XLMR, KDM5C-related: KDM5C Gene Deletion/Duplication

Condition Description

Mutations in the KDM5C gene (Xp11.22-p11.21) have beenshown to cause an X-linked recessive syndromic mental retardation syndrome.Phenotypic features that have been reported include facial hypotonia, maxillaryhypoplasia, strabismus, large ears with raised lobes, big hands with largefingers and proximal thumbs, prominent and separated superior incisors, scrotaltongue, and pectus excavatum. Other features of this syndrome can include slowlyprogressive spastic paraplegia, epileptic seizures, short stature,microcephaly, hypermetropia, and small feet, testes, and penis. Aggressivebehavior and an overfriendly and anxious character have also been reported.

The phenotype associatedwith mutations in the KDM5C gene isvariable with regard to dysmorphism and cognitive impairment. In some families,the X-linked mental retardation seems to be nonsyndromic, with no dysmorphicfeatures. It has been estimated that the frequency of mutations in the KDM5C gene may account for 2.8% to3.3% of families with XLMR.

Click here for the OMIM summary on this condition.

Genes (1)

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This test is indicated for:

  • Confirmation of a clinical diagnosis of KDM5C-related syndromic XLMR in individuals who have tested negative for sequence analysis
  • Carrier testing in adult females with a family history of KDM5C-related syndromic XLMR who have tested negative for sequence analysis


DNA isolated from peripheral blood is hybridized to a CGH array to detect deletions and duplications. The targeted CGH array has overlapping probes which cover the entire genomic region.


Detection is limited to duplications and deletions. The CGH array will not detect point or intronic mutations.Results of molecular analysis must be interpreted in the context of the patient's clinical and/or biochemical phenotype.

Specimen Requirements

Listed below are EGL's preferred sample criteria. For any questions, please call 470.378.2200 and ask to speak with a laboratory genetic counselor (eglgc@egl-eurofins.com).
Submit only 1 of the following specimen types
Whole Blood (EDTA)

EDTA (Purple Top)
Infants and Young Children (<2 years of age): 2-3 ml
Children > 2 years of age to 10 years old: 3-5 ml
Older Children & Adults: 5-10 ml
Autopsy: 2-3 ml unclotted cord or cardiac blood
Collection and Shipping
Ship sample at room temperature for receipt at EGL within 72 hours of collection. Do not freeze.
DNA, Isolated

Isolation using the Perkin Elmer™Chemagen™ Chemagen™ Automated Extraction method or Qiagen™ Puregene kit for DNA extraction is recommended.
Collection and Shipping
Refrigerate until time of shipment in 100 ng/µL in TE buffer. Ship sample at room temperature with overnight delivery.

Special Instructions

Submit copies of diagnostic biochemical test results with the sample, if appropriate. Contact the laboratory if further information is needed.

Sequence analysis is required before deletion/duplication analysis by targeted CGH array. If sequencing is performed outside of EGL Genetics, please submit a copy of the sequencing report with the test requisition.

  • Sequencing analysis of the KDM5C  gene is available (YJ) and is required before deletion/duplication analysis.
  • ACGH array-based test for deletion/duplication analysis of 64 differentX-linked intellectual disability genes is available (OL).
  • Prenataltesting is available to adult females who are confirmed carriers ofmutations. Please contact the laboratory genetic counselor to discussappropriate testing prior to collecting a prenatal specimen.

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