CPN2

carboxypeptidase N subunit 2, the group of M14 carboxypeptidases

Basic information

Region (hg38): 3:194339767-194351328

Previous symbols: [ "ACBP" ]

Links

ENSG00000178772 ∙ NCBI:1370 ∙ OMIM:603104 ∙ HGNC:2313 ∙ Uniprot:P22792 ∙ 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 CPN2 gene.

• Inborn genetic diseases (30 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CPN2 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	1
missense			29	1	1	31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	1	2

Variants in CPN2

This is a list of pathogenic ClinVar variants found in the CPN2 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-194341106-G-A		not specified	Uncertain significance (Feb 16, 2023)
3-194341205-G-A		not specified	Uncertain significance (Mar 11, 2022)
3-194341226-C-T		not specified	Uncertain significance (Aug 30, 2021)
3-194341255-T-C		not specified	Uncertain significance (Feb 09, 2023)
3-194341259-T-C		not specified	Uncertain significance (Mar 31, 2023)
3-194341266-G-C		not specified	Uncertain significance (Mar 23, 2022)
3-194341267-C-T		not specified	Uncertain significance (Dec 27, 2023)
3-194341331-A-G		not specified	Uncertain significance (Jan 26, 2022)
3-194341358-G-A		not specified	Uncertain significance (Aug 02, 2021)
3-194341406-G-C		not specified	Uncertain significance (Apr 25, 2022)
3-194341457-G-A		not specified	Uncertain significance (Mar 01, 2023)
3-194341460-C-T		not specified	Uncertain significance (Aug 14, 2023)
3-194341559-C-T		not specified	Uncertain significance (Dec 21, 2023)
3-194341594-T-C		not specified	Likely benign (Jan 17, 2024)
3-194341598-A-G		not specified	Uncertain significance (Sep 07, 2022)
3-194341658-G-A		not specified	Uncertain significance (Jun 29, 2023)
3-194341694-C-T		not specified	Uncertain significance (Jan 03, 2024)
3-194341753-G-T		not specified	Uncertain significance (Aug 28, 2023)
3-194341769-G-C		not specified	Uncertain significance (Jan 18, 2023)
3-194341772-G-A		not specified	Uncertain significance (May 18, 2022)
3-194341948-G-A			Benign (Aug 01, 2018)
3-194341955-G-A		not specified	Uncertain significance (Oct 17, 2023)
3-194342002-G-A		not specified	Uncertain significance (Mar 14, 2023)
3-194342014-G-A		not specified	Uncertain significance (Feb 27, 2024)
3-194342036-A-G		not specified	Uncertain significance (Mar 07, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CPN2	protein_coding	protein_coding	ENST00000323830	1	11564

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00260	0.940	125724	0	24	125748	0.0000954

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.293	292	306	0.953	0.0000181	3519
Missense in Polyphen		63	81.636	0.77172		1073
Synonymous	-1.58	179	154	1.16	0.0000100	1197
Loss of Function	1.66	6	12.3	0.489	5.37e-7	129

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000456	0.000456
Ashkenazi Jewish	0.00	0.00
East Asian	0.000217	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.0000708	0.0000703
Middle Eastern	0.000217	0.000217
South Asian	0.0000980	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: The 83 kDa subunit binds and stabilizes the catalytic subunit at 37 degrees Celsius and keeps it in circulation. Under some circumstances it may be an allosteric modifier of the catalytic subunit.
• Pathway: Innate Immune System;Immune System;Regulation of Complement cascade;Complement cascade (Consensus)

Recessive Scores

• pRec: 0.172

Intolerance Scores

• loftool: 0.640
• rvis_EVS: 0.29
• rvis_percentile_EVS: 71.62

Haploinsufficiency Scores

• pHI: 0.203
• hipred: N
• hipred_score: 0.146

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.196

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cpn2

Gene ontology

• Biological process: proteolysis;regulation of complement activation;regulation of catalytic activity;protein stabilization
• Cellular component: extracellular region;extracellular space;extracellular matrix;extracellular exosome;blood microparticle
• Molecular function: metallocarboxypeptidase activity;enzyme regulator activity