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Primary immunodeficiency

Gene: HAVCR2

Green List (high evidence)

HAVCR2 (hepatitis A virus cellular receptor 2)
EnsemblGeneIds (GRCh38): ENSG00000135077
EnsemblGeneIds (GRCh37): ENSG00000135077
OMIM: 606652, Gene2Phenotype
HAVCR2 is in 2 panels

4 reviews

Arina Puzriakova (Genomics England Curator)

The rating of this gene has been updated following NHS Genomic Medicine Service approval.
Created: 4 Mar 2022, 10:17 a.m. | Last Modified: 4 Mar 2022, 10:17 a.m.
Panel Version: 2.529
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, 2:57 p.m. | Last Modified: 20 Oct 2020, 2:57 p.m.
Panel Version: 2.338

Sarah Leigh (Genomics England Curator)

Comment on list classification: Associated with relevant phenotype in OMIM, but not associated with phenotype in Gen2Phen. At least 3 variants reported in at least 20 families. PMID 30374066 haplotype analysis identified at least 12 distinct chromosome backgrounds within 7 families homozygous for rs184868814, suggestive of recurrant occurrence.
Created: 7 May 2020, 2:51 p.m. | Last Modified: 7 May 2020, 2:51 p.m.
Panel Version: 2.168

Zornitza Stark (Australian Genomics)

Green List (high evidence)

Over 20 unrelated individuals reported, note germline confirmation not in all. Some variants are recurrent: c.245A>G (p.Tyr82Cys) and c.291A>G (p.Ile97Met).
Created: 10 Apr 2020, 7:47 a.m. | Last Modified: 10 Apr 2020, 7:47 a.m.
Panel Version: 2.51

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
T-cell lymphoma, subcutaneous panniculitis-like, MIM# 618398

Publications

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

Publications

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
  • IUIS Classification December 2019
Phenotypes
  • T-cell lymphoma, subcutaneous panniculitis-like, 618398
  • Tim-3 deficiency
  • Autoinflammatory Disorders
OMIM
606652
Clinvar variants
Variants in HAVCR2
Penetrance
None
Publications
Panels with this gene

History Filter Activity

4 Mar 2022, Gel status: 3

Removed Tag

Arina Puzriakova (Genomics England Curator)

Tag for-review was removed from gene: HAVCR2.

4 Mar 2022, Gel status: 3

Added New Source, Status Update

Arina Puzriakova (Genomics England Curator)

Source Expert Review Green was added to HAVCR2. Rating Changed from Amber List (moderate evidence) to Green List (high evidence)

20 Oct 2020, Gel status: 2

Entity classified by Genomics England curator

Arina Puzriakova (Genomics England Curator)

Gene: havcr2 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: HAVCR2.

7 May 2020, Gel status: 3

Entity classified by Genomics England curator

Sarah Leigh (Genomics England Curator)

Gene: havcr2 has been classified as Green List (High Evidence).

7 May 2020, Gel status: 1

Set Phenotypes

Sarah Leigh (Genomics England Curator)

Phenotypes for gene: HAVCR2 were changed from Tim-3 deficiency; T-cell lymphoma, subcutaneous panniculitis-like, HLH; T-cell lymphoma, subcutaneous panniculitis-like, 618398; Autoinflammatory Disorders to T-cell lymphoma, subcutaneous panniculitis-like, 618398; Tim-3 deficiency; Autoinflammatory Disorders

28 Feb 2020, Gel status: 1

Set publications

Louise Daugherty (Genomics England Curator)

Publications for gene HAVCR2 were updated from 32086639; 32048120 to 30792187; 32086639; 32048120; 30374066

26 Feb 2020, Gel status: 1

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

Louise Daugherty (Genomics England Curator)

gene: HAVCR2 was added gene: HAVCR2 was added to Primary immunodeficiency. Sources: IUIS Classification December 2019 Mode of inheritance for gene: HAVCR2 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: HAVCR2 were set to 32086639; 32048120 Phenotypes for gene: HAVCR2 were set to Tim-3 deficiency; T-cell lymphoma, subcutaneous panniculitis-like, HLH; T-cell lymphoma, subcutaneous panniculitis-like, 618398; Autoinflammatory Disorders