CPA2

carboxypeptidase A2, the group of M14 carboxypeptidases

Basic information

Region (hg38): 7:130266863-130289798

Links

ENSG00000158516 ∙ NCBI:1358 ∙ OMIM:600688 ∙ HGNC:2297 ∙ Uniprot:P48052 ∙ 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 CPA2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CPA2 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					1	1
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	0	3

Variants in CPA2

This is a list of pathogenic ClinVar variants found in the CPA2 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-130266925-A-G		not specified	Uncertain significance (Oct 04, 2022)
7-130269713-C-T			Benign (Aug 04, 2018)
7-130269714-G-A			Benign (May 08, 2018)
7-130269729-G-A		not specified	Uncertain significance (Feb 03, 2022)
7-130269766-A-G		not specified	Uncertain significance (Jul 28, 2021)
7-130269798-G-A		not specified	Uncertain significance (May 05, 2023)
7-130270709-A-T		not specified	Uncertain significance (Mar 07, 2023)
7-130270750-G-A		not specified	Uncertain significance (Jun 05, 2024)
7-130273096-C-G		not specified	Uncertain significance (Dec 19, 2022)
7-130273100-G-A		not specified	Uncertain significance (Oct 26, 2022)
7-130273115-G-T		not specified	Uncertain significance (Dec 13, 2022)
7-130273125-G-A		not specified	Uncertain significance (Jun 16, 2024)
7-130273134-A-T		not specified	Uncertain significance (Mar 23, 2023)
7-130275176-A-G			Benign (May 31, 2018)
7-130275177-T-C		not specified	Uncertain significance (Jul 15, 2021)
7-130275195-T-C		not specified	Uncertain significance (Feb 08, 2023)
7-130275204-G-A		not specified	Uncertain significance (Jul 25, 2023)
7-130276640-T-C		not specified	Uncertain significance (Nov 08, 2022)
7-130276661-A-G		not specified	Uncertain significance (May 18, 2023)
7-130276673-G-T		not specified	Uncertain significance (May 21, 2024)
7-130276698-C-T		not specified	Uncertain significance (Dec 14, 2023)
7-130277830-G-A		not specified	Uncertain significance (Feb 06, 2023)
7-130277848-G-C		not specified	Uncertain significance (Sep 01, 2021)
7-130277855-G-T		not specified	Uncertain significance (Dec 02, 2022)
7-130277877-G-A		not specified	Uncertain significance (Jan 30, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CPA2	protein_coding	protein_coding	ENST00000222481	11	22972

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.40e-15	0.0123	125636	0	112	125748	0.000445

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0768	236	233	1.01	0.0000121	2756
Missense in Polyphen		80	85.125	0.93979		1044
Synonymous	-0.202	89	86.6	1.03	0.00000460	799
Loss of Function	0.0539	23	23.3	0.988	0.00000114	265

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00117	0.00110
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000326	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.000564	0.000563
Middle Eastern	0.000326	0.000326
South Asian	0.000330	0.000327
Other	0.000489	0.000489

dbNSFP

Source: dbNSFP

• Pathway: Protein digestion and absorption - Homo sapiens (human);Pancreatic secretion - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.129

Intolerance Scores

• loftool: 0.866
• rvis_EVS: -0.38
• rvis_percentile_EVS: 28.01

Haploinsufficiency Scores

• pHI: 0.611
• hipred: N
• hipred_score: 0.144
• ghis: 0.419

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.128

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cpa2
• Phenotype: homeostasis/metabolism phenotype; reproductive system phenotype

Gene ontology

• Biological process: proteolysis;protein catabolic process in the vacuole
• Cellular component: extracellular region;extracellular space;vacuole
• Molecular function: carboxypeptidase activity;metallocarboxypeptidase activity;zinc ion binding