PTPN1

protein tyrosine phosphatase non-receptor type 1, the group of Protein tyrosine phosphatases non-receptor type

Basic information

Region (hg38): 20:50510320-50585241

Previous symbols: [ "PTP1B" ]

Links

ENSG00000196396 ∙ NCBI:5770 ∙ OMIM:176885 ∙ HGNC:9642 ∙ Uniprot:P18031 ∙ 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 PTPN1 gene.

• Inborn genetic diseases (6 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PTPN1 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					1	1
missense			5	2		7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	5	2	1

Variants in PTPN1

This is a list of pathogenic ClinVar variants found in the PTPN1 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-50565018-C-T		not specified	Likely benign (Feb 06, 2024)
20-50565047-A-G		not specified	Uncertain significance (Aug 11, 2022)
20-50574654-A-G		PTPN1-related disorder	Benign (Nov 16, 2019)
20-50578421-C-T		not specified	Uncertain significance (Jul 21, 2021)
20-50578558-G-A		not specified	Likely benign (Apr 08, 2022)
20-50578616-C-G		not specified	Uncertain significance (Jan 09, 2024)
20-50579178-G-A		not specified	Uncertain significance (Sep 16, 2021)
20-50579743-C-T			Likely benign (May 01, 2022)
20-50579896-C-G		not specified	Uncertain significance (Sep 12, 2023)
20-50581309-G-A		not specified	Uncertain significance (May 04, 2022)
20-50581362-G-A		not specified	Likely benign (Feb 17, 2024)
20-50581418-C-T		PTPN1-related disorder	Benign (Mar 12, 2019)
20-50582818-C-CG		Insulin resistance, susceptibility to	risk factor (Mar 01, 2002)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PTPN1	protein_coding	protein_coding	ENST00000371621	10	74409

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.813	0.187	125735	0	13	125748	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.79	129	254	0.507	0.0000145	2883
Missense in Polyphen		22	83.316	0.26406		893
Synonymous	0.413	96	101	0.948	0.00000653	783
Loss of Function	3.98	5	27.5	0.182	0.00000166	287

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.00	0.00
Finnish	0.000139	0.000139
European (Non-Finnish)	0.0000618	0.0000615
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Tyrosine-protein phosphatase which acts as a regulator of endoplasmic reticulum unfolded protein response. Mediates dephosphorylation of EIF2AK3/PERK; inactivating the protein kinase activity of EIF2AK3/PERK. May play an important role in CKII- and p60c-src-induced signal transduction cascades. May regulate the EFNA5-EPHA3 signaling pathway which modulates cell reorganization and cell-cell repulsion. May also regulate the hepatocyte growth factor receptor signaling pathway through dephosphorylation of MET. {ECO:0000269|PubMed:18819921, ECO:0000269|PubMed:21135139, ECO:0000269|PubMed:22169477}.
• Pathway: Adherens junction - Homo sapiens (human);Insulin resistance - Homo sapiens (human);Insulin signaling pathway - Homo sapiens (human);IGF-Ncore;JAK-STAT-Ncore;Leptin signaling pathway;Prolactin Signaling Pathway;JAK-STAT;VEGFA-VEGFR2 Signaling Pathway;Angiopoietin Like Protein 8 Regulatory Pathway;Insulin Signaling;Signaling by PTK6;Signal Transduction;Growth hormone receptor signaling;Cytokine Signaling in Immune system;Regulation of IFNG signaling;Integrin alphaIIb beta3 signaling;Immune System;PTK6 Down-Regulation;Platelet Aggregation (Plug Formation);Platelet activation, signaling and aggregation;EGFR1;Integrin signaling;Hemostasis;Signaling events mediated by TCPTP;Signaling by Non-Receptor Tyrosine Kinases;Posttranslational regulation of adherens junction stability and dissassembly;Interferon gamma signaling;Regulation of IFNA signaling;Interferon alpha/beta signaling;Negative regulation of MET activity;Signaling by MET;Signaling by Receptor Tyrosine Kinases;Insulin Pathway;Signaling events mediated by Hepatocyte Growth Factor Receptor (c-Met);N-cadherin signaling events;Calcineurin-regulated NFAT-dependent transcription in lymphocytes;Interferon Signaling;IGF1 pathway;PDGFR-beta signaling pathway;Signaling events mediated by PTP1B (Consensus)

Recessive Scores

• pRec: 0.425

Intolerance Scores

• loftool: 0.380
• rvis_EVS: -0.36
• rvis_percentile_EVS: 29.16

Haploinsufficiency Scores

• pHI: 0.492
• hipred: Y
• hipred_score: 0.684
• ghis: 0.527

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.996

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ptpn1
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); skeleton phenotype; growth/size/body region phenotype; endocrine/exocrine gland phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); homeostasis/metabolism phenotype

Gene ontology

• Biological process: protein dephosphorylation;activation of JUN kinase activity;insulin receptor signaling pathway;regulation of signal transduction;negative regulation of signal transduction;regulation of endocytosis;negative regulation of vascular endothelial growth factor receptor signaling pathway;endoplasmic reticulum unfolded protein response;actin cytoskeleton reorganization;regulation of intracellular protein transport;cellular response to unfolded protein;peptidyl-tyrosine dephosphorylation;platelet-derived growth factor receptor-beta signaling pathway;IRE1-mediated unfolded protein response;negative regulation of MAP kinase activity;negative regulation of insulin receptor signaling pathway;regulation of type I interferon-mediated signaling pathway;JAK-STAT cascade involved in growth hormone signaling pathway;positive regulation of protein tyrosine kinase activity;negative regulation of ERK1 and ERK2 cascade;regulation of hepatocyte growth factor receptor signaling pathway;negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway;positive regulation of IRE1-mediated unfolded protein response;negative regulation of PERK-mediated unfolded protein response;peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity;positive regulation of receptor catabolic process
• Cellular component: early endosome;endoplasmic reticulum;cytosol;plasma membrane;protein-containing complex;sorting endosome;cytoplasmic side of endoplasmic reticulum membrane
• Molecular function: RNA binding;protein tyrosine phosphatase activity;insulin receptor binding;protein binding;zinc ion binding;enzyme binding;protein kinase binding;receptor tyrosine kinase binding;cadherin binding;ephrin receptor binding;protein phosphatase 2A binding