CPA5

carboxypeptidase A5, the group of M14 carboxypeptidases

Basic information

Region (hg38): 7:130344816-130368730

Links

ENSG00000158525 ∙ NCBI:93979 ∙ OMIM:609561 ∙ HGNC:15722 ∙ Uniprot:Q8WXQ8 ∙ 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 CPA5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CPA5 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				2		2
missense			30	2		32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	30	4	0

Variants in CPA5

This is a list of pathogenic ClinVar variants found in the CPA5 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-130346511-C-G		not specified	Uncertain significance (Apr 17, 2023)
7-130346540-C-G		not specified	Uncertain significance (Nov 02, 2023)
7-130346580-T-G		not specified	Likely benign (Oct 29, 2021)
7-130347780-G-A		not specified	Uncertain significance (Nov 08, 2022)
7-130349988-G-A		not specified	Uncertain significance (Dec 28, 2022)
7-130350000-G-A		not specified	Uncertain significance (Dec 10, 2024)
7-130350009-T-C		not specified	Uncertain significance (Aug 23, 2021)
7-130350026-G-A		not specified	Uncertain significance (Feb 06, 2024)
7-130350093-T-C		not specified	Uncertain significance (Mar 08, 2024)
7-130359631-C-T		not specified	Uncertain significance (Mar 18, 2024)
7-130359632-G-A		not specified	Uncertain significance (Feb 15, 2023)
7-130359641-G-A		not specified	Uncertain significance (Jun 07, 2023)
7-130361189-T-C		not specified	Uncertain significance (Dec 03, 2021)
7-130361205-T-G		not specified	Uncertain significance (Dec 14, 2023)
7-130362456-C-T		not specified	Uncertain significance (Jan 17, 2024)
7-130362457-G-A		not specified	Likely benign (Dec 30, 2023)
7-130362466-C-T		not specified	Uncertain significance (Mar 28, 2023)
7-130362498-G-A		not specified	Uncertain significance (Mar 29, 2023)
7-130362933-C-T		not specified	Uncertain significance (Aug 19, 2024)
7-130362938-G-A		not specified	Uncertain significance (Nov 08, 2024)
7-130362948-T-C		not specified	Uncertain significance (Jan 03, 2024)
7-130363431-C-T		not specified	Uncertain significance (Sep 10, 2024)
7-130363470-G-A		not specified	Uncertain significance (Nov 17, 2022)
7-130363493-G-C		not specified	Uncertain significance (Aug 12, 2024)
7-130367392-C-T		not specified	Uncertain significance (Aug 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CPA5	protein_coding	protein_coding	ENST00000485477	11	23942

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000182	0.995	125716	0	32	125748	0.000127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.591	235	262	0.897	0.0000154	2854
Missense in Polyphen		81	100.21	0.80833		1196
Synonymous	0.610	96	104	0.924	0.00000663	835
Loss of Function	2.46	10	22.6	0.442	0.00000111	256

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000333	0.000333
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.000132	0.000132
Middle Eastern	0.000218	0.000217
South Asian	0.000170	0.000163
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.164

Intolerance Scores

• loftool: 0.786
• rvis_EVS: 0.36
• rvis_percentile_EVS: 74.63

Haploinsufficiency Scores

• pHI: 0.192
• hipred: N
• hipred_score: 0.414
• ghis: 0.390

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.121

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cpa5

Gene ontology

• Biological process: proteolysis
• Cellular component: extracellular space
• Molecular function: metallocarboxypeptidase activity;zinc ion binding