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STRs in panel
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COVID-19 research

Gene: LIG1

Green List (high evidence)

LIG1 (DNA ligase 1)
EnsemblGeneIds (GRCh38): ENSG00000105486
EnsemblGeneIds (GRCh37): ENSG00000105486
OMIM: 126391, Gene2Phenotype
LIG1 is in 5 panels

3 reviews

Sophie Hambleton (Newcastle University)

Red List (low evidence)

There does not seem to be consensus that this is a real disease gene so probably best kept out of this panel
Created: 29 Jun 2018, 2:22 p.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Olivia Niblock (Genomics England Curator)

I don't know

GRID V2.0
ESID Registry 20171117
Expert Review Amber
Created: 15 May 2018, 10:12 a.m.

Louise Daugherty (Genomics England Curator)

I don't know

Added publication referenced by IUIS december 2019 update
Created: 28 Feb 2020, 8:49 p.m. | Last Modified: 28 Feb 2020, 8:49 p.m.
Panel Version: 2.36
Comment on list classification: Changed from Amber to Red. Until further evidence from GRID this gene is rated Red. Also, External expert review notes Red status due to no consensus on gene pertinence for immunodeficiency.
Created: 4 Jul 2018, 11:26 a.m.
OriginaI Metadata from IUIS classification table (February, 2018) downloaded 20180614. IUIS Genetic defect (original gene symbol in IUIS download): LIG1 .PanelApp HGNC gene symbol check: LIG1 . IUIS Disease: Ligase I deficiency . IUIS Inheritance: AR .T cells: T cell lymphopenia, reduced nave T cells, .B cells: Normal, .IUIS Other affected cells: N/A. IUIS Associated features: Recurrent respiratory infections, growth retardation, sun sensitivity, lymphoma, radiation sensitivity. IUIS Major category: Combined immunodeficiencies with associated or syndromic features. IUIS Subcategory: DNA Repair Defects other than those listed in Table 1
Created: 2 Jul 2018, 10:35 a.m.
Kept as amber until further evidence in the literature or from external expert review input. Ligase I deficiency is associated to Recurrent respiratory infections but there is currently no confirmed gene-disease associations
Created: 19 Jun 2018, 4:34 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: LIG1, PanelApp HGNC gene symbol check: LIG1, ESID classification: Main_category/ Sub_category/ PID_Diagnosis Other well defined PIDs / DNA-breakage disorder / DNA-ligase 1 ATP-dependent deficiency (LIG1)
Created: 17 Apr 2018, 12:29 p.m.
Original metadata supplied by GRID. GRID Gene Symbol HGNC PanelApp check: LIG1, GRID_Gene_Symbol: LIG1, GRID_Transcript_ENS_Community submitted: ENST00000263274, GRID_Transcript_RefSeq: NM_000234.1, GRID_Transcript_ENS_used_on_Production: ENST00000263274
Created: 17 Apr 2018, 12:12 p.m.

Publications

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Literature
  • Emory Genetics Laboratory
  • Other
  • Expert Review
Phenotypes
  • DNA ligase I deficiency
  • Combined immunodeficiencies with associated or syndromic features
  • DNA-ligase 1 ATP-dependent deficiency (LIG1)
  • Recurrent respiratory infections, growth retardation, sun sensitivity, lymphoma, radiation sensitivity
OMIM
126391
Clinvar variants
Variants in LIG1
Penetrance
None
Publications
Panels with this gene

History Filter Activity

2 Apr 2020, Gel status: 3

Added New Source, Set Phenotypes, Status Update

Ellen McDonagh (Genomics England Curator)

Source Expert Review Green was added to LIG1. Added phenotypes DNA ligase I deficiency; Combined immunodeficiencies with associated or syndromic features; DNA-ligase 1 ATP-dependent deficiency (LIG1); Recurrent respiratory infections, growth retardation, sun sensitivity, lymphoma, radiation sensitivity for gene: LIG1 Rating Changed from Red List (low evidence) to Green List (high evidence)

1 Apr 2020, Gel status: 1

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

Ellen McDonagh (Genomics England Curator)

gene: LIG1 was added gene: LIG1 was added to Viral susceptibility. Sources: Emory Genetics Laboratory,Expert Review,Other,IUIS Classification December 2019,Expert Review Red,Literature,IUIS Classification February 2018 Mode of inheritance for gene: LIG1 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: LIG1 were set to 30395541; 1581963; 32086639; 32048120 Phenotypes for gene: LIG1 were set to DNA ligase I deficiency; Combined immunodeficiencies with associated or syndromic features; DNA-ligase 1 ATP-dependent deficiency (LIG1); Recurrent respiratory infections, growth retardation, sun sensitivity, lymphoma, radiation sensitivity