CPO

carboxypeptidase O, the group of M14 carboxypeptidases

Basic information

Region (hg38): 2:206939518-206969474

Links

ENSG00000144410 ∙ NCBI:130749 ∙ OMIM:609563 ∙ HGNC:21011 ∙ Uniprot:Q8IVL8 ∙ 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 CPO gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CPO 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			36	2		38
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	36	2	0

Variants in CPO

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

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

Position	Type	Phenotype	Significance	ClinVar
2-206939612-C-G		not specified	Uncertain significance (Feb 05, 2025)
2-206949646-T-C		not specified	Uncertain significance (Nov 08, 2024)
2-206949653-G-T		not specified	Uncertain significance (Dec 26, 2023)
2-206949657-G-T		not specified	Uncertain significance (Apr 26, 2024)
2-206949671-C-A		not specified	Uncertain significance (Dec 06, 2023)
2-206949693-A-G		not specified	Uncertain significance (Feb 18, 2025)
2-206949699-C-T		not specified	Uncertain significance (Jan 26, 2022)
2-206958311-C-T		not specified	Uncertain significance (Apr 12, 2023)
2-206958323-C-T		not specified	Uncertain significance (Sep 06, 2022)
2-206958358-G-A		not specified	Uncertain significance (Dec 16, 2022)
2-206958367-T-G		not specified	Uncertain significance (Feb 07, 2025)
2-206958397-G-C		not specified	Uncertain significance (Jul 16, 2024)
2-206959635-T-C		not specified	Uncertain significance (Jun 24, 2022)
2-206959644-A-G		not specified	Uncertain significance (Feb 09, 2022)
2-206959649-G-C		not specified	Uncertain significance (Jun 11, 2024)
2-206959655-T-A		not specified	Uncertain significance (Feb 14, 2025)
2-206959664-C-T		not specified	Uncertain significance (Oct 29, 2024)
2-206959665-G-A		not specified	Likely benign (Sep 20, 2024)
2-206959668-A-C		not specified	Uncertain significance (Dec 27, 2023)
2-206959674-T-G		not specified	Uncertain significance (Oct 09, 2024)
2-206959719-G-A		not specified	Uncertain significance (Dec 14, 2023)
2-206959725-T-G		not specified	Uncertain significance (Jul 19, 2022)
2-206959730-A-G		not specified	Uncertain significance (Sep 30, 2024)
2-206960873-C-T		not specified	Uncertain significance (Apr 09, 2024)
2-206960879-C-T		not specified	Likely benign (Apr 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CPO	protein_coding	protein_coding	ENST00000272852	9	29921

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.27e-21	0.000131	125528	1	209	125738	0.000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.479	183	202	0.905	0.0000101	2440
Missense in Polyphen		50	53.933	0.92707		711
Synonymous	-0.375	80	75.8	1.05	0.00000404	705
Loss of Function	-1.32	27	20.5	1.32	0.00000102	247

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00751	0.00741
Ashkenazi Jewish	0.00	0.00
East Asian	0.000329	0.000326
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000406	0.000404
Middle Eastern	0.000329	0.000326
South Asian	0.000817	0.000817
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Carboxypeptidase which preferentially cleaves C-terminal acidic residues from peptides and proteins. Can also cleave C- terminal hydrophobic amino acids, with a preference for small residues over large residues. {ECO:0000269|PubMed:21921028}.

Recessive Scores

• pRec: 0.0942

Intolerance Scores

• loftool: 0.917
• rvis_EVS: 0.67
• rvis_percentile_EVS: 84.61

Haploinsufficiency Scores

• pHI: 0.0953
• hipred: N
• hipred_score: 0.219
• ghis: 0.433

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.000726

Gene Damage Prediction

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

Gene ontology

• Biological process: proteolysis
• Cellular component: extracellular space;apical plasma membrane;anchored component of plasma membrane
• Molecular function: metallocarboxypeptidase activity;zinc ion binding