PTPRK

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

Basic information

Region (hg38): 6:127968785-128520616

Links

ENSG00000152894 ∙ NCBI:5796 ∙ OMIM:602545 ∙ HGNC:9674 ∙ Uniprot:Q15262 ∙ 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 PTPRK gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PTPRK 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	3
missense			53	1		54
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	53	1	3

Variants in PTPRK

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

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

Position	Type	Phenotype	Significance	ClinVar
6-127973023-G-A		not specified	Uncertain significance (Jul 08, 2022)
6-127973095-C-T		Hereditary breast ovarian cancer syndrome	Uncertain significance (Aug 01, 2020)
6-127973096-G-A		not specified	Uncertain significance (Jul 05, 2023)
6-127973105-T-C		not specified	Uncertain significance (Mar 06, 2023)
6-127973114-C-T		not specified	Uncertain significance (Mar 07, 2024)
6-127973116-A-T		not specified	Uncertain significance (Nov 02, 2023)
6-127973802-T-C		not specified	Uncertain significance (Feb 12, 2024)
6-127981127-C-T		not specified	Uncertain significance (Feb 17, 2022)
6-127981205-T-C		not specified	Uncertain significance (Mar 01, 2024)
6-127981210-C-T		not specified	Uncertain significance (Sep 29, 2023)
6-127981265-G-C		not specified	Uncertain significance (Jan 26, 2023)
6-127981272-G-C			Benign (May 24, 2018)
6-127982883-A-G			Uncertain significance (Mar 01, 2022)
6-127982886-T-C		not specified	Uncertain significance (Apr 24, 2024)
6-127983262-T-C		not specified	Uncertain significance (Jun 19, 2024)
6-127983267-C-T		not specified	Uncertain significance (Jul 13, 2022)
6-127983268-G-A		not specified	Uncertain significance (May 30, 2024)
6-127985832-G-A		not specified	Uncertain significance (Oct 30, 2023)
6-127985856-C-T		not specified	Uncertain significance (Dec 22, 2023)
6-127990849-C-T		not specified	Uncertain significance (Jun 09, 2022)
6-127998845-A-G		not specified	Uncertain significance (Aug 17, 2022)
6-127998871-C-T		not specified	Uncertain significance (May 18, 2023)
6-127998874-C-A		not specified	Uncertain significance (Nov 18, 2023)
6-128005125-A-G		not specified	Uncertain significance (Nov 07, 2022)
6-128005131-T-A		not specified	Uncertain significance (Sep 15, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PTPRK	protein_coding	protein_coding	ENST00000368213	31	551947

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.903	0.0971	125694	1	53	125748	0.000215

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.17	551	804	0.685	0.0000428	9473
Missense in Polyphen		219	404.06	0.542		4897
Synonymous	-0.272	294	288	1.02	0.0000160	2755
Loss of Function	6.68	17	82.5	0.206	0.00000472	920

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00162	0.00162
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.00	0.00
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000142	0.000141
Middle Eastern	0.00	0.00
South Asian	0.000132	0.000131
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulation of processes involving cell contact and adhesion such as growth control, tumor invasion, and metastasis. Negative regulator of EGFR signaling pathway. Forms complexes with beta-catenin and gamma-catenin/plakoglobin. Beta-catenin may be a substrate for the catalytic activity of PTPRK/PTP-kappa. {ECO:0000269|PubMed:19836242}.
• Pathway: Signal Transduction;EGFR downregulation;Signaling by EGFR;EGFR1;Signaling by Receptor Tyrosine Kinases;Calcineurin-regulated NFAT-dependent transcription in lymphocytes (Consensus)

Intolerance Scores

• loftool: 0.665
• rvis_EVS: -1.72
• rvis_percentile_EVS: 2.47

Haploinsufficiency Scores

• pHI: 0.395
• hipred: Y
• hipred_score: 0.694
• ghis: 0.561

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.654

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Ptprk

Gene ontology

• Biological process: protein dephosphorylation;cell adhesion;signal transduction;transforming growth factor beta receptor signaling pathway;negative regulation of cell population proliferation;negative regulation of keratinocyte proliferation;cell migration;negative regulation of cell migration;neuron projection development;protein localization to cell surface;cellular response to reactive oxygen species;cellular response to UV;peptidyl-tyrosine dephosphorylation;negative regulation of cell cycle;negative regulation of transcription, DNA-templated;focal adhesion assembly
• Cellular component: photoreceptor outer segment;plasma membrane;integral component of plasma membrane;cell-cell junction;adherens junction;cell surface;integral component of membrane;cell junction;axon;dendrite;leading edge membrane;neuronal cell body;intracellular membrane-bounded organelle
• Molecular function: protein tyrosine phosphatase activity;transmembrane receptor protein tyrosine phosphatase activity;protein binding;beta-catenin binding;protein kinase binding;gamma-catenin binding