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Primary Microcephaly, Autosomal Recessive, via the MCPH1 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
MCPH1 81479 81479,81479 $990
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
9943MCPH181479 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


  • Renee Bend, PhD

Clinical Features and Genetics

Clinical Features

Autosomal recessive primary microcephaly (MCPH) is a neurodevelopmental disorder that results from hypoplasia of the cerebral cortex. The hallmark clinical feature of MCPH is head circumference at least three standard deviations below the population mean for age and sex (Jackson et al. Am J Hum Genet 63:541-546, 1998; Passemard et al. GeneReviews, 2009, www.genetests.org). In MCPH patients, microcephaly is usually detectable by the 32nd week of gestation and is apparent at birth (Woods et al. Am J Hum Genet 76:717-728, 2005). Typically, microcephaly persists throughout the patient’s lifetime. Additional features often include a sloping forehead, various degrees of cognitive disabilities, seizures, congenital hearing loss, and short stature. Brain imaging findings may include reduction of the cerebral cortical volume with simplification of the gyral cortical pattern, pachygyria with cortical thickening, lissencephaly, and polymicrogyria (Jackson et al. Am J Hum Genet 71:136-142, 2002; Passemard et al. Neurology 73:962-969, 2009; Nicholas et al. Nat Genet 42:1010-1014, 2010; Yu et al. Nat Genet 42:1015-1020, 2010; Bacino et al. Am J Med Genet A 158A:622-625, 2012). MCPH is pan ethnic. However, its incidence is variable and ranges from 1 in 30,000 to 1 in 250,000 living births (Passemard et al. GeneReviews, 2009, www.genetests.org). Incidence is highest in populations where consanguineous marriages are broadly practiced (Bundey and Alam. Eur J Hum Genet 1:206-219, 1993).


MCPH is a genetically heterogeneous disorder.  To date, eight genes (ASPM, WDR62, MCPH1, CEP152, CENPJ, STIL, CDK5RAP2 and CEP135) have been implicated in the disorder (Bond et al. Nat Genet 32:316-320, 2002; Bilgüvar et al.  Nature 467:207-210, 2010; Jackson, 2002; Guernsey et al. Am J Hum Genet 87:40-51, 2010; Bond et al. Nat Genet 37:353–355, 2005; Kumar et al. Am J Hum Genet 84:286–290, 2009; Hussain et al. Am J Hum Genet 90:871-878, 2012).  MCPH1 mutations account for less than 5% of cases with known mutations (Passemard, 2009).  To date about 10 mutations have been reported.  With the exception of three missense mutations, Thr27Arg, His49Glu and Ser72Leu, all pathogenic variants are predicted to result in truncated proteins and include nonsense mutations, splicing mutations, small insertions and large deletions.  Patients with MCPH1 pathogenic variants have a head circumference of 5-10 standard deviations below the mean, a stature of 2-3 standard deviations below the mean, mild to moderate mental retardation, with no structural anomalies or other clinical features (Jackson, 2002).  MPCH1 encodes microcephalin, which is involved in the regulation of chromosome condensation during neurogenesis (Trimborn et al. Am J Hum Genet 75:261-266, 2004).

Clinical Sensitivity - Sequencing with CNV PGxome

This test will detect mutations in less than 5% of patients with a clinical diagnosis of primary microcephaly (Passemard et al. GeneReviews, 2009, www.genetests.org).

Testing Strategy

This test provides full coverage of all coding exons of the MCPH1 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

Patients with head circumference at least three standard deviations below the age and sex mean, with or without central nervous system anomalies, and with a family history consistent with autosomal recessive mode of inheritance and no mutations in the ASPM or WDR62 genes (Bacino et al. Am J Med Genet A 158A:622-625, 2012, Passemard et al. GeneReviews, 2009). This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in MCPH1.


Official Gene Symbol OMIM ID
MCPH1 607117
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


Name Inheritance OMIM ID
Primary Autosomal Recessive Microcephaly 1 251200

Related Tests

CENPJ-Related Disorders via the CENPJ Gene
Primary Microcephaly, Autosomal Recessive, via the CDK5RAP2 Gene
Primary Microcephaly, Autosomal Recessive, via the STIL Gene
Primary Microcephaly, Autosomal Recessive, via the WDR62 Gene


  • Bacino et al. 2012. PubMed ID: 22308068
  • Bacino et al. 2012. PubMed ID: 22308068
  • Bilgüvar et al. 2010. PubMed ID: 20729831
  • Bond et al. 2005. PubMed ID: 15793586
  • Bond et al. ASPM is a major determinant of cerebral cortical size. Nat Genet 32:316-320, 2002. PubMed ID: 12355089
  • Bundey and Alam. 1993. PubMed ID: 8044647
  • Guernsey et al. 2010. PubMed ID: 20598275
  • Hussain et al. 2012. PubMed ID: 22521416
  • Jackson et al. 1998. PubMed ID: 9683597
  • Jackson et al. 2002. PubMed ID: 12046007
  • Jackson et al.  Identification of microcephalin, a protein implicated in determining the size of the human brain. Am J Hum Genet 71:136–142, 2002. PubMed ID: 12046007
  • Kumar et al. 2009. PubMed ID: 19215732
  • Nicholas et al. 2010. PubMed ID: 20890279
  • Passemard et al. Expanding the clinical and neuroradiologic phenotype of primary microcephaly due to ASPM mutations. Neurology 73:962-969, 2009. PubMed ID: 19770472
  • Passemard et al. GeneReviews, 2009
  • Trimborn et al.  Mutations in microcephalin cause aberrant regulation of chromosome condensation. Am J Hum Genet 75:261-266, 2004. PubMed ID: 15199523
  • Verloes et al. 2013. PubMed ID: 20301772
  • Verloes et al. 2013. PubMed ID: 20301772
  • Verloes et al. 2013. PubMed ID: 20301772
  • Woods et al. 2005. PubMed ID: 15806441
  • Yu et al. 2010. PubMed ID: 20890278


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