PTPN1
protein tyrosine phosphatase non-receptor type 1, the group of Protein tyrosine phosphatases non-receptor type
Basic information
Region (hg38): 20:50510321-50585241
Previous symbols: [ "PTP1B" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
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 | 2 | |||||
| missense | 9 | |||||
| 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 | 6 | 4 | 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 (Jun 21, 2018) | ||
| 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) | |||
| 20-50579776-C-T | not specified | Uncertain significance (May 16, 2024) | ||
| 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 (Dec 13, 2017) | ||
| 20-50581448-C-A | Neoplasm | - (-) | ||
| 20-50582818-C-CG | Insulin resistance, susceptibility to | risk factor (Mar 01, 2002) |
GnomAD
Source:
| 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:
- 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