CPA3

carboxypeptidase A3, the group of M14 carboxypeptidases

Basic information

Region (hg38): 3:148865296-148897203

Links

ENSG00000163751 ∙ NCBI:1359 ∙ OMIM:114851 ∙ HGNC:2298 ∙ Uniprot:P15088 ∙ 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 CPA3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CPA3 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	2
missense			32	1	2	35
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	32	2	3

Variants in CPA3

This is a list of pathogenic ClinVar variants found in the CPA3 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-148865318-T-A		not specified	Uncertain significance (Dec 11, 2024)
3-148865350-G-A		not specified	Uncertain significance (Aug 14, 2024)
3-148865362-G-A		not specified	Uncertain significance (Feb 14, 2023)
3-148865366-G-A		not specified	Uncertain significance (Apr 13, 2023)
3-148868927-T-C		not specified	Uncertain significance (Dec 20, 2023)
3-148868936-G-A		not specified	Uncertain significance (Jan 22, 2024)
3-148868976-G-A		not specified	Uncertain significance (Jan 27, 2025)
3-148868988-A-G		not specified	Uncertain significance (May 13, 2024)
3-148878445-T-G		not specified	Uncertain significance (Feb 15, 2025)
3-148878451-C-T		not specified	Uncertain significance (Jan 04, 2022)
3-148878454-G-C		not specified	Uncertain significance (Nov 24, 2024)
3-148878482-T-C		not specified	Uncertain significance (May 26, 2022)
3-148878490-A-C		not specified	Uncertain significance (Feb 22, 2024)
3-148878505-G-A		not specified	Uncertain significance (May 24, 2023)
3-148878520-G-A		not specified	Uncertain significance (Jan 07, 2022)
3-148878674-G-T		not specified	Uncertain significance (Aug 10, 2023)
3-148878675-A-C		not specified	Uncertain significance (Nov 12, 2024)
3-148878721-T-G			Likely benign (Jun 13, 2018)
3-148879842-G-A		not specified	Uncertain significance (Mar 18, 2024)
3-148879850-A-C		not specified	Uncertain significance (Dec 11, 2024)
3-148879888-A-G		not specified	Uncertain significance (Aug 22, 2023)
3-148881557-C-G			Benign (Apr 04, 2018)
3-148881569-C-A		not specified	Uncertain significance (Aug 17, 2021)
3-148882509-G-A		not specified	Uncertain significance (Jun 10, 2024)
3-148882526-C-T		not specified	Uncertain significance (Jun 25, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CPA3	protein_coding	protein_coding	ENST00000296046	11	31941

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.04e-16	0.0147	125595	0	152	125747	0.000605

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.695	259	229	1.13	0.0000120	2754
Missense in Polyphen		102	82.964	1.2294		1025
Synonymous	-0.0591	79	78.3	1.01	0.00000395	748
Loss of Function	0.266	25	26.5	0.944	0.00000154	290

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00305	0.00305
Ashkenazi Jewish	0.00	0.00
East Asian	0.000545	0.000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000282	0.000281
Middle Eastern	0.000545	0.000544
South Asian	0.00162	0.00160
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Pathway: Renin-angiotensin system - Homo sapiens (human);Protein digestion and absorption - Homo sapiens (human);Pancreatic secretion - Homo sapiens (human);Peptide hormone metabolism;Metabolism of proteins;Metabolism of Angiotensinogen to Angiotensins (Consensus)

Recessive Scores

• pRec: 0.147

Intolerance Scores

• loftool: 0.963
• rvis_EVS: 1.51
• rvis_percentile_EVS: 95.45

Haploinsufficiency Scores

• pHI: 0.170
• hipred: N
• hipred_score: 0.169
• ghis: 0.415

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0624

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cpa3
• Phenotype: renal/urinary system phenotype; immune system phenotype; hematopoietic system phenotype; reproductive system 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); homeostasis/metabolism phenotype; cellular phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan)

Gene ontology

• Biological process: angiotensin maturation;proteolysis
• Cellular component: extracellular region;extracellular space;transport vesicle;secretory granule;collagen-containing extracellular matrix
• Molecular function: metallocarboxypeptidase activity;zinc ion binding