PRCP

prolylcarboxypeptidase, the group of M14 carboxypeptidases|Minor histocompatibility antigens

Basic information

Region (hg38): 11:82822936-82970584

Links

ENSG00000137509 ∙ NCBI:5547 ∙ OMIM:176785 ∙ HGNC:9344 ∙ Uniprot:P42785 ∙ 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 PRCP gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRCP 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			36	1	2	39
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	36	1	2

Variants in PRCP

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

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

Position	Type	Phenotype	Significance	ClinVar
11-82824954-C-T		not specified	Uncertain significance (Oct 10, 2023)
11-82824958-T-C		not specified	Uncertain significance (Aug 15, 2024)
11-82824993-C-T		not specified	Uncertain significance (Nov 09, 2021)
11-82825018-C-T		not specified	Uncertain significance (Apr 06, 2022)
11-82825019-G-A		not specified	Uncertain significance (Jan 17, 2023)
11-82825055-C-A		not specified	Uncertain significance (Aug 17, 2022)
11-82825093-C-T		not specified	Uncertain significance (Jun 02, 2023)
11-82825107-G-T			not provided (-)
11-82838408-G-A		not specified	Uncertain significance (Aug 28, 2024)
11-82838418-T-C		not specified	Uncertain significance (Sep 22, 2023)
11-82838421-T-C		not specified	Uncertain significance (Sep 03, 2024)
11-82838436-T-C		not specified	Uncertain significance (Aug 10, 2021)
11-82838439-T-G		not specified	Uncertain significance (Feb 22, 2023)
11-82838513-T-C		not specified	Uncertain significance (Aug 12, 2024)
11-82838532-C-T		not specified	Uncertain significance (Jul 05, 2023)
11-82839298-G-T			Benign (Dec 13, 2017)
11-82839356-G-C		not specified	Uncertain significance (Aug 17, 2021)
11-82849105-C-T		not specified	Uncertain significance (Jul 02, 2024)
11-82849115-A-T		not specified	Uncertain significance (Aug 02, 2022)
11-82849948-C-A		not specified	Uncertain significance (Jan 17, 2023)
11-82849977-C-T		not specified	Uncertain significance (Feb 01, 2023)
11-82849984-C-G		not specified	Uncertain significance (Oct 26, 2021)
11-82850001-C-T		not specified	Uncertain significance (Sep 09, 2024)
11-82850016-C-T		not specified	Uncertain significance (Nov 26, 2024)
11-82850039-A-G		not specified	Uncertain significance (May 03, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRCP	protein_coding	protein_coding	ENST00000393399	10	147083

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.76e-12	0.263	125701	0	44	125745	0.000175

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0402	270	268	1.01	0.0000126	3369
Missense in Polyphen		95	98.973	0.95986		1221
Synonymous	-0.657	106	97.7	1.08	0.00000461	984
Loss of Function	0.965	20	25.2	0.793	0.00000114	301

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000443	0.000416
Ashkenazi Jewish	0.00	0.00
East Asian	0.000231	0.000217
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000222	0.000220
Middle Eastern	0.000231	0.000217
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cleaves C-terminal amino acids linked to proline in peptides such as angiotensin II, III and des-Arg9-bradykinin. This cleavage occurs at acidic pH, but enzymatic activity is retained with some substrates at neutral pH.
• Pathway: Renin-angiotensin system - Homo sapiens (human);Protein digestion and absorption - Homo sapiens (human);Neutrophil degranulation;Innate Immune System;Immune System;Intrinsic Pathway of Fibrin Clot Formation;Hemostasis;Formation of Fibrin Clot (Clotting Cascade) (Consensus)

Recessive Scores

• pRec: 0.210

Intolerance Scores

• loftool: 0.466
• rvis_EVS: 0.2
• rvis_percentile_EVS: 67.3

Haploinsufficiency Scores

• pHI: 0.422
• hipred: N
• hipred_score: 0.177
• ghis: 0.492

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0137

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Prcp
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); homeostasis/metabolism phenotype

Gene ontology

• Biological process: regulation of thyroid hormone mediated signaling pathway;plasma kallikrein-kinin cascade;negative regulation of systemic arterial blood pressure;proteolysis;blood coagulation, intrinsic pathway;glucose homeostasis;neutrophil degranulation;regulation of blood vessel endothelial cell migration;angiogenesis involved in wound healing;energy homeostasis;regulation of reactive oxygen species metabolic process
• Cellular component: plasma membrane;azurophil granule membrane;basal part of cell;extracellular exosome;ficolin-1-rich granule membrane
• Molecular function: serine-type carboxypeptidase activity;protein binding;dipeptidyl-peptidase activity