CALCR

calcitonin receptor, the group of MicroRNA protein coding host genes|Calcitonin receptors

Basic information

Region (hg38): 7:93424486-93574730

Links

ENSG00000004948 ∙ NCBI:799 ∙ OMIM:114131 ∙ HGNC:1440 ∙ Uniprot:P30988 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• osteoporosis (No Known Disease Relationship), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CALCR gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CALCR 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				2	2	4
missense			25	4	2	31
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	2	3
non coding					50	50
Total	0	0	26	6	54

Variants in CALCR

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

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

Position	Type	Phenotype	Significance	ClinVar
7-93426338-G-A			Benign (Nov 10, 2018)
7-93426384-T-G		not specified	Uncertain significance (May 30, 2024)
7-93426391-G-A		not specified	Uncertain significance (Mar 19, 2024)
7-93426412-C-T		CALCR-related disorder	Likely benign (Jun 06, 2019)
7-93426422-GT-G		not specified	Uncertain significance (Jun 22, 2021)
7-93426432-T-C		not specified	Uncertain significance (Oct 06, 2022)
7-93426441-A-G		Bone mineral density quantitative trait locus 15 • CALCR-related disorder	Benign (Nov 10, 2018)
7-93426442-G-T		not specified	Uncertain significance (Jun 23, 2023)
7-93426496-C-A			Likely benign (May 21, 2018)
7-93426516-G-C		not specified	Uncertain significance (Mar 21, 2023)
7-93426534-C-T		not specified	Uncertain significance (Oct 18, 2021)
7-93426555-A-G		not specified	Uncertain significance (Jan 10, 2022)
7-93426915-A-G			Benign (Nov 10, 2018)
7-93434086-G-T			Benign (Nov 10, 2018)
7-93434389-G-GA			Benign (Jun 18, 2021)
7-93434389-G-GAA			Benign (Jun 18, 2021)
7-93434389-G-GAAAA			Benign (Jun 19, 2021)
7-93434510-G-A			Benign (Nov 10, 2018)
7-93434532-A-T			Benign (Nov 10, 2018)
7-93434594-GA-G			Benign (Jun 20, 2021)
7-93434594-G-GAA			Benign (Jun 18, 2021)
7-93435803-G-C			Benign (Jun 18, 2021)
7-93435814-T-A			Benign (Jun 18, 2021)
7-93435824-TAATA-T			Benign (Jun 18, 2021)
7-93435827-T-A			Benign (Jun 18, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CALCR	protein_coding	protein_coding	ENST00000359558	14	150244

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.12e-9	0.918	125683	0	61	125744	0.000243

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.515	263	288	0.915	0.0000158	3343
Missense in Polyphen		105	117.34	0.8948		1434
Synonymous	0.239	102	105	0.970	0.00000618	915
Loss of Function	1.86	18	28.8	0.625	0.00000155	323

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000519	0.000516
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.000218	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.000302	0.000299
Middle Eastern	0.000218	0.000217
South Asian	0.000360	0.000359
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: This is a receptor for calcitonin. The activity of this receptor is mediated by G proteins which activate adenylyl cyclase. The calcitonin receptor is thought to couple to the heterotrimeric guanosine triphosphate-binding protein that is sensitive to cholera toxin.
• Pathway: Neuroactive ligand-receptor interaction - Homo sapiens (human);Osteoclast differentiation - Homo sapiens (human);RANKL-RANK (Receptor activator of NFKB (ligand)) Signaling Pathway;GPCRs, Class B Secretin-like;Signaling by GPCR;Signal Transduction;G alpha (s) signalling events;Calcitonin-like ligand receptors;Class B/2 (Secretin family receptors);GPCR ligand binding;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.475

Intolerance Scores

• loftool: 0.939
• rvis_EVS: 0.09
• rvis_percentile_EVS: 60.57

Haploinsufficiency Scores

• pHI: 0.181
• hipred: N
• hipred_score: 0.452

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.718

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Calcr
• Phenotype: homeostasis/metabolism phenotype; limbs/digits/tail phenotype; normal 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); hematopoietic system phenotype; skeleton phenotype; immune system phenotype

Gene ontology

• Biological process: cell surface receptor signaling pathway;G protein-coupled receptor signaling pathway;adenylate cyclase-activating G protein-coupled receptor signaling pathway;activation of adenylate cyclase activity;positive regulation of cytosolic calcium ion concentration;positive regulation of gene expression;positive regulation of protein kinase A signaling;positive regulation of cell death;positive regulation of peptidyl-serine phosphorylation;cross-receptor inhibition within G protein-coupled receptor heterodimer;response to glucocorticoid;positive regulation of protein kinase B signaling;positive regulation of ERK1 and ERK2 cascade;amylin receptor signaling pathway;response to amyloid-beta;positive regulation of calcium ion import across plasma membrane
• Cellular component: plasma membrane;integral component of plasma membrane;axon;amylin receptor complex 1;amylin receptor complex 2;amylin receptor complex 3
• Molecular function: amyloid-beta binding;calcitonin gene-related peptide receptor activity;calcitonin receptor activity;protein binding;calcitonin binding;amylin receptor activity