Craniofrontonasal Syndrome via the EFNB1 Gene

  • Summary and Pricing
  • Clinical Features and Genetics
  • Citations
  • Methods
  • Ordering/Specimens
Order Kits


Test Code Test Copy GenesIndividual Gene PriceCPT Code Copy CPT Codes
2297 EFNB1$580.00 81479 Add to Order
Targeted Testing

For ordering targeted known variants, please proceed to our Targeted Variants landing page.

Turnaround Time

The great majority of tests are completed within 18 days.

Clinical Sensitivity
EFNB1 pathogenic variants were detected in 33 out of 38 unrelated clinical suspected craniofrontonasal dysplasia patients (Wieland et al. 2005).

See More

See Less

Clinical Features
EFNB1-related craniofrontonasal syndrome is mainly characterized by hypertelorism, broad nasal tip, brachycephaly, coronal suture synostosis, strabismus, frontal bossing, bifid nasal tip, and high-arched palate. Some less common features include asymmetric lower limbs, grooved nails, thick/wiry hair, webbed neck/short neck, cleft lip and/or palate, and corpus callosum hypoplasia or agenesis. Over 98% of patients had normal mental development (Wieacker and Wieland 2005).
EFNB1-related craniofrontonasal dysplasia shows an unusual X-linked inheritance pattern. Heterozygous female patients generally present more severe clinical features than hemizygous male patients (Wieland et al. 2005). Male patients may only have hypertelorism, however, a few males mosaic for an EFNB1 pathogenic variant had severe clinical presentations (Twigg et al. 2013). The EFNB1 protein is a member of the ligand of Eph-related receptor tyrosine kinases, which may play roles during embryonic morphogenesis. Over 100 EFNB1 pathogenic variants have been reported. They include: missense (37%), nonsense: (10%), splicing (10%), small deletion/insertions (33%), gross deletion/insertion (10%) and one pre-coding point pathogenic variant (Wieland et al. 2005; Twigg et al. 2006; Twigg et al. 2013; Human Gene Mutation Database). Wieland et al. studied 9 familial and 29 sporadic craniofrontonasal dysplasia patients and identified pathogenic variants in 8/9 familial cases and 25/29 sporadic cases, respectively. De novo variants were seen in 6 out of the 25 sporadic cases. The c.196C>T (p.Arg66*) variant was seen in one familial and four sporadic cases (Wieland et al. 2005).
Testing Strategy
The EFNB1 protein is coded by exons 1 to 5 of the EFNB1 gene on chromosome Xq12. Testing involves PCR amplification from genomic DNA and bidirectional Sanger sequencing of the coding exons and ~20 bp of adjacent noncoding sequences. We will also sequence any single exon (Test #100) in family members of patients with a known mutation or to confirm research results.
Indications for Test
Candidates for this test are patients with symptoms consistent with X-linked Craniofrontonasal syndrome, and the family members of patients who have known EFNB1 pathogenic variants.


Official Gene Symbol OMIM ID
EFNB1 300035
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


Name Inheritance OMIM ID
Craniofrontonasal Dysplasia 304110

Related Tests

FGFR1-Related Disorders via the FGFR1 Gene
FGFR2-Related Disorders via the FGFR2 Gene
FGFR3-Related Disorders via the FGFR3 Gene
Achondroplasia via the FGFR3 Gene, Exon 10
Craniosynostosis and Related Disorders Sequencing Panel
Craniosynostosis via the MSX2 Gene
Craniosynostosis via the TCF12 Gene
Frontonasal Dysplasia (Frontorhiny) via the ALX3 Gene
Hypochondroplasia via the FGFR3 Gene
Saethre-Chotzen Syndrome Via the TWIST1 Gene
Thanatophoric Dysplasia (TD) via the FGFR3 Gene


Genetic Counselors
  • Human Gene Mutation Database (Bio-base).
  • Twigg S.R. et al. 2006. American Journal of Human Genetics. 78: 999-1010. PubMed ID: 16685650
  • Twigg S.R. et al. 2013. Human Molecular Genetics. 22: 1654-62. PubMed ID: 23335590
  • Wieacker P., Wieland I. 2005. Molecular Genetics and Metabolism. 86: 110-6. PubMed ID: 16143553
  • Wieland I. et al. 2005. Human Mutation. 26: 113-8. PubMed ID: 15959873
Order Kits

Bi-Directional Sanger Sequencing

Test Procedure

Nomenclature for sequence variants was from the Human Genome Variation Society (  As required, DNA is extracted from the patient specimen.  PCR is used to amplify the indicated exons plus additional flanking non-coding sequence.  After cleaning of the PCR products, cycle sequencing is carried out using the ABI Big Dye Terminator v.3.0 kit.  Products are resolved by electrophoresis on an ABI 3730xl capillary sequencer.  In most cases, sequencing is performed in both forward and reverse directions; in some cases, sequencing is performed twice in either the forward or reverse directions.  In nearly all cases, the full coding region of each exon as well as 20 bases of non-coding DNA flanking the exon are sequenced.

Analytical Validity

As of March 2016, we compared 17.37 Mb of Sanger DNA sequence generated at PreventionGenetics to NextGen sequence generated in other labs. We detected only 4 errors in our Sanger sequences, and these were all due to allele dropout during PCR. For Proficiency Testing, both external and internal, in the 12 years of our lab operation we have Sanger sequenced roughly 8,800 PCR amplicons. Only one error has been identified, and this was due to sequence analysis error.

Our Sanger sequencing is capable of detecting virtually all nucleotide substitutions within the PCR amplicons. Similarly, we detect essentially all heterozygous or homozygous deletions within the amplicons. Homozygous deletions which overlap one or more PCR primer annealing sites are detectable as PCR failure. Heterozygous deletions which overlap one or more PCR primer annealing sites are usually not detected (see Analytical Limitations). All heterozygous insertions within the amplicons up to about 100 nucleotides in length appear to be detectable. Larger heterozygous insertions may not be detected. All homozygous insertions within the amplicons up to about 300 nucleotides in length appear to be detectable. Larger homozygous insertions may masquerade as homozygous deletions (PCR failure).

Analytical Limitations

In exons where our sequencing did not reveal any variation between the two alleles, we cannot be certain that we were able to PCR amplify both of the patient’s alleles. Occasionally, a patient may carry an allele which does not amplify, due for example to a deletion or a large insertion. In these cases, the report contains no information about the second allele.

Similarly, our sequencing tests have almost no power to detect duplications, triplications, etc. of the gene sequences.

In most cases, only the indicated exons and roughly 20 bp of flanking non-coding sequence on each side are analyzed. Test reports contain little or no information about other portions of the gene, including many regulatory regions.

In nearly all cases, we are unable to determine the phase of sequence variants. In particular, when we find two likely causative mutations for recessive disorders, we cannot be certain that the mutations are on different alleles.

Our ability to detect minor sequence variants, due for example to somatic mosaicism is limited. Sequence variants that are present in less than 50% of the patient’s nucleated cells may not be detected.

Runs of mononucleotide repeats (eg (A)n or (T)n) with n >8 in the reference sequence are generally not analyzed because of strand slippage during PCR and cycle sequencing.

Unless otherwise indicated, the sequence data that we report are based on DNA isolated from a specific tissue (usually leukocytes). Test reports contain no information about gene sequences in other tissues.

Order Kits

Ordering Options

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.
  • 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.


(Delivery accepted Monday - Saturday)

  • Collect 3 ml -5 ml (5 ml preferred) of whole blood in EDTA (purple top tube) or ACD (yellow top tube). For Test #500-DNA Banking only, collect 10 ml -20 ml of whole blood.
  • For small babies, we require a minimum of 1 ml of blood.
  • Only one blood tube is required for multiple tests.
  • Ship blood tubes at room temperature in an insulated container. Do not freeze blood.
  • During hot weather, include a frozen ice pack in the shipping container. Place a paper towel or other thin material between the ice pack and the blood tube.
  • In cold weather, include an unfrozen ice pack in the shipping container as insulation.
  • At room temperature, blood specimen is stable for up to 48 hours.
  • If refrigerated, blood specimen is stable for up to one week.
  • Label the tube with the patient name, date of birth and/or ID number.


(Delivery accepted Monday - Saturday)

  • Send in screw cap tube at least 5 µg -10 µg of purified DNA at a concentration of at least 20 µg/ml for NGS and Sanger tests and at least 5 µg of purified DNA at a concentration of at least 100 µg/ml for gene-centric aCGH, MLPA, and CMA tests, minimum 2 µg for limited specimens.
  • For requests requiring more than one test, send an additional 5 µg DNA per test ordered when possible.
  • DNA may be shipped at room temperature.
  • Label the tube with the composition of the solute, DNA concentration as well as the patient’s name, date of birth, and/or ID number.
  • We only accept genomic DNA for testing. We do NOT accept products of whole genome amplification reactions or other amplification reactions.


(Delivery preferred Monday - Thursday)

  • PreventionGenetics should be notified in advance of arrival of a cell culture.
  • Culture and send at least two T25 flasks of confluent cells.
  • Some panels may require additional flasks (dependent on size of genes, amount of Sanger sequencing required, etc.). Multiple test requests may also require additional flasks. Please contact us for details.
  • Send specimens in insulated, shatterproof container overnight.
  • Cell cultures may be shipped at room temperature or refrigerated.
  • Label the flasks with the patient name, date of birth, and/or ID number.
  • We strongly recommend maintaining a local back-up culture. We do not culture cells.
loading Loading... ×