CPN2

protein-coding

carboxypeptidase N subunit 2, the group of M14 carboxypeptidases

Gene summary

Predicted to enable signaling receptor activity. Predicted to be involved in protein stabilization. Located in blood microparticle and extracellular exosome. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

ACBP

MANE transcript

NM_001080513.4

Inheritance

—

ClinVar variants

U:87B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.49

Max pathogenic AF

—

Genomic locus

chr3:194,339,768-194,351,328

External References & Databases

Ensembl (ENSG00000178772)

Transcript & Mutation Effects

hg38 • Region Span ~11.6 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 CPN2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 88

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001080513.4. 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			87 clinvar	4 clinvar	1 clinvar	92
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	87	4	2	93

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 35 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001080513.4	RefSeq	NP_001073982.3	1	MANE Select
ENST00000323830.4	Ensembl	ENSP00000319464.3	1	MANE Select
NM_001291988.2	RefSeq	NP_001278917.1	1	Standard
ENST00000429275.1	Ensembl	ENSP00000402232.1	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Innate Immune System
Immune System
Regulation of Complement cascade
Complement cascade

Biological Process

proteolysis
regulation of complement activation
regulation of catalytic activity
protein stabilization

Molecular Function

metallocarboxypeptidase activity
enzyme regulator activity

Cellular Component

extracellular region
extracellular space
extracellular matrix
extracellular exosome
blood microparticle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000323830
Coding exons: 1
Length: 11564
Individuals with no LoFs: 125724
Homozygous LoFs: 0
Heterozygous LoFs: 24
Defined: 125748
p: 0.0000954

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.293	292	306	0.953	0.0000181	3519
Missense (PolyPhen)		63	81.636	0.77172		1073
Synonymous	-1.58	179	154	1.16	0.0000100	1197
Loss of Function	1.66	6	12.3	0.489	5.37e-7	129

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00037	0.00037	rare
Latino/Admixed American	0.000087	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00022	0.00022	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000071	0.000070	rare
South Asian	0.000098	0.000098	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: The 83 kDa subunit binds and stabilizes the catalytic subunit at 37 degrees Celsius and keeps it in circulation. Under some circumstances it may be an allosteric modifier of the catalytic subunit.;

Recessive Scores

pRec: 0.172

Intolerance Scores

LoFtool: 0.640
RVIS EVS: 0.29
RVIS percentile EVS: 71.62

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.196

Gene Damage Prediction

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