CALCRL
calcitonin receptor like receptor, the group of Calcitonin receptors
Basic information
Region (hg38): 2:187341964-187448460
Links
Phenotypes
GenCC
Source:
- lymphatic malformation 8 (Limited), mode of inheritance: Unknown
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Lymphatic malformation 8 | AR | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Cardiovascular | 30115739 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (24 variants)
- not_provided (2 variants)
- EBV-positive_nodal_T-_and_NK-cell_lymphoma (1 variants)
- Lymphatic_malformation_8 (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CALCRL gene is commonly pathogenic or not. These statistics are base on transcript: NM_000005795.6. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | |||||
| missense | 22 | 25 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 22 | 2 | 2 |
Highest pathogenic variant AF is 6.8625e-7
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CALCRL | protein_coding | protein_coding | ENST00000409998 | 12 | 105332 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.985 | 0.0147 | 125700 | 0 | 11 | 125711 | 0.0000438 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.09 | 144 | 234 | 0.615 | 0.0000110 | 3047 |
| Missense in Polyphen | 28 | 62.721 | 0.44642 | 870 | ||
| Synonymous | 0.626 | 76 | 83.3 | 0.913 | 0.00000433 | 812 |
| Loss of Function | 4.18 | 3 | 26.0 | 0.115 | 0.00000118 | 326 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000290 | 0.0000290 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000884 | 0.0000880 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Receptor for calcitonin-gene-related peptide (CGRP) together with RAMP1 and receptor for adrenomedullin together with RAMP3 (By similarity). Receptor for adrenomedullin together with RAMP2. The activity of this receptor is mediated by G proteins which activate adenylyl cyclase. {ECO:0000250, ECO:0000269|PubMed:22102369}.;
- Pathway
- Vascular smooth muscle contraction - Homo sapiens (human);Neuroactive ligand-receptor interaction - Homo sapiens (human);Endothelin Pathways;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
- 0.107
Intolerance Scores
- loftool
- 0.401
- rvis_EVS
- 0.17
- rvis_percentile_EVS
- 65.76
Haploinsufficiency Scores
- pHI
- 0.373
- hipred
- Y
- hipred_score
- 0.728
- ghis
- 0.497
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.774
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Calcrl
- Phenotype
- muscle phenotype; cellular phenotype; 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); endocrine/exocrine gland phenotype; digestive/alimentary phenotype; immune system phenotype; embryo phenotype; reproductive 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); hematopoietic system 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);
Zebrafish Information Network
- Gene name
- calcrla
- Affected structure
- trunk vasculature
- Phenotype tag
- abnormal
- Phenotype quality
- morphology
Gene ontology
- Biological process
- angiogenesis;calcium ion transport;cell surface receptor signaling pathway;G protein-coupled receptor signaling pathway;G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger;adenylate cyclase-activating G protein-coupled receptor signaling pathway;heart development;protein transport;receptor internalization;negative regulation of smooth muscle contraction;positive regulation of smooth muscle cell proliferation;negative regulation of inflammatory response;cellular response to sucrose stimulus;calcitonin gene-related peptide receptor signaling pathway;adrenomedullin receptor signaling pathway
- Cellular component
- cytoplasm;lysosome;endosome;endoplasmic reticulum;plasma membrane;integral component of plasma membrane;adrenomedullin receptor complex;CGRP receptor complex
- Molecular function
- adrenomedullin receptor activity;calcitonin gene-related peptide receptor activity;G protein-coupled receptor activity;calcitonin receptor activity;protein binding;protein transporter activity;adrenomedullin binding