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Intellectual Disability, X-linked, Claes-Jensen Type via the KDM5C 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
KDM5C 81407 81407,81479 $990
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
8017KDM5C81407 81407,81479 $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


  • Li Fan, MD, PhD, FCCMG, FACMG

Clinical Features and Genetics

Clinical Features

Intellectual disability, X-linked and syndromic, Claes-Jensen type is characterized by mild to severe intellectual disability, often accompanied by symptoms such as epilepsy, behavioral disturbances, short stature and hyperreflexia (Abidi et al. 2008; Brookes et al. 2015). A KDM5C pathogenic variant has also been reported in autism spectrum disorder, Huntington’s disease and drug addiction (Brookes et al. 2015).

Female carriers have been reported to have mild intellectual disability or learning difficulties (Abidi et al. 2008; Rujirabanjerd et al. 2010).


Pathogenic variants in KDM5C cause intellectual disability, syndromic, Claes-Jensen type which is inherited in an X-linked recessive manner (Abidi et al. 2008; Gonçalves et al. 2014; Brookes et al. 2015). The majority of pathogenic variants reported in KDM5C are missense. Others include nonsense, splicing, small deletions/duplications, as well as a large deletion compassing the KDM5C locus (Human Gene Mutation Database).

The KDM5C gene (also known as JARID1C and SMCX) encodes lysine-specific demethylase 5C which is a histone demethylase. This demethylase removes di- and tri-methylation of histone H3 lysine 4 [H3K4me2/3], leading to modification of the associated gene activation. Malfunction of KDM5C could lead to alterations in chromatin landscape and may contribute to disease (Brookes et al. 2015).

Clinical Sensitivity - Sequencing with CNV PGxome

Pathogenic variants in the KDM5C gene account for 1–4% of X-linked intellectual disability (Brookes et al. 2015) and in another study for 0.7% among males with probable X-linked intellectual disability in Latin America (Gonçalves et al. 2014).

A large deletion with several genes, including the KDM5C gene, has been reported (Fieremans et al. 2015). To date, no large cohort study on deletions/duplications of KDM5C has been published.

Testing Strategy

This test provides full coverage of all coding exons of the KDM5C 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

Sequencing of KDM5C is considered for patients who are suspected to have intellectual disability, X-linked and syndromic, Claes-Jensen type.


Official Gene Symbol OMIM ID
KDM5C 314690
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


  • Abidi F.E. et al. 2008. Journal of Medical Genetics. 45: 787-93. PubMed ID: 18697827
  • Brookes E. et al. 2015. Human Molecular Genetics. 24: 2861-72. PubMed ID: 25666439
  • Fieremans N. et al. 2015. European Journal of Medical Genetics. 58: 324-7. PubMed ID: 25858702
  • Gonçalves T.F. et al. 2014. European Journal of Medical Genetics. 57: 138-44. PubMed ID: 24583395
  • Human Gene Mutation Database (Bio-base).
  • Rujirabanjerd S. et al. 2010. European Journal of Human Genetics. 18: 330-5. PubMed ID: 19826449


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

1) Select Test Method (Platform)

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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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