Test

Testing can be performed in tiers, moving to the next tier only if the preceding test is negative. Testing can also be performed concurrently, or in any order requested. The following strategy is suggested for cardiofaciocutaneous (CFC) syndrome testing.

• Tier 1: Sequencing of exons 6 and 11 through 16 of BRAF
• Tier 2: Sequencing of exons 2, 3, 6 and 7 of MEK1 and MEK2
• Tier 3: Sequencing of the entire coding region of KRAS

Testing will detect point mutations, small deletions and small insertions in the regions of the genes that are analyzed. It will not detect a partial or whole gene deletion or duplication.

For CFC syndrome, mutations are detected in:

• Exons 6 or 11 through 16 of BRAF in 75 percent to 80 percent of affected individuals
• Exons 2 or 3 of MEK1 or MEK2 in 10 percent to 15 percent of affected individuals
• KRAS in less than 5 percent of affected individuals

A negative test does not completely rule out a diagnosis of CFC syndrome, since it is unclear at this time if all the genes associated with CFC syndrome have been identified. Clinical overlap is seen between CFC syndrome, Noonan syndrome and Costello syndrome. Tests for Noonan syndrome and Costello syndrome are also available in our lab and can be requested if clinically indicated.

Sample Requirements

Draw one or two 4-cc tubes of blood in EDTA/purple-top tube (minimum of 1-2 cc for infants).

Turnaround time: 10-14 business days for each gene; about 3-4 weeks for all 3 tiers

CPT Codes and Cost

Additional Information

• GeneReview
• OMIM entries

Gene: PAX8
Protein: paired box protein Pax-8

Clinical characteristics

• Thyroid dysgenesis — agenesis, hypoplasia or ectopia
• Mild to severe hypothyroidism:
  • elevated TSH
  • low to normal total and free T4
• Variable expressivity

Inheritance Pattern: Autosomal dominant with reduced penetrance

What Can Be Learned From This Test

Testing is performed by sequencing the entire coding region and the promoter of the PAX8 gene. This will detect point mutations, small deletions and small insertions. It will not detect a partial or whole gene deletion or duplication.

A negative test result does not rule out a genetic cause of congenital hypothyroidism. Other genes are known to be associated with this condition, and this test will only detect mutations in PAX8.

Sample Requirements

Draw one or two 4cc tubes of blood in EDTA/purple top tube (minimum of 1-2 cc for infants)

Turnaround time: 10-14 business days

CPT Codes and Cost

Additional Information

• OMIM entries

Gene: HRAS
Protein: GTPase HRas

Clinical characteristics

• feeding difficulty
• postnatal short stature
• characteristic facial features:
  • full lips and/or large mouth
  • coarse features
  • full cheeks
• loose skin and deep palmar or plantar skin creases
• curly or sparse, fine hair
• deep, hoarse, or whispery voice
• papillomas of face and perianal region - typically absent in infancy but may appear in childhood
• characteristic hand posture — splayed fingers and ulnar deviation of wrists
• congenital heart problems — most commonly pulmonic stenosis, hypertrophic cardiomyopathy, and atrial tachycardia
• increased occurrence of benign and malignant solid tumors
• developmental delay or mental retardation
• social, outgoing personality

Inheritance pattern: Autosomal dominant

What Can Be Learned From This Test

Testing is performed by sequencing exons 2 and 3 and the surrounding intronic regions of the HRAS gene. Sequencing of all coding exons can also be performed upon request. This assay will detect point mutations, small deletions and small insertions. It will not detect a partial or whole gene deletion or duplication.

HRAS is the only gene known to be associated with Costello syndrome. Sequence analysis of exon 2 detects a mutation in 80 percent to 90 percent of individuals with Costello syndrome. Mutations in other exons have also been reported. A negative test result does not rule out somatic mosaicism of an HRAS mutation, which has been described in individuals with Costello syndrome.

Costello syndrome is one of a group of related disorders caused by abnormal functioning of the Ras-mitogen-activated protein kinase (RAS/MapK) pathway. A negative HRAS test does not rule out all of these disorders, and additional testing may be indicated.

Sample Requirements

Draw one or two 4-cc tubes of blood in EDTA/purple-top tube (minimum of 1-2 cc for infants).

Turnaround time: 10-14 business days

CPT Codes and Cost

Additional Information

• Gene Review
• OMIM entries
• The International Costello syndrome support group

Gene: SLITRK6
Protein: SLIT and NTRK-like family, member 6

Clinical Characteristics

• Sensorineural hearing loss
  • bilateral
  • moderate to profound
  • congenital or prelingual
  • can present as auditory neuropathy spectrum disorder with progressive hearing loss
• High myopia
  • diagnosed in infancy or early childhood
  • greater than -6 diopters

Inheritance pattern: Autosomal recessive

What this test can tell us:

Testing is performed by sequencing all exons and the surrounding intronic regions of the SLITRK6 gene. This will detect point mutations, small deletions, and small insertions. It will not detect a partial or whole gene deletion or duplication. To date, no large deletions or duplications have been reported.

A negative test result does not rule out a genetic cause of hearing loss. Other genes are known to be associated with hearing loss and this test will only detect mutations in SLITRK6, associated with deafness and myopia syndrome.

Sample Requirements

Draw one or two 4cc tubes of blood in EDTA/ purple top tube (minimum of 1-2 cc for infants).

Turnaround time: 10-14 business days

CPT Code and Cost

Full Gene Sequencing:

• Code: 81479
• Cost: $600

Known Variant Testing:

• Code: 81479
• Cost: $225

Additional Information

• GeneReview
• OMIM entries

Gene: DFNB59 /PJVK
Protein: pejvakin

Clinical Characteristics

• sensorineural hearing loss with or without auditory neuropathy spectrum disorder
  • bilateral
  • congenital or prelingual
  • can be stable or progressive

Inheritance pattern: Autosomal recessive

What this test can tell us:

Testing is performed by sequencing all exons and the surrounding intronic regions of the DFNB59 gene. This will detect point mutations, small deletions, and small insertions. It will not detect a partial or whole gene deletion or duplication. To date, no large deletions or duplications have been reported.

A negative test result does not rule out a genetic cause of hearing loss. Other genes are known to be associated with hearing loss and this test will only detect mutations in the DFNB59 gene. 

Sample Requirements

Draw one or two 4cc tubes of blood in EDTA/ purple top tube (minimum of 1-2 cc for infants).

Turnaround time: 10-14 business days

CPT Code and Cost

Full Gene Sequencing:

• Code: 81405
• Cost: $600

Known Variant Testing:

• Code: 81479
• Cost: $225

Additional Information

• OMIM entries

Gene: DMD
Protein: dystrophin

Clinical Characteristics

Duchenne Muscular Dystrophy (DMD)

• affects males
• progressive symmetrical muscular weakness, proximal greater than distal
• calf pseudohypertrophy
• onset before age five years
• wheelchair dependency before age 13 years
• serum creatine phosphokinase (CK) concentration greater than 10 times normal

Becker Muscular Dystrophy (BMD)

• affects males
• later onset of symptoms
• wheelchair dependency after age 16 years; some remain ambulatory
• serum CK concentration greater than 5 times normal

DMD-Associated Dilated Cardiomyopathy

• affects males and females
• dilated cardiomyopathy (DCM) with congestive heart failure
  • males with onset between ages 20 and 40 years with rapid progression
  • females with onset later in life with slower progression
• usually no clinical evidence of skeletal muscle disease

Inheritance pattern: X-linked; carrier females may be affected with dilated cardiomyopathy

What Can Be Learned From This Test

Testing is performed by multiplex PCR of select exons of the DMD gene. Of the 79 exons in the DMD gene, 47 are amplified. These 47 exons are located throughout the gene and concentrated in regions that are known to be frequently deleted. Deletions that include one or more of these exons will be detected by this assay. Deletions account for 65 percent of the mutations in DMD and 85 percent of the mutations in BMD. This test will not detect large duplications, small deletions or insertions, point mutations or splicing mutations. Our lab does not perform sequencing of the DMD gene.

A negative test result does not rule out a diagnosis of Duchenne or Becker muscular dystrophy, since 15 percent to 35 percent of mutations are nondeletion mutations. There are no other genes known to be associated with Duchenne and Becker muscular dystrophies.

A negative test does not rule out a genetic cause of muscular dystrophy. There are many other genes associated with different types of muscular dystrophy.

Our lab does not perform carrier testing in females for mutations in the DMD gene.

Sample Requirements

Draw one or two 4-cc tubes of blood in EDTA/purple-top tube (minimum of 1-2 cc for infants).

Turnaround time: 10-14 business days

CPT Code and Cost

Select Exon Deletion Testing

• Code: 81161
• Cost: $525

Additional Information

• GeneReview
• OMIM entries

Gene: EMD
Protein: emerin

Clinical Characteristics

• joint contractures beginning in early childhood — especially of elbows, ankles and neck
• slowly progressive muscle weakness, beginning in upper arms and lower legs and progressing to shoulders and hips.
• cardiac disease with conduction defects and arrhythmias
• female carriers are at risk for cardiac disease

Inheritance pattern: X-linked; carrier females may be affected with cardiac disease.

What Can Be Learned From This Test

Testing is performed by sequencing the entire coding region of EMD. This will detect point mutations, small deletions and small insertions. For females, the assay will not detect a partial or whole gene deletion. For males, a partial or whole gene deletion may appear as failure to amplify a region of the gene.

This assay will detect mutations in EMD in greater than 99 percent of individuals with a clear pattern of X-linked inheritance and/or with no emerin detected by immunodetection methods.

A negative test result does not rule out a diagnosis of Emery-Dreifuss muscular dystrophy (EDMD). X-linked EDMD can be caused by mutations in either EMD or FHL1. Autosomal dominant and autosomal recessive forms of EDMD can be caused by mutations in LMNA.

A negative test does not rule out a genetic cause of muscular dystrophy. There are many other genes associated with different types of muscular dystrophy, some of which have features in common with EDMD.

Sample Requirements

Draw one or two 4-cc tubes of blood in EDTA/purple-top tube (minimum of 1-2 cc for infants).

Turnaround time: 10-14 business days

CPT Codes and Cost

Gene: CHRNG
Protein: Acetylcholine receptor subunit gamma

Clinical Characteristics

• decreased fetal movement
• joint contractures
• multiple pterygium (webbing) of neck, elbows, knees, axillae
• respiratory distress
• cleft palate
• cryptorchidism
• scoliosis
• short stature
• Characteristic facial features
  • ptosis, epicanthal folds, and downslanting palpebral fissures
  • low-set ears
  • micrognathia with downturning corners of mouth
  • long philtrum
  • decreased facial expression
• Lethal multiple pterygium syndrome is a more severe presentation
  • pterygia can also be present at ankles, inner thighs and chin to sternum
  • most are stillborn or die in the neonatal period due to pulmonary hypoplasia
  • intrauterine growth retardation
  • cystic hygroma and hydrops
  • cardiac hypoplasia
  • generalized amyoplasia

Inheritance pattern: Autosomal recessive

What Can Be Learned From This Test

Testing is performed by sequencing the entire coding region and the surrounding intronic regions of the CHRNG gene. This will detect point mutations, small deletions and small insertions. It will not detect a partial or whole gene deletion or duplication.

CHRNG is the only gene known to be associated with Escobar syndrome. Lethal multiple pterygium syndrome has been associated with CHRNG mutations, as well as mutations in the related genes, CHRNA1 and CHRND.

Sample Requirements

Draw one or two 4-cc tubes of blood in EDTA/purple-top tube (minimum of 1-2 cc for infants).

Turnaround time: 10-14 business days

CPT Codes and Cost

Additional Information

• OMIM entries

Clinical Characteristics

• hypercholesterolemia, usually present from birth
  • heterozygous
    • total cholesterol of 250-450 mg/dl
    • LDL-cholesterol of 200-400 mg/dl
  • homozygous
    • total cholesterol greater than 500 mg/dl
    • LDL-cholesterol greater than 450 mg/dl
• corneal arcus
• xanthomas – around eyelids, on tendons and between fingers
• increased risk of coronary heart disease (CHD) at an early age
  • heterozygous – CHD in 40’s or 50’s if untreated
  • homozygous – severe CHD often fatal before age 20 if untreated

Inheritance pattern: Autosomal co-dominant

What Can Be Learned From This Test

Testing is performed by a tiered approach.  Tier 1 includes sequencing exons 1-4, 9-11, and 17 of LDLR, exon 7 of PCSK9, and the portion of exon 26 in APOB containing common pathogenic variants.  Tier 2 includes sequencing the remaining exons of LDLR and PCSK9, an additional fragment of exon 26 of APOB containing other published pathogenic variants, and deletion/ duplication testing of select exons of LDLR and PCSK9. The sequencing tests will detect point mutations, small deletions, and small insertions. The deletion/ duplication tests may not detect a partial copy number variant, but will detect a whole gene deletion or duplication.  Large deletions and duplications in LDLR have been reported.

Sample Requirements

Draw one or two 4cc tubes of blood in EDTA/purple top tube (minimum of 1-2cc for infants).

Turnaround time: 10-14 business days per tier

Tier 1 CPT Codes: 81401, 81406, 81479 Cost: $370
Tier 2 CPT Codes 81401, 81405, 81406, 81479 x3 Cost: $1,050
Both Tiers CPT Codes: 81401, 81405, 81406 x2, 81479 Cost: $1,420

Known Variant Testing:
LDLR, PCSK9 or APOB CPT Code: 81479 Cost: $225

Additional Resources

• GeneReview
• OMIM
  

Gene: GCM2 – glial cells missing 2
Protein: Chorion-specific transcription factor GCMb

Clinical Characteristics

• hypocalcemia
• hyperphosphatemia
• hypoparathyroidism
• absence of syndromic features

Symptoms of acute hypocalcemia:

• seizures or muscle spasms
• tingling of lips, tongue, fingers, and toes

Symptoms of chronic hypocalcemia:

• may be asymptomatic
• muscle spasms or muscle stiffness
• calcium and iron deposits found on CT scan of the brain
• abnormal involuntary movements or decrease of voluntary movements
• cataracts
• coarse brittle hair or hair loss
• abnormalities of the teeth
• mental retardation
• personality disorders

Inheritance pattern:

• autosomal recessive
• autosomal dominant (reported in 2 families)

What Can Be Learned From This Test

Testing is performed by sequencing the entire coding region of the GCM2 gene. This will detect point mutations, small deletions and small insertions. It will not detect a partial or whole gene deletion or duplication.

A negative test result does not rule out a diagnosis of familial isolated hypoparathyroidism (FIH). Other genes are known to be associated with FIH and this test will only detect mutations in GCM2.

Sample Requirements

Draw one or two 4cc tubes of blood in EDTA/ purple top tube (minimum of 1-2 cc for infants).

Turnaround time: 10-14 business days

CPT Codes and Cost

Additional Resources

• OMIM entries

Due To Cytochrome C Oxidase Deficiency

Gene: SCO2
Protein: Protein SCO2 homolog, mitochondrial

Clinical Characteristics

• hypertrophic cardiomyopathy, onset may be several months after birth
• encephalopathy or Leigh syndrome (subacute necrotizing encephalopathy)
• lactic acidosis
• Muscle biopsy findings:
  • decreased activity of cytochrome c oxidase (COX deficiency)
  • neurogenic changes or SMA-like pattern of muscle fibers
• hypotonia
• respiratory difficulty and/or inspiratory stridor
• developmental delay
• spasticity or seizures
• decreased extraocular movement (ptosis, strabismus)
• history of miscarriages or stillbirths

Inheritance pattern: Autosomal recessive

What Can Be Learned From This Test

Testing is performed by sequencing the entire coding region (exon 2) and surrounding intronic regions of SCO2. This will detect point mutations, small deletions and small insertions. It will not detect a partial or whole gene deletion or duplication.

A negative test does not rule out a genetic cause of COX deficiency or a neuromuscular disorder, as there are many other genes, both nuclear and mitochondrial, associated with different types of neuromuscular disorders.

Sample Requirements

Draw one or two 4-cc tubes of blood in EDTA/ purple top tube (minimum of 1-2 cc for infants)

Turnaround time: 10-14 business days

CPT Codes and Cost

Download the Testing Packet »

Additional Resources

• OMIM Entries

Feingold syndrome 1

Gene: MYCN
Protein: N-myc proto-oncogene protein

Feingold syndrome 2

Gene: MIR17HG
Transcript: MIR17-92 cluster (primary transcript for microRNAs MIR17, MIR18, MIR19A, MIR19B, MIR20 and MIR92)

Clinical Characteristics

• microcephaly
• short palpebral fissures
• gastrointestinal atresia
• digital abnormalities
  • brachymesophalangy 2 and 5
  • thumb hypoplasia
  • 2-3 or 4-5 toe syndactyly
• normal intelligence or mild to moderate learning disability
• variable expressivity within and between families

Inheritance pattern: Autosomal dominant

What Can Be Learned From This Test

Testing is performed by sequencing exon 1, coding exons 2 and 3, and the surrounding intronic regions of the MYCN gene. Gene dosage by capillary electrophoresis will be performed (on mutation negative samples) to detect a whole or partial gene deletion, since deletions of the entire MYCN gene have been reported in affected individuals.

Gene deletion testing of the MIR17-92 cluster region will be performed by capillary electrophoresis to determine copy number within the MIR17HG gene.

Sequence analysis of MYCN detects mutations in 65 percent of individuals with a clinical suspicion of Feingold syndrome. Deletion testing of MYCN detects another 10 percent. Deletion of MIR17HG accounts for additional cases of Feingold syndrome, but specific detection rate is unknown. MYCN and MIR17HG are the only genes known to be associated with Feingold syndrome. A negative test for both genes does not rule out a diagnosis of Feingold syndrome, since there may be other genes involved.

Sample Requirements

Draw one or two 4-cc tubes of blood in EDTA/purple-top tube (minimum of 1-2 cc for infants).

Turnaround time: 10-14 business days per gene

CPT Codes and Cost

Additional Information:

• GeneReview
• OMIM entries

Nonsyndromic sensorineural hearing loss, DFNB1

Gene: ACNT4, ALG1, ALMS1, APOL1, ARGHDIA, ARHGAP24, CD2AP, CD151, CFH, COL4A3, COL4A4, COL4A5, COQ2, COQ6, COQ7, COQ9, COQ8B, CRB2, CUBN, CYP11B2, CYP24A1, DGKE, EMP2, E2F3, INF2, ITGA3, ITGB4, KANK2, LAMB2, LMX1B, MED28, MEFV, MYH9, MYO1E, NEIL1, NPHS1, NPHS2, PDSS2, PLCE1, PMM2, PTPRO, SCARB2, SMARCAL1, TRPC6, WT1, ZMPSTE24

Clinical Characteristics

Steroid Resistant Nephrotic Syndromes (SRNS) are a clinically and genetically diverse group of disorders that can present with proteinuria, edema, hypoalbuminemia and hyperlipidemia. Rare monogenic forms of Focal Segmental Glomerulosclerosis Syndrome (FSGS) and nephrotic syndrome can present with symptoms at birth or may present later in life, including adulthood. Monogenic forms of FSGS, Alport syndrome, nephrotic syndromes, and other rare diseases of the kidney are associated with variants in 46 genes expressed in the podocyte or the glomerular basement membrane. This panel includes both nonsyndromic and syndromic causes of kidney pathology.

What Can Be Learned From This Test

As many of these conditions are not steroid or immunosuppression responsive, genetic testing provides key information to physicians to help determine course of treatment. Additionally, identification of a genetic syndrome may indicate additional screening and intervention to prevent secondary complications of the disorder.

Testing is performed by next generation sequencing followed by analysis software alignment to the gene reference transcripts.

A negative test result does not rule out a diagnosis of a nephrotic syndrome disorder. Other genes are known to be associated with some of these conditions, and this test will only detect gene variants in the genes listed above. Copy number changes will not be detected through this assay.

Sample Requirements

• Infants/Children: one purple top (EDTA) tube > 2ml
• Adults: one purple top (EDTA) tube > 3ml
• DNA previously isolated may be accepted; requires minimum of 5 micrograms DNA in TE buffer. DNA from FFPE (formalin fixed paraffin embedded) samples will not be accepted.
• Complete the NGS Sample Submission form

Turnaround time: 12-16 weeks

CPT Codes and Cost

Additional Resources

• Gene Testing (PDF)

Clinical Characteristics

DFNB1

• sensorineural hearing loss
  • typically congenital
  • usually nonprogressive
  • mild to profound
• no associated medical findings

DFNA3

• sensorineural hearing loss
  • typical onset in childhood
  • usually progressive
  • moderate to severe
  • high frequencies more severely affected
• no associated medical findings

Allelic Dermatologic Conditions

• GJB2
  • Palmoplantar keratoderma with deafness
  • Keratitis-ichthyosis-deafness (KID) syndrome
  • Hystrix-like ichthyosis-deafness (HID) syndrome
  • Vohwinkel syndrome (deafness, keratopachydermia, constrictions of fingers and toes)
  • Bart-Pumphrey syndrome (knuckle pads, leukonychia, deafness)
• GJB6
  • hidrotic ectodermal dysplasia 2 (Clouston syndrome)

Inheritance Pattern:

• autosomal recessive for DFNB1
• autosomal dominant for DFNA3 and allelic dermatologic conditions

What Can Be Learned From This Test

Testing is performed by sequencing untranslated exon 1, coding exon 2, and the surrounding intronic regions of GJB2. This will detect point mutations, small deletions and small insertions. It will not detect a partial or whole gene deletion or duplication. GJB6 is analyzed for the common 309 kb deletion, and coding exon 3 is sequenced.

A negative test result does not rule out a genetic cause of sensorineural hearing loss as there are many other genes associated with this trait. This test will only detect mutations in GJB2 and GJB6.

Sample Requirements

Draw one or two 4cc tubes of blood in EDTA/ purple top tube (minimum of 1-2 cc for infants).

Turnaround time: 10-14 business days

CPT Codes and Cost

Additional Information

GeneReviews

• DFNB1
• DFNA3
• Hidrotic Ectodermal Dysplasia 2

More Resources

• OMIM entries
• National Institute on Deafness and Other Communication Disorders
• My Baby’s Hearing

Also known as: McArdle Disease, myophosphorylase deficiency, GSD5

Gene: PYGM
Protein: glycogen phosphorylase, muscle form

Clinical Characteristics

• Exercise intolerance with isometric or sustained aerobic exercise
  • rapid fatigue
  • muscle pain and cramps
  • “second wind” phenomenon — relief of pain and fatigue after a few minutes of rest
• Onset in second or third decade of life
• Muscle weakness
  • Nonprogressive muscle weakness in one third of affected individuals.
  • Progressive weakness in some affected individuals in the sixth or seventh decade of life.
• Myoglobinuria in about 50 percent of affected individuals, can result in acute renal failure
• Supportive lab findings
  • increased resting serum creatine kinase
  • no increase in plasma lactate on the forearm exercise test
  • cycle test — decrease in heart rate from the seventh to the fifteenth minute of stationary cycling
• Rare severe form with rapid progression and onset shortly after birth

Inheritance pattern: Autosomal recessive

What This Test Can Tell Us

Testing is performed by sequencing the entire coding region of PYGM. This will detect point mutations, small deletions and small insertions. It will not detect a partial or whole gene deletion or duplication. Partial sequencing of exons 1 and 5 can be carried out; please note on submission form if this tiered approach is being requested.

A negative test result does not rule out a genetic cause of myopathy. There are many other genetic forms of myopathy, and this test will only detect mutations associated with glycogen storage disease type V, caused by deficiency of glycogen phosphorylase, muscle form.

Sample Requirements

Draw one or two 4-cc tubes of blood in EDTA/purple-top tube (minimum of 1-2 cc for infants).

Turnaround time: 10-14 business days

CPT Codes and Cost

Additional Resources

• GeneReview
• OMIM entries

Also known as Hypomyelinating Leukodystrophy 5 (HLD5)

Gene: FAM126A (also known as DRCTNNB1A)
Protein: hyccin

Clinical Characteristics

• bilateral congenital cataracts
• normal psychomotor development in first year of life
• progressive ataxia and spasticity
• mild to moderate cognitive impairment
• hypotonia
• dysarthria
• truncal titubation and intention tremor
• peripheral neuropathy
• progressive scoliosis
• Characteristic MRI findings:
  • diffusely abnormal supratentorial white matter
  • sparing of the cortical and deep gray matter structures
  • hypomyelination of supratentorial white matter +/- deep cerebellar white matter
  • increased white matter water content
  • white matter bulk loss and gliosis in older individuals

Inheritance pattern: Autosomal recessive

What This Test Can Tell Us

Testing is performed by sequencing the entire coding region and intron-exon junctions of FAM126A. This assay will detect point mutations, small deletions and small insertions. It will not detect a partial or whole gene deletion or duplication.

A negative test does not rule out a genetic cause of a neurologic disorder. There are many other genes associated with different types of neurologic disorders and leukodystrophies, some of which are available for testing in our laboratory and can be performed if clinically indicated. 

Sample Requirements

Draw one or two 4-cc tubes of blood in EDTA/purple-top tube (minimum of 1-2 cc for infants).

Turn-around time: 10-14 business days

CPT Codes and Cost

Additional Information

• GeneReview
• OMIM Entries

Gene: RARS
Protein: arginine--tRNA ligase, cytoplasmic

Clinical characteristics

• delayed motor development
• spasticity
• nystagmus
• onset in the first year of life
• diffuse hypomyelination affecting all regions of the brain
• ataxia and dystonia may be present
• mild intellectual disability may be present
• phenotype is variable and severe symptoms with early brain atrophy have been reported

Inheritance pattern: Autosomal recessive

What This Test Can Tell Us

Testing is performed by sequencing the entire coding region and surrounding intronic regions of RARS. This will detect point mutations, small deletions, and small insertions. It will not detect a partial or whole gene deletion or duplication.

A negative test does not rule out a genetic cause of hypomyelinating leukodystrophy. There may be a mutation in a region of the RARS gene not analyzed, or a partial or whole gene deletion or duplication. Mutations in multiple other genes are known to cause other forms of hypomyelinating leukodystrophy. Testing of other genes associated with hypomyelinating leukodystrophy is available in our laboratory and can be performed if clinically indicated.

Sample Requirements

Draw one or two 4cc tubes of blood in EDTA/purple top tube (minimum of 1-2 cc for infants).

Turnaround time: 10-14 business days

CPT Codes and Cost

• Code: 81479
• Cost: $900

Known Familial Variant

• Code: 81479
• Cost: $225

Additional Resources

• OMIM Entries
• Leukodystrophy Overview in GeneReviews
• United Leukodystrophy Foundation

Hypomyelinating Leukodystrophy 11

Gene: POLR1C
Protein: DNA-directed RNA polymerases I and III subunit RPAC1

Clinical Characteristics

• similar to disorders (HLD7 and HLD8) due to mutations in POLR3A and POLR3B
• delayed motor development
• loss or lack of independent ambulation
• tremors
• ataxia, other signs of cerebellar dysfunction
• MRI findings
  • thin corpus callosum
  • hypomyelination
  • with or without cerebellar atrophy
• Some individuals may have
  • intellectual disability
  • dental abnormalities
  • hypogonadotropic hypogonadism
  • myopia
• Onset typically in early childhood
• Different mutations in POLR1C are associated with autosomal recessive Treacher-Collins  syndrome

Inheritance pattern: Autosomal recessive

What Can Be Learned From This Test

Testing is performed by sequencing all exons and at least 40 base pairs of the surrounding intronic regions of the POLR1C gene. This will detect point mutations, small deletions, and small insertions. It will not detect a partial or whole gene deletion or duplication. To date, no large deletions or duplications have been reported.

Sample Requirements

Draw one or two 4-cc tubes of blood in EDTA/purple-top tube (minimum of 1-2 cc for infants).

Turn-around time: 10-14 business days per tier

CPT Codes and Cost

Full Gene Sequencing

• Code: 81479
• Cost: $350

Known Variant Testing

• Code: 81479
• Cost: $225

Additional Information

• OMIM entries
• United Leukodystrophy Foundation
• Myelin Disorders Bioregistry Project

Hypomyelinating Leukodystrophy with Atrophy of the Basal Ganglia and Cerebellum (H  ABC) and Autosomal Dominant Torsion Dystonia 4 (DYT4)

Gene: TUBB4A (also known as TUBB4, TUBB5)
Protein: tubulin, beta 4

Clinical Characteristics

• H-ABC
  • also known as Hypomyelinating Leukodystrophy 6
  • infancy to early childhood onset
  • developmental delay
  • progressive deterioration of motor skills
  • extrapyramidal movement disorders
    • dystonia
    • choreoathetosis
    • rigidity
    • opisthotonus
    • oculogyric crises
  • progressive spastic tetraplegia
  • ataxia
  • cognition relatively preserved
  • mRI features:
    • hypomyelination
    • cerebellar atrophy
    • absence or disappearance of putamen
• DYT4
  • onset in second to fourth decade
  • progressive spasmodic “whispering” dysphonia
  • cervical or generalized dystonia
  • characteristic “hobby horse” gait ataxia
  • normal MRI

Inheritance Pattern: Autosomal dominant or sporadic

What Can Be Learned From This Test

Testing is performed by sequencing the entire coding region of the TUBB4A gene. This will detect point mutations, small deletions and small insertions. It will not detect a partial or whole gene deletion or duplication. Targeted mutation analysis for the common mutations c.745G>A; p.Asp249Asn in H-ABC or c.4C>G; p.Arg2Gly in DYT4 can be carried out; please note on submission form if this targeted approach is being requested. A negative test result does not rule out a genetic cause of hypomyelinating leukodystrophy, since there are many other genes associated with leukodystrophies, some of which are available for testing in our laboratory. 

Sample Requirements

Draw one or two 4cc tubes of blood in EDTA/purple top tube (minimum of 1-2cc for infants)

Turnaround time: 7-10 business days

CPT Codes and Cost

Gene: CYP24A1
Protein: 1,25-dihydroxyvitamin D(3) 24-hydroxylase, mitochondrial

Clinical Characteristics

• hypercalcemia
• hypercalciuria
• suppressed intact PTH
• symptoms of hypercalcemia can include:
  • failure to thrive
  • vomiting
  • dehydration
  • nephrocalcinosis
  • nephrolithiasis
• variable age of onset
  • severe form presents in infancy
  • mild to severe symptoms presenting in adulthood

Inheritance pattern: Autosomal recessive; carriers with either subclinical biochemical phenotypes or clinical symptoms have been reported.

What Can Be Learned From This Test

Testing is performed by sequencing coding exons 1-11, and a portion of exon 12 in the 3’UTR. This test will detect point mutations, small deletions and small insertions. The gene dosage assay will detect some partial and all whole gene deletions or duplications. Large deletions and duplications in CYP24A1 have not been reported.

Common pathogenic variants have been reported in exons 2, 3, 6, 7, 9.  Partial sequencing in regions known to carry mutations can be carried out and may be ordered as Tier 1 testing; please note on submission form if this tiered approach is being requested.

Sample Requirements

Draw one or two 4cc tubes of blood in EDTA/purple top tube (minimum of 1-2cc for infants).

Turnaround time: 10-14 business days

CPT Codes and Cost

Additional Resources

• OMIM entries

Gene: AARS1; AARS2; DARS1; DARS2; EARS2; FAM126A; GJC2; HEPACAM; LMNB1; MARS2; MLC1; PLP1; POLR3A; POLR3B; POLR1C; RARS1; SLC16A2; TUBB4A

Clinical Characteristics

Pediatric and Adult-onset leukodystrophies are a clinically and genetically diverse group of disorders comprised of white matter neurodegeneration and varying neurological symptoms. Rare monogenic forms can present with symptoms at birth or may present later in life, including adulthood. The diverse genetic etiology and clinical overlap of phenotypes can make a definitive diagnosis a challenge. Patients may present with hypomyelination; nystagmus; hypotonia; spasticity; ataxia; dysarthria; stridor; progressive pyramidal and cerebellar signs; dysmyelination of the brain; cerebellar atrophy. This panel includes both non-syndromic and syndromic causes of progressive movement disorders, and can be associated with gene variants in one of these 18 genes. Copy number changes will not be detected through this assay. Inheritance patterns: autosomal dominant, autosomal recessive, X-linked

What Can Be Learned From This Test

Testing is performed by next generation sequencing followed by analysis software alignment to the gene reference transcripts.

A negative test result does not rule out a diagnosis of a leukodystrophy related disorder. Other genes are known to be associated with some of these conditions, and this test will only detect gene variants in the genes listed above.

Sample Requirements

• Infants/Children: one purple top (EDTA) tube > 2ml
• Adults: one purple top (EDTA) tube > 3ml
• DNA previously isolated may be accepted; requires minimum of 5 micrograms DNA in TE buffer. DNA from FFPE (formalin fixed paraffin embedded) samples will not be accepted.
• Complete the NGS Sample Submission form

Turnaround time: 12-16 weeks

CPT Codes and Cost

Additional Resources

• Gene List (PDF)

Gene: DARS2
Protein: mitochondrial aspartyl-tRNA synthetase 2

Clinical Characteristics

• Slowly progressive cerebellar ataxia with onset usually in childhood or adolescence
• Spasticity
• Dorsal column dysfunction involving the legs more than the arms (decreased sense of position and vibration)
• Characteristic MRI findings (major diagnostic criteria)
  • Signal abnormalities in the periventricular cerebral white matter
  • Signal abnormalities in the dorsal columns and lateral corticospinal tracts of the spinal cord
  • Signal abnormalities in the pyramids in the medulla oblongata
• Supportive MRI findings (supportive diagnostic criteria)
  • Signal abnormalities in other specific areas
  • Elevated lactate in the abnormal cerebral white matter, as measured by MRS
• Wide phenotypic spectrum
  • Rare cases of individuals with infantile onset, rapid disease progression, and death in early childhood
  • Some individuals with adult onset and mild symptoms, remaining ambulatory without support

Inheritance Pattern: Autosomal recessive

What This Test Can Tell Us:

The diagnosis of LBSL is based on characteristic abnormalities observed on brain and spinal cord MRI and the identification of two alleles with mutations in DARS2. Finding two disease-causing mutations in DARS2 confirms the diagnosis of LBSL. However, absence of DARS2 mutations does not exclude the diagnosis when the clinical and MRI findings are characteristic, especially if all major diagnostic criteria and at least one supportive criterion are met.

Testing can be performed in tiers, moving to the next tier only if the preceding test is negative. Full gene sequencing can also be performed. The following strategy is suggested:

Tier 1: Sequencing of exons 3 , 5, and adjacent intronic regions of DARS2, which covers the three most common pathogenic variants: c.228-21_-20delTTinsC (rs367543010), c.455G>T (rs121918208), and c.492+2T>C (rs14243333).

Tier 2: Sequencing of the remaining exons and intronic boundaries of DARS2.

This will detect point mutations, small deletions, and small insertions. It will not detect a partial or whole gene deletion or duplication.

Sample Requirements

Draw one or two 4cc tubes of blood in EDTA/purple top tube (minimum of 1-2cc for infants)

Turnaround time: 10-14 days per tier

CPT Codes and Cost

Tier 1: (81479): $300
Tier 2: (81479): $725
Full Gene Sequencing: (81479): $1025
Known Variant Testing: (81479): $225

Additional Resources

• OMIM
• GeneReview
• United Leukodystrophy Foundation

Gene: LIG4
Protein: DNA ligase 4

Clinical Characteristics

• pancytopenia
  
• immunodeficiencySensitivity to ionizing radiation
• microcephaly
• developmental delay
• growth delay
• increased risk for malignancies including leukemia and lymphoma
• can have severe combined immunodeficiency (SCID) and/or radiosensitivity without other features
• Characteristic Facial Features
  • similar to Seckel syndrome
  • low anterior hairline
  • prominent or broad nasal bridge
  • epicanthal folds

Inheritance Pattern: Autosomal recessive

What Can Be Learned From This Test

Testing is performed by sequencing both exons of the LIG4 gene as well as partial intronic regions. This will detect point mutations, small deletions and small insertions. It will not detect a partial or whole gene deletion or duplication. To date, no large deletions or duplications have been reported.

Sample Requirements

Draw one or two 4cc tubes of blood in EDTA/purple top tube (minimum of 1-2cc for infants)

Turnaround time: 10-14 business days

CPT Codes and Cost

Additional Resources

• LIG4 on OMIM

Clinical Characteristics

MLC1/ MLC2A: Classical Phenotype

• macrocephaly present at birth or within first year of life
• epileptic seizures
• normal to delayed early development, usually progressing to independent walking
• ataxia and spasticity in early childhood
• extrapyrimadal movement abnormalities
• mild intellectual deterioration in early teens
• MRI findings:
  • Abnormal and swollen white matter, especially in cerebral hemisphere.
  • Subcortical cysts in anterior temporal and frontoparietal regions.

MLC2B: Improving Phenotype

• macrocephaly present at birth or within first year of life
• normal to delayed early development, progressing to independent walking
• no regression of mental or motor function
• improved motor function after second or third year of life
• epileptic seizures may occur
• normal cognition to stable intellectual disability with or without autism
• MRI findings:
  • Same abnormalities as MLC1 and MLC2A in the first year
    of life.
  • Improvement seen on subsequent MRI’s.

Inheritance Pattern:

• autosomal recessive for MLC1 and MLC2A
• autosomal dominant for MLC2B

What Can Be Learned From This Test

The diagnosis of MLC is based on diagnostic criteria, including brain MRI. A negative test result does not rule out a diagnosis of MLC since a mutation may not be identifiable with test methods used, or a mutation may be in another gene. This test will only detect mutations in MLC1 and HEPACAM.

Mutations in MLC1 and HEPACAM are found in 75 percent and 20 percent of affected individuals, respectively. Testing can be performed in tiers, moving to the next tier only if the preceding test is negative. Testing can also be performed concurrently, or in any order requested. The following strategy is suggested:

• Tier 1: Sequencing of untranslated exon 1 and the entire coding region of MLC1
• Tier 2: Sequencing of the entire coding region of HEPACAM

This will detect point mutations, small deletions, and small insertions. It will not detect a partial or whole gene deletion or duplication. Sequencing will identify the majority of mutations, but partial gene deletions have been reported in MLC1 (Ilja Boor et al, 2006).

Sample Requirements

Draw one or two 4cc tubes of blood in EDTA/purple top tube (minimum of 1-2cc for infants)

Turnaround time: 10-14 business days per tier

CPT Codes and Cost

Additional Resources

• OMIM
• GeneReview
• United Leukodystrophy Foundation

Ear, Patella, Short stature syndrome (EPS) or Absent patellae, micrognathia syndrome

Clinical Characteristics

Severe intrauterine and postnatal growth retardation (usually <3rd percentile)

Infancy Period

• feeding problems, failure to thrive
• characteristic facial features
  • microstomia
  • full lips
  • beaked nose
  • micrognathia

Craniofacial features

• microcephaly
• bilateral microtia
• atretic/ small external auditory canals
• mandibular hypoplasia

Skeletal Features

• delayed bone age
• aplasia or hypoplasia of patellaes
• slender long bones
• joint abnormalities

Inheritance Pattern: Autosomal recessive for all genes: ORC1, ORC4, ORC6, CDT1, CDC6

What Can Be Learned From This Test

Testing is performed by sequencing all exons of the ORC1, ORC4, ORC6, CDT1 and CDC6 genes as well as partial intronic regions. This will detect point mutations, small deletions and small insertions. It will not detect a partial or whole gene deletion or duplication. To date, only nonsense and frameshift mutations with single nucleotide insertions or deletions have been detected. Testing of genes can be completed simultaneously or by a tiered approach.

Sample Requirements

Draw one or two 4cc tubes of blood in EDTA/purple top tube (minimum of 1-2cc for infants)

Turnaround time: 10-14 business days per gene

CPT Codes and Cost

Testing in a new patient:

Known Variant Testing

• Code: 81479
• Cost: $225

Additional Resources

• OMIM entries
  
• Potentials Foundation (support organization)
  

(Taybi – Linder syndrome)

Gene: RNU4ATAC
Transcript: U4atac small nuclear RNA

Clinical Characteristics

• Marked intrauterine and postnatal growth retardation
• Microcephaly
• Skeletal abnormalities
  • vertebral and pelvic anomalies
  • short bowed long bones
  • wide metaphyses
  • delayed epiphyseal maturation
• Brain malformations
  • agenesis of the corpus callosum or cerebellar vermis
  • lissencephaly or other gyral abnormalities
  • hypoplastic frontal lobes
• Dysmorphic facial features
  • prominent nose with a downturned tip
  • sloping forehead
  • protruding eyes
  • low-set ears
  • micrognathia
• Sparse hair and dry skin
• Developmental delay
• Death typically occurs in the first year of life

Inheritance pattern: Autosomal recessive

What Can Be Learned From This Test

Testing is performed by sequencing the entire RNU4ATAC gene and surrounding regions. This will detect point mutations, small deletions and small insertions. It will not detect a whole gene deletion or duplication.

RNU4ATAC is the only gene known to be associated with microcephalic osteodysplastic primordial dwarfism, type I (MOPD I). A negative test does not rule out a diagnosis of MOPD I since a mutation could be in a region not sequenced or in another gene.

Sample Requirements

Draw one 4cc tube of blood in EDTA/ purple top tube (only 1-2 cc needed for infants)

Turnaround time: 10-14 business days

CPT Codes and Cost

Additional Resources

• OMIM entry for MOPD I
• OMIM entry for RNU4ATAC
• Potentials Foundation

Gene: PCNT2
Protein: pericentrin

Clinical characteristics

• progressive intrauterine growth retardation
• small for gestational age, typical birth weight is 3 pounds
• relative microcephaly appears over time
• disproportionately small forearms with progressive shortening of distal limbs
• thin delicate bones with progressive metaphyseal widening, may be subtle in newborns
• prominent nose and eyes
• microdontia, hypodontia, or dysplastic teeth
• fine sparse hair
• pigmentary dysplasia of the skin
• cerebral vascular abnormalities (moyamoya disease) in 20 percent, can predispose to stroke

Inheritance pattern: Autosomal recessive

What This Test Can Tell Us

Testing is performed by sequencing all exons and surrounding intronic regions of the PCNT gene. This will detect point mutations, small deletions and small insertions. It will not detect a partial or whole gene deletion or duplication.

PCNT2 is the only gene known to be associated with microcephalic osteodysplastic primordial dwarfism, type II (MOPD2). A negative test does not rule out a diagnosis of MOPD II since a mutation could be in a region not sequenced or in another gene.

Sample Requirements

Draw one or two 4-cc tubes of blood in EDTA/ purple top tube (minimum of 1-2 cc for infants)

Turnaround time: 4 weeks or less

CPT Codes and Cost

Additional Resources

• OMIM Entries
• MOPD II information from Nemours

Noonan syndrome and related disorders

Gene: Protein

• PTPN11: tyrosine-protein phosphatase non-receptor type 11
• SOS1: son of sevenless homolog 1
• RAF1: RAF proto-oncogene serine/threonine-protein kinase
• KRAS: GTPase KRas
• SHOC2: leucine-rich repeat protein SHOC-2
• BRAF: serine/threonine-protein kinase B-raf
• MAP2K1/MEK1: dual specificity mitogen-activated protein kinase kinase 1

Clinical Characteristics

Noonan syndrome

• heart defects including hypertrophic cardiomyopathy and pulmonic valve stenosis
• facial dysmorphology
• short stature
• chest wall deformities
• developmental delay

LEOPARD syndrome

• acronym for multiple lentigines, electrocardiogram abnormalities, ocular hypertelorism, pulmonic valvular stenosis, abnormalities of genitalia, retardation of growth, sensorineural deafness
• lentigines may or may not be present
• heart defects including hypertrophic cardiomyopathy and pulmonic valve stenosis
• cryptorchidism
• postnatal growth retardation
• mild facial dysmorphology
• mild mental retardation

Noonan-like syndrome with loose anagen hair

• features of Noonan syndrome
• actively growing hair that is easy to pluck, sparse, thin and slow-growing

Inheritance pattern: Autosomal dominant

What Can Be Learned From This Test

Testing can be performed in tiers, moving to the next tier only if the preceding test is negative. Testing can also be performed concurrently or in any order requested. The following strategy is suggested for Noonan syndrome testing: Tier 1 and 3 is suggested if an individual has findings suggestive of LEOPARD syndrome; Tier 5 is suggested if an individual has loose anagen hair.

Tier 1: Sequencing of the entire coding region of PTPN11

Tier 2: Sequencing of the entire coding region of SOS1

Tier 3: Sequencing of exons 7, 14 and 17 of RAF1

Tier 4: Sequencing of the entire coding region of KRAS

Tier 5: Sequencing of part of exon 2 for reported mutation in SHOC2

Tier 6: Sequencing of exons 6 and 11 through 16 of BRAF

Tier 7: Sequencing of exons 2, 3, 6 and 7 of MAP2K1 (MEK1)

Sequencing tests will detect point mutations, small deletions and small insertions in the regions of the genes that are analyzed. It will not detect a partial or whole gene deletion or duplication.

For Noonan syndrome, mutations are detected in:
 

• PTPN11 in about 50 percent of affected individuals
• SOS1 in about 10 percent of affected individuals
• Exon 7, 12, 14, or 17 of RAF1 in 3 percent to 17 percent of affected individuals
• KRAS in less than 5 percent of affected individuals
• Exon 2 of SHOC2 in individuals with Noonan-like syndrome with loose anagen hair
• BRAF in less than 2 percent of affected individuals
• MAP2K1 (MEK1) in less than 2 percent of individuals

For LEOPARD syndrome, mutations are detected in:

• Exon 7, 12, 14, or 17 of RAF1 in about 3 percent of affected individuals

A negative test does not completely rule out a diagnosis of Noonan syndrome or LEOPARD syndrome, since mutations in these five genes do not account for 100 percent of cases. Clinical overlap is seen between Noonan syndrome, Costello syndrome and cardiofaciocutaneous (CFC) syndrome. Tests for Costello syndrome and CFC syndrome are also available in our lab and can be requested if clinically indicated.

Sample Requirements

Draw one or two 4-cc tubes of blood in EDTA/purple-top tube (minimum of 2-3 cc for infants due to large number of assays).

Turnaround time: 7-10 business days for each gene; about 4 weeks for all 7 tiers

CPT Codes and Cost

Additional Information

• GeneReview for Noonan syndrome
• GeneReview for LEOPARD syndrome
• OMIM entries

Gene: PLP1
Protein: myelin proteolipid protein

Clinical Characteristics

• spectrum of phenotypes, ranging from severe neurodegenerative disorder to spastic paraparesis without central nervous system involvement
• nystagmus
• hypotonia
• diffuse leukoencephalopathy
• cognitive impairment may or may not be present
• spasticity
• ataxia
• choreoathetosis
• dysarthria
• pharyngeal weakness and stridor
• head titubation

Inheritance pattern: X-linked; carrier females may have mild to moderate symptoms

Testing

Duplication Testing

Testing is performed by quantitative multiplex PCR to determine copy number of PLP1. Fluorescent primers are used to amplify select exons of the PLP1 gene, along with several reference genes. The quantity of each PCR product is determined by measuring the intensity of the fluorescence. Copy number is calculated based on the normalized ratio of the PLP1 gene to each of the reference genes for the patient and controls.

Duplications of variable size and other dosage changes (deletions, triplications, quintuplications) are found in at least 50 percent of males with PLP1-related disorders. This test will detect duplications and other dosage changes that are in tandem as well as duplications that are inserted elsewhere in the genome. Duplication testing alone will not detect point mutations or smaller deletions or insertions.

Sequencing

Testing is performed by sequencing the entire coding region and intron-exon junctions of PLP1. This assay will detect point mutations, small deletions and small insertions. Sequencing alone will not detect a partial or whole gene deletion or duplication.

Point mutations are found in 15 percent or less of males with PLP1-related disorders. A negative result will exclude the presence of a mutation in the regions tested with greater than 99 percent sensitivity. However, a negative result does not exclude the possibility that mutations are present in other regions of the PLP1 gene or in other genes.

Sensitivity

If duplication testing and sequencing are both negative, it does not rule out a PLP1-related disorder. Approximately 40 percent of males with clinical findings consistent with the PLP1-related disorders do not have an identifiable mutation in the PLP1 gene, suggesting that mutations may occur in regions of the gene that are not analyzed or in another gene.

A negative test does not rule out a genetic cause of a neurologic disorder. There are many other genes associated with different types of neurologic disorders and leukodystrophies, some of which are available for testing in our laboratory and can be performed if clinically indicated.

Sample Requirements

Draw one or two 4-cc tubes of blood in EDTA/purple-top tube (minimum of 1-2 cc for infants).

Turn-around time: 10-14 business days per tier

CPT Codes and Cost

Online Resources:

• United Leukodystrophy Foundation
• Myelin Disorders Bioregistry Project
• PMD Foundation
• Gene Review

Also known as hypomyelinating leukodystrophy 2 (HLD2)

Gene: GJC2 (previously known as GJA12)
Protein: gap junction gamma-2 protein (also known as connexin 46.6)

Clinical Characteristics

• Symptoms resemble Pelizaeus-Merzbacher disease and can include:
  • nystagmus
  • hypotonia
  • diffuse leukoencephalopathy
  • cognitive impairment - may or may not be present
  • progressive spasticity
  • ataxia
  • choreoathetosis
  • dysarthria
  • pharyngeal weakness and stridor
  • head titubation
• Brainstem auditory evoked potentials are present in PMLD (typically absent in PMD)

Inheritance Pattern: Autosomal recessive

Testing

Testing is performed by sequencing the entire coding region of GJC2. This assay will detect point mutations, small deletions and small insertions. To date (December 2014), no reports of whole gene duplications or deletions have been documented in the literature.

There is a report in the literature that autosomal dominant missense mutations in GJC2 cause lymphedema (Ferrell et al., AJHG 86:943-948, 2010).

A negative test does not rule out a genetic cause of a leukodystrophy. There are many other genes associated with different types of neurologic disorders and leukodystrophies, some of which are available for testing in our laboratory and can be performed if clinically indicated. 

Sample Requirements

Draw one or two 4-cc tubes of blood in EDTA/purple-top tube (minimum of 1-2 cc for infants).

Turn-around time: 10-14 business days

CPT Codes and Cost

Online Resources

• United Leukodystrophy Foundation
• Myelin Disorders Bioregistry Project
• PMD Foundation

Gene: SLC26A4
Protein: pendrin

Clinical Characteristics

Pendred syndrome

• Sensorineural hearing loss
  • usually bilateral
  • usually severe to profound
  • onset typically at birth or in early childhood
• Temporal bone abnormalities
  • enlarged vestibular aqueduct
  • cochlear hypoplasia may or may not be present
• Significant variability within and between families
  • enlarged vestibular aqueduct is typical
  • cochlear hypoplasia may or may not be present
• Euthyroid goiter, onset in early adulthood

DFNB4

• nonsyndromic sensorineural hearing loss
• temporal bone abnormalities

Absence of thyroid defects

Inheritance pattern: Autosomal recessive

What Can Be Learned From This Test

Molecular testing of the SLC26A4 gene should be considered for individuals with hearing loss and enlarged vestibular aqueduct (EVA). Testing is performed by sequencing all exons and the surrounding intronic regions of the SLC26A4 gene. This assay will detect point mutations, small deletions and small insertions. It will not detect a partial or whole gene deletion or duplication.

SLC26A4 mutations are identified in 80 percent to 90 percent of familial cases of Pendred syndrome, and in about 30 percent of cases with no family history. Mutations have been identified throughout the SLC26A4 gene and include point mutations, small insertions or deletions, and splice site mutations. Deletions of single and multiple exons have also been reported.

The detection of two pathogenic mutations in SLC26A4 is consistent with a diagnosis of Pendred syndrome or DFNB4. However, single heterozygous mutations have been identified in SLC26A4 in 20 percent to 30 percent of individuals who meet criteria for Pendred syndrome or DFNB4. It is hypothesized that a second unidentified mutation is present in SLC26A4 or in another gene. There is some evidence to suggest that individuals with one identified mutation in SLC26A4 are less likely to develop thyroid manifestations than individuals with two identified mutations.

Sample Requirements

Draw one or two 4-cc tubes of blood in EDTA/purple-top tube (minimum of 1-2 cc for infants).

Turnaround time: 10-14 business days

CPT Codes and Cost

Additional Information

• GeneReview
• OMIM entries

4H syndrome; hypomyelinating leukodystrophy with or without hypodontia and/or hypogonadotropic hypogonadism: HLD7 and HLD8

Clinical Characteristics

• Cerebellar signs
  • progressive ataxia
  • intention tremor
  • dysarthria, dysmetria, dysdiadochokinesis
• Progressive upper motor neuron dysfunction
  • spasticity
  • mild hyperreflexia
• MRI findings
  • hypomyelination
  • cerebellar atrophy
  • hypoplastic corpus callosum
• childhood or juvenile onset (reported ages range from 1–20 years)
• extrapyramidal dysfunction such as dystonia
• dental abnormalities (delayed dentition, hypodontia, etc.)
• hypogonadotropic hypogonadism
• eye movement abnormalities and myopia
• mild to moderate intellectual disability with or without cognitive regression
• sensory deficits (sensorineural hearing loss, myopia, optic atrophy)
• inter- and intrafamilial variability

Inheritance Pattern: Autosomal recessive for both POLR3A and POLR3B

What Can Be Learned From This Test

Testing is performed by sequencing the entire coding region of POLR3A and POLR3B. This will detect point mutations, small deletions and small insertions. It will not detect a partial or whole gene deletion or duplication. A negative test result does not rule out a genetic cause of hypomyelinating leukodystrophy, since there are many other genes associated with leukodystrophies, some of which are available for testing in our lab.

Sequencing of POLR3A with reflex to sequencing of POLR3B is recommended, however, testing can be done concurrently or in any order specified.

Sample Requirements

Draw one or two 4cc tubes of blood in EDTA/purple top tube (minimum of 1-2cc for infants)

Turnaround time: 10-14 business days per gene

CPT Codes and Cost

Additional Resources

• OMIM
• United Leukodystrophy Foundation
• Myelin Disorders Bioregistry Project

Gene: SLC22A12 (URAT1)
Protein: Solute carrier family 22, member 12

Gene: SLC2A9 (GLUT9)
Protein: Solute carrier family 2, facilitated glucose transporter member 9

Clinical Characteristics

• impaired reabsorption of uric acid by the kidney
  • decreased serum uric acid level of less than 2.0 mg/dL (<119 umol/L)
  • increased fractional excretion of uric acid (FEUA) of greater than 10%
• majority of individuals are asymptomatic
• some have urolithiasis
• some are predisposed to exercise-induced acute kidney injury (EI-AKI)
• RHUC1 is due to SLC22A12 mutations
• RHUC2 is due to SLC2A9 mutations

Inheritance pattern: Autosomal recessive

What this test can tell us:

Testing is performed by sequencing all exons and the surrounding intronic regions of the SLC22A12 and SLC2A9 genes. This will detect point mutations, small deletions, and small insertions. It will not detect a partial or whole gene deletion or duplication. To date, a deletion of exon 7 as well as a large duplication of exons 1a – 11, have been reported in the SLC2A9 gene. A copy number assay for these regions of SLC2A9 can also be performed.

Sample Requirements

Draw one or two 4cc tubes of blood in EDTA/ purple top tube (minimum of 1-2 cc for infants).

Turnaround time: 10-14 business days

CPT Code and Cost

Additional Information

• OMIM entries

Gene: MECP2
Protein: Methyl-CpG-binding protein 2

Clinical Characteristics

Classic Rett syndrome

• typically affects females (males with mosaicism or 47,XXY have been reported)
• normal prenatal and newborn history
• apparently normal psychomotor development for first 6 to 18 months of life
• short developmental plateau followed by regression in language and motor skills
• cognitive impairment/mental retardation without further regression
• repetitive, stereotypic hand movements with loss of purposeful hand movements
• autistic features
• acquired microcephaly
• seizures
• bruxism (teeth grinding)
• impaired sleeping pattern
• breathing disturbances

Atypical Rett syndrome

• typically affects females
• loss or reduction of hand skills, speech, and other communication skills
• acquired microcephaly
• regression followed by recovery of interaction
• may or may not have other features of classic Rett syndrome
• other presentations with variable courses and different ages of onset

Severe neonatal encephalopathy

• affects males; rare in females
• severe neonatal-onset encephalopathy with microcephaly
• abnormal tone and involuntary movements
• severe seizures
• breathing abnormalities
• often die before second year of life

PPM-X syndrome

• females - mild nonprogressive mental retardation
• males - severe mental retardation associated with
  • “PPM” (Psychosis, Pyramidal signs, Macro-orchidism)
  • Parkinsonian features - resting tremor, slowness of movements, and ataxia

MECP2 duplication syndrome

• affects males; can affect females with an associated translocation or insertion
• infantile hypotonia
• severe mental retardation
• poor speech development
• progressive spasticity
• recurrent respiratory infections
• seizures

Inheritance pattern: X-linked

What Can Be Learned From This Test

Tier 1 testing is performed by sequencing the entire coding region of MECP2. This will detect point mutations, small deletions and small insertions. Reflexive testing for a partial or whole gene deletion by fragment analysis can be carried out; please note on submission form if this tiered approach is being requested.

A negative test result does not rule out a diagnosis of Rett syndrome. Sequencing alone will detect mutations in about 80 percent of individuals with classic Rett syndrome and in about 40 percent of individuals with atypical Rett syndrome. Deletion/duplication testing increases the detection rates to about 88 percent and 43 percent, respectively.

Sample Requirements

Draw one or two 4-cc tubes of blood in EDTA/purple-top tube (minimum of 1-2 cc for infants).

Turnaround time: 10-14 business days per tier

CPT Codes and Cost

Full Gene Sequencing (Tier 1)

• Code: 81302
• Cost: $685

Dosage (Tier 2)

• Code: 81304
• Cost: $300

Known Variant Testing

• Code: 81303
• Cost: $225

Additional Resources

• GeneReview for MECP2- Related Disorders
• GeneReview for MECP2 duplication syndrome
• OMIM entries
• International Rett Syndrome Foundation

Smith-McCort Dysplasia

Gene: RAB33B
Protein: Ras-related protein Rab-33B

Clinical Characteristics

• spondyloepimetaphyseal dysplasia
• normal birth parameters with progressive skeletal abnormalities
• short stature
• pectus carinatum
• exaggerated lordosis
• platyspondyly with double-hump or notched appearance of vertebrae
• decreased joint mobility
  • limited elbow extension
  • limited flexion of interphalangeal joints causing incomplete fist formation

Inheritance Pattern: Autosomal recessive

What Can Be Learned From This Test

Testing is performed by sequencing all exons and surrounding intronic regions of the RAB33B gene. This will detect point mutations, small deletions and small insertions. It will not detect a partial or whole gene deletion or duplication.

A negative test does not rule out a diagnosis of Smith-McCort dysplasia (SMC). A mutation could be present in a region not sequenced or in another gene. Mutations in the DYM gene have also been associated with SMC.

Dyggve-Melchior-Clausen syndrome (DMC) is a disorder that is similar to SMC, but also includes intellectual disability and microcephaly. Mutations in the DYM gene have been associated with both phenotypes, SMC and DMC. Mutations identified to date in RAB33B have been identified in individuals with phenotypes consistent with SMC. At this time, it is not clear if some cases of DMC are due to RAB33B mutations.

Sample Requirements

Draw one or two 4cc tubes of blood in EDTA/ purple top tube (minimum of 1-2 cc for infants)

Turnaround time: 10-14 business days

CPT Codes and Cost

Additional Information

• OMIM entries
• Little People of America, Inc.

Gene: PLP1
Protein: myelin proteolipid protein

Clinical Characteristics

• spectrum of phenotypes, ranging from severe neurodegenerative disorder to spastic paraparesis without central nervous system involvement
• nystagmus
• hypotonia
• diffuse leukoencephalopathy
• cognitive impairment may or may not be present
• spasticity
• ataxia
• choreoathetosis
• dysarthria
• pharyngeal weakness and stridor
• head titubation

Inheritance pattern: X-linked; carrier females may have mild to moderate symptoms

What Can Be Learned From This Test

Duplication test:
Testing is performed by quantitative multiplex PCR to determine copy number of PLP1. Fluorescent primers are used to amplify select exons of the PLP1 gene, along with several reference genes. The quantity of each PCR product is determined by measuring the intensity of the fluorescence. Copy number is calculated based on the normalized ratio of the PLP1 gene to each of the reference genes for the patient and controls.

Duplications of variable size and other dosage changes (deletions, triplications, quintuplications) are found in at least 50 percent of males with PLP1-related disorders. This test will detect duplications and other dosage changes that are in tandem as well as duplications that are inserted elsewhere in the genome. Duplication testing alone will not detect point mutations or smaller deletions or insertions.

Sequencing:
Testing is performed by sequencing the entire coding region and intron-exon junctions of PLP1. This assay will detect point mutations, small deletions and small insertions. Sequencing alone will not detect a partial or whole gene deletion or duplication.

Point mutations are found in 15 percent or less of males with PLP1-related disorders. A negative result will exclude the presence of a mutation in the regions tested with greater than 99 percent sensitivity. However, a negative result does not exclude the possibility that mutations are present in other regions of the PLP1 gene or in other genes.

Sensitivity:
If duplication testing and sequencing are both negative, it does not rule out a PLP1-related disorder. Approximately 40 percent of males with clinical findings consistent with the PLP1-related disorders do not have an identifiable mutation in the PLP1 gene, suggesting that mutations may occur in regions of the gene that are not analyzed or in another gene.

A negative test does not rule out a genetic cause of a neurologic disorder. There are many other genes associated with different types of neurologic disorders and leukodystrophies, some of which are available for testing in our laboratory and can be performed if clinically indicated.

Sample Requirements

Draw one or two 4-cc tubes of blood in EDTA/purple-top tube (minimum of 1-2 cc for infants).

Turn-around time: 10-14 business days per tier

CPT Codes and Cost

Additional Resources

• GeneReview
• OMIM entries
• The PMD Foundation
  

Gene: SMN1
Protein: survival motor neuron protein

Clinical Characteristics

• progressive, symmetric proximal muscle weakness
• respiratory failure
• muscle atrophy due to degeneration of lower motor neurons of the spinal cord and lower brainstem
• spectrum of phenotypes with age of onset ranging from prenatal to adulthood
  • Prenatal
    • athrogryposis multiplex congenita
    • minimal facial weakness
  • Onset prior to 6 months - SMA type I
    • (Werdnig-Hoffmann disease)
    • absent reflexes
    • able to sit with support
    • tongue fasciculations
    • mild contractures of large joints
    • life span typically less than 2 years
  • Onset between 6 and 12 months of age – SMA type II
    • able to sit independently when placed in a sitting position
    • postural tremor of fingers
    • life span ranges from early adulthood to normal
  • Onset in childhood after 12 months of age - SMA type III
    • able to walk independently
    • loss of ambulation in adolescence or adulthood
    • normal life expectancy
  • Adult onset - SMA type IV
    • achieve typical motor milestones
    • onset of muscle weakness in second or third decade of life
    • normal life expectancy

Inheritance pattern: Autosomal recessive

What Can Be Learned From This Test

Deletion testing:

In approximately 95 percent of cases, SMA is caused by homozygous deletion of SMN1. Deletion testing is performed to detect the presence or absence of SMN1. This test does not detect heterozygous carriers of an SMN1 deletion.

Indications:

Confirm or rule out a suspected diagnosis of SMA

Sequence analysis:

About 5 percent of the time, SMA is caused by a deletion of SMN1 on one allele in combination with an intragenic mutation on the other allele. Gene sequencing can be performed for individuals who test negative by deletion testing. The entire coding regions of SMN1 and SMN2 are sequenced. Large duplications and deletions within the gene may not be detected.

Indications:

• Confirm or rule out a suspected diagnosis of SMA after negative deletion testing (deletion testing must be completed prior to the sequencing test, either in our lab or another facility).
• Carrier testing in an adult for a known familial intragenic mutation (Please note: Our lab does not offer sequence analysis for general population carrier screening.).

Sensitivity:

SMN1 is the only gene known to be associated with this form of SMA. These assays will detect mutations in greater than 99 percent of individuals with this form of SMA. There are other disorders that include muscular atrophy and loss of lower motor neurons. A negative SMN1 test does not rule out a genetic cause of muscle weakness, and additional testing may be indicated.

Sample Requirements

Draw one or two 4-cc tubes of blood in EDTA/purple-top tube (minimum of 1-2 cc for infants).

Turnaround time:

• Deletion testing: 7-10 business days
• Dosage analysis: 7-10 business days
• Sequence analysis: 10-14 business days
  

CPT Codes and Cost

Additional Resources

• GeneReview
• OMIM entries

(Distal Spinal Muscular Atrophy: DSMA1, Distal Hereditary Motor Neuronopathy type VI: dHMN6 or HMN6)

Gene: IGHMBP2
Protein: Immunoglobulin Mu-Binding Protein 2

Clinical Characteristics

• sudden onset of respiratory symptoms
  • stridor/weak cry
  • diaphragmatic paralysis within first year of life
• muscle weakness
  • initially distal, progressing to generalized
• intrauterine growth retardation
• premature birth
• foot deformities
• autonomic nervous system dysfunction
• seizures
• phenotypic variability between and within families

Inheritance pattern: Autosomal recessive

What Can Be Learned From This Test

Testing is performed by sequencing all exons and partial intronic regions of IGHMBP2. This will detect point mutations, small deletions and small insertions. It will not detect a partial or whole gene deletion or duplication.

Sample Requirements

Draw one or two 4-cc tubes of blood in EDTA/purple-top tube (minimum of 1-2 cc for infants).

Turnaround time: 10-14 business days

CPT Codes and Cost

Additional Resources

• Smard 1 on OMIM
• IGHMBP2 on OMIM

Spondyloocular syndrome (SOS)

Gene: XYLT2
Protein: xylosyltransferase II

Clinical characteristics

• Skeletal findings
  • osteopenia or osteoporosis predisposing to multiple vertebral compression fractures and long-bone fractures
  • platyspondyly
  • kyphosis
• Sensorineural hearing loss
• Vision impairment
  • cataracts
  • retinal detachment
• Cardiac defects
  • atrial septal defect
  • mitral valve prolapse
• Learning difficulties in some individuals

Inheritance pattern: Autosomal recessive

What this test can tell us

Testing is performed by sequencing all exons and the surrounding intronic regions of the XYLT2 gene. This will detect point mutations, small deletions, and small insertions. It will not detect a partial or whole gene deletion or duplication. To date, no large deletions or duplications have been reported.

Sample requirements: Draw one or two 4cc tubes of blood in EDTA/ purple top tube (minimum of 1-2 cc for infants)

Turn-around time: 10-14 business days

CPT codes and cost:
Full Gene Sequencing: 81479 $700
Known Variant Testing: 81479 $225

Links :

OMIM entries

Gene: RBM10
Protein: RNA-binding protein 10

Clinical Characteristics

• talipes equinovarus
• atrial septal defect
• robin sequence
• persistence of the left superior vena cava
• low-set ears
• cryptorchidism
• pulmonary hypoplasia
• prenatal or postnatal lethality

Inheritance pattern: X-linked

What Can Be Learned From This Test

Testing is performed by sequencing the entire RBM10 gene and surrounding regions. This will detect point mutations, small deletions and small insertions. It will not detect a whole gene deletion or duplication.

RBM10 is the only gene known to be associated with TARP syndrome. A negative test does not rule out a diagnosis of TARP syndrome since a mutation could be in a region not sequenced or in another gene.

Sample Requirements

Draw one or two 4cc tubes of blood in EDTA/purple top tube (minimum of 1-2 cc for infants)

Turnaround time: 10-14 business days

CPT Codes and Cost

Additional Resources

• OMIM entries

Gene: CACNA1C
Protein: Voltage-dependent L-type calcium channel subunit alpha-1C

Clinical Characteristics

• prolonged QT interval
• other EKG abnormalities
  • 2:1 atrioventricular block
  • macroscopic T-wave alternans
• syndactyly
  • bilateral cutaneous syndactyly of toes two and three
  • unilateral or bilateral cutaneous syndactyly variably involving fingers 2, 3, 4, and 5
• congenital heart defects
• dysmorphic facial features
• thin scalp hair and poor tooth enamel
• neurologic features
  • hypotonia
  • developmental delay
  • autism
  • seizures

Inheritance pattern:

• autosomal dominant
• typically de novo; germline mosaicism has been reported

What Can Be Learned From This Test

Testing is performed by sequencing exons 8 and 8A (alternatively transcribed coding exons) and the surrounding intronic regions of the CACNA1C gene. This will detect point mutations, small deletions and small insertions. It will not detect a partial or whole gene deletion or duplication.

A negative test result does not rule out a genetic cause of long QT syndrome (LQTS). Other genes are known to be associated with LQTS and this test will only detect mutations associated with Timothy syndrome. This test will not detect mutations in other regions of the gene, such as those associated with Brugada syndrome.

Sample Requirements

Draw one or two 4cc tubes of blood in EDTA/ purple top tube (minimum of 1-2 cc for infants).

Turnaround time: 10-14 business days

CPT Codes and Cost

Additional Resources

• GeneReviews
• OMIM entries

Gene: TRPV4
Protein: Transient receptor potential cation channel, subfamily V, member 4

Clinical characteristics

Congenital distal spinal muscular atrophy

• congenital weakness of lower limbs
• weakness of pelvic girdle and trunk may or may not be present
• congenital contractures may or may not be present
• nonprogressive

Scapuloperoneal spinal muscular atrophy

(also known as neurogenic scapuloperoneal amyotrophy)

• congenital amyoplasia
• progressive scapuloperoneal atrophy and weakness
• laryngeal palsy

Hereditary motor and sensory neuropathy, type IIC

(also known as Charcot-Marie-Tooth disease type 2C)

• progressive weakness of limb, diaphragm, intercostal and laryngeal muscles
• sensory involvement may be mild or asymptomatic

Inheritance pattern: Autosomal dominant

What This Test Can Tell Us

Mutations in exons 3, 5 and 6 of TRPV4 have been associated with the three neuromuscular disorders listed above, which show overlap in their clinical symptoms. Testing can be performed by sequencing exons 3, 5 and 6, or by sequencing the entire coding region. This will detect point mutations, small deletions and small insertions. It will not detect a partial or whole gene deletion or duplication.

TRPV4 is the only gene known to be associated with these specific disorders. A negative test does not rule out a genetic cause of neuromuscular problems, as there are many other genes associated with different types of neuromuscular disorders.

Certain mutations in exons 6 and 11 through 16 of TRPV4 have been associated with three specific types of autosomal dominant skeletal dysplasias. One of these mutations may be identified during this test. This will be reported to the ordering provider.

Sample Requirements

Draw one or two 4cc tubes of blood in EDTA/purple top tube (minimum of 1-2 cc for infants)

Turnaround time: 10-14 business days

CPT Codes and Cost

Additional Resources

• GeneReview for Hereditary Motor and Sensory Neuropathy, type II
• OMIM entries

Gene: TRPV4
Protein: transient receptor potential cation channel, subfamily V, member 4

Clinical Characteristics

Spondylometaphyseal dysplasia, Koslowski type

• typically diagnosed around 2 years of age
• short stature of postnatal onset
• progressive kyphoscoliosis
• waddling gait
• radiographic findings
  • odontoid hypoplasia
  • delayed bone age
  • platyspondyly and widely spaced vertebral pedicles
  • metaphyseal irregularities
  • short square ilia, flat acetabular roofs, wide proximal femoral epiphyses

Metatropic dysplasia

• short limbs and long narrow trunk in newborn period
• joint contractures and enlargement
• progressive kyphoscoliosis resulting in short trunk and relatively longer limbs
• platyspondyly
• metaphyseal enlargement

Brachyolmia type 3

• short trunk
• mild short stature
• severe kyphoscoliosis
• flattened irregular cervical vertebrae
• metaphyseal and epiphyseal abnormalities may be minimal

Recent evidence that TRPV4 mutations also cause

• spondyloepiphyseal dysplasia, Maroteaux type/
  Brachyolmia Type 2
  
• parastremmatic dysplasia

Inheritance pattern: Autosomal dominant

What Can Be Learned From This Test

Testing is performed by sequencing the entire coding region of TRPV4. This will detect point mutations, small deletions and small insertions. It will not detect a partial or whole gene deletion or duplication. Partial sequencing in regions known to carry mutations can be carried out; please note on submission form if this tiered approach is being requested.

TRPV4 is the only gene known to be associated with these specific disorders. There are other types of spondylometaphyseal dysplasia and brachyolmia that are not associated with mutations in TRPV4. A negative test does not rule out a genetic cause of a skeletal dysplasia, as there are many other genes associated with different types of skeletal dysplasias.

Certain mutations in TRPV4 have been associated with 3 specific types of autosomal dominant neuromuscular disorders. One of these mutations may be identified during this test. This will be reported to the ordering provider.

Sample Requirements

Draw one or two 4cc tubes of blood in EDTA/ purple top tube (minimum of 1-2 cc for infants)

Turnaround time: 10-14 business days

CPT Codes and Cost:

Additional Resources

• OMIM entries