CPB2

carboxypeptidase B2, the group of M14 carboxypeptidases

Basic information

Region (hg38): 13:46053185-46105033

Links

ENSG00000080618 ∙ NCBI:1361 ∙ OMIM:603101 ∙ HGNC:2300 ∙ Uniprot:Q96IY4 ∙ 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 CPB2 gene.

• Inborn genetic diseases (7 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CPB2 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	2
missense			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	7	1	1

Variants in CPB2

This is a list of pathogenic ClinVar variants found in the CPB2 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-46053671-A-G		CPB2-related disorder	Likely benign (Aug 14, 2019)
13-46053702-A-G		not specified	Uncertain significance (Feb 14, 2023)
13-46055768-T-C		not specified	Uncertain significance (Jan 20, 2023)
13-46055809-A-G		CPB2-related disorder	Benign (Oct 17, 2019)
13-46055831-C-T		not specified	Uncertain significance (Dec 07, 2022)
13-46055843-C-A		not specified	Uncertain significance (Jul 25, 2023)
13-46064691-G-A		CPB2-related disorder	Benign (Nov 19, 2019)
13-46064707-G-A		not specified	Uncertain significance (Jul 05, 2023)
13-46064709-A-G			Likely benign (Apr 04, 2018)
13-46067331-A-G		CPB2-related disorder	Benign (Oct 17, 2019)
13-46067346-T-C		CPB2-related disorder	Benign (Oct 16, 2019)
13-46073912-T-C		CPB2-related disorder	Likely benign (Jun 18, 2019)
13-46073959-C-T		CPB2-related disorder	Benign (Oct 17, 2019)
13-46078860-A-G			Benign (Jul 16, 2018)
13-46078900-A-G		not specified	Uncertain significance (Dec 09, 2023)
13-46082472-G-A		not specified	Uncertain significance (Jul 14, 2023)
13-46082476-C-A		not specified	Likely benign (Oct 20, 2023)
13-46082534-A-G		CPB2-related disorder	Benign (Oct 16, 2019)
13-46084226-G-A		not specified	Uncertain significance (Jan 17, 2024)
13-46084238-C-T		not specified	Uncertain significance (Mar 05, 2024)
13-46084297-T-G		not specified	Uncertain significance (Aug 04, 2023)
13-46087824-G-C			Likely benign (Jul 16, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CPB2	protein_coding	protein_coding	ENST00000181383	11	51891

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.71e-17	0.00860	125629	0	119	125748	0.000473

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.953	192	233	0.824	0.0000118	2775
Missense in Polyphen		65	93.819	0.69282		1168
Synonymous	-0.783	95	85.8	1.11	0.00000492	786
Loss of Function	0.162	26	26.9	0.966	0.00000144	297

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00225	0.00219
Ashkenazi Jewish	0.00	0.00
East Asian	0.000435	0.000435
Finnish	0.00	0.00
European (Non-Finnish)	0.000185	0.000185
Middle Eastern	0.000435	0.000435
South Asian	0.00138	0.00137
Other	0.000653	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cleaves C-terminal arginine or lysine residues from biologically active peptides such as kinins or anaphylatoxins in the circulation thereby regulating their activities. Down- regulates fibrinolysis by removing C-terminal lysine residues from fibrin that has already been partially degraded by plasmin. {ECO:0000269|PubMed:10574983}.
• Pathway: Complement and coagulation cascades - Homo sapiens (human);Protein digestion and absorption - Homo sapiens (human);Pancreatic secretion - Homo sapiens (human);Dengue-2 Interactions with Complement and Coagulation Cascades;Complement and Coagulation Cascades;Peptide hormone metabolism;fibrinolysis pathway;Metabolism of proteins;Metabolism of Angiotensinogen to Angiotensins;Innate Immune System;Immune System;Regulation of Complement cascade;Complement cascade (Consensus)

Recessive Scores

• pRec: 0.212

Intolerance Scores

• loftool: 0.866
• rvis_EVS: -0.22
• rvis_percentile_EVS: 37.43

Haploinsufficiency Scores

• pHI: 0.0412
• hipred: N
• hipred_score: 0.243
• ghis: 0.476

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.462

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cpb2
• Phenotype: growth/size/body region phenotype; homeostasis/metabolism phenotype; immune system phenotype; renal/urinary system phenotype; respiratory system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: positive regulation of extracellular matrix constituent secretion;proteolysis;blood coagulation;response to heat;negative regulation of plasminogen activation;regulation of complement activation;response to drug;fibrinolysis;negative regulation of fibrinolysis;cellular response to glucose stimulus;liver regeneration;negative regulation of hepatocyte proliferation
• Cellular component: extracellular region;extracellular space;cell;extracellular exosome
• Molecular function: metallocarboxypeptidase activity;zinc ion binding