RCAN1
regulator of calcineurin 1
Basic information
Region (hg38): 21:34513142-34615113
Previous symbols: [ "DSCR1" ]
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 RCAN1 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 RCAN1
This is a list of pathogenic ClinVar variants found in the RCAN1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 21-34518098-T-C | not specified | Uncertain significance (Feb 28, 2023) | ||
| 21-34518124-T-C | not specified | Uncertain significance (Dec 17, 2021) | ||
| 21-34518225-G-T | not specified | Uncertain significance (Apr 20, 2023) | ||
| 21-34518250-T-G | not specified | Uncertain significance (Feb 12, 2024) | ||
| 21-34521517-T-C | not specified | Uncertain significance (Jun 16, 2024) | ||
| 21-34521577-C-T | not specified | Uncertain significance (Dec 03, 2024) | ||
| 21-34521589-C-T | not specified | Uncertain significance (Apr 23, 2024) | ||
| 21-34521627-G-A | not specified | Uncertain significance (Jun 18, 2021) | ||
| 21-34521637-G-A | not specified | Uncertain significance (Mar 26, 2024) | ||
| 21-34523595-C-T | not specified | Uncertain significance (Oct 05, 2022) | ||
| 21-34523610-G-A | not specified | Uncertain significance (Sep 23, 2023) | ||
| 21-34614911-G-T | RCAN1-related disorder | Likely benign (May 16, 2023) | ||
| 21-34614941-G-A | not specified | Uncertain significance (Jul 20, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| RCAN1 | protein_coding | protein_coding | ENST00000313806 | 4 | 102002 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0167 | 0.896 | 125739 | 0 | 7 | 125746 | 0.0000278 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.02 | 88 | 119 | 0.738 | 0.00000629 | 1635 |
| Missense in Polyphen | 33 | 63.599 | 0.51888 | 778 | ||
| Synonymous | 1.04 | 41 | 50.4 | 0.813 | 0.00000317 | 481 |
| Loss of Function | 1.44 | 4 | 8.54 | 0.469 | 4.58e-7 | 115 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000123 | 0.000123 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000264 | 0.0000264 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000654 | 0.0000653 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Inhibits calcineurin-dependent transcriptional responses by binding to the catalytic domain of calcineurin A (PubMed:12809556). Could play a role during central nervous system development (By similarity). {ECO:0000250|UniProtKB:Q9JHG6, ECO:0000269|PubMed:12809556}.;
- Pathway
- Oxytocin signaling pathway - Homo sapiens (human);Kaposi,s sarcoma-associated herpesvirus infection - Homo sapiens (human);Thyroid hormone signaling pathway - Homo sapiens (human);MicroRNAs in cardiomyocyte hypertrophy;VEGFA-VEGFR2 Signaling Pathway;Notch-mediated HES/HEY network;Role of Calcineurin-dependent NFAT signaling in lymphocytes;Calcium signaling in the CD4+ TCR pathway
(Consensus)
Recessive Scores
- pRec
- 0.234
Intolerance Scores
- loftool
- 0.214
- rvis_EVS
- -0.05
- rvis_percentile_EVS
- 49.76
Haploinsufficiency Scores
- pHI
- 0.161
- hipred
- Y
- hipred_score
- 0.645
- ghis
- 0.518
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.663
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rcan1
- Phenotype
- growth/size/body region phenotype; endocrine/exocrine gland phenotype; cellular phenotype; homeostasis/metabolism phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); reproductive system phenotype; 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); neoplasm; immune system phenotype;
Zebrafish Information Network
- Gene name
- rcan1a
- Affected structure
- dorsal longitudinal anastomotic vessel
- Phenotype tag
- abnormal
- Phenotype quality
- arrested
Gene ontology
- Biological process
- regulation of transcription, DNA-templated;signal transduction;central nervous system development;blood circulation;calcineurin-NFAT signaling cascade;regulation of phosphoprotein phosphatase activity;regulation of calcineurin-NFAT signaling cascade;negative regulation of calcineurin-NFAT signaling cascade
- Cellular component
- nucleus;cytoplasm
- Molecular function
- DNA binding;DNA-binding transcription factor activity;protein binding;calcium-dependent protein serine/threonine phosphatase regulator activity