CPXM2

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

Basic information

Region (hg38): 10:123706207-123940267

Links

ENSG00000121898 ∙ NCBI:119587 ∙ OMIM:617348 ∙ HGNC:26977 ∙ Uniprot:Q8N436 ∙ 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 CPXM2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CPXM2 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						0
missense			52	3	1	56
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding					1	1
Total	0	0	52	3	2

Variants in CPXM2

This is a list of pathogenic ClinVar variants found in the CPXM2 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-123746771-C-T		not specified	Uncertain significance (Jun 30, 2023)
10-123746792-C-T		not specified	Uncertain significance (Sep 16, 2021)
10-123746804-C-G		not specified	Uncertain significance (Jun 11, 2021)
10-123746996-C-T		not specified	Uncertain significance (May 01, 2022)
10-123754686-C-A		not specified	Uncertain significance (Mar 31, 2024)
10-123754752-C-T		not specified	Uncertain significance (Feb 16, 2023)
10-123754756-G-A		not specified	Uncertain significance (Jan 24, 2024)
10-123754772-A-G			Benign (Aug 03, 2017)
10-123757242-G-A		not specified	Uncertain significance (Mar 03, 2022)
10-123757301-T-C		not specified	Uncertain significance (Nov 03, 2022)
10-123757305-T-C		not specified	Uncertain significance (Jun 28, 2022)
10-123757319-C-T		not specified	Uncertain significance (Jul 14, 2023)
10-123761881-C-T		not specified	Uncertain significance (Jul 06, 2022)
10-123761901-T-C		not specified	Uncertain significance (Dec 07, 2021)
10-123761919-T-C			Benign (Aug 03, 2017)
10-123761965-T-C		not specified	Uncertain significance (Nov 01, 2022)
10-123761971-G-A		not specified	Uncertain significance (Feb 28, 2024)
10-123761988-G-A		not specified	Uncertain significance (May 12, 2024)
10-123762004-G-A		not specified	Uncertain significance (Jul 15, 2021)
10-123762016-C-T		not specified	Uncertain significance (Dec 13, 2021)
10-123762019-C-T		not specified	Uncertain significance (Jan 03, 2024)
10-123766980-T-C		not specified	Uncertain significance (Jan 23, 2023)
10-123767013-T-C		not specified	Uncertain significance (Jul 26, 2021)
10-123767020-T-C		not specified	Uncertain significance (May 05, 2023)
10-123767046-C-T		not specified	Likely benign (Apr 25, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CPXM2	protein_coding	protein_coding	ENST00000241305	14	234061

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.49e-13	0.800	125588	2	158	125748	0.000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.170	457	467	0.978	0.0000290	4923
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00110	0.00110
Ashkenazi Jewish	0.00	0.00
East Asian	0.000707	0.000707
Finnish	0.00	0.00
European (Non-Finnish)	0.000573	0.000571
Middle Eastern	0.000707	0.000707
South Asian	0.00195	0.00186
Other	0.000653	0.000652

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.256
• hipred: N
• hipred_score: 0.334
• ghis: 0.536

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.215

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cpxm2

Gene ontology

• Biological process: peptide metabolic process;protein processing
• Cellular component: extracellular space
• Molecular function: metallocarboxypeptidase activity;zinc ion binding