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Fetal anomalies

Gene: KDM1A

Amber List (moderate evidence)
KDM1A (lysine demethylase 1A)
EnsemblGeneIds (GRCh38): ENSG00000004487
EnsemblGeneIds (GRCh37): ENSG00000004487
OMIM: 609132, Gene2Phenotype
KDM1A is in 6 panels

5 reviews

Arina Puzriakova (Genomics England Curator)

I don't know

Amber rating has been maintained, inline with the recent review by the R21 Clinical Oversight Group.
Created: 5 Sep 2025, 4:41 p.m. | Last Modified: 5 Sep 2025, 4:41 p.m.
Panel Version: 6.29
Created: 5 Sep 2025, 4:41 p.m.
Last Modified: 5 Sep 2025, 4:41 p.m.
Panel version: 6.29

Esther Kinning (NHS Greater Glasgow and Clyde)

I don't know

This gene and phenotype were reviewed during meetings in June & July 2025. The meetings included representatives of the North Thames and Central & South R21 testing GLHs and from the R21 Clinical Oversight Group. Clinical review and curation was performed by Natalie Chandler & Elizabeth Scotchman (North Thames GLH), Natalie Bibb, Stephanie Allen & Sarah Graham (Central & South GLH) and Alice Gardham, Esther Kinning, Vicki Harrison, Anna DeBurca, Natalie Canham, Elizabeth Wall, Sunayna Best, Soo-Mi Park & Sahar Mansour (R21 Clinical Oversight Group).
Created: 5 Sep 2025, 4:31 p.m. | Last Modified: 5 Sep 2025, 4:31 p.m.
Panel Version: 6.28
no new literature, postnatal cleft palate and thin corpus callosum seen in 3 individuals
Created: 5 Sep 2025, 2:55 p.m. | Last Modified: 5 Sep 2025, 2:55 p.m.
Panel Version: 6.24

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Phenotypes
Cleft palate, psychomotor retardation, and distinctive facial features

Publications

Created: 5 Sep 2025, 2:55 p.m.
Last Modified: 5 Sep 2025, 2:55 p.m.
Panel version: 6.28

Achchuthan Shanmugasundram (Genomics England Curator)

This gene and phenotype were reviewed during meetings between November 2023 & July 2024. The meetings included representatives of the North Thames and Central & South R21 testing GLHs and from the R21 Clinical Oversight Group. Clinical review and curation was performed by Natalie Chandler, Alison Male and Lyn Chitty (North Thames GLH), Stephanie Allen, Natalie Bibb, Esther Kinning and Denise Williams (Central & South GLH) and Natalie Canham, Anna De Burca and Samantha Doyle R21 Clinical Oversight Group.
Created: 29 Aug 2024, 8:33 p.m. | Last Modified: 29 Aug 2024, 8:33 p.m.
Panel Version: 4.36
Created: 29 Aug 2024, 8:33 p.m.
Last Modified: 29 Aug 2024, 8:33 p.m.
Panel version: 4.36

Natalie Bibb (C&S GLH)

I don't know

Green R27, R29. PMID:26656649 - 3 patients with ID de novo variants - VUS, 1 also has ANKRD11 VUS ?associated with Kabuki. PMID:24838796 - same patient as in PMID:26656649 with ANKRD11 VUS. Functional models in E.coli suggestive of functional effect - not included as evidence. Insufficent evidence Amber - needs more cases
Created: 29 Aug 2024, 8:07 p.m. | Last Modified: 29 Aug 2024, 8:07 p.m.
Panel Version: 4.35

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Phenotypes
Cleft palate, psychomotor retardation, and distinctive facial features, OMIM:616728

Publications

Created: 29 Aug 2024, 8:07 p.m.
Last Modified: 29 Aug 2024, 8:07 p.m.
Panel version: 4.35

Rebecca Foulger (Genomics England curator)

I don't know

DDG2P rating in original PAGE list: Probable for Developmental delay and distinctive facial features
Created: 11 Dec 2018, 9:05 a.m.
In the original PAGE file, MOP listed as Uncertain.
Created: 8 Nov 2018, 4:45 p.m.

Mode of pathogenicity
Other - please provide details in the comments

Created: 8 Nov 2018, 4:45 p.m.

Panel version: 0.9

Details

Mode of Inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Sources
  • NHS GMS
  • Expert Review Amber
  • PAGE DD-Gene2Phenotype
Phenotypes
  • Cleft palate, psychomotor retardation, and distinctive facial features, OMIM:616728
  • Cleft palate, psychomotor retardation, and distinctive facial features
OMIM
609132
Clinvar variants
Variants in KDM1A
Penetrance
None
Publications
Panels with this gene

History Filter Activity

5 Sep 2025, Gel status: 2

Set Phenotypes, Set publications

Arina Puzriakova (Genomics England Curator)

Added phenotypes Cleft palate, psychomotor retardation, and distinctive facial features for gene: KDM1A Publications for gene: KDM1A were updated from 27094131; 24838796; 26656649 to 27094131; 24838796; 26656649

30 Aug 2024, Gel status: 2

Set Phenotypes

Achchuthan Shanmugasundram (Genomics England Curator)

Phenotypes for gene: KDM1A were changed from Cleft palate, psychomotor retardation, and distinctive facial features, OMIM:616728; Developmental delay and distinctive facial features to Cleft palate, psychomotor retardation, and distinctive facial features, OMIM:616728

29 Aug 2024, Gel status: 2

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

Achchuthan Shanmugasundram (Genomics England Curator)

Source NHS GMS was added to KDM1A. Mode of inheritance for gene KDM1A was changed from MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Added phenotypes Cleft palate, psychomotor retardation, and distinctive facial features, OMIM:616728 for gene: KDM1A Publications for gene: KDM1A were updated from to 27094131; 24838796; 26656649

8 Nov 2018, Gel status: 2

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

Rebecca Foulger (Genomics England curator)

gene: KDM1A was added gene: KDM1A was added to Fetal anomalies. Sources: PAGE DD-Gene2Phenotype,Expert Review Amber Mode of inheritance for gene: KDM1A was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Phenotypes for gene: KDM1A were set to Developmental delay and distinctive facial features