PTPRCAP

protein tyrosine phosphatase receptor type C associated protein

Basic information

Region (hg38): 11:67435510-67437682

Links

ENSG00000213402 ∙ NCBI:5790 ∙ OMIM:601577 ∙ HGNC:9667 ∙ Uniprot:Q14761 ∙ 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 PTPRCAP gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PTPRCAP 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						0
missense			15	2		17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	2	0

Variants in PTPRCAP

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

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

Position	Type	Phenotype	Significance	ClinVar
11-67435785-T-C		not specified	Uncertain significance (May 15, 2024)
11-67435810-C-A		not specified	Uncertain significance (Jan 19, 2025)
11-67435870-C-T		not specified	Likely benign (Jan 02, 2024)
11-67435885-C-T		not specified	Uncertain significance (Mar 21, 2023)
11-67435917-C-T		not specified	Likely benign (Dec 03, 2021)
11-67435941-G-A		not specified	Uncertain significance (Mar 08, 2024)
11-67435944-G-A		not specified	Uncertain significance (Apr 20, 2024)
11-67435968-T-G		not specified	Uncertain significance (Aug 20, 2024)
11-67436002-C-T		not specified	Uncertain significance (Dec 31, 2024)
11-67436061-C-G		not specified	Uncertain significance (Mar 31, 2023)
11-67436073-C-T		not specified	Uncertain significance (Mar 21, 2024)
11-67436116-G-A		not specified	Uncertain significance (Oct 22, 2024)
11-67436118-C-T		not specified	Uncertain significance (May 18, 2023)
11-67436129-C-A		not specified	Uncertain significance (Jun 26, 2024)
11-67436136-G-A		not specified	Uncertain significance (Jan 17, 2025)
11-67436148-C-T		not specified	Uncertain significance (Jan 18, 2025)
11-67436149-G-A		not specified	Uncertain significance (Jul 13, 2021)
11-67436179-G-A		not specified	Uncertain significance (Mar 07, 2024)
11-67436188-G-A		not specified	Uncertain significance (Feb 22, 2025)
11-67436190-C-T		not specified	Uncertain significance (Dec 06, 2023)
11-67436248-C-T		not specified	Uncertain significance (May 09, 2023)
11-67436326-C-A		not specified	Uncertain significance (Dec 19, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PTPRCAP	protein_coding	protein_coding	ENST00000326294	2	2558

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.540	0.408	123561	0	2	123563	0.00000809

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.299	118	127	0.926	0.00000878	1263
Missense in Polyphen		36	32.311	1.1142		269
Synonymous	-0.0795	65	64.2	1.01	0.00000468	483
Loss of Function	1.41	0	2.30	0.00	9.72e-8	35

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000899	0.00000897
Middle Eastern	0.00	0.00
South Asian	0.0000329	0.0000328
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: TNF alpha Signaling Pathway (Consensus)

Recessive Scores

• pRec: 0.111

Haploinsufficiency Scores

• pHI: 0.106
• hipred: N
• hipred_score: 0.250
• ghis: 0.410

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.782

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ptprcap
• Phenotype: hematopoietic system phenotype; normal phenotype; immune system phenotype

Gene ontology

• Biological process: defense response
• Cellular component: plasma membrane;integral component of membrane