CPVL

carboxypeptidase vitellogenic like, the group of M14 carboxypeptidases

Basic information

Region (hg38): 7:28995234-29195451

Links

ENSG00000106066 ∙ NCBI:54504 ∙ OMIM:609780 ∙ HGNC:14399 ∙ Uniprot:Q9H3G5 ∙ 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 CPVL gene.

• Inborn genetic diseases (17 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CPVL 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			17	2		19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	2	0

Variants in CPVL

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

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

Position	Type	Phenotype	Significance	ClinVar
7-28995780-C-A		not specified	Uncertain significance (Feb 06, 2024)
7-28995812-C-T			Likely benign (May 09, 2018)
7-29030638-T-G		not specified	Uncertain significance (Sep 12, 2023)
7-29030651-T-C		not specified	Uncertain significance (Jan 23, 2023)
7-29030680-T-C		not specified	Uncertain significance (Aug 17, 2022)
7-29030726-C-T		not specified	Uncertain significance (Nov 17, 2023)
7-29064087-A-C		not specified	Uncertain significance (Oct 29, 2021)
7-29064111-T-C		not specified	Uncertain significance (Aug 02, 2023)
7-29064135-C-G		not specified	Uncertain significance (Feb 10, 2023)
7-29064231-G-A		not specified	Uncertain significance (Aug 28, 2023)
7-29066049-T-G		not specified	Uncertain significance (Jan 23, 2024)
7-29072332-G-A		not specified	Uncertain significance (Jan 19, 2024)
7-29086486-C-G		not specified	Uncertain significance (Sep 12, 2023)
7-29092653-T-G		not specified	Uncertain significance (Jan 23, 2024)
7-29092666-C-T		not specified	Uncertain significance (Feb 27, 2023)
7-29095102-C-T		not specified	Uncertain significance (Aug 02, 2023)
7-29095139-C-T		not specified	Uncertain significance (Oct 05, 2022)
7-29096107-C-G		not specified	Uncertain significance (Dec 14, 2021)
7-29096171-G-A		not specified	Uncertain significance (Jan 03, 2024)
7-29096204-T-A		not specified	Uncertain significance (Sep 16, 2021)
7-29112766-C-T		not specified	Uncertain significance (Jan 17, 2023)
7-29112795-A-G		not specified	Uncertain significance (Feb 12, 2024)
7-29120916-A-G		not specified	Uncertain significance (Jan 23, 2024)
7-29120977-T-C		not specified	Uncertain significance (Dec 22, 2023)
7-29121006-G-A		not specified	Uncertain significance (Nov 10, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CPVL	protein_coding	protein_coding	ENST00000409850	12	200221

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.35e-11	0.496	125525	2	221	125748	0.000887

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.608	230	257	0.893	0.0000130	3116
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00152	0.00152
Ashkenazi Jewish	0.00	0.00
East Asian	0.00255	0.00229
Finnish	0.000140	0.000139
European (Non-Finnish)	0.000995	0.000994
Middle Eastern	0.00255	0.00229
South Asian	0.000730	0.000653
Other	0.000817	0.000815

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.0700
• hipred: N
• hipred_score: 0.197
• ghis: 0.411

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.177

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cpvl
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: proteolysis involved in cellular protein catabolic process
• Cellular component: extracellular exosome
• Molecular function: serine-type carboxypeptidase activity