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COVID-19 research

Gene: LAT

Green List (high evidence)

LAT (linker for activation of T-cells)
EnsemblGeneIds (GRCh38): ENSG00000213658
EnsemblGeneIds (GRCh37): ENSG00000213658
OMIM: 602354, Gene2Phenotype
LAT is in 6 panels

5 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
Comment on list classification: Changed Amber to Green. After internal clinical review it was agreed that as there are two unrelated cases, two variants (frameshifting) and a supportive mouse model for T cell deficits plus a Green rating from external expert review this gene could be promoted to Green
Created: 11 Jul 2018, 4:09 p.m.
OriginaI Metadata from IUIS classification table (February, 2018) downloaded 20180614. IUIS Genetic defect (original gene symbol in IUIS download): LAT .PanelApp HGNC gene symbol check: LAT . IUIS Disease: LAT deficiency . IUIS Inheritance: AR .T cells: N/A, .B cells: Nl to low, .IUIS Other affected cells: N/A. IUIS Associated features: Adenopathy, splenomegaly, recurrent infections, autoimmunity. IUIS Major category: Immunodeficiencies affecting cellular and humoral immunity. IUIS Subcategory: T-B+ Severe Combined Immune Deficiency (SCID)
Created: 2 Jul 2018, 10:35 a.m.
This gene was present in the original PanelApp PID panel dataset (review in April 2018) rated as Amber. The gene is absent from 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, 10:30 a.m.

Rebecca Foulger (Genomics England curator)

Comment on list classification: 2 independent cases and 2 variants (a 2 bp deletion and a 1 bp insertion) reported in OMIM: 1 Arab family in Keller et al 2016/PMID:27242165, and 1 Pakistani family in Bacchelli et al 2017/PMID:27522155). No more current publications and not yet associated with a disease in DD-G2P. Therefore currently insufficient cases to rate green so rated as Amber and added 'watchlist' tag in anticipation of further publications.
Created: 29 Aug 2017, 9:31 a.m.
Added to this panel as advised by Helen Brittain after a new gene-disorder association was reported in OMIM in June 2017 (Immunodeficiency 52, MIM:617514).
Created: 29 Aug 2017, 9:26 a.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Immunodeficiency 52, 617514

Publications

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
Phenotypes
  • Immunodeficiencies affecting cellular and humoral immunity
  • Immunodeficiency 52, 617514
  • Adenopathy, splenomegaly, recurrent infections, autoimmunity
OMIM
602354
Clinvar variants
Variants in LAT
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: LAT was added gene: LAT was added to Viral susceptibility. Sources: Expert Review Green,Combined B and T cell defect v1.12,North West GLH,NHS GMS,London North GLH,A- or hypo-gammaglobulinaemia v1.25,SCID v1.6,IUIS Classification February 2018 Mode of inheritance for gene: LAT was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: LAT were set to 27522155; 27242165 Phenotypes for gene: LAT were set to Immunodeficiencies affecting cellular and humoral immunity; Immunodeficiency 52, 617514; Adenopathy, splenomegaly, recurrent infections, autoimmunity