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Acrofacial Dysostosis 1, Nagar Type via the SF3B4 Gene

Summary and Pricing

Test Method

Exome Sequencing with CNV Detection
Test Code Test Copy GenesTest CPT Code Gene CPT Codes Copy CPT Codes Base Price
4233 SF3B4 81479 81479,81479 $890 Order Options and Pricing
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
4233SF3B481479 81479,81479 $890 Order Options and Pricing

Pricing Comments

Our favored testing approach is exome based NextGen sequencing with CNV analysis. This will allow cost effective reflexing to PGxome or other exome based tests. However, if full gene Sanger sequencing is desired for STAT turnaround time, insurance, or other reasons, please see link below for Test Code, pricing, and turnaround time information.

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

Click here for costs to reflex to whole PGxome (if original test is on PGxome Sequencing backbone).

Click here for costs to reflex to whole PGnome (if original test is on PGnome Sequencing backbone).

The Sanger Sequencing method for this test is NY State approved.

For Sanger Sequencing click here.

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

  • Stela Berisha, PhD, FACMG

Clinical Features and Genetics

Clinical Features

Acrofacial dysostosis, Nager type is characterized by malformation of the craniofacial area and the limbs. The major craniofacial features are: downslanted palpebral fissures, midface retrusion, and micrognathia. The upper limb defects consist of small or absent thumbs, triphalangeal thumbs, radial hypoplasia or aplasia, and radioulnar synostosis. Some other features include, but are not limited to, cleft palate, tracheotomy and hearing loss. Acrofacial dysostosis, Nager type shares some features with Miller syndrome (Bernier et al. 2012).

Genetics

SF3B4-related Acrofacial dysostosis, Nager type is inherited in an autosomal dominant manner. One SF3B4 de novo pathogenic variant was found in a patient affected with Rodriguez syndrome, a severe acrofacial dysostosis, phocomelia with pre- and post-axial limb defects, fibular agenesis, rib, and shoulder girdle anomalies (McPherson et al. 2014). In a study of 14 families, at least five of the sporadic cases were de novo, suggesting complete penetrance (Petit et al. 2014). The SF3B4 protein is a component of the U2 pre-mRNA spliceosomal complex involving RNA-binding activity. To date, ~30 unique pathogenic variants have been documented in HGMD (Human Gene Mutation Database): missense (6%); nonsense (20%), splicing (13%), small deletion/insertion (61%). No large deletions/insertions have been reported (Bernier et al. 2012; Petit et al. 2014; Castori et al. 2014; HGMD).

Clinical Sensitivity - Sequencing with CNV PGxome

Bernier et al. (2012) identified 18 different heterozygous SF3B4 pathogenic variants in 20 (57%) of 35 families affected by Acrofacial dysostosis, Nager type. Analytical sensitivity should be high because almost all of the documented SF3B4 pathogenic variants are point mutations, and small deletion/insertions which are expected to be detected by direct sequencing of genomic DNA.

Testing Strategy

This test provides full coverage of all coding exons of the SF3B4 gene plus 10 bases of flanking noncoding DNA in all available transcripts along with other non-coding regions in which pathogenic variants have been identified at PreventionGenetics or reported elsewhere. We define full coverage as >20X NGS reads or Sanger sequencing. PGnome panels typically provide slightly increased coverage over the PGxome equivalent. PGnome sequencing panels have the added benefit of additional analysis and reporting of deep intronic regions (where applicable).

Dependent on the sequencing backbone selected for this testing, discounted reflex testing to any other similar backbone-based test is available (i.e., PGxome panel to whole PGxome; PGnome panel to whole PGnome).

Indications for Test

Candidates for this test are patients with symptoms consistent with SF3B4 and the family members of patients who have known SF3B4 mutations.

Gene

Official Gene Symbol OMIM ID
SF3B4 605593
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Disease

Name Inheritance OMIM ID
Acrofacial Dysostosis 1, Nager Type AD 154400

Citations

  • Bernier et al. 2012. PubMed ID: 22541558
  • Castori M, Bottillo I, D’Angelantonio D, Morlino S, Bernardo C De, Scassellati Sforzolini G, Silvestri E, Grammatico P. 2014. A 22-Week-Old Fetus with Nager Syndrome and Congenital Diaphragmatic Hernia due to a Novel SF3B4 Mutation. Mol Syndromol 5: 241-244. PubMed ID: 25337072
  • Human Gene Mutation Database (Bio-base).
  • McPherson et al. 2014. PubMed ID: 24715698
  • Petit et al. 2014. PubMed ID: 24003905

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

PGxome (Exome) Sequencing Panel

PGnome (Genome) Sequencing Panel

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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.
Total Price: $
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