PTPRJ
protein tyrosine phosphatase receptor type J, the group of Fibronectin type III domain containing|Protein tyrosine phosphatases receptor type|MicroRNA protein coding host genes|CD molecules
Basic information
Region (hg38): 11:47980425-48170839
Links
Phenotypes
GenCC
Source:
- colorectal cancer (No Known Disease Relationship), mode of inheritance: Unknown
- hereditary nonpolyposis colon cancer (Limited), mode of inheritance: AD
- thrombocytopenia 10 (Limited), mode of inheritance: AR
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Thrombocytopenia 10 | AR | Hematologic | The condition may involve mild bleeding tendency, and awareness may be beneficial related to prevention and management of bleeding episodes | Hematologic | 30591527 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (158 variants)
- PTPRJ-related_disorder (33 variants)
- not_provided (19 variants)
- Thrombocytopenia_10 (2 variants)
- Carcinoma_of_colon (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PTPRJ gene is commonly pathogenic or not. These statistics are base on transcript: NM_000002843.4. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 16 | 18 | ||||
| missense | 152 | 20 | 179 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | |||||
| splice donor/acceptor (+/-2bp) | 1 | |||||
| Total | 3 | 0 | 152 | 36 | 8 |
Highest pathogenic variant AF is 0.000035946166
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PTPRJ | protein_coding | protein_coding | ENST00000418331 | 25 | 187558 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.29e-11 | 1.00 | 125695 | 0 | 52 | 125747 | 0.000207 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.965 | 674 | 748 | 0.901 | 0.0000424 | 8704 |
| Missense in Polyphen | 199 | 245.85 | 0.80942 | 2947 | ||
| Synonymous | 1.22 | 269 | 296 | 0.909 | 0.0000192 | 2692 |
| Loss of Function | 3.92 | 29 | 62.4 | 0.465 | 0.00000319 | 756 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000291 | 0.000291 |
| Ashkenazi Jewish | 0.0000995 | 0.0000992 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.000139 | 0.000139 |
| European (Non-Finnish) | 0.000283 | 0.000281 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.000163 | 0.000163 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Tyrosine phosphatase which dephosphorylates or contributes to the dephosphorylation of CTNND1, FLT3, PDGFRB, MET, RET (variant MEN2A), KDR, LYN, SRC, MAPK1, MAPK3, EGFR, TJP1, OCLN, PIK3R1 and PIK3R2. Plays a role in cell adhesion, migration, proliferation and differentiation. Involved in vascular development. Regulator of macrophage adhesion and spreading. Positively affects cell-matrix adhesion. Positive regulator of platelet activation and thrombosis. Negative regulator of cell proliferation. Negative regulator of PDGF-stimulated cell migration; through dephosphorylation of PDGFR. Positive regulator of endothelial cell survival, as well as of VEGF-induced SRC and AKT activation; through KDR dephosphorylation. Negative regulator of EGFR signaling pathway; through EGFR dephosphorylation. Enhances the barrier function of epithelial junctions during reassembly. Negatively regulates T-cell receptor (TCR) signaling. Upon T-cell TCR activation, it is up-regulated and excluded from the immunological synapses, while upon T-cell-antigen presenting cells (APC) disengagement, it is no longer excluded and can dephosphorylate PLCG1 and LAT to down-regulate prolongation of signaling. {ECO:0000269|PubMed:10821867, ECO:0000269|PubMed:11259588, ECO:0000269|PubMed:12062403, ECO:0000269|PubMed:12370829, ECO:0000269|PubMed:12475979, ECO:0000269|PubMed:12913111, ECO:0000269|PubMed:14709717, ECO:0000269|PubMed:16682945, ECO:0000269|PubMed:16778204, ECO:0000269|PubMed:18348712, ECO:0000269|PubMed:18936167, ECO:0000269|PubMed:19332538, ECO:0000269|PubMed:19494114, ECO:0000269|PubMed:19836242, ECO:0000269|PubMed:19922411, ECO:0000269|PubMed:21091576, ECO:0000269|PubMed:21262971, ECO:0000269|PubMed:9531590, ECO:0000269|PubMed:9780142}.;
- Pathway
- Adherens junction - Homo sapiens (human);miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;VEGFA-VEGFR2 Signaling Pathway;Neutrophil degranulation;Signal Transduction;Phosphorylation of CD3 and TCR zeta chains;TCR signaling;Innate Immune System;Immune System;Adaptive Immune System;Negative regulation of MET activity;Signaling by MET;Signaling by Receptor Tyrosine Kinases;Signaling events mediated by Hepatocyte Growth Factor Receptor (c-Met);PDGFR-beta signaling pathway;Signaling events mediated by VEGFR1 and VEGFR2
(Consensus)
Recessive Scores
- pRec
- 0.147
Intolerance Scores
- loftool
- 0.737
- rvis_EVS
- 0.75
- rvis_percentile_EVS
- 86.42
Haploinsufficiency Scores
- pHI
- 0.0838
- hipred
- Y
- hipred_score
- 0.568
- ghis
- 0.454
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.829
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ptprj
- Phenotype
- homeostasis/metabolism phenotype; muscle phenotype; growth/size/body region phenotype; embryo phenotype; immune system phenotype; neoplasm; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system 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); normal phenotype; reproductive system phenotype; respiratory system phenotype; liver/biliary system phenotype;
Zebrafish Information Network
- Gene name
- ptprjb.1
- Affected structure
- dorsal aorta
- Phenotype tag
- abnormal
- Phenotype quality
- morphology
Gene ontology
- Biological process
- negative regulation of cell population proliferation;negative regulation of platelet-derived growth factor receptor signaling pathway;regulation of cell adhesion;B cell differentiation;negative regulation of cell growth;negative regulation of cell migration;positive regulation of tumor necrosis factor production;peptidyl-tyrosine dephosphorylation;calcium-mediated signaling using intracellular calcium source;negative regulation of epidermal growth factor receptor signaling pathway;negative regulation of vascular permeability;neutrophil degranulation;negative regulation of MAP kinase activity;positive regulation of MAPK cascade;positive regulation of cell adhesion;platelet-derived growth factor receptor signaling pathway;positive regulation of peptidyl-tyrosine phosphorylation;T cell receptor signaling pathway;negative regulation of T cell receptor signaling pathway;positive chemotaxis;positive regulation of focal adhesion assembly;positive regulation of protein kinase B signaling;negative regulation of protein kinase B signaling;contact inhibition;positive regulation of Fc-gamma receptor signaling pathway involved in phagocytosis
- Cellular component
- immunological synapse;plasma membrane;integral component of plasma membrane;cell-cell junction;cell surface;ruffle membrane;specific granule membrane;extracellular exosome
- Molecular function
- protein tyrosine phosphatase activity;platelet-derived growth factor receptor binding;protein binding;beta-catenin binding;phosphatase activity;protein kinase binding;gamma-catenin binding;mitogen-activated protein kinase binding;delta-catenin binding