PTPRU

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

Basic information

Region (hg38): 1:29236515-29326813

Links

ENSG00000060656 ∙ NCBI:10076 ∙ OMIM:602454 ∙ HGNC:9683 ∙ Uniprot:Q92729 ∙ 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 PTPRU gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PTPRU 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				16	3	19
missense			87	2	3	92
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				3		3
non coding						0
Total	0	0	87	18	6

Variants in PTPRU

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

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

Position	Type	Phenotype	Significance	ClinVar
1-29255340-G-A		not specified	Uncertain significance (Dec 19, 2023)
1-29255382-C-T		not specified	Uncertain significance (Sep 16, 2021)
1-29255383-G-A		not specified	Uncertain significance (Feb 28, 2024)
1-29255394-G-C		not specified	Uncertain significance (Jul 25, 2023)
1-29258558-G-C		not specified	Uncertain significance (Oct 03, 2022)
1-29258561-A-G		not specified	Uncertain significance (Jul 06, 2022)
1-29258624-C-T		not specified	Uncertain significance (Dec 20, 2023)
1-29258629-C-T		PTPRU-related disorder	Likely benign (Aug 15, 2019)
1-29258677-C-T		PTPRU-related disorder	Benign (Nov 26, 2019)
1-29258715-A-C		not specified	Uncertain significance (Jul 25, 2023)
1-29258717-G-A		not specified	Uncertain significance (Apr 13, 2023)
1-29258733-A-C		not specified	Uncertain significance (Jan 22, 2024)
1-29259313-A-G		not specified	Uncertain significance (Jun 02, 2023)
1-29259504-C-T		PTPRU-related disorder	Likely benign (Feb 17, 2023)
1-29259505-G-T		not specified	Uncertain significance (Aug 02, 2021)
1-29259513-C-A		not specified	Uncertain significance (Dec 22, 2023)
1-29259521-T-C		not specified	Uncertain significance (Jun 06, 2022)
1-29259881-G-A		PTPRU-related disorder	Benign (Oct 28, 2019)
1-29259961-G-A		not specified	Uncertain significance (Aug 02, 2021)
1-29260025-C-T		PTPRU-related disorder	Likely benign (Nov 12, 2019)
1-29260618-A-G		not specified	Uncertain significance (Oct 27, 2022)
1-29260621-C-T		not specified	Uncertain significance (Jul 19, 2023)
1-29260674-G-T		not specified	Uncertain significance (Oct 17, 2023)
1-29260700-A-G		not specified	Uncertain significance (Dec 15, 2021)
1-29260723-A-G		not specified	Uncertain significance (Mar 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PTPRU	protein_coding	protein_coding	ENST00000345512	31	90298

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.393	0.607	125704	0	44	125748	0.000175

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.45	725	936	0.775	0.0000624	9373
Missense in Polyphen		282	395.68	0.7127		3798
Synonymous	0.793	364	384	0.949	0.0000258	2916
Loss of Function	6.23	17	75.3	0.226	0.00000414	789

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000210	0.000210
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.000167	0.000163
Finnish	0.0000955	0.0000924
European (Non-Finnish)	0.000240	0.000237
Middle Eastern	0.000167	0.000163
South Asian	0.0000980	0.0000980
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Tyrosine-protein phosphatase which dephosphorylates CTNNB1. Regulates CTNNB1 function both in cell adhesion and signaling. May function in cell proliferation and migration and play a role in the maintenance of epithelial integrity. May play a role in megakaryocytopoiesis. {ECO:0000269|PubMed:10397721, ECO:0000269|PubMed:12501215, ECO:0000269|PubMed:16574648}.
• Pathway: EPO Receptor Signaling;Signal Transduction;KitReceptor;Signaling by SCF-KIT;Signaling by Receptor Tyrosine Kinases (Consensus)

Recessive Scores

• pRec: 0.134

Intolerance Scores

• loftool: 0.366
• rvis_EVS: -1.78
• rvis_percentile_EVS: 2.28

Haploinsufficiency Scores

• pHI: 0.346
• hipred: Y
• hipred_score: 0.782
• ghis: 0.531

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.938

Gene Damage Prediction

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

Mouse Genome Informatics

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

Gene ontology

• Biological process: protein dephosphorylation;cell adhesion;transmembrane receptor protein tyrosine phosphatase signaling pathway;negative regulation of cell population proliferation;cell differentiation;negative regulation of cell migration;animal organ regeneration;homotypic cell-cell adhesion;protein localization to cell surface;peptidyl-tyrosine dephosphorylation;response to glucocorticoid;negative regulation of canonical Wnt signaling pathway;positive regulation of cell-cell adhesion mediated by cadherin
• Cellular component: plasma membrane;integral component of plasma membrane;cell-cell junction
• Molecular function: protein tyrosine phosphatase activity;transmembrane receptor protein tyrosine phosphatase activity;protein binding;beta-catenin binding