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Intellectual disability
Gene: KDM2B

KDM2B (lysine demethylase 2B)
EnsemblGeneIds (GRCh38): ENSG00000089094
EnsemblGeneIds (GRCh37): ENSG00000089094
OMIM: 609078, Gene2Phenotype
KDM2B is in 3 panels

5 reviews

Ida Ertmanska (Genomics England Curator)

Comment on phenotypes: OMIM phenotype updated 20 Mar 2026.
Created: 20 Mar 2026, 11:56 a.m. | Last Modified: 20 Mar 2026, 11:56 a.m.

Panel Version: 9.338

Created: 20 Mar 2026, 11:56 a.m.
Last Modified: 20 Mar 2026, 11:56 a.m.
Panel version: 9.338

Eleanor Williams (Genomics England Curator)

This gene is not currently associated with a disease phenotype in OMIM, but checked PMID:36322151 to make sure it is the same gene listed in the publication as on this panel and it is, so added the gene-checked tag
Created: 16 Oct 2023, 7:43 p.m. | Last Modified: 16 Oct 2023, 7:43 p.m.

Panel Version: 5.313

Created: 16 Oct 2023, 7:43 p.m.
Last Modified: 16 Oct 2023, 7:43 p.m.
Panel version: 5.313

Arina Puzriakova (Genomics England Curator)

Green List (high evidence)

The rating of this gene has been updated to Green following NHS Genomic Medicine Service approval.
Created: 11 Oct 2023, 9:34 a.m. | Last Modified: 11 Oct 2023, 9:34 a.m.

Panel Version: 5.286

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Created: 11 Oct 2023, 9:34 a.m.
Last Modified: 11 Oct 2023, 9:34 a.m.
Panel version: 5.286

Achchuthan Shanmugasundram (Genomics England Curator)

Green List (high evidence)

Comment on list classification: There is sufficient evidence for this gene to be promoted to GREEN rating at the next GMS update.
Created: 3 May 2023, 4:31 p.m. | Last Modified: 3 May 2023, 4:31 p.m.

Panel Version: 5.90

As reviewed by Mike Spiller (Sheffield Children's Hospital), 25 out of 27 patients (21/22 unrelated cases) reported in PMID:36322151 had developmental delay. Out of these, seven unrelated cases had intellectual disability (ranging from mild to severe) and four had global developmental delay among other clinical manifestations.
Created: 3 May 2023, 4:22 p.m. | Last Modified: 3 May 2023, 4:22 p.m.

Panel Version: 5.86

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Phenotypes
neurodevelopmental disorder, MONDO:0700092; intellectual disability, MONDO:0001071

Publications

36322151

Created: 3 May 2023, 4:22 p.m.
Last Modified: 3 May 2023, 4:22 p.m.
Panel version: 5.86

Mike Spiller (Sheffield Children's Hospital)

Green List (high evidence)

van Jaarsveld et al 2022 PMID: 36322151

Majority of variants are missense, strong evidence for hotspot in CXXC domain.(7 different de Novo missenses + 1 de Novo in frame del. Same inframe del also found de novo in NHS GMS patient. All absent from gnomAD, region highly constrained).

Also 3 LOF SNVs and 3 patients with deletions including this gene, although not all are de novo and most also have potential alternate causes.

All have developmental delay. Almost all have intellectual disability ranging from mild to moderate, speech delay common..7 with cardiac abnormalities, 4 with kidney abnormalities.

Also 2 variants published in this region in PMID: 35710456, 35904121.

KDM2B methylation episignature recorded. CXXC variants show strong clustering, highly distinct from control dataset. LOF variants (including dels) also reported to show distinct episignature from controls, and from CXXC variants. While the data supports a KDM2B LOF episignature, this is not as clear, and may not be as specific, as the CXXC signature.

Mouse model also supports importance of CXXC domain, with mice heterozygous for CXXC-deleted KDM2B showing neurological defects (PMID: 35128353).

Evidence very strong for CXXC missenses less clear for haploinsufficiency.

Overall sufficient evidence from cases and episignature evidence to include as green for ID.
Sources: Literature
Created: 25 Jan 2023, 3:53 p.m.

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Publications

Created: 25 Jan 2023, 3:53 p.m.

Panel version: 4.51

Details

Mode of Inheritance

MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Sources

Expert Review Green
NHS GMS

Phenotypes

Neurodevelopmental disorder with congenital cardiac defects and variable renal and ocular abnormalities, OMIM:621474

OMIM

609078

Clinvar variants

Variants in KDM2B

Penetrance

None

Publications

Panels with this gene

History Filter Activity

20 Mar 2026, Gel status: 3

Set publications

Ida Ertmanska (Genomics England Curator)

Publications for gene: KDM2B were set to 36322151

20 Mar 2026, Gel status: 3

Set Phenotypes

Ida Ertmanska (Genomics England Curator)

Phenotypes for gene: KDM2B were changed from neurodevelopmental disorder, MONDO:0700092; intellectual disability, MONDO:0001071 to Neurodevelopmental disorder with congenital cardiac defects and variable renal and ocular abnormalities, OMIM:621474

20 Mar 2026, Gel status: 3

Removed Tag

Ida Ertmanska (Genomics England Curator)

Tag gene-checked was removed from gene: KDM2B.

16 Oct 2023, Gel status: 3

Added Tag

Eleanor Williams (Genomics England Curator)

Tag gene-checked tag was added to gene: KDM2B.

11 Oct 2023, Gel status: 3

Removed Tag

Arina Puzriakova (Genomics England Curator)

Tag Q2_23_promote_green was removed from gene: KDM2B.

11 Oct 2023, Gel status: 3

Added New Source, Added New Source, Status Update

Arina Puzriakova (Genomics England Curator)

Source NHS GMS was added to KDM2B. Source Expert Review Green was added to KDM2B. Rating Changed from Amber List (moderate evidence) to Green List (high evidence)

3 May 2023, Gel status: 2