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Primary immunodeficiency

Gene: KDM6A

Red List (low evidence)

KDM6A (lysine demethylase 6A)
EnsemblGeneIds (GRCh38): ENSG00000147050
EnsemblGeneIds (GRCh37): ENSG00000147050
OMIM: 300128, Gene2Phenotype
KDM6A is in 18 panels

5 reviews

Arina Puzriakova (Genomics England Curator)

Infection susceptibility can be seen in a subset of patients with KDM6A-related Kabuki syndrome so inclusion on this panel may be of benefit in some cases. However, as this is not a prominent feature in the majority, this gene will be flagged for GMS expert review to determine the pertinence to this panel.
Created: 21 Sep 2021, 3:44 p.m. | Last Modified: 21 Sep 2021, 3:44 p.m.
Panel Version: 2.465

Dmitrijs Rots (RadboudUMC)

Green List (high evidence)

Immunodeficiency is a well-known and common feature of KS. Recent study shows:
"Overall, 44.1% (78/177) and 58.2% (46/79) of KS individuals exhibited infection susceptibility and hypogammaglobulinemia, respectively"

The gene is also included in Inborn errors of immunity classification: PMID 31953710
Created: 12 Sep 2021, 11:11 a.m. | Last Modified: 24 Sep 2021, 12:16 p.m.
Panel Version: 2.468

Mode of inheritance
X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males)

Phenotypes
Hypogammaglobulinemia; intellectual disability; short stature

Publications

Eleanor Williams (Genomics England Curator)

The following PubMed IDs were added to gene KDM6A (OMIM gene MIM#300128): 23076834;22197486. These publications have been associated with the gene by the immunodeficiencies subgroup of the Human Phenotype Ontology Immune Mediated Disorders Consortium (https://hpo-immune-mediated-disorders.groups.io/g/update) in August 2020.
Created: 13 Oct 2020, 9:36 a.m. | Last Modified: 13 Oct 2020, 9:36 a.m.
Panel Version: 2.208

Publications

Louise Daugherty (Genomics England Curator)

Comment on publications: Immunological abnormalities and KS were systematically analyzed for the first time in 2005, Hoffman JD et al. (2005) PMID:15887282. Although it was noted that no studies have analyzed in detail the functional consequences of KMT2D and KDM6A mutations on the immune system of patients with KS, and no mechanistic models accounting for such abnormalities have been proposed. Low serum immunoglobulin levels and reduced memory T and B lymphocytes have been reported Lin JL et al. (2015) PMID:25142838. Also increased occurrence of autoimmune manifestations, such as idiopathic thrombocytopenic purpura (ITP), hemolytic anemia, autoimmune thyroiditis, and vitiligo has been reported by Ming JE et al. (2005) PMID:15523604, suggests that both KMT2D and KDM6A genes may play a relevant, still undisclosed, role in the immune homeostasis.
Created: 6 Jul 2018, 2:23 p.m.
Comment on publications: Added publications to support immunodeficiency phenotype and KS. Stagi S et al. (2016) PMID: 26411453 noted that most KS patients show increased susceptibility to infections and have reduced serum immunoglobulin levels, while some suffer also from autoimmune manifestations, such as idiopathic thrombocytopenic purpura, hemolytic anemia, autoimmune thyroiditis, and vitiligo. They reviewed the immunological aspects of KS and proposed a novel model to account for the immune dysfunction observed in this condition.
Created: 6 Jul 2018, 2:17 p.m.
OriginaI Metadata from IUIS classification table (February, 2018) downloaded 20180614. IUIS Genetic defect (original gene symbol in IUIS download): KDM6A .PanelApp HGNC gene symbol check: KDM6A . IUIS Disease: Kabuki Syndrome 2 due to KDM6A deficiency . IUIS Inheritance: XL (females may be affected) .T cells: N/A, .B cells: Normal, .IUIS Other affected cells: N/A. IUIS Associated features: N/A. IUIS Major category: Combined immunodeficiencies with associated or syndromic features. IUIS Subcategory: Other Combined immunodeficiencies with associated or syndromic features
Created: 6 Jul 2018, 12:29 p.m.

Sophie Hambleton (Newcastle University)

I don't know

Immunodeficiency has not been described in patients with Kabuki syndrome 2 to my knowledge
Created: 29 Jun 2018, 9:36 p.m.

Phenotypes
Kabuki syndrome 2

Details

Mode of Inheritance
X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males)
Sources
  • Other
  • IUIS Classification December 2019
  • Expert Review Red
  • IUIS Classification February 2018
Phenotypes
  • Kabuki syndrome 2, OMIM:300867
  • Recurrent infections (otitis media, pneumonia)
  • Autoimmunity
  • Combined immunodeficiencies with associated or syndromic features
Tags
Q3_21_expert_review
OMIM
300128
Clinvar variants
Variants in KDM6A
Penetrance
None
Publications
Panels with this gene

History Filter Activity

29 Sep 2021, Gel status: 1

Set publications

Arina Puzriakova (Genomics England Curator)

Publications for gene: KDM6A were set to 25142838; 15523604; 32048120; 25546742; 15887282; 32086639; 26411453; 22197486; 23076834; 31363182

21 Sep 2021, Gel status: 1

Set Phenotypes

Arina Puzriakova (Genomics England Curator)

Phenotypes for gene: KDM6A were changed from Typical facial abnormalities, cleft or high arched palate, skeletal abnormalities, short stature, intellectual disability, congenital heart defects, recurrent infections (otitis media, pneumonia) in 50% of patients. Autoimmunity may be present; Kabuki Syndrome 2 due to KDM6A deficiency; Combined immunodeficiencies with associated or syndromic features to Kabuki syndrome 2, OMIM:300867; Recurrent infections (otitis media, pneumonia); Autoimmunity; Combined immunodeficiencies with associated or syndromic features

21 Sep 2021, Gel status: 1

Set publications

Arina Puzriakova (Genomics England Curator)

Publications for gene: KDM6A were set to 25142838; 15523604; 32048120; 25546742; 15887282; 32086639; 26411453; 22197486; 23076834

21 Sep 2021, Gel status: 1

Added Tag

Arina Puzriakova (Genomics England Curator)

Tag Q3_21_expert_review tag was added to gene: KDM6A.

13 Oct 2020, Gel status: 1

Added New Source, Set publications

Eleanor Williams (Genomics England Curator)

Source Other was added to KDM6A. Publications for gene KDM6A were updated from 25546742; 25142838; 32048120; 15887282; 15523604; 26411453; 32086639 to 25142838; 15523604; 32048120; 25546742; 15887282; 32086639; 26411453; 22197486; 23076834

28 Feb 2020, Gel status: 1

Added New Source, Set Phenotypes, Set publications

Louise Daugherty (Genomics England Curator)

Source IUIS Classification December 2019 was added to KDM6A. Added phenotypes Typical facial abnormalities, cleft or high arched palate, skeletal abnormalities, short stature, intellectual disability, congenital heart defects, recurrent infections (otitis media, pneumonia) in 50% of patients. Autoimmunity may be present; Combined immunodeficiencies with associated or syndromic features for gene: KDM6A Publications for gene KDM6A were updated from 26411453; 25546742; 15887282; 25142838; 15523604 to 25546742; 25142838; 32048120; 15887282; 15523604; 26411453; 32086639

12 Jul 2018, Gel status: 1

Panel promoted to version 1.0

Louise Daugherty (Genomics England Curator)

2018-07-12 Louise Daugherty (Genomics England Curator) promoted panel to v1.0. Reviews were assessed, and panel was revised according to expert reviews and further in-house curation based on PanelApp guidelines. Previous panels (A- or hypo-gammaglobulinaemia, Congenital neutropaenia, Agranulocytosis, Combined B and T cell defect, Inherited complement deficiency and SCID panels) that were merged with this panel, were checked again for any changes/new reviews prior to versioning of this panel, these merged panels are now retired/made internal.

6 Jul 2018, Gel status: 1

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: kdm6a has been classified as Red List (Low Evidence).

6 Jul 2018, Gel status: 1

Set publications

Louise Daugherty (Genomics England Curator)

Publications for gene: KDM6A were set to 26411453; 25546742; 15887282; 25142838; 15523604

6 Jul 2018, Gel status: 1

Set publications

Louise Daugherty (Genomics England Curator)

Publications for gene: KDM6A were set to 26411453; 25546742

6 Jul 2018, Gel status: 1

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for gene: KDM6A were set to Kabuki Syndrome 2 due to KDM6A deficiency; Combined immunodeficiencies with associated or syndromic features

6 Jul 2018, Gel status: 1

Set mode of inheritance

Louise Daugherty (Genomics England Curator)

Mode of inheritance for gene: KDM6A was changed from to X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males)

1 Jul 2018, Gel status: 1

Set penetrance

Louise Daugherty (Genomics England Curator)

Phenotypes for gene KDM6A were set to N/A, Combined immunodeficiencies with associated or syndromic features

26 Jun 2018, Gel status: 1

Added New Source

Louise Daugherty (Genomics England Curator)

KDM6A was added to Primary immunodeficiency disorders panel. Sources: IUIS Classification February 2018

26 Jun 2018, Gel status: 1

Created

Louise Daugherty (Genomics England Curator)

KDM6A was created by Louise Daugherty