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): 11:47980424-48170839

Links

ENSG00000149177 ∙ NCBI:5795 ∙ OMIM:600925 ∙ HGNC:9673 ∙ Uniprot:Q12913 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• colorectal cancer (No Known Disease Relationship), mode of inheritance: Unknown
• hereditary nonpolyposis colon cancer (Limited), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

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 ClinVar and linked to the PTPRJ gene.

• Inborn genetic diseases (36 variants)
• not provided (17 variants)
• PTPRJ-related condition (4 variants)
• not specified (3 variants)
• Carcinoma of colon (1 variants)
• Colorectal cancer (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.

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				3	1	4
missense			41	5	6	52
nonsense						0
start loss						0
frameshift						0
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding						0
Total	0	0	42	8	7

Variants in PTPRJ

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

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

Position	Type	Phenotype	Significance	ClinVar
11-47980920-C-T		not specified	Uncertain significance (Oct 05, 2023)
11-47980977-C-CGCT		PTPRJ-related disorder	Uncertain significance (Jul 02, 2023)
11-47980997-C-T		not specified	Uncertain significance (Oct 04, 2022)
11-48110056-A-G		Thrombocytopenia 10	Pathogenic (Apr 02, 2024)
11-48110061-C-T			Likely benign (Dec 31, 2019)
11-48110066-C-T		PTPRJ-related disorder	Likely benign (Jul 25, 2019)
11-48112761-C-A		not specified	Uncertain significance (Sep 14, 2022)
11-48112803-A-T		PTPRJ-related disorder	Uncertain significance (Nov 19, 2022)
11-48112834-T-G		not specified	Uncertain significance (May 17, 2023)
11-48112873-C-A		not specified	Uncertain significance (Dec 16, 2023)
11-48112911-G-A		not specified	Uncertain significance (Aug 13, 2021)
11-48112913-T-C			Likely benign (Aug 01, 2022)
11-48121097-C-T			Likely benign (May 01, 2022)
11-48121099-A-C		PTPRJ-related disorder	Uncertain significance (Dec 18, 2023)
11-48121113-C-T		PTPRJ-related disorder	Uncertain significance (Aug 16, 2023)
11-48121158-T-C		not specified	Likely benign (Dec 20, 2023)
11-48121225-A-G			Benign (Dec 31, 2019)
11-48121232-T-A		PTPRJ-related disorder	Likely benign (Apr 08, 2021)
11-48123616-C-T		not specified	Uncertain significance (Apr 25, 2022)
11-48123636-C-T		Carcinoma of colon	Pathogenic (Jul 01, 2002)
11-48123661-A-G		not specified	Uncertain significance (Feb 13, 2024)
11-48123711-C-T		not specified	Uncertain significance (Dec 20, 2022)
11-48123775-C-T		PTPRJ-related disorder • not specified	Uncertain significance (Jan 04, 2024)
11-48123796-A-T		not specified	Uncertain significance (Sep 25, 2023)
11-48123811-C-T		not specified	Likely benign (Jun 06, 2023)

GnomAD

Source: gnomAD

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: dbNSFP

• 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