Primary immunodeficiency or monogenic inflammatory bowel disease
Gene: PTPN2EnsemblGeneIds (GRCh38): ENSG00000175354
EnsemblGeneIds (GRCh37): ENSG00000175354
OMIM: 176887, Gene2Phenotype
PTPN2 is in 3 panels
5 reviews
Sarah Leigh (Genomics England Curator)
The rating of this gene has been updated to green and the mode of inheritance set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted following NHS Genomic Medicine Service approval.Created: 3 May 2024, 8:36 p.m. | Last Modified: 3 May 2024, 8:36 p.m.
Panel Version: 5.3
Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Achchuthan Shanmugasundram (Genomics England Curator)
Comment on list classification: There are two unrelated cases and a Ptpn2 deficient mouse model in support of the association of PTPN2 to this panel. Hence, this gene can be promoted to green rating in the next GMS review.Created: 2 Nov 2023, 2:57 p.m. | Last Modified: 2 Nov 2023, 2:57 p.m.
Panel Version: 4.116
Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications
Hannah Knight (NIHR BioResource - University of Cambridge)
PMID: 32721438 reported a girl with IBD with a de novo missense variant in PTPN2Created: 17 Oct 2023, 1:53 p.m. | Last Modified: 17 Oct 2023, 1:53 p.m.
Panel Version: 4.50
Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Phenotypes
Very early onset inflammatory bowel disease
Publications
Arina Puzriakova (Genomics England Curator)
Comment on list classification: Rating Amber as additional cases required for inclusion of PTPN2 on a diagnostic panel.Created: 10 Aug 2020, 3:18 p.m. | Last Modified: 10 Aug 2020, 3:18 p.m.
Panel Version: 2.180
Zornitza Stark (Australian Genomics)
A single family with a proband diagnosed with CVID and arthiritis (among other features) with an intronic expression quantitative trait loci (eQTL) rs2847297-G in trans with a stopgain variant. The stopgain variant was also identified in the proband's mother, who was diagnosed with lupus. A Ptpn2 deficient mouse model also demonstrates an autoimmune phenotype.
Sources: LiteratureCreated: 3 Aug 2020, 11:02 a.m.
Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Phenotypes
Lupus; arthritis; common variable immunodeficiency
Publications
Details
- Mode of Inheritance
- MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
- Sources
-
- Expert Review Green
- NHS GMS
- Phenotypes
-
- Lupus
- arthritis
- common variable immunodeficiency
- Very early onset inflammatory bowel disease
- Tags
- OMIM
- 176887
- Clinvar variants
- Variants in PTPN2
- Penetrance
- None
- Publications
- Panels with this gene
History Filter Activity
Added Tag
Eleanor Williams (Genomics England Curator)Tag gene-checked tag was added to gene: PTPN2.
Removed Tag, Removed Tag
Achchuthan Shanmugasundram (Genomics England Curator)Tag Q4_23_promote_green was removed from gene: PTPN2. Tag Q4_23_NHS_review was removed from gene: PTPN2.
Added New Source, Added New Source, Status Update
Achchuthan Shanmugasundram (Genomics England Curator)Source NHS GMS was added to PTPN2. Source Expert Review Green was added to PTPN2. Rating Changed from Amber List (moderate evidence) to Green List (high evidence)
Entity classified by Genomics England curator
Achchuthan Shanmugasundram (Genomics England Curator)Gene: ptpn2 has been classified as Amber List (Moderate Evidence).
Set Phenotypes
Achchuthan Shanmugasundram (Genomics England Curator)Phenotypes for gene: PTPN2 were changed from Lupus; arthritis; common variable immunodeficiency to Lupus; arthritis; common variable immunodeficiency; Very early onset inflammatory bowel disease
Set publications
Achchuthan Shanmugasundram (Genomics England Curator)Publications for gene: PTPN2 were set to 32499645; 27658548
Added Tag, Added Tag
Achchuthan Shanmugasundram (Genomics England Curator)Tag Q4_23_promote_green tag was added to gene: PTPN2. Tag Q4_23_NHS_review tag was added to gene: PTPN2.
Entity classified by Genomics England curator
Arina Puzriakova (Genomics England Curator)Gene: ptpn2 has been classified as Amber List (Moderate Evidence).
Created, Added New Source, Set mode of inheritance, Set publications, Set Phenotypes
Zornitza Stark (Australian Genomics)gene: PTPN2 was added gene: PTPN2 was added to Primary immunodeficiency. Sources: Literature Mode of inheritance for gene: PTPN2 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: PTPN2 were set to 32499645; 27658548 Phenotypes for gene: PTPN2 were set to Lupus; arthritis; common variable immunodeficiency Review for gene: PTPN2 was set to AMBER