PTPRH

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

Basic information

Region (hg38): 19:55181247-55209506

Links

ENSG00000080031 ∙ NCBI:5794 ∙ OMIM:602510 ∙ HGNC:9672 ∙ Uniprot:Q9HD43 ∙ 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 PTPRH gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PTPRH 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				1		1
missense			107	15		122
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	107	16	0

Variants in PTPRH

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

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

Position	Type	Phenotype	Significance	ClinVar
19-55181822-A-G		not specified	Uncertain significance (Jul 16, 2024)
19-55181846-C-A		not specified	Uncertain significance (Jan 09, 2024)
19-55181894-C-T		not specified	Uncertain significance (Nov 12, 2021)
19-55182038-C-T		not specified	Uncertain significance (Nov 05, 2021)
19-55182040-A-C		not specified	Uncertain significance (Jan 29, 2024)
19-55182054-T-C		not specified	Uncertain significance (Apr 12, 2024)
19-55182072-G-C		not specified	Uncertain significance (Feb 03, 2025)
19-55182089-G-A		not specified	Uncertain significance (Dec 14, 2023)
19-55182102-G-A		not specified	Uncertain significance (Jul 14, 2021)
19-55182123-T-C		not specified	Uncertain significance (Dec 15, 2023)
19-55182137-C-G		not specified	Uncertain significance (May 24, 2023)
19-55182137-C-T		not specified	Uncertain significance (Jun 03, 2024)
19-55182144-C-T		not specified	Uncertain significance (Jan 01, 2025)
19-55185527-C-T		not specified	Uncertain significance (Mar 07, 2024)
19-55185532-A-C		not specified	Uncertain significance (Feb 05, 2024)
19-55185536-T-C		not specified	Uncertain significance (May 15, 2024)
19-55185542-C-T		not specified	Uncertain significance (Dec 26, 2023)
19-55185574-A-T		not specified	Uncertain significance (Oct 17, 2024)
19-55185576-C-G		not specified	Uncertain significance (Apr 04, 2024)
19-55185602-C-T		not specified	Uncertain significance (Jul 15, 2021)
19-55185656-C-T		not specified	Uncertain significance (Mar 18, 2024)
19-55185881-C-T		not specified	Uncertain significance (Sep 10, 2024)
19-55185903-C-T		not specified	Uncertain significance (Jan 09, 2025)
19-55185908-T-A		not specified	Uncertain significance (Oct 05, 2023)
19-55185909-C-G		not specified	Uncertain significance (Sep 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PTPRH	protein_coding	protein_coding	ENST00000376350	20	28259

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.03e-36	0.0000209	124373	9	1366	125748	0.00548

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.793	711	654	1.09	0.0000378	7192
Missense in Polyphen		198	203.36	0.97365		2328
Synonymous	-0.502	294	283	1.04	0.0000192	2279
Loss of Function	0.375	57	60.1	0.948	0.00000319	594

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00722	0.00720
Ashkenazi Jewish	0.0247	0.0243
East Asian	0.00131	0.00131
Finnish	0.000973	0.000971
European (Non-Finnish)	0.00609	0.00603
Middle Eastern	0.00131	0.00131
South Asian	0.00438	0.00435
Other	0.00819	0.00818

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Protein phosphatase that may contribute to contact inhibition of cell growth and motility by mediating the dephosphorylation of focal adhesion-associated substrates and thus negatively regulating integrin-promoted signaling processes. Induces apoptotic cell death by at least two distinct mechanisms: inhibition of cell survival signaling mediated by PI 3-kinase, Akt, and ILK and activation of a caspase-dependent proapoptotic pathway. Inhibits the basal activity of LCK and its activation in response to TCR stimulation and TCR-induced activation of MAP kinase and surface expression of CD69. Inhibits TCR-induced tyrosine phosphorylation of LAT and ZAP70. Inhibits both basal activity of DOK1 and its CD2-induced tyrosine phosphorylation. Induces dephosphorylation of BCAR1, focal adhesion kinase and SRC. Reduces migratory activity of activity of Jurkat cells. Reduces tyrosine phosphorylation of CEACAM20 and thereby contributes to suppress the intestinal immune response CEACAM20 (By similarity). {ECO:0000250|UniProtKB:E9Q0N2, ECO:0000269|PubMed:11278335, ECO:0000269|PubMed:12101188, ECO:0000269|PubMed:12837766, ECO:0000269|PubMed:15850787}.
• Pathway: TCR (Consensus)

Intolerance Scores

• loftool: 0.573
• rvis_EVS: 1.11
• rvis_percentile_EVS: 92.07

Haploinsufficiency Scores

• pHI: 0.0771
• hipred: N
• hipred_score: 0.147
• ghis: 0.364

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.581

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ptprh
• Phenotype: neoplasm

Gene ontology

• Biological process: protein dephosphorylation;apoptotic process;peptidyl-tyrosine dephosphorylation
• Cellular component: cytoplasm;integral component of plasma membrane;apical plasma membrane;microvillus membrane
• Molecular function: transmembrane receptor protein tyrosine phosphatase activity;protein binding