PTPRCAP

protein-coding

protein tyrosine phosphatase receptor type C associated protein

Gene summary

The protein encoded by this gene was identified as a transmembrane phosphoprotein specifically associated with tyrosine phosphatase PTPRC/CD45, a key regulator of T- and B-lymphocyte activation. The interaction with PTPRC may be required for the stable expression of this protein. [provided by RefSeq, Jul 2008]

MANE transcript

NM_005608.3

Inheritance

—

ClinVar variants

U:35B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr11:67,435,510-67,437,682

External References & Databases

Ensembl (ENSG00000213402)

Transcript & Mutation Effects

hg38 • Region Span ~2.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PTPRCAP variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 36

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_005608.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			33 clinvar	3 clinvar		36
nonsense						0
start loss			1 clinvar			1
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	35	3	0	38

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 2 of 2 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_005608.3	RefSeq	NP_005599.1	2	MANE Select
ENST00000326294.4	Ensembl	ENSP00000325589.3	2	MANE Select

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

TNF alpha Signaling Pathway

Biological Process

defense response

Cellular Component

plasma membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000326294
Coding exons: 2
Length: 2558
Individuals with no LoFs: 123561
Homozygous LoFs: 0
Heterozygous LoFs: 2
Defined: 123563
p: 0.00000809

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.299	118	127	0.926	0.00000878	1263
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.0000090	0.0000090	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.111

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.782

Gene Damage Prediction

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