CPVL

protein-coding

carboxypeptidase vitellogenic like, the group of M14 carboxypeptidases

Gene summary

The protein encoded by this gene is a carboxypeptidase and bears strong sequence similarity to serine carboxypeptidases. Carboxypeptidases are a large class of proteases that act to cleave a single amino acid from the carboxy termini of proteins or peptides. The exact function of this protein, however, has not been determined. [provided by RefSeq, Jan 2017]

MANE transcript

NM_031311.5

Inheritance

—

ClinVar variants

U:73B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.74

Max pathogenic AF

—

Genomic locus

chr7:28,995,235-29,195,451

External References & Databases

Ensembl (ENSG00000106066)

Transcript & Mutation Effects

hg38 • Region Span ~200.2 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 CPVL variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 62

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_031311.5. 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			4 clinvar			4
missense			69 clinvar	3 clinvar		72
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	73	3	0	76

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 101 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_031311.5	RefSeq	NP_112601.3	12	MANE Select
ENST00000265394.10	Ensembl	ENSP00000265394.5	12	MANE Select
NM_001348052.1	RefSeq	NP_001334981.1	12	Standard
NM_001348054.1	RefSeq	NP_001334983.1	12	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

proteolysis involved in cellular protein catabolic process

Molecular Function

serine-type carboxypeptidase activity

Cellular Component

extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000409850
Coding exons: 12
Length: 200221
Individuals with no LoFs: 125525
Homozygous LoFs: 2
Heterozygous LoFs: 221
Defined: 125748
p: 0.000887

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.608	230	257	0.893	0.0000130	3116
Missense (PolyPhen)		104	114.38	0.90923		1397
Synonymous	0.00516	96	96.1	0.999	0.00000526	864
Loss of Function	1.27	20	27.1	0.737	0.00000129	330

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00068	0.00068	rare
Latino/Admixed American	0.00084	0.00084	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.0026	0.0023	notable
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.00099	0.00099	rare
South Asian	0.00073	0.00065	rare
Other	0.00082	0.00081	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be involved in the digestion of phagocytosed particles in the lysosome, participation in an inflammatory protease cascade, and trimming of peptides for antigen presentation.;

Recessive Scores

pRec: 0.102

Intolerance Scores

LoFtool: 0.384
RVIS EVS: 1.33
RVIS percentile EVS: 94.21

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.177

Gene Damage Prediction

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