PTPRB

protein tyrosine phosphatase receptor type B, the group of Fibronectin type III domain containing|Protein tyrosine phosphatases receptor type

Basic information

Region (hg38): 12:70515870-70637440

Previous symbols: [ "PTPB" ]

Links

ENSG00000127329 ∙ NCBI:5787 ∙ OMIM:176882 ∙ HGNC:9665 ∙ Uniprot:P23467 ∙ 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 PTPRB gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PTPRB 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	3	5
missense			101	10		111
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding				1		1
Total	0	0	101	13	3

Variants in PTPRB

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

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

Position	Type	Phenotype	Significance	ClinVar
12-70524555-C-T		not specified	Uncertain significance (Oct 02, 2023)
12-70532073-C-T		not specified	Uncertain significance (Jul 08, 2022)
12-70532078-A-G		not specified	Uncertain significance (Sep 01, 2021)
12-70534512-G-A		not specified	Uncertain significance (Mar 16, 2022)
12-70534602-A-G		not specified	Uncertain significance (Sep 20, 2023)
12-70534621-G-A		not specified	Uncertain significance (Sep 12, 2023)
12-70534853-G-A		not specified	Uncertain significance (Sep 20, 2023)
12-70534930-G-A		not specified	Uncertain significance (Sep 22, 2023)
12-70536039-C-G		not specified	Uncertain significance (Jan 23, 2023)
12-70536057-C-T		not specified	Uncertain significance (Sep 01, 2021)
12-70536069-C-T		not specified	Uncertain significance (Dec 14, 2022)
12-70536070-G-C		not specified	Uncertain significance (Dec 22, 2023)
12-70536153-T-C		not specified	Uncertain significance (May 23, 2023)
12-70538219-C-T		not specified	Uncertain significance (Dec 12, 2023)
12-70538981-C-T		not specified	Uncertain significance (Sep 12, 2023)
12-70538995-C-T		not specified	Uncertain significance (Feb 28, 2023)
12-70539627-C-G		not specified	Uncertain significance (Oct 17, 2023)
12-70539645-G-T		not specified	Uncertain significance (May 01, 2024)
12-70539973-G-A		not specified	Uncertain significance (Apr 26, 2023)
12-70539991-T-A		not specified	Uncertain significance (Dec 05, 2022)
12-70540862-C-T		not specified	Uncertain significance (Aug 17, 2022)
12-70540937-C-G		not specified	Uncertain significance (Jun 17, 2024)
12-70544603-T-C			Benign/Likely benign (Nov 01, 2022)
12-70552948-A-G			Uncertain significance (Feb 10, 2021)
12-70552949-T-C		not specified	Uncertain significance (May 09, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PTPRB	protein_coding	protein_coding	ENST00000334414	34	120591

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.502	0.498	124618	0	39	124657	0.000156

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.66	1022	1.18e+3	0.864	0.0000628	14495
Missense in Polyphen		276	396.99	0.69524		4780
Synonymous	1.37	419	456	0.919	0.0000254	4279
Loss of Function	7.46	24	107	0.223	0.00000581	1221

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000656	0.000656
Ashkenazi Jewish	0.00	0.00
East Asian	0.000167	0.000167
Finnish	0.000146	0.000139
European (Non-Finnish)	0.000144	0.000133
Middle Eastern	0.000167	0.000167
South Asian	0.000164	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays an important role in blood vessel remodeling and angiogenesis. Not necessary for the initial formation of blood vessels, but is essential for their maintenance and remodeling. Can induce dephosphorylation of TEK/TIE2, CDH5/VE-cadherin and KDR/VEGFR-2. Regulates angiopoietin-TIE2 signaling in endothelial cells. Acts as a negative regulator of TIE2, and controls TIE2 driven endothelial cell proliferation, which in turn affects blood vessel remodeling during embryonic development and determines blood vessel size during perinatal growth. Essential for the maintenance of endothelial cell contact integrity and for the adhesive function of VE-cadherin in endothelial cells and this requires the presence of plakoglobin (By similarity). {ECO:0000250, ECO:0000269|PubMed:19116766, ECO:0000269|PubMed:19136612}.
• Pathway: Adherens junction - Homo sapiens (human);Ectoderm Differentiation;Neutrophil degranulation;sprouty regulation of tyrosine kinase signals;Innate Immune System;Immune System (Consensus)

Recessive Scores

• pRec: 0.139

Intolerance Scores

• loftool: 0.753
• rvis_EVS: 0.34
• rvis_percentile_EVS: 73.68

Haploinsufficiency Scores

• pHI: 0.283
• hipred: Y
• hipred_score: 0.708
• ghis: 0.489

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.828

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ptprb
• Phenotype: homeostasis/metabolism phenotype; cellular phenotype; muscle phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); 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); 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); embryo phenotype

Zebrafish Information Network

• Gene name: ptprb
• Affected structure: blood vessel endothelial cell
• Phenotype tag: abnormal
• Phenotype quality: has fewer parts of type

Gene ontology

• Biological process: angiogenesis;protein dephosphorylation;phosphate-containing compound metabolic process;dephosphorylation;peptidyl-tyrosine dephosphorylation;neutrophil degranulation
• Cellular component: plasma membrane;integral component of plasma membrane;specific granule membrane;receptor complex;tertiary granule membrane
• Molecular function: transmembrane receptor protein tyrosine phosphatase activity;protein binding