PTPRR

protein tyrosine phosphatase receptor type R, the group of Protein tyrosine phosphatases receptor type

Basic information

Region (hg38): 12:70638072-70920738

Previous symbols: [ "PTPRQ" ]

Links

ENSG00000153233 ∙ NCBI:5801 ∙ OMIM:602853 ∙ HGNC:9680 ∙ Uniprot:Q15256 ∙ 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 PTPRR gene.

• Inborn genetic diseases (26 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PTPRR 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			24	1	1	26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2			2
Total	0	0	26	2	1

Variants in PTPRR

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

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

Position	Type	Phenotype	Significance	ClinVar
12-70639237-G-A		not specified	Uncertain significance (Jul 08, 2022)
12-70660956-C-T		not specified	Uncertain significance (Oct 26, 2021)
12-70662550-A-C		not specified	Uncertain significance (Apr 27, 2023)
12-70684260-T-A		not specified	Uncertain significance (Jul 22, 2022)
12-70698306-G-A		not specified	Uncertain significance (Feb 05, 2024)
12-70701172-C-A		not specified	Uncertain significance (Jun 12, 2023)
12-70701172-C-T		not specified	Uncertain significance (Aug 12, 2021)
12-70701192-C-T		not specified	Uncertain significance (Apr 22, 2022)
12-70701201-A-G		not specified	Uncertain significance (Aug 02, 2023)
12-70701202-T-A		not specified	Uncertain significance (May 17, 2023)
12-70701231-G-T		not specified	Uncertain significance (May 08, 2023)
12-70701258-G-A		not specified	Uncertain significance (Oct 10, 2023)
12-70701312-T-C		not specified	Uncertain significance (Jan 04, 2024)
12-70745873-C-T		not specified	Uncertain significance (Jan 26, 2022)
12-70745902-C-T		not specified	Uncertain significance (Jun 23, 2023)
12-70746007-G-A		not specified	Uncertain significance (Jul 12, 2023)
12-70746010-G-A		not specified	Uncertain significance (Apr 14, 2022)
12-70746080-A-G			Likely benign (Aug 01, 2022)
12-70754208-T-C		not specified	Uncertain significance (Jul 16, 2021)
12-70754279-T-C		not specified	Uncertain significance (Jan 18, 2023)
12-70754295-C-T		not specified	Uncertain significance (Jul 05, 2023)
12-70761538-C-T		not specified	Uncertain significance (Jun 07, 2022)
12-70761583-C-T		not specified	Uncertain significance (Jan 25, 2023)
12-70761588-T-C		not specified	Uncertain significance (Nov 14, 2023)
12-70764673-G-A			Benign (May 31, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PTPRR	protein_coding	protein_coding	ENST00000283228	14	282771

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.74e-7	0.999	125719	0	29	125748	0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.868	311	357	0.871	0.0000182	4304
Missense in Polyphen		68	97.978	0.69403		1170
Synonymous	-0.470	140	133	1.05	0.00000723	1260
Loss of Function	2.95	16	34.8	0.460	0.00000188	403

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.000695	0.000695
East Asian	0.00	0.00
Finnish	0.0000926	0.0000924
European (Non-Finnish)	0.000133	0.000132
Middle Eastern	0.00	0.00
South Asian	0.000108	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Sequesters mitogen-activated protein kinases (MAPKs) such as MAPK1, MAPK3 and MAPK14 in the cytoplasm in an inactive form. The MAPKs bind to a dephosphorylated kinase interacting motif, phosphorylation of which by the protein kinase A complex releases the MAPKs for activation and translocation into the nucleus (By similarity). {ECO:0000250}.
• Pathway: MAPK signaling pathway - Homo sapiens (human);MAPK Signaling Pathway;EGF-EGFR Signaling Pathway;erk1/erk2 mapk signaling pathway;EGFR1 (Consensus)

Recessive Scores

• pRec: 0.130

Intolerance Scores

• loftool: 0.428
• rvis_EVS: 0.53
• rvis_percentile_EVS: 81.01

Haploinsufficiency Scores

• pHI: 0.451
• hipred: Y
• hipred_score: 0.747
• ghis: 0.531

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.605

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ptprr
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: in utero embryonic development;protein dephosphorylation;negative regulation of epithelial cell migration;peptidyl-tyrosine dephosphorylation;ERBB2 signaling pathway;negative regulation of ERK1 and ERK2 cascade;regulation of homophilic cell adhesion
• Cellular component: extracellular space;cytosol;plasma membrane;integral component of membrane;cell junction;perinuclear region of cytoplasm
• Molecular function: protein tyrosine phosphatase activity;transmembrane receptor protein tyrosine phosphatase activity;protein binding;protein kinase binding