CPXM1

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

Basic information

Region (hg38): 20:2794074-2800627

Previous symbols: [ "CPXM" ]

Links

ENSG00000088882 ∙ NCBI:56265 ∙ OMIM:609555 ∙ HGNC:15771 ∙ Uniprot:Q96SM3 ∙ 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 CPXM1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CPXM1 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					2	2
missense			41	5		46
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	41	5	2

Variants in CPXM1

This is a list of pathogenic ClinVar variants found in the CPXM1 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-2794213-G-A		not specified	Uncertain significance (Jun 28, 2022)
20-2794221-C-T		not specified	Uncertain significance (Feb 27, 2023)
20-2794263-A-G		not specified	Uncertain significance (Apr 29, 2024)
20-2794264-G-A			Benign (Jan 01, 2023)
20-2794272-A-G		not specified	Uncertain significance (Sep 28, 2022)
20-2794338-C-T		not specified	Uncertain significance (Jul 15, 2021)
20-2794339-G-A		not specified	Uncertain significance (Dec 19, 2022)
20-2794344-T-C		not specified	Likely benign (Jun 23, 2023)
20-2794348-G-A		not specified	Uncertain significance (Sep 23, 2023)
20-2794551-T-C		not specified	Uncertain significance (Aug 26, 2022)
20-2794567-C-T		not specified	Uncertain significance (Oct 02, 2023)
20-2794599-G-A		not specified	Uncertain significance (Apr 26, 2023)
20-2794602-T-C		not specified	Uncertain significance (Jan 04, 2024)
20-2795610-G-A		not specified	Uncertain significance (Aug 17, 2022)
20-2795626-C-G		not specified	Uncertain significance (May 12, 2024)
20-2795641-C-T		not specified	Uncertain significance (Dec 27, 2023)
20-2795647-C-A		not specified	Likely benign (Oct 25, 2023)
20-2795673-C-A		not specified	Uncertain significance (Apr 18, 2024)
20-2795673-C-T		not specified	Uncertain significance (Aug 23, 2021)
20-2795688-T-C		not specified	Uncertain significance (Jan 09, 2023)
20-2795709-G-A		not specified	Uncertain significance (Jan 13, 2023)
20-2795731-G-T		not specified	Uncertain significance (Sep 30, 2022)
20-2795743-C-T		not specified	Uncertain significance (Nov 09, 2021)
20-2795764-C-T		not specified	Uncertain significance (Apr 06, 2024)
20-2795766-C-A		not specified	Uncertain significance (Oct 25, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CPXM1	protein_coding	protein_coding	ENST00000380605	14	6569

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.76e-12	0.914	125648	0	99	125747	0.000394

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.50	363	453	0.802	0.0000288	4730
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000981	0.000980
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.000870	0.000870
Finnish	0.0000950	0.0000924
European (Non-Finnish)	0.000168	0.000167
Middle Eastern	0.000870	0.000870
South Asian	0.000982	0.000980
Other	0.000490	0.000489

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.181
• hipred: N
• hipred_score: 0.287
• ghis: 0.511

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.153

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cpxm1

Gene ontology

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