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Intellectual disability

Gene: KDM2A

Amber List (moderate evidence)
KDM2A (lysine demethylase 2A)
EnsemblGeneIds (GRCh38): ENSG00000173120
EnsemblGeneIds (GRCh37): ENSG00000173120
OMIM: 605657, Gene2Phenotype
KDM2A is in 2 panels

1 review

Achchuthan Shanmugasundram (Genomics England Curator)

Green List (high evidence)

Comment on list classification: There is sufficient evidence available (17 unrelated patients) for the association of KDM2A gene with syndromic intellectual disability. Hence, this gene can be promoted to green rating in the next GMS update.
Created: 9 Jan 2026, 3 p.m. | Last Modified: 9 Jan 2026, 3 p.m.
Panel Version: 9.231
PMID:41468891 (2025) reported a cohort of 18 unrelated individuals including one foetus with heterozygous de novo variants in KDM2A gene and with a neurodevelopmental disorder.

All individuals, excluding the foetus, exhibited developmental delay and/or intellectual disability, with the severity of developmental delay or intellectual disability ranging from learning disabilities to severe intellectual disability. The majority of individuals were affected by mild developmental delay/intellectual disability (11/17) or learning disabilities (2/17), while four individuals presented with severe developmental delay/intellectual disability.

The other reported phenotypes include microcephaly (six individuals including the foetus - none of them had OFC beyond -3 SD), seizures (five), hypotonia (four), IUGR (eight), short stature (nine), feeding difficulties (six) and dysmorphic facial features (twelve).

The study proposed dual mechanism of pathogenicity: loss of nuclear function for some variants tested and additional cytoplasmic gain-of-function toxicity for c.704C>T (p.Pro235Leu), as eliminating endogenous Drosophila Kdm2 did not produce noticeable neurodevelopmental phenotypes.

This gene has not yet been associated with relevant phenotypes in OMIM (last accessed 09 January 2026), Gene2Phenotype or ClinGen.
Sources: Literature
Created: 9 Jan 2026, 2:58 p.m. | Last Modified: 9 Jan 2026, 3:14 p.m.
Panel Version: 9.231

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Phenotypes
neurodevelopmental disorder, MONDO:0700092

Publications

Created: 9 Jan 2026, 2:57 p.m.
Last Modified: 9 Jan 2026, 3:14 p.m.
Panel version: 9.230

Details

Mode of Inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Sources
  • Expert Review Amber
  • Literature
Phenotypes
  • neurodevelopmental disorder, MONDO:0700092
Tags
Q1_26_promote_green
OMIM
605657
Clinvar variants
Variants in KDM2A
Penetrance
None
Publications
Panels with this gene

History Filter Activity

9 Jan 2026, Gel status: 2

Entity classified by Genomics England curator

Achchuthan Shanmugasundram (Genomics England Curator)

Gene: kdm2a has been classified as Amber List (Moderate Evidence).

9 Jan 2026, Gel status: 1

Added Tag

Achchuthan Shanmugasundram (Genomics England Curator)

Tag Q1_26_promote_green tag was added to gene: KDM2A.

9 Jan 2026, Gel status: 1

Created, Added New Source, Set mode of inheritance, Set publications, Set Phenotypes

Achchuthan Shanmugasundram (Genomics England Curator)

gene: KDM2A was added gene: KDM2A was added to Intellectual disability. Sources: Literature Mode of inheritance for gene: KDM2A was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: KDM2A were set to 41468891 Phenotypes for gene: KDM2A were set to neurodevelopmental disorder, MONDO:0700092 Review for gene: KDM2A was set to GREEN