PTPN7

protein tyrosine phosphatase non-receptor type 7, the group of Protein tyrosine phosphatases non-receptor type

Basic information

Region (hg38): 1:202147012-202161588

Links

ENSG00000143851 ∙ NCBI:5778 ∙ OMIM:176889 ∙ HGNC:9659 ∙ Uniprot:P35236 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PTPN7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PTPN7 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			20			20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			5			5
Total	0	0	25	0	0

Variants in PTPN7

This is a list of pathogenic ClinVar variants found in the PTPN7 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-202150356-C-T		not specified	Uncertain significance (Jan 27, 2022)
1-202150386-C-T		not specified	Uncertain significance (Mar 17, 2023)
1-202152556-G-C		not specified	Uncertain significance (Nov 21, 2022)
1-202152611-C-T		not specified	Uncertain significance (Feb 10, 2023)
1-202152612-G-A		not specified	Uncertain significance (Oct 05, 2021)
1-202153732-G-T		not specified	Uncertain significance (May 30, 2024)
1-202153741-C-T		not specified	Uncertain significance (Jul 13, 2021)
1-202153780-C-T		not specified	Uncertain significance (Dec 13, 2022)
1-202153795-C-T		not specified	Uncertain significance (Jul 11, 2022)
1-202153828-A-C		not specified	Uncertain significance (Jan 22, 2024)
1-202154199-C-T		not specified	Uncertain significance (Oct 12, 2022)
1-202154262-G-A		not specified	Uncertain significance (Nov 08, 2022)
1-202155552-A-T		not specified	Uncertain significance (Jun 03, 2022)
1-202155597-C-T		not specified	Uncertain significance (Mar 24, 2023)
1-202157772-C-T		not specified	Uncertain significance (Nov 09, 2021)
1-202158169-C-A		not specified	Uncertain significance (Oct 17, 2023)
1-202158252-C-T		not specified	Uncertain significance (Mar 28, 2023)
1-202158271-G-C		not specified	Uncertain significance (Mar 15, 2024)
1-202159348-C-T		not specified	Uncertain significance (May 04, 2023)
1-202159365-G-A		not specified	Likely benign (Mar 29, 2024)
1-202159384-C-A		not specified	Uncertain significance (Jan 29, 2024)
1-202159409-G-T		not specified	Uncertain significance (Aug 28, 2023)
1-202159423-C-T		not specified	Uncertain significance (Apr 25, 2023)
1-202160596-T-C		not specified	Uncertain significance (Dec 01, 2022)
1-202160599-G-T		not specified	Uncertain significance (Dec 21, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PTPN7	protein_coding	protein_coding	ENST00000309017	10	14576

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.41e-14	0.252	125666	0	82	125748	0.000326

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.20	229	286	0.800	0.0000173	2969
Missense in Polyphen		82	107.33	0.764		1143
Synonymous	0.540	107	114	0.936	0.00000692	950
Loss of Function	1.14	24	30.9	0.778	0.00000180	280

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000183	0.000181
Ashkenazi Jewish	0.000100	0.0000992
East Asian	0.000163	0.000163
Finnish	0.000188	0.000185
European (Non-Finnish)	0.000553	0.000545
Middle Eastern	0.000163	0.000163
South Asian	0.000229	0.000229
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Protein phosphatase that acts preferentially on tyrosine-phosphorylated MAPK1. Plays a role in the regulation of T and B-lymphocyte development and signal transduction. {ECO:0000269|PubMed:10206983, ECO:0000269|PubMed:10559944, ECO:0000269|PubMed:10702794, ECO:0000269|PubMed:1510684, ECO:0000269|PubMed:1530918, ECO:0000269|PubMed:9624114}.
• Pathway: MAPK signaling pathway - Homo sapiens (human);MAPK Signaling Pathway;t cell receptor signaling pathway;Ras signaling in the CD4+ TCR pathway;Downstream signaling in naïve CD8+ T cells (Consensus)

Recessive Scores

• pRec: 0.150

Intolerance Scores

• loftool: 0.466
• rvis_EVS: 0.0000761
• rvis_percentile_EVS: 53.98

Haploinsufficiency Scores

• pHI: 0.246
• hipred: Y
• hipred_score: 0.558
• ghis: 0.530

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.939

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	High
Cancer	High	Medium	High

Mouse Genome Informatics

• Gene name: Ptpn7
• Phenotype: normal phenotype

Gene ontology

• Biological process: protein dephosphorylation;peptidyl-tyrosine dephosphorylation;cellular response to cytokine stimulus
• Cellular component: nucleoplasm;cytoplasm;cytosol;cytoskeleton;cytoplasmic side of plasma membrane
• Molecular function: protein tyrosine phosphatase activity;protein binding