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Intellectual disability

Gene: KDM1A

Green List (high evidence)

KDM1A (lysine demethylase 1A)
EnsemblGeneIds (GRCh38): ENSG00000004487
EnsemblGeneIds (GRCh37): ENSG00000004487
OMIM: 609132, Gene2Phenotype
KDM1A is in 5 panels

4 reviews

Caroline Wright (Sanger)

Red List (low evidence)

Olivia Niblock (Genomics England Curator)

Red List (low evidence)

Mouse studies are available detailing deletions in this gene - which were found to be lethal. PMID 26077434 notes that only one KDM1A variant has been described in a developmental disorder so far, but it does not detail this finding. In PMID 24838796, one case is described in a patient with a variant in this gene along with a variant in ANKRD11. The phenotypes listed include clefting, hypospadias and choradee, patent foramen ovale, global developmental delay and hypotonia. The authors of the paper hypothesise that both variants are contributing to the patient's overall disorder phenotype.
Created: 31 Oct 2017, 10:36 a.m.

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown

Phenotypes
Cleft palate, psychomotor retardation, and distinctive facial features

Publications

Louise Daugherty (Genomics England Curator)

Green List (high evidence)

As a result of watchlist tag audit the watchlist tag was removed from KDM1A- this is now a green gene with sufficient evidence/review
Created: 13 Jan 2020, 3:40 p.m. | Last Modified: 13 Jan 2020, 3:40 p.m.
Panel Version: 3.0
Comment on list classification: Changed from Red to Green. Publications support gene-disease association and rating of this gene to Green on the ID panel
Created: 27 Sep 2018, 4:07 p.m.
Comment on list classification: Changed from Red to Green. Publications support gene-disease association and rating of this gene to Green on the ID panel
Created: 27 Sep 2018, 4:04 p.m.
Comment on phenotypes: added MIMid
Created: 27 Sep 2018, 3:59 p.m.
Recommendation that this gene should be Green. Three patients https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4902791/, there is functional characterisation of the three described mutations https://www.ncbi.nlm.nih.gov/pubmed/27094131?dopt=Abstract and the patients seem to share a similar phenotype, which recapitulates features of other deleterious mutations in better-characterised lysine demethylase and chromatin remodelling genes. There is also a recurrent de novo variant p.Tyr831Cys which has been reported in two separate "autism spectrum" patients in large cohort studies. The gene is also extensively constrained against both missense and LOF variation in humans http://exac.broadinstitute.org/gene/ENSG00000004487. I think what's been reported so far is probably robust enough to use the gene clinically.Pers comm. Ian Berry (NHS Leeds Genetics Laboratory)
Created: 27 Sep 2018, 3:55 p.m.
Comment on publications: Three unrelated cases for the disorder: Cleft palate, psychomotor retardation, and distinctive facial features, this would suggest the status for this gene is changed from Red to Green. The finding of the second and third unrelated cases are in a paper published August 2016 (PMID: 26656649), which is after this gene on this panel was reviewed by experts in February 2016, both reviewed the gene and denoted the evidence as being low (Red), likely due to not enough published evidence at the time. Need to recheck with reviewers.
Created: 27 Jan 2017, 1:30 p.m.

Lu Raymond (university of cambridge )

Red List (low evidence)

Details

Mode of Inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Sources
  • Radboud University Medical Center, Nijmegen
Phenotypes
  • Cleft palate, psychomotor retardation, and distinctive facial features, 616728
  • Developmental delay
OMIM
609132
Clinvar variants
Variants in KDM1A
Penetrance
Complete
Publications
Panels with this gene

History Filter Activity

13 Jan 2020, Gel status: 3

Removed Tag

Louise Daugherty (Genomics England Curator)

Tag watchlist was removed from gene: KDM1A.

28 Sep 2018, Gel status: 4

Added New Source

Louise Daugherty (Genomics England Curator)

Source Victorian Clinical Genetics Services was added to KDM1A.

27 Sep 2018, Gel status: 3

Set Phenotypes

Louise Daugherty (Genomics England Curator)

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

27 Sep 2018, Gel status: 3

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: kdm1a has been classified as Green List (High Evidence).

27 Sep 2018, Gel status: 3

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: kdm1a has been classified as Green List (High Evidence).

27 Sep 2018, Gel status: 3

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: kdm1a has been classified as Green List (High Evidence).

27 Sep 2018, Gel status: 1

Set publications

Louise Daugherty (Genomics England Curator)

Publications for gene: KDM1A were set to 26077434; 24838796

27 Sep 2018, Gel status: 1

Set Phenotypes

Louise Daugherty (Genomics England Curator)

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

12 Mar 2018, Gel status: 1

Panel promoted to version 2.0

Ellen McDonagh (Genomics England Curator)

12.03.2018: Due to major updates completed (Phase 1, 2 and 3), this panel was promoted to Version 2 in order to reflect the major updates since November 2017 which have resulted in reviews for 836 genes added by Genomics England Curators and the Clinical Team, 130 new Green genes added to the interpretation pipeline (from 751 to 881 Green genes), and the gene total has increased from 1879 to 1927.

29 Nov 2017, Gel status: 1

Set publications

Ellen McDonagh (Genomics England Curator)

Publications for gene KDM1A was set to ['26077434', ' 24838796']

27 Jan 2017, Gel status: 1

Set publications

Louise Daugherty (Genomics England Curator)

Publications for KDM1A were set to 24838796; 26656649; 23020937

27 Jan 2017, Gel status: 1

Set Mode of Inheritance

Louise Daugherty (Genomics England Curator)

Mode of inheritance for KDM1A was changed to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown

27 Jan 2017, Gel status: 1

Set Mode of Inheritance

Louise Daugherty (Genomics England Curator)

Mode of inheritance for KDM1A was changed to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown

27 Jan 2017, Gel status: 1

Set publications

Louise Daugherty (Genomics England Curator)

Publications for KDM1A were set to 24838796; 26656649; 23020937;

27 Jan 2017, Gel status: 1

Upload gene information

Louise Daugherty (Genomics England Curator)

KDM1A was added to Intellectual disabilitypanel. Sources: Radboud University Medical Center, Nijmegen

13 Nov 2015, Gel status: 1

gel status update

GEL ()

The Gel status was updated for this whole panel

13 Nov 2015, Gel status: 2

gel status update

GEL ()

The Gel status was updated for this whole panel

13 Nov 2015, Gel status: 0

Added New Source

Ellen McDonagh (Genomics England Curator)

KDM1A was added to Intellectual disabilitypanel. Sources: Expert Review Red

13 Nov 2015, Gel status: 0

Created

Ellen McDonagh (Genomics England Curator)

KDM1A was created by ellenmcdonagh