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SLC26A2-Related Disorders via the SLC26A2 Gene

Summary and Pricing

Test Method

Sequencing and CNV Detection via NextGen Sequencing using PG-Select Capture Probes
Test Code Test Copy GenesTest CPT Code Gene CPT Codes Copy CPT Codes Base Price
7827 SLC26A2 81479 81479,81479 $640 Order Options and Pricing
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
7827SLC26A281479 81479,81479 $640 Order Options and Pricing

Pricing Comments

This test is also offered via our exome backbone with CNV detection (click here). The exome-based test may be higher priced, but permits reflex to the entire exome or to any other set of clinically relevant genes.

An additional 25% charge will be applied to STAT orders. STAT orders are prioritized throughout the testing process.

Turnaround Time

18 days on average for standard orders or 13 days on average for STAT orders.

Please note: Once the testing process begins, an Estimated Report Date (ERD) range will be displayed in the portal. This is the most accurate prediction of when your report will be complete and may differ from the average TAT published on our website. About 85% of our tests will be reported within or before the ERD range. We will notify you of significant delays or holds which will impact the ERD. Learn more about turnaround times here.

Targeted Testing

For ordering sequencing of targeted known variants, go to our Targeted Variants page.

EMAIL CONTACTS

Genetic Counselors

Geneticist

  • Juan Dong, PhD, FACMG

Clinical Features and Genetics

Clinical Features

Pathogenic variants in the SLC26A2 gene are known to cause the following autosomal recessive conditions:

Achondrogenesis type 1B (ACG1B) is characterized by extremely short limbs with short fingers and toes, flat face, short neck, hypoplasia of the thorax, protuberant abdomen, and hydropic fetal appearance caused by the abundance of soft tissue relative to the short skeleton (Bonafé et al. 2013. PubMed ID: 20301689). Death occurs prenatally or shortly after birth.

Atelosteogenesis type 2 (AO2) is characterized by rhizomelic limb shortening with normal-sized skull, hitchhiker thumbs, small chest, protuberant abdomen, cleft palate, and distinctive facial features (midface hypoplasia, depressed nasal bridge, epicanthus, micrognathia). Other typical findings include ulnar deviation of the fingers, gap between the first and second toes, and clubfoot (Bonafé et al. 2014. PubMed ID: 20301493). AO2 is lethal at birth or shortly thereafter because of pulmonary hypoplasia and tracheobronchomalacia.

Diastrophic dysplasia is characterized by limb shortening, normal-sized skull, hitchhiker thumbs, spinal deformities (scoliosis, exaggerated lumbar lordosis, cervical kyphosis), and contractures of the large joints with deformities and early-onset osteoarthritis. Other typical findings include ulnar deviation of the fingers, gap between the first and second toes, and clubfoot. On occasion the disease can be lethal at birth, but most affected individuals survive the neonatal period and develop physical limitations with normal intelligence (Bonafé et al. 2013. PubMed ID: 20301524).

Multiple epiphyseal dysplasia (MED) is characterized by joint pain (usually in the hips or knees); malformations of hands, feet, and knees; and scoliosis. Approximately half of the affected individuals have some abnormal finding at birth such as clubfoot or clinodactyly. Onset of articular pain is variable, but usually occurs in late childhood. Stature is usually within the normal range prior to puberty; in adulthood, stature is only slightly diminished. Functional disability is mild (Bonafé et al. 2014. PubMed ID: 20301483).

Genetics

SLC26A2-related conditions are inherited in an autosomal recessive manner with complete penetrance. SLC26A2 encodes solute carrier family 26 member A2, a sulfate transporter. This transmembrane protein transports sulfate into chondrocytes to maintain adequate sulfation of proteoglycans. Undersulfation of proteoglycans affects the composition of the extracellular matrix and leads to impaired proteoglycan deposition, which is necessary for proper enchondral bone formation (Corsi et al. 2001. PubMed ID: 11570921; Forlino et al. 2005. PubMed ID: 15703192).

To date, ~50 pathogenic variants have been documented (missense: ~60%; truncating: 37%, splicing: ~4%). The Finnish founder mutation c.-26+2T>C has been reported in several SLC26A2-related conditions (Zechi-Ceide et al. 2013. PubMed ID: 23840040); this variant has been also observed in a public database with allele frequency up to ~0.7% in European Finnish populations, and up to 0.1% in the general European population (http://gnomad.broadinstitute.org/variant/5-149340544-T-C). The other three common pathogenic variants are: c.532C>T, p.Arg178*; c.835C>T, p.Arg279Trp, and c.1957T>A, p.Cys653Ser (Bonafé et al. 2014. PubMed ID: 20301493). The c.835C>T, p.Arg279Trp has been observed up to ~0.2% in Ashkenazi Jewish populations, and ~0.15% European populations (http://gnomad.broadinstitute.org/variant/5-149359991-C-T). In the compound heterozygous condition, the c.-26+2T>C variant, along with c.835C>T, p.Arg279Trp has also been found in several Swedish patients with autosomal recessive multiple epiphyseal dysplasia (Mäkitie et al. 2015. PubMed ID: 24598000).

Clinical Sensitivity - Sequencing with CNV PG-Select

This test is predicted to detect causative pathogenic variants in >95% of individuals affected with Atelosteogenesis type 2 (AO2) (Rossi & Superti-Furga. 2001 PubMed ID: 11241838).

This test is predicted to detect causative pathogenic variants in ~70% of individuals with clinical and radiologic features compatible with autosomal recessive multiple epiphyseal dysplasia (MED) (Jackson et al. 2012. PubMed ID: 21922596). The radiologic sign of double-layered patella in lateral knee radiograph is specific for autosomal recessive MED; the c.1957T>A, p.Cys653Ser variant was found in three patients with this sign (Mäkitie et al. 2003. PubMed ID: 12966518).

No disease related large deletions/duplications have been reported in the SLC26A2 gene.

Testing Strategy

This test provides full coverage of all coding exons of the SLC26A2 gene, plus ~10 bases of flanking noncoding DNA. We define full coverage as >20X NGS reads or Sanger sequencing.

This test also includes coverage of the c.-26+2T>C variant.

Indications for Test

Candidates for this test are newborns with abnormal clinical and radiologic/histologic features consistent with Achondrogenesis type 1B, Atelosteogenesis type 2, Diastrophic dysplasia, and autosomal recessive multiple epiphyseal dysplasia.

Gene

Official Gene Symbol OMIM ID
SLC26A2 606718
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Related Test

Name
Short Rib Skeletal Dysplasia Panel

Citations

  • Bonafé et al. 2013. PubMed ID: 20301524
  • Bonafé et al. 2013. PubMed ID: 20301689
  • Bonafé et al. 2014. PubMed ID: 20301493
  • Bonafé et al. 2014. PubMed ID: 20301483
  • Corsi et.al. 2001. PubMed ID: 11570921
  • Forlino et.al. 2005. PubMed ID: 15703192
  • Jackson et al. 2012. PubMed ID: 21922596
  • Mäkitie et al. 2003. PubMed ID: 12966518
  • Mäkitie et al. 2015. PubMed ID: 24598000
  • Rossi and Superti-Furga. 2001. PubMed ID: 11241838
  • Zechi-Ceide et al. 2013. PubMed ID: 23840040

Ordering/Specimens

Ordering Options

We offer several options when ordering sequencing tests. For more information on these options, see our Ordering Instructions page. To view available options, click on the Order Options button within the test description.

myPrevent - Online Ordering

  • The test can be added to your online orders in the Summary and Pricing section.
  • Once the test has been added log in to myPrevent to fill out an online requisition form.
  • PGnome sequencing panels can be ordered via the myPrevent portal only at this time.

Requisition Form

  • A completed requisition form must accompany all specimens.
  • Billing information along with specimen and shipping instructions are within the requisition form.
  • All testing must be ordered by a qualified healthcare provider.

For Requisition Forms, visit our Forms page


Specimen Types

Specimen Requirements and Shipping Details

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ORDER OPTIONS

View Ordering Instructions

1) Select Test Method (Backbone)


1) Select Test Type


2) Select Additional Test Options

STAT and Prenatal Test Options are not available with Patient Plus.

No Additional Test Options are available for this test.

Note: acceptable specimen types are whole blood and DNA from whole blood only.
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