CPA2

protein-coding

carboxypeptidase A2, the group of M14 carboxypeptidases

Gene summary

Three different forms of human pancreatic procarboxypeptidase A have been isolated. The encoded protein represents the A2 form, which is a monomeric protein with different biochemical properties from the A1 and A3 forms. The A2 form of pancreatic procarboxypeptidase acts on aromatic C-terminal residues and is a secreted protein. [provided by RefSeq, Dec 2008]

MANE transcript

NM_001869.3

Inheritance

—

ClinVar variants

U:58B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.99

Max pathogenic AF

—

Genomic locus

chr7:130,266,863-130,289,798

External References & Databases

Ensembl (ENSG00000158516)

Transcript & Mutation Effects

hg38 • Region Span ~22.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CPA2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 57

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001869.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous					1 clinvar	1
missense			58 clinvar		2 clinvar	60
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	58	0	3	61

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 4 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001869.3	RefSeq	NP_001860.2	11	MANE Select
ENST00000222481.9	Ensembl	ENSP00000222481.4	11	MANE Select
ENST00000416698.1	Ensembl	ENSP00000395582.1	6	Standard
ENST00001134685.1	Ensembl	ENSP00000801780.1	11	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Protein digestion and absorption - Homo sapiens (human)
Pancreatic secretion - Homo sapiens (human)

Biological Process

proteolysis
protein catabolic process in the vacuole

Molecular Function

carboxypeptidase activity
metallocarboxypeptidase activity
zinc ion binding

Cellular Component

extracellular region
extracellular space
vacuole

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000222481
Coding exons: 11
Length: 22972
Individuals with no LoFs: 125636
Homozygous LoFs: 0
Heterozygous LoFs: 112
Defined: 125748
p: 0.000445

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.0768	236	233	1.01	0.0000121	2756
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00062	0.00055	rare
Latino/Admixed American	0.00055	0.00055	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00033	0.00033	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00056	0.00056	rare
South Asian	0.00033	0.00033	rare
Other	0.00049	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.129

Intolerance Scores

LoFtool: 0.866
RVIS EVS: -0.38
RVIS percentile EVS: 28.01

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.128

Gene Damage Prediction

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