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Primary immunodeficiency

Gene: HAVCR2

Amber List (moderate 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)

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 Amber
  • IUIS Classification December 2019
Phenotypes
  • T-cell lymphoma, subcutaneous panniculitis-like, 618398
  • Tim-3 deficiency
  • Autoinflammatory Disorders
Tags
for-review
OMIM
606652
Clinvar variants
Variants in HAVCR2
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: 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