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Primary immunodeficiency

Gene: LIG1

Amber List (moderate evidence)

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

6 reviews

Arina Puzriakova (Genomics England Curator)

Comment on list classification: Changed rating from Green to Amber so that Green genes on this panel reflect the NHS signed-off version. This will be reviewed at the next GMS panel update (added 'for-review' tag).
Created: 20 Oct 2020, 3:18 p.m. | Last Modified: 20 Oct 2020, 3:18 p.m.
Panel Version: 2.345

Rebecca Foulger (Genomics England curator)

Comment on list classification: Updated rating from Red to Green. Red review pre-dates paper PMID:30395541 which provides 5 patients (3 kindreds) for evidence of association with immunodeficiency. Although severity of phenotype is variable, just sufficient cases for inclusion.
Created: 30 Apr 2020, 9:30 a.m. | Last Modified: 30 Apr 2020, 9:30 a.m.
Panel Version: 2.139
PMID:30395541. Maffucci et al., 2018 report 5 patients form 3 kindreds with biallelic LIG1 variants and immunodeficiency of variable severity. Note that Sophie Hambelton's review pre-dates this IUIS paper, and LIG1 is on the IUIS 2019 update based on PMID:30395541.
Created: 30 Apr 2020, 9:29 a.m. | Last Modified: 30 Apr 2020, 9:29 a.m.
Panel Version: 2.138

Zornitza Stark (Australian Genomics)

Green List (high evidence)

Five individuals from three families.
Created: 11 Apr 2020, 3:36 a.m. | Last Modified: 11 Apr 2020, 3:36 a.m.
Panel Version: 2.51

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Combined immunodeficiency; Lymphopaenia; Hypogammaglobulinaemia; Recurrent bacterial and viral infections; Growth retardation; Sun sensitivity, radiation sensitivity; Macrocytosis

Publications

Variants in this GENE are reported as part of current diagnostic practice

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
  • Expert Review Amber
  • IUIS Classification December 2019
  • IUIS Classification February 2018
  • Literature
  • Emory Genetics Laboratory
  • Other
  • Expert Review
Phenotypes
  • Combined immunodeficiencies with associated or syndromic features
  • Recurrent respiratory infections, growth retardation, sun sensitivity, lymphoma, radiation sensitivity
  • DNA-ligase 1 ATP-dependent deficiency (LIG1)
  • DNA ligase I deficiency
Tags
for-review
OMIM
126391
Clinvar variants
Variants in LIG1
Penetrance
None
Publications
Panels with this gene

History Filter Activity

20 Oct 2020, Gel status: 2

Entity classified by Genomics England curator

Arina Puzriakova (Genomics England Curator)

Gene: lig1 has been classified as Amber List (Moderate Evidence).

20 Oct 2020, Gel status: 3

Added Tag

Arina Puzriakova (Genomics England Curator)

Tag for-review tag was added to gene: LIG1.

30 Apr 2020, Gel status: 3

Entity classified by Genomics England curator

Rebecca Foulger (Genomics England curator)

Gene: lig1 has been classified as Green List (High Evidence).

28 Feb 2020, Gel status: 1

Set publications

Louise Daugherty (Genomics England Curator)

Publications for gene LIG1 were updated from 32048120; 1581963; 32086639 to 30395541; 1581963; 32086639; 32048120

28 Feb 2020, Gel status: 1

Added New Source, Set Phenotypes, Set publications

Louise Daugherty (Genomics England Curator)

Source IUIS Classification December 2019 was added to LIG1. Added phenotypes Recurrent respiratory infections, growth retardation, sun sensitivity, lymphoma, radiation sensitivity; Combined immunodeficiencies with associated or syndromic features for gene: LIG1 Publications for gene LIG1 were updated from 1581963 to 32048120; 1581963; 32086639

12 Jul 2018, Gel status: 1

Panel promoted to version 1.0

Louise Daugherty (Genomics England Curator)

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.

4 Jul 2018, Gel status: 1

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: lig1 has been classified as Red List (Low Evidence).

4 Jul 2018, Gel status: 1

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: lig1 has been classified as Red List (Low Evidence).

1 Jul 2018, Gel status: 2

Set penetrance

Louise Daugherty (Genomics England Curator)

Phenotypes for gene LIG1 were set to DNA ligase I deficiency, DNA-ligase 1 ATP-dependent deficiency (LIG1), Recurrent respiratory infections, growth retardation, sun sensitivity, lymphoma, radiation sensitivity, Combined immunodeficiencies with associated or syndromic features

26 Jun 2018, Gel status: 2

Added New Source

Louise Daugherty (Genomics England Curator)

IUIS Classification February 2018 was added to LIG1. Panel: Primary immunodeficiency disorders

15 May 2018, Gel status: 2

Gene classified by Genomics England curator

Olivia Niblock (Genomics England Curator)

This gene has been classified as Amber List (Moderate Evidence).

15 May 2018, Gel status: 1

Added New Source, Added New Source, Set penetrance, Set publications

Olivia Niblock (Genomics England Curator)

Emory Genetics Laboratory was added to LIG1. Panel: Primary immunodeficiency disorders Literature was added to LIG1. Panel: Primary immunodeficiency disorders Phenotypes for gene LIG1 were set to DNA ligase I deficiency, DNA-ligase 1 ATP-dependent deficiency (LIG1) Publications for gene LIG1 was set to ['1581963']

15 May 2018, Gel status: 1

Added New Source, Added New Source, Set penetrance

Olivia Niblock (Genomics England Curator)

Expert Review was added to LIG1. Panel: Primary immunodeficiency disorders Other was added to LIG1. Panel: Primary immunodeficiency disorders Phenotypes for gene LIG1 were set to DNA ligase I deficiency, DNA-ligase 1 ATP-dependent deficiency (LIG1)

15 May 2018, Gel status: 0

Clear Sources

Olivia Niblock (Genomics England Curator)

LIG1 All sources for gene: LIG1 were removed

20 Apr 2018, Gel status: 2

Added New Source

Louise Daugherty (Genomics England Curator)

Expert Review Amber was added to LIG1. Panel: Primary immunodeficiency disorders

17 Apr 2018, Gel status: 1

Added New Source, Set penetrance

Louise Daugherty (Genomics England Curator)

ESID Registry 20171117 was added to LIG1. Panel: Primary immunodeficiency disorders Phenotypes for gene LIG1 were set to DNA ligase I deficiency, DNA-ligase 1 ATP-dependent deficiency (LIG1)

17 Apr 2018, Gel status: 1

Set penetrance

Louise Daugherty (Genomics England Curator)

Phenotypes for gene LIG1 were set to DNA ligase I deficiency

17 Apr 2018, Gel status: 1

Added New Source

Louise Daugherty (Genomics England Curator)

LIG1 was added to Primary immunodeficiency disorders panel. Sources: GRID V2.0

17 Apr 2018, Gel status: 1

Created

Louise Daugherty (Genomics England Curator)

LIG1 was created by Louise Daugherty