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Mental Retardation with Cerebellar Hypoplasia and Distinctive Facial Appearance via the OPHN1 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
OPHN1 81479 81479,81479 $990
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
9857OPHN181479 81479,81479 $990 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. If the Sanger option is selected, CNV detection may be ordered through Test #600.

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 platform).

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

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

For Sanger Sequencing click here.

Turnaround Time

3 weeks on average for standard orders or 2 weeks 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.


Genetic Counselors


  • Sali Farhan, PhD

Clinical Features and Genetics

Clinical Features

X-linked mental retardation with cerebellar hypoplasia and distinctive facial appearance (OMIM 300486) is a clinically heterogeneous disorder with intrafamilial and interfamilial phenotypic variability (Zanni et al. Neurology 65:1364-1369, 2005). X-linked mental retardation with cerebellar hypoplasia and distinctive facial appearance is mainly characterized by moderate to severe mental retardation and cerebellar anomalies, particularly cerebellar vermis hypoplasia presented as isolated vermis hypoplasia and common facial features such as prominent supraorbital ridges, hypotelorism, deep-set eyes, long tubular nose, short philtrum, thin upper lip, and prominent chin (Billuart et al. Nature 392:923-926, 1998; Philip et al. J Med Genet 40:441-446, 2003; Zanni et al. 2005). Brain imaging (MRI) may also reveal cerebral atrophy, ventriculomegaly, and rarely hydrocephalus (Zanni et al. 2005). Other clinical findings such as tall stature, macrocephaly, hypotonia, developmental delay, seizures, oculomotor problems, language problems, and neurological and behavioral problems such as dysmetria, adiadochokinesia, hyperactivity, and anxiety have been occasionally reported (Philip et al. 2003; Zanni et al. 2005).


X-linked mental retardation with cerebellar hypoplasia is inherited as X-linked recessive disorder, where males are more severely affected than females. However heterozygous females may have mild cognitive impairments (Zanni et al. Neurology 65: 1364-1369, 2005). X-linked mental retardation with cerebellar hypoplasia is caused by variants in the oligophrenin-1 (OPHN1) gene (Billuart et al. Nature 392: 923-926, 1998). OPHN1 gene encodes the oligophrenin-1 protein, which contains a domain common in Rho-GTPase-activating proteins suggesting a role in cell migration and outgrowth of axons and dendrites, neuronal morphogenesis and synapse maturation (Billuart et al. 1998; Zanni et al 2005). A mix of nonsense, splice site, frameshift, and single- and multiple-exon deletion variants have been reported in the OPHN1 gene (Billuart et al. 1998; Philip et al. J Med Genet 40: 441-446, 2003; Bergmann et al. Brain 126:1537-1544, 2003, Chabrol et al. Am J Med Genet 138: 314-317, 2005).

Clinical Sensitivity - Sequencing with CNV PGxome

OPHN1 variants were found in approximately 12% of patients with mental retardation with known cerebellar anomalies and in about 1% of X-linked mental retardation patients (Zanni et al. Neurology 65:1364-9, 2005).

Testing Strategy

This test provides full coverage of all coding exons of the OPHN1 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 X-linked mental retardation with cerebellar hypoplasia and family members of patients who have known OPHN1 variants.


Official Gene Symbol OMIM ID
OPHN1 300127
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


  • Bergmann, C., et.al. (2003). PubMed ID: 12805098
  • Billuart, P., et.al. (1998). PubMed ID: 9582072
  • Chabrol, B., et.al. (2005). PubMed ID: 16158428
  • Philip, N., et.al. (2003). PubMed ID: 12807966
  • Zanni, G., et.al. (2005). PubMed ID: 16221952


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

If ordering a Duo or Trio test, the proband and all comparator samples are required to initiate testing. If we do not receive all required samples for the test ordered within 21 days, we will convert the order to the most effective testing strategy with the samples available. Prior authorization and/or billing in place may be impacted by a change in test code.

Specimen Types

Specimen Requirements and Shipping Details

PGxome (Exome) Sequencing Panel

PGnome (Genome) Sequencing Panel

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View Ordering Instructions

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2) Select Additional Test Options

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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