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.

not_specified (234 variants)
not_provided (9 variants)
PTPRB-related_disorder (1 variants)

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. These statistics are base on transcript: NM_001109754.4. 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				2 clinvar	2 clinvar	4
missense			222 clinvar	16 clinvar		238
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	222	18	2

Loading clinvar variants...

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