CPXM1

protein-coding

carboxypeptidase X, M14 family member 1, the group of M14 carboxypeptidases

Gene summary

This gene likely encodes a member of the carboxypeptidase family of proteins. Cloning of a comparable locus in mouse indicates that the encoded protein contains a discoidin domain and a carboxypeptidase domain, but the protein appears to lack residues necessary for carboxypeptidase activity.[provided by RefSeq, May 2010]

Previous symbols:

CPXM

MANE transcript

NM_019609.5

Inheritance

—

ClinVar variants

U:105B:14

Top phenotype

EBV-positive nodal T- and NK-cell lymphoma

gnomAD constraint

pLI —, LoF o/e 0.64

Max pathogenic AF

—

Genomic locus

chr20:2,794,074-2,800,627

External References & Databases

Ensembl (ENSG00000088882)

Transcript & Mutation Effects

hg38 • Region Span ~6.6 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 CPXM1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 108

not providedTotal: 3

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

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_019609.5. 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			2 clinvar	1 clinvar	2 clinvar	5
missense			99 clinvar	11 clinvar		110
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	105	12	2	119

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 25 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_019609.5	RefSeq	NP_062555.1	14	MANE Select
ENST00000380605.3	Ensembl	ENSP00000369979.2	14	MANE Select
NM_001184699.2	RefSeq	NP_001171628.1	14	Standard
ENST00000867057.1	Ensembl	ENSP00000537116.1	14	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: ENST00000380605
Coding exons: 14
Length: 6569
Individuals with no LoFs: 125648
Homozygous LoFs: 0
Heterozygous LoFs: 99
Defined: 125747
p: 0.000394

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.50	363	453	0.802	0.0000288	4730
Missense (PolyPhen)		133	174.36	0.76278		1840
Synonymous	0.901	168	184	0.915	0.0000120	1496
Loss of Function	2.01	24	37.3	0.644	0.00000210	367

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00043	0.00043	rare
Latino/Admixed American	0.00055	0.00055	rare
Ashkenazi Jewish	0.00030	0.00030	rare
East Asian	0.00087	0.00087	rare
Finnish	0.000095	0.000092	rare
European (Non-Finnish)	0.00017	0.00017	rare
South Asian	0.00098	0.00098	rare
Other	0.00049	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be involved in cell-cell interactions. No carboxypeptidase activity was found yet (By similarity). {ECO:0000250}.;

Recessive Scores

pRec: 0.107

Intolerance Scores

LoFtool: 0.333
RVIS EVS: -1.17
RVIS percentile EVS: 6.03

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.153

Gene Damage Prediction

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