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STRs in panel
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COVID-19 research

Gene: LCK

Green List (high evidence)

LCK (LCK proto-oncogene, Src family tyrosine kinase)
EnsemblGeneIds (GRCh38): ENSG00000182866
EnsemblGeneIds (GRCh37): ENSG00000182866
OMIM: 153390, Gene2Phenotype
LCK is in 3 panels

4 reviews

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)

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): 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 Immunodeficiency
Created: 2 Jul 2018, 10:35 a.m.
Comment on list classification: Changed Amber to Green from external expert review
Created: 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 phenotype
Created: 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 immunodeficiency
Created: 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: ENST00000336890
Created: 17 Apr 2018, 12:12 p.m.

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
Phenotypes
  • Severe combined immunodeficiency due to LCK deficiency
  • Recurrent infections, immune dysregulation, autoimmunity
  • Combined immunodeficiency
  • Immunodeficiency 22, 615758
  • Immunodeficiencies affecting cellular and humoral immunity
  • LCK deficiency
OMIM
153390
Clinvar variants
Variants in LCK
Penetrance
None
Publications
Panels with this gene

History Filter Activity

1 Apr 2020, Gel status: 3

Created, Added New Source, Set mode of inheritance, Set publications, Set Phenotypes

Ellen McDonagh (Genomics England Curator)

gene: LCK was added gene: LCK was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018 Mode of inheritance for gene: LCK was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: LCK were set to 11351273; 9664084; 22985903 Phenotypes for gene: LCK were set to Severe combined immunodeficiency due to LCK deficiency; Recurrent infections, immune dysregulation, autoimmunity; Combined immunodeficiency; Immunodeficiency 22, 615758; Immunodeficiencies affecting cellular and humoral immunity; LCK deficiency