Primary immunodeficiency or monogenic inflammatory bowel disease
Gene: STK4Comment 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
agree with green geneCreated: 17 Sep 2019, 3:18 p.m. | Last Modified: 17 Sep 2019, 3:18 p.m.
Panel Version: 1.94
YES- this is covered on our targeted exomeCreated: 17 Sep 2019, 3:18 p.m. | Last Modified: 17 Sep 2019, 3:18 p.m.
Panel Version: 1.94
Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal
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 ImmunodeficiencyCreated: 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 miceCreated: 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 immunodeficiencyCreated: 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: ENST00000372806Created: 17 Apr 2018, 12:12 p.m.
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.
Gene: stk4 has been classified as Green List (High Evidence).
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)
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
Source NHS GMS was added to STK4.
Source North West GLH was added to STK4.
Source London North GLH was added to STK4.
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.
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
IUIS Classification February 2018 was added to STK4. Panel: Primary immunodeficiency disorders
Victorian Clinical Genetics Services was added to STK4. Panel: Primary immunodeficiency disorders
Gene: stk4 has been classified as Green List (High Evidence).
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
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
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
STK4 was added to Primary immunodeficiency disorders panel. Sources: Expert Review Green, Combined B and T cell defect v1.12
STK4 was created by Louise Daugherty