CALCA
calcitonin related polypeptide alpha, the group of Neuropeptides
Basic information
Region (hg38): 11:14966622-14972354
Previous symbols: [ "CALC1" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CALCA 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 | |||||
| missense | 7 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 6 | |||||
| Total | 0 | 0 | 13 | 0 | 2 |
Variants in CALCA
This is a list of pathogenic ClinVar variants found in the CALCA 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) | ||
| 11-14967729-G-A | not specified | Uncertain significance (Sep 09, 2024) | ||
| 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 (Apr 02, 2025) | ||
| 11-14968816-G-T | not specified | Uncertain significance (Nov 28, 2024) | ||
| 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) | |||
| 11-14968974-C-G | not specified | Uncertain significance (Jan 08, 2025) | ||
| 11-14970040-G-A | not specified | Uncertain significance (Mar 08, 2025) | ||
| 11-14970056-G-T | not specified | Uncertain significance (Nov 13, 2024) | ||
| 11-14971141-A-T | not specified | Uncertain significance (Dec 22, 2023) | ||
| 11-14971143-A-G | not specified | Uncertain significance (Dec 07, 2024) | ||
| 11-14971162-C-T | not specified | Uncertain significance (Aug 10, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CALCA | protein_coding | protein_coding | ENST00000331587 | 3 | 5687 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0156 | 0.712 | 125741 | 0 | 7 | 125748 | 0.0000278 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.598 | 94 | 79.0 | 1.19 | 0.00000417 | 930 |
| Missense in Polyphen | 20 | 20.609 | 0.97046 | 277 | ||
| Synonymous | -1.28 | 42 | 32.7 | 1.28 | 0.00000183 | 277 |
| Loss of Function | 0.676 | 3 | 4.56 | 0.658 | 1.94e-7 | 52 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000119 | 0.000119 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000462 | 0.0000462 |
| European (Non-Finnish) | 0.0000264 | 0.0000264 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Calcitonin causes a rapid but short-lived drop in the level of calcium and phosphate in blood by promoting the incorporation of those ions in the bones.;
- Pathway
- Endothelin Pathways;Myometrial Relaxation and Contraction Pathways;Lung fibrosis;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
- 0.616
Intolerance Scores
- loftool
- 0.899
- rvis_EVS
- 0.91
- rvis_percentile_EVS
- 89.44
Haploinsufficiency Scores
- pHI
- 0.0667
- hipred
- N
- hipred_score
- 0.139
- ghis
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.00787
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Calca
- Phenotype
- renal/urinary system phenotype; skeleton phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); hearing/vestibular/ear phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); 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); normal phenotype; neoplasm; respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan);
Zebrafish Information Network
- Gene name
- calca
- Affected structure
- integument
- Phenotype tag
- abnormal
- Phenotype quality
- has extra parts of type
Gene ontology
- Biological process
- artery vasodilation involved in baroreceptor response to increased systemic arterial blood pressure;monocyte chemotaxis;inflammatory response;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;neuropeptide signaling pathway;embryo implantation;aging;feeding behavior;regulation of heart contraction;response to heat;regulation of signaling receptor activity;negative regulation of ossification;activation of protein kinase activity;cellular protein metabolic process;negative regulation of bone resorption;negative regulation of transcription, DNA-templated;negative regulation of smooth muscle contraction;response to pain;detection of temperature stimulus involved in sensory perception of pain;regulation of cytosolic calcium ion concentration;positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G protein-coupled signaling pathway;cellular response to tumor necrosis factor;cellular response to nerve growth factor stimulus
- Cellular component
- extracellular region;extracellular space;nucleus;cytoplasm;neuronal cell body;terminal bouton
- Molecular function
- hormone activity;protein binding;calcitonin receptor binding;identical protein binding