CPA4

carboxypeptidase A4, the group of M14 carboxypeptidases

Basic information

Region (hg38): 7:130293134-130324180

Links

ENSG00000128510 ∙ NCBI:51200 ∙ OMIM:607635 ∙ HGNC:15740 ∙ Uniprot:Q9UI42 ∙ 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 CPA4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CPA4 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			29			29
nonsense				1		1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	1	0

Variants in CPA4

This is a list of pathogenic ClinVar variants found in the CPA4 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-130298771-A-G		not specified	Uncertain significance (Nov 18, 2022)
7-130299304-G-A		not specified	Uncertain significance (Jul 25, 2023)
7-130299315-G-A		not specified	Uncertain significance (Feb 14, 2023)
7-130299321-G-A		not specified	Uncertain significance (Aug 30, 2022)
7-130299348-A-G		not specified	Uncertain significance (May 14, 2024)
7-130299369-G-A		not specified	Uncertain significance (Jan 22, 2024)
7-130299402-C-A		not specified	Uncertain significance (Jan 23, 2024)
7-130300877-A-G		not specified	Uncertain significance (Mar 01, 2024)
7-130304487-G-A		not specified	Uncertain significance (Jan 26, 2023)
7-130304494-A-G		not specified	Uncertain significance (Mar 16, 2022)
7-130304537-G-T		not specified	Uncertain significance (Aug 12, 2021)
7-130304559-C-T		not specified	Uncertain significance (Nov 15, 2021)
7-130305844-C-T		not specified	Uncertain significance (Jul 15, 2021)
7-130306821-C-T		not specified	Uncertain significance (Aug 10, 2023)
7-130306834-G-T		not specified	Uncertain significance (Dec 15, 2023)
7-130306875-G-T		not specified	Uncertain significance (Mar 29, 2022)
7-130308381-G-A		CPA4-related disorder	Likely benign (Jul 24, 2017)
7-130310837-G-A		not specified	Uncertain significance (Feb 06, 2024)
7-130310841-A-G		not specified	Uncertain significance (Dec 16, 2021)
7-130310844-C-T		not specified	Uncertain significance (Jan 19, 2024)
7-130310850-T-C		not specified	Uncertain significance (Apr 13, 2022)
7-130310917-C-G		not specified	Uncertain significance (May 17, 2023)
7-130310925-C-T		not specified	Uncertain significance (May 30, 2023)
7-130310949-G-A		not specified	Uncertain significance (Dec 17, 2023)
7-130312048-C-T		not specified	Uncertain significance (Jun 17, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CPA4	protein_coding	protein_coding	ENST00000222482	11	31047

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.39e-18	0.00461	124887	0	861	125748	0.00343

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.525	223	246	0.906	0.0000140	2780
Missense in Polyphen		75	86.182	0.87025		1017
Synonymous	0.599	96	104	0.925	0.00000688	789
Loss of Function	-0.0471	26	25.7	1.01	0.00000145	268

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00484	0.00484
Ashkenazi Jewish	0.00377	0.00378
East Asian	0.00131	0.00131
Finnish	0.00476	0.00477
European (Non-Finnish)	0.00431	0.00432
Middle Eastern	0.00131	0.00131
South Asian	0.00242	0.00242
Other	0.00310	0.00310

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Metalloprotease that could be involved in the histone hyperacetylation pathway (PubMed:10383164). Releases a C-terminal amino acid, with preference for -Phe, -Leu, -Ile, -Met, -Tyr and -Val (PubMed:20385563). {ECO:0000269|PubMed:10383164, ECO:0000269|PubMed:20385563}.

Recessive Scores

• pRec: 0.114

Intolerance Scores

• loftool: 0.976
• rvis_EVS: -0.31
• rvis_percentile_EVS: 32.17

Haploinsufficiency Scores

• pHI: 0.270
• hipred: N
• hipred_score: 0.170
• ghis: 0.497

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.748

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cpa4

Gene ontology

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