CPM

carboxypeptidase M, the group of M14 carboxypeptidases

Basic information

Region (hg38): 12:68842197-68971570

Links

ENSG00000135678 ∙ NCBI:1368 ∙ OMIM:114860 ∙ HGNC:2311 ∙ Uniprot:P14384 ∙ 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 CPM gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CPM 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			23			23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	0	0

Variants in CPM

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

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

Position	Type	Phenotype	Significance	ClinVar
12-68856483-C-G		not specified	Uncertain significance (Aug 01, 2024)
12-68856493-T-C		not specified	Uncertain significance (Jan 26, 2023)
12-68856535-T-C		not specified	Uncertain significance (Nov 18, 2022)
12-68856538-G-A		not specified	Uncertain significance (Dec 27, 2023)
12-68856591-A-G		not specified	Uncertain significance (May 08, 2023)
12-68858996-T-C		not specified	Uncertain significance (Nov 17, 2022)
12-68858997-G-A		not specified	Uncertain significance (May 31, 2022)
12-68859062-C-A		not specified	Uncertain significance (Oct 01, 2024)
12-68859062-C-T		not specified	Uncertain significance (Dec 10, 2024)
12-68866904-A-G		not specified	Uncertain significance (Aug 09, 2021)
12-68866936-G-C		not specified	Uncertain significance (Oct 05, 2023)
12-68866940-T-C		not specified	Uncertain significance (Feb 03, 2022)
12-68866970-C-T		not specified	Uncertain significance (Nov 11, 2024)
12-68866971-G-A		not specified	Uncertain significance (Mar 17, 2023)
12-68866971-G-C		not specified	Uncertain significance (Dec 05, 2022)
12-68869343-A-T		not specified	Uncertain significance (Dec 26, 2023)
12-68869360-C-G		Autism	Uncertain significance (-)
12-68869463-G-T		not specified	Uncertain significance (Mar 23, 2022)
12-68869487-C-A		not specified	Uncertain significance (Nov 17, 2022)
12-68870281-C-T		not specified	Uncertain significance (Jan 17, 2024)
12-68870382-T-C		not specified	Uncertain significance (May 08, 2023)
12-68871835-G-A		not specified	Uncertain significance (Feb 14, 2023)
12-68871895-T-C		not specified	Uncertain significance (Oct 11, 2024)
12-68871896-C-A		not specified	Uncertain significance (Nov 16, 2021)
12-68871910-G-A		not specified	Uncertain significance (Apr 04, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CPM	protein_coding	protein_coding	ENST00000551568	8	129374

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000166	0.970	125596	0	152	125748	0.000605

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.97	153	239	0.641	0.0000118	2925
Missense in Polyphen		59	93.816	0.62889		1154
Synonymous	0.0391	92	92.5	0.995	0.00000485	819
Loss of Function	1.98	11	20.7	0.531	0.00000102	264

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00689	0.00686
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.000163	0.000163
Finnish	0.000462	0.000462
European (Non-Finnish)	0.0000708	0.0000703
Middle Eastern	0.000163	0.000163
South Asian	0.000200	0.000196
Other	0.000331	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Specifically removes C-terminal basic residues (Arg or Lys) from peptides and proteins. It is believed to play important roles in the control of peptide hormone and growth factor activity at the cell surface, and in the membrane-localized degradation of extracellular proteins. {ECO:0000269|PubMed:12457462}.
• Pathway: Post-translational modification: synthesis of GPI-anchored proteins;Post-translational protein modification;Metabolism of proteins (Consensus)

Recessive Scores

• pRec: 0.191

Intolerance Scores

• loftool: 0.703
• rvis_EVS: 0.48
• rvis_percentile_EVS: 79.25

Haploinsufficiency Scores

• pHI: 0.164
• hipred: N
• hipred_score: 0.421
• ghis: 0.442

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0509

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cpm

Gene ontology

• Biological process: peptide metabolic process;anatomical structure morphogenesis;protein processing
• Cellular component: extracellular region;extracellular space;plasma membrane;cell surface;anchored component of membrane;extracellular exosome
• Molecular function: carboxypeptidase activity;metallocarboxypeptidase activity;zinc ion binding