CPD

carboxypeptidase D, the group of M14 carboxypeptidases

Basic information

Region (hg38): 17:30378927-30469989

Links

ENSG00000108582 ∙ NCBI:1362 ∙ OMIM:603102 ∙ HGNC:2301 ∙ Uniprot:O75976 ∙ 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 CPD gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CPD 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				1	2	3
missense			68	3	2	73
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	68	4	4

Variants in CPD

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

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

Position	Type	Phenotype	Significance	ClinVar
17-30378993-C-A			Benign (May 30, 2017)
17-30378998-C-G		not specified	Likely benign (Feb 27, 2023)
17-30379006-C-A		not specified	Uncertain significance (Mar 31, 2023)
17-30379068-C-T		not specified	Uncertain significance (May 05, 2023)
17-30379117-C-T		not specified	Uncertain significance (Jul 13, 2022)
17-30379150-G-C		not specified	Uncertain significance (Jul 07, 2022)
17-30379207-T-G		not specified	Uncertain significance (Dec 03, 2021)
17-30379213-G-T		not specified	Uncertain significance (Apr 07, 2022)
17-30379335-C-G		not specified	Uncertain significance (Oct 12, 2022)
17-30379350-C-T		not specified	Uncertain significance (Nov 09, 2021)
17-30379392-A-G		not specified	Uncertain significance (May 13, 2022)
17-30379440-C-T		not specified	Uncertain significance (Oct 12, 2021)
17-30379450-C-T		not specified	Uncertain significance (Apr 11, 2023)
17-30379461-C-T		not specified	Uncertain significance (Sep 03, 2024)
17-30379477-G-T		not specified	Uncertain significance (Jun 03, 2022)
17-30379495-A-C		not specified	Uncertain significance (Feb 27, 2023)
17-30379495-A-G		not specified	Uncertain significance (Jan 23, 2023)
17-30379598-C-G		not specified	Uncertain significance (Jan 25, 2023)
17-30379603-G-C		not specified	Uncertain significance (Nov 17, 2023)
17-30379665-C-A		not specified	Uncertain significance (Jul 19, 2023)
17-30379665-C-G		not specified	Uncertain significance (May 23, 2023)
17-30379665-C-T		not specified	Uncertain significance (Apr 07, 2022)
17-30379701-C-T		not specified	Uncertain significance (Aug 20, 2024)
17-30379717-G-A		not specified	Uncertain significance (Oct 19, 2024)
17-30385115-G-T		not specified	Uncertain significance (Sep 08, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CPD	protein_coding	protein_coding	ENST00000225719	21	91085

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000741	0.999	125698	0	50	125748	0.000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.59	513	707	0.725	0.0000347	8954
Missense in Polyphen		197	327.81	0.60096		4125
Synonymous	0.867	241	259	0.931	0.0000128	2699
Loss of Function	5.15	18	61.6	0.292	0.00000331	754

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000275	0.000275
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000273	0.000272
Finnish	0.000786	0.000786
European (Non-Finnish)	0.000167	0.000167
Middle Eastern	0.000273	0.000272
South Asian	0.0000980	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Golgi Associated Vesicle Biogenesis;Clathrin derived vesicle budding;trans-Golgi Network Vesicle Budding;Vesicle-mediated transport;Membrane Trafficking (Consensus)

Intolerance Scores

• loftool: 0.608
• rvis_EVS: -0.02
• rvis_percentile_EVS: 52.25

Haploinsufficiency Scores

• pHI: 0.863
• hipred: Y
• hipred_score: 0.567
• ghis: 0.549

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.254

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cpd

Gene ontology

• Biological process: peptide metabolic process;protein processing
• Cellular component: extracellular space;plasma membrane;membrane;integral component of membrane;extracellular exosome
• Molecular function: metallocarboxypeptidase activity;serine-type carboxypeptidase activity;zinc ion binding