Primary immunodeficiency or monogenic inflammatory bowel disease
Gene: LCKComment 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, 1:16 p.m. | Last Modified: 14 Oct 2020, 1:16 p.m.
Panel Version: 2.270
The following PubMed IDs were added to entity LCK: 22985903;11351273;9664084. These publications have been associated with OMIM phenotype MIM#615758, 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
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): LCK .PanelApp HGNC gene symbol check: LCK . IUIS Disease: LCK deficiency . IUIS Inheritance: AR .T cells: N/A, .B cells: Normal, .IUIS Other affected cells: N/A. IUIS Associated features: Recurrent infections, immune dysregulation, autoimmunity. 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.
Comment on list classification: Changed Amber to Green from external expert reviewCreated: 27 Jun 2018, 6:35 p.m.
Comment on list classification: Kept as amber until further evidence in the literature or from external expert review input. Although three unrelated cases, there is only one confirmed pathogenic variant (missense)Created: 19 Jun 2018, 4:48 p.m.
Comment on publications: added publications to support to phenotypeCreated: 19 Jun 2018, 4:43 p.m.
This gene was absent from the original PanelApp PID panel dataset (review April 2018). However it was listed in external expert immunodeficiency diagnostic gene list(s) GOSH or GRID. In this combined PID panel, this gene has been rated as AMBER and needs further curational review to assess pertinence prior to v1.Created: 20 Apr 2018, 12:25 p.m.
Original metadata downloaded from ESID Registry. ESID_Gene_original: LCK, PanelApp HGNC gene symbol check: LCK, 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: LCK, GRID_Gene_Symbol: LCK, GRID_Transcript_ENS_Community submitted: ENST00000336890, GRID_Transcript_RefSeq: NM_005356.4, GRID_Transcript_ENS_used_on_Production: ENST00000336890Created: 17 Apr 2018, 12:12 p.m.
Gene: lck has been classified as Green List (High Evidence).
Source Other was added to LCK. Publications for gene LCK were updated from 22985903; 9664084; 11351273 to 22985903; 11351273; 9664084 Rating Changed from Green List (high evidence) to Red List (low evidence)
Source NHS GMS was added to LCK.
Source North West GLH was added to LCK.
Source London North GLH was added to LCK.
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 LCK were set to Immunodeficiency 22, 615758, LCK deficiency, Combined immunodeficiency, Severe combined immunodeficiency due to LCK deficiency, Recurrent infections, immune dysregulation, autoimmunity, Immunodeficiencies affecting cellular and humoral immunity
Gene: lck has been classified as Green List (High Evidence).
Gene: lck has been classified as Green List (High Evidence).
IUIS Classification February 2018 was added to LCK. Panel: Primary immunodeficiency disorders
Victorian Clinical Genetics Services was added to LCK. Panel: Primary immunodeficiency disorders
Gene: lck has been classified as Amber List (Moderate Evidence).
Publications for gene: LCK were set to 22985903; 9664084; 11351273
Phenotypes for gene: LCK were set to Immunodeficiency 22, 615758; LCK deficiency; Combined immunodeficiency; Severe combined immunodeficiency due to LCK deficiency
Phenotypes for LCK were set to Immunodeficiency 22/ LCK deficiency; Combined immunodeficiency
Expert Review Amber was added to LCK. Panel: Primary immunodeficiency disorders
ESID Registry 20171117 was added to LCK. Panel: Primary immunodeficiency disorders Phenotypes for gene LCK were set to Immunodeficiency 22/ LCK deficiency, Immunodeficiency 22/ LCK deficiency, Combined immunodeficiency
Phenotypes for gene LCK were set to Immunodeficiency 22/ LCK deficiency, Immunodeficiency 22/ LCK deficiency
LCK was added to Primary immunodeficiency disorders panel. Sources: GRID V2.0
LCK was created by Louise Daugherty