CPB1

carboxypeptidase B1, the group of M14 carboxypeptidases

Basic information

Region (hg38): 3:148791102-148860187

Links

ENSG00000153002 ∙ NCBI:1360 ∙ OMIM:114852 ∙ HGNC:2299 ∙ Uniprot:P15086 ∙ 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 CPB1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CPB1 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				3		3
missense			18	4	6	28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	2	3
non coding						0
Total	0	0	18	7	6

Variants in CPB1

This is a list of pathogenic ClinVar variants found in the CPB1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-148827858-T-C		not specified	Uncertain significance (Aug 29, 2024)
3-148828002-C-T		CPB1-related disorder	Benign (May 23, 2019)
3-148828025-T-C		not specified	Uncertain significance (Aug 16, 2022)
3-148828054-C-T		not specified	Uncertain significance (Aug 02, 2021)
3-148828055-G-A		CPB1-related disorder	Benign (May 22, 2019)
3-148834542-C-T		CPB1-related disorder	Likely benign (Nov 08, 2019)
3-148834543-A-G		CPB1-related disorder	Likely benign (Jun 11, 2019)
3-148834559-G-A		not specified	Likely benign (Jun 22, 2023)
3-148834574-A-G		not specified	Uncertain significance (Jan 08, 2024)
3-148840695-A-G		not specified	Uncertain significance (Dec 06, 2024)
3-148840784-C-T		not specified	Uncertain significance (Dec 04, 2024)
3-148840880-G-A		not specified	Uncertain significance (Oct 09, 2024)
3-148840895-G-A		not specified	Uncertain significance (Oct 30, 2023)
3-148840895-G-C		not specified	Uncertain significance (Jun 22, 2023)
3-148840897-C-T			Likely benign (Jun 01, 2022)
3-148840898-G-A		not specified	Uncertain significance (Sep 09, 2024)
3-148841858-C-A		not specified	Uncertain significance (Oct 12, 2024)
3-148841864-C-A		CPB1-related disorder	Benign (Feb 27, 2019)
3-148841919-A-G		not specified	Uncertain significance (May 17, 2023)
3-148844478-G-T		not specified	Uncertain significance (Aug 19, 2023)
3-148844484-C-T		not specified	Uncertain significance (Nov 01, 2022)
3-148844485-G-A		CPB1-related disorder	Benign (Feb 01, 2024)
3-148844496-C-T		not specified	Uncertain significance (Mar 25, 2024)
3-148844497-G-A		not specified	Uncertain significance (Aug 11, 2024)
3-148844522-C-T		CPB1-related disorder	Benign (Aug 20, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CPB1	protein_coding	protein_coding	ENST00000491148	11	69086

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.61e-22	0.000132	125560	1	186	125747	0.000744

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.336	229	244	0.939	0.0000138	2713
Missense in Polyphen		98	105.66	0.92752		1206
Synonymous	0.0375	90	90.5	0.995	0.00000515	815
Loss of Function	-0.959	30	24.8	1.21	0.00000127	278

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00407	0.00407
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.000218	0.000217
Finnish	0.00185	0.00180
European (Non-Finnish)	0.000475	0.000475
Middle Eastern	0.000218	0.000217
South Asian	0.000393	0.000392
Other	0.000490	0.000489

dbNSFP

Source: dbNSFP

• Pathway: Protein digestion and absorption - Homo sapiens (human);Pancreatic secretion - Homo sapiens (human);Peptide hormone metabolism;Metabolism of proteins;Metabolism of Angiotensinogen to Angiotensins (Consensus)

Recessive Scores

• pRec: 0.160

Intolerance Scores

• loftool: 0.929
• rvis_EVS: 0.44
• rvis_percentile_EVS: 77.85

Haploinsufficiency Scores

• pHI: 0.604
• hipred: N
• hipred_score: 0.190
• ghis: 0.364

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.100

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cpb1
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: proteolysis
• Cellular component: extracellular space
• Molecular function: carboxypeptidase activity;metallocarboxypeptidase activity;zinc ion binding