CPXM2

protein-coding

carboxypeptidase X, M14 family member 2, the group of M14 carboxypeptidases

Gene summary

Predicted to enable metallocarboxypeptidase activity and zinc ion binding activity. Predicted to be involved in proteolysis. Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_198148.3

Inheritance

—

ClinVar variants

U:148B:6

Top phenotype

EBV-positive nodal T- and NK-cell lymphoma

gnomAD constraint

pLI —, LoF o/e 0.68

Max pathogenic AF

—

Genomic locus

chr10:123,706,207-123,940,267

External References & Databases

Ensembl (ENSG00000121898)

Transcript & Mutation Effects

hg38 • Region Span ~234.1 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 CPXM2 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 146

not providedTotal: 3

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

Breast ductal adenocarcinomaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_198148.3. 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			145 clinvar	4 clinvar	1 clinvar	150
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	148	4	2	154

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 24 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_198148.3	RefSeq	NP_937791.2	14	MANE Select
ENST00000241305.4	Ensembl	ENSP00000241305.3	14	MANE Select
ENST00000615851.4	Ensembl	ENSP00000483180.1	5	Standard
ENST00000909347.1	Ensembl	ENSP00000579406.1	13	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

peptide metabolic process
protein processing

Molecular Function

metallocarboxypeptidase activity
zinc ion binding

Cellular Component

extracellular space

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000241305
Coding exons: 14
Length: 234061
Individuals with no LoFs: 125588
Homozygous LoFs: 2
Heterozygous LoFs: 158
Defined: 125748
p: 0.000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.170	457	467	0.978	0.0000290	4923
Missense (PolyPhen)		213	206.21	1.0329		2046
Synonymous	1.03	167	185	0.904	0.0000116	1470
Loss of Function	1.81	25	36.9	0.678	0.00000188	406

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00092	0.00092	rare
Latino/Admixed American	0.00017	0.00017	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00071	0.00071	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00057	0.00057	rare
South Asian	0.0020	0.0019	notable
Other	0.00065	0.00065	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be involved in cell-cell interactions.;

Recessive Scores

pRec: 0.104

Intolerance Scores

LoFtool: 0.287
RVIS EVS: -0.28
RVIS percentile EVS: 33.53

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.215

Gene Damage Prediction

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