CALCB

calcitonin related polypeptide beta, the group of Neuropeptides

Basic information

Region (hg38): 11:14904997-15082342

Previous symbols: [ "CALC2" ]

Links

ENSG00000175868 ∙ NCBI:797 ∙ OMIM:114160 ∙ HGNC:1438 ∙ Uniprot:P10092 ∙ 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 CALCB gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CALCB 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			12			12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	0	0

Variants in CALCB

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

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

Position	Type	Phenotype	Significance	ClinVar
11-14967707-G-T		not specified	Uncertain significance (Jun 29, 2023)
11-14967715-G-A		not specified	Uncertain significance (Nov 17, 2023)
11-14967804-C-T		not specified	Uncertain significance (Oct 22, 2021)
11-14967805-G-A		not specified	Uncertain significance (Jul 19, 2022)
11-14967810-G-T		not specified	Uncertain significance (Mar 01, 2023)
11-14968069-A-A		Calcitonin polymorphism	Benign (Sep 25, 2012)
11-14968847-C-T			Benign (Jul 10, 2018)
11-14968891-C-A		not specified	Uncertain significance (Apr 18, 2023)
11-14968907-G-A			Benign (Dec 28, 2017)
11-14970040-G-A		not specified	Uncertain significance (Dec 19, 2022)
11-14971141-A-T		not specified	Uncertain significance (Dec 22, 2023)
11-14971162-C-T		not specified	Uncertain significance (Aug 10, 2021)
11-15074789-A-G		not specified	Uncertain significance (Mar 07, 2023)
11-15075076-C-G		not specified	Uncertain significance (Jan 31, 2024)
11-15075085-C-G		not specified	Uncertain significance (Apr 08, 2024)
11-15075087-C-T		not specified	Uncertain significance (Nov 30, 2021)
11-15075106-G-T		not specified	Uncertain significance (Oct 29, 2021)
11-15075110-G-A		not specified	Uncertain significance (Nov 10, 2022)
11-15075172-G-C		not specified	Uncertain significance (Sep 28, 2021)
11-15075180-A-C		not specified	Uncertain significance (May 15, 2024)
11-15075188-C-A		not specified	Uncertain significance (Nov 10, 2022)
11-15075191-G-A		not specified	Uncertain significance (Nov 10, 2022)
11-15077291-C-G		not specified	Uncertain significance (Dec 20, 2023)
11-15077335-C-T		not specified	Uncertain significance (Dec 15, 2022)
11-15077399-T-G		not specified	Uncertain significance (Jan 02, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CALCB	protein_coding	protein_coding	ENST00000533448	3	177346

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0971	0.781	125734	0	14	125748	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0567	76	74.6	1.02	0.00000391	820
Missense in Polyphen		22	26.244	0.8383		304
Synonymous	-0.278	33	31.0	1.06	0.00000151	269
Loss of Function	1.18	2	4.80	0.417	2.03e-7	57

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.0000440	0.0000439
Middle Eastern	0.00	0.00
South Asian	0.000196	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: CGRP induces vasodilation. It dilates a variety of vessels including the coronary, cerebral and systemic vasculature. Its abundance in the CNS also points toward a neurotransmitter or neuromodulator role.
• Pathway: Signaling by GPCR;Signal Transduction;GPCR signaling-G alpha q;GPCR signaling-cholera toxin;GPCR signaling-pertussis toxin;G alpha (s) signalling events;Calcitonin-like ligand receptors;Class B/2 (Secretin family receptors);GPCR ligand binding;GPCR signaling-G alpha s Epac and ERK;GPCR signaling-G alpha s PKA and ERK;GPCR signaling-G alpha i;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.116

Intolerance Scores

• loftool: 0.592
• rvis_EVS: -0.14
• rvis_percentile_EVS: 42.88

Haploinsufficiency Scores

• pHI: 0.0401
• hipred: N
• hipred_score: 0.112
• ghis: 0.429

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0874

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Calcb

Gene ontology

• Biological process: cellular calcium ion homeostasis;signal transduction;G protein-coupled receptor signaling pathway;adenylate cyclase-activating G protein-coupled receptor signaling pathway;regulation of signaling receptor activity;regulation of cytosolic calcium ion concentration
• Cellular component: extracellular region;extracellular space;cell
• Molecular function: neuropeptide hormone activity;calcitonin receptor binding