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Primary immunodeficiency

Gene: STK4

Green List (high evidence)

STK4 (serine/threonine kinase 4)
EnsemblGeneIds (GRCh38): ENSG00000101109
EnsemblGeneIds (GRCh37): ENSG00000101109
OMIM: 604965, Gene2Phenotype
STK4 is in 5 panels

6 reviews

Eleanor Williams (Genomics England Curator)

Comment on list classification: Changed rating of gene from Red to Green. This gene was rated as Green in v2.208 and incorrectly automatically demoted to Red in v2.209. This was due to a defect in the automatic PanelApp uploading tool when a set of publications was added to the panel with the source ‘Other’, and under certain conditions associated to previous sources listed, resulted in the rating of the gene being automatically changed when it should not have been.
Created: 14 Oct 2020, 4:29 p.m. | Last Modified: 14 Oct 2020, 4:29 p.m.
Panel Version: 2.317
The following PubMed IDs were added to entity STK4: 22174160;26801501;26117625;22294732. These publications have been associated with OMIM phenotype MIM#614868, which is listed for this entity, 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

Kimberly Gilmour (Great Ormond Street Hopsital)

Green List (high evidence)

agree with green gene
Created: 17 Sep 2019, 3:18 p.m. | Last Modified: 17 Sep 2019, 3:18 p.m.
Panel Version: 1.94

Tracy Briggs (Manchester Genomic Medicine Centre)

Green List (high evidence)

YES- this is covered on our targeted exome
Created: 17 Sep 2019, 3:18 p.m. | Last Modified: 17 Sep 2019, 3:18 p.m.
Panel Version: 1.94

Sophie Hambleton (Newcastle University)

Green List (high evidence)

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Louise Daugherty (Genomics England Curator)

Green List (high evidence)

Gene rating submitted by Kimberly Gilmour and Austen Worth on behalf of London North GLH for the GMS Immunology specialist test group. As discussed with the GMS Immunology Specialist Test Group during webex call 28th March 2019 and confirmed in follow up email 6th September the Specialist Test Group all agreed there is enough evidence to rate this gene Green.
Created: 17 Sep 2019, 3:18 p.m. | Last Modified: 17 Sep 2019, 3:18 p.m.
Panel Version: 1.94
Gene rating submitted by Tracy Briggs, David Gokhale and Abigal Rousseau on behalf of North West GLH for the GMS Immunology specialist test group. As discussed with the GMS Immunology Specialist Test Group during webex call 28th March 2019 and confirmed in follow up email on 20th June the Specialist Test Group all agreed there is enough evidence to rate this gene Green.
Created: 17 Sep 2019, 3:18 p.m. | Last Modified: 17 Sep 2019, 3:18 p.m.
Panel Version: 1.94
OriginaI Metadata from IUIS classification table (February, 2018) downloaded 20180614. IUIS Genetic defect (original gene symbol in IUIS download): STK4 .PanelApp HGNC gene symbol check: STK4 . IUIS Disease: MST1 deficiency . IUIS Inheritance: AR .T cells: N/A, .B cells: Low , .IUIS Other affected cells: N/A. IUIS Associated features: Intermittent neutropenia, bacterial, viral (HPV), candidal infections, EBV lymphoproliferation, autoimmune cytopenias, lymphoma, congenital heart disease. IUIS Major category: Immunodeficiencies affecting cellular and humoral immunity. IUIS Subcategory: Combined Immunodeficiencies Generally Less Profound than Severe Combined Immunodeficiency
Created: 2 Jul 2018, 10:35 a.m.
Ellen McDonagh (Genomics England Curator) 6 Jun 2016, 3:20 p.m. review. PMID: 22174160 Nehme NT MST1 mutations in autosomal recessive primary immunodeficiency characterized by defective naive T-cell survival.Blood. 2012 Apr 12 119(15):3458-68;PMID: 22294732;PMID: 26801501;PMID: 26117625;PMID: 24453252 knockout mice
Created: 18 Apr 2018, 3:44 p.m.
Original metadata downloaded from ESID Registry. ESID_Gene_original: MST1 (STK4), PanelApp HGNC gene symbol check: STK4, ESID classification: Main_category/ Sub_category/ PID_Diagnosis Combined immunodeficiencies / Combined immunodeficiency (CID) / Combined immunodeficiency
Created: 17 Apr 2018, 12:29 p.m.
Original metadata supplied by GRID. GRID Gene Symbol HGNC PanelApp check: STK4, GRID_Gene_Symbol: STK4, GRID_Transcript_ENS_Community submitted: ENST00000372806, GRID_Transcript_RefSeq: NM_006282.2, GRID_Transcript_ENS_used_on_Production: ENST00000372806
Created: 17 Apr 2018, 12:12 p.m.

Ellen McDonagh (Genomics England Curator)

Comment on list classification: This gene was added by an expert reviewer. There are three cases/families reported in OMIM, and a literature review revealed further cases with multiple variants in patients from different ethnicities (see PMID: 26117625 for a summary table of variants identified in patients).
Created: 6 Jun 2016, 2:20 p.m.

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
  • Other
  • NHS GMS
  • North West GLH
  • London North GLH
  • IUIS Classification February 2018
  • Victorian Clinical Genetics Services
  • ESID Registry 20171117
  • GRID V2.0
  • Combined B and T cell defect v1.12
Phenotypes
  • Hypergammaglobulinaemia, lymphopenia, combined immunodeficiency, congenital heart disease, autoimmunity
  • T-cell immunodeficiency, recurrent infections, autoimmunity, and cardiac malformations, 614868
  • AR hyperimmunoglobulin E syndrome
  • Combined immunodeficiency
  • Intermittent neutropenia, bacterial, viral (HPV), candidal infections, EBV lymphoproliferation, autoimmune cytopenias, lymphoma, congenital heart disease
  • Immunodeficiencies affecting cellular and humoral immunity
OMIM
604965
Clinvar variants
Variants in STK4
Penetrance
None
Publications
Panels with this gene

History Filter Activity

14 Oct 2020, Gel status: 3

Entity classified by Genomics England curator

Eleanor Williams (Genomics England Curator)

Gene: stk4 has been classified as Green List (High Evidence).

13 Oct 2020, Gel status: 1

Added New Source, Set publications, Status Update

Eleanor Williams (Genomics England Curator)

Source Other was added to STK4. Publications for gene STK4 were updated from 22174160; 22294732; 26801501; 26117625; 24453252 to 22294732; 26801501; 24453252; 26117625; 22174160 Rating Changed from Green List (high evidence) to Red List (low evidence)

22 Sep 2020, Gel status: 3

Set Phenotypes

Eleanor Williams (Genomics England Curator)

Phenotypes for gene: STK4 were changed from Hypergammaglobulinaemia, lymphopenia, combined immunodeficiency, congenital heart disease, autoimmunity; T-cell immunodeficiency, recurrent infections, autoimmunity, and cardiac malformations; AR hyperimmunoglobulin E syndrome; Combined immunodeficiency; Intermittent neutropenia, bacterial, viral (HPV), candidal infections, EBV lymphoproliferation, autoimmune cytopenias, lymphoma, congenital heart disease; Immunodeficiencies affecting cellular and humoral immunity to Hypergammaglobulinaemia, lymphopenia, combined immunodeficiency, congenital heart disease, autoimmunity; T-cell immunodeficiency, recurrent infections, autoimmunity, and cardiac malformations, 614868; AR hyperimmunoglobulin E syndrome; Combined immunodeficiency; Intermittent neutropenia, bacterial, viral (HPV), candidal infections, EBV lymphoproliferation, autoimmune cytopenias, lymphoma, congenital heart disease; Immunodeficiencies affecting cellular and humoral immunity

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source NHS GMS was added to STK4.

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source North West GLH was added to STK4.

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source London North GLH was added to STK4.

12 Jul 2018, Gel status: 4

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.

1 Jul 2018, Gel status: 4

Set penetrance

Louise Daugherty (Genomics England Curator)

Phenotypes for gene STK4 were set to Hypergammaglobulinaemia, lymphopenia, combined immunodeficiency, congenital heart disease, autoimmunity, T-cell immunodeficiency, recurrent infections, autoimmunity, and cardiac malformations, AR hyperimmunoglobulin E syndrome, Combined immunodeficiency, Intermittent neutropenia, bacterial, viral (HPV), candidal infections, EBV lymphoproliferation, autoimmune cytopenias, lymphoma, congenital heart disease, Immunodeficiencies affecting cellular and humoral immunity

26 Jun 2018, Gel status: 4

Added New Source

Louise Daugherty (Genomics England Curator)

IUIS Classification February 2018 was added to STK4. Panel: Primary immunodeficiency disorders

26 Jun 2018, Gel status: 4

Added New Source

Louise Daugherty (Genomics England Curator)

Victorian Clinical Genetics Services was added to STK4. Panel: Primary immunodeficiency disorders

13 Jun 2018, Gel status: 4

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: stk4 has been classified as Green List (High Evidence).

17 Apr 2018, Gel status: 4

Added New Source, Set penetrance

Louise Daugherty (Genomics England Curator)

ESID Registry 20171117 was added to STK4. Panel: Primary immunodeficiency disorders Phenotypes for gene STK4 were set to Hypergammaglobulinaemia, lymphopenia, combined immunodeficiency, congenital heart disease, autoimmunity, T-cell immunodeficiency, recurrent infections, autoimmunity, and cardiac malformations, AR hyperimmunoglobulin E syndrome, Combined immunodeficiency

17 Apr 2018, Gel status: 4

Set penetrance

Louise Daugherty (Genomics England Curator)

Phenotypes for gene STK4 were set to Hypergammaglobulinaemia, lymphopenia, combined immunodeficiency, congenital heart disease, autoimmunity, T-cell immunodeficiency, recurrent infections, autoimmunity, and cardiac malformations, AR hyperimmunoglobulin E syndrome

17 Apr 2018, Gel status: 4

Added New Source, Set penetrance

Louise Daugherty (Genomics England Curator)

GRID V2.0 was added to STK4. Panel: Primary immunodeficiency disorders Phenotypes for gene STK4 were set to Hypergammaglobulinaemia, lymphopenia, combined immunodeficiency, congenital heart disease, autoimmunity, T-cell immunodeficiency, recurrent infections, autoimmunity, and cardiac malformations, AR hyperimmunoglobulin E syndrome

29 Mar 2018, Gel status: 4

Added New Source

Louise Daugherty (Genomics England Curator)

STK4 was added to Primary immunodeficiency disorders panel. Sources: Expert Review Green, Combined B and T cell defect v1.12

29 Mar 2018, Gel status: 4

Created

Louise Daugherty (Genomics England Curator)

STK4 was created by Louise Daugherty