RCAN2
Basic information
Region (hg38): 6:46220736-46491972
Previous symbols: [ "DSCR1L1" ]
Links
Phenotypes
GenCC
Source:
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 RCAN2 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 | 7 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 6 | 0 | 1 |
Variants in RCAN2
This is a list of pathogenic ClinVar variants found in the RCAN2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 6-46223277-C-G | not specified | Uncertain significance (Dec 21, 2023) | ||
| 6-46246858-T-C | not specified | Uncertain significance (Oct 26, 2022) | ||
| 6-46246874-G-C | not specified | Uncertain significance (Aug 08, 2022) | ||
| 6-46246905-C-G | not specified | Uncertain significance (Feb 01, 2023) | ||
| 6-46248728-C-A | not specified | Uncertain significance (Mar 28, 2024) | ||
| 6-46248849-G-T | not specified | Uncertain significance (Sep 13, 2023) | ||
| 6-46325428-C-T | not specified | Uncertain significance (May 24, 2023) | ||
| 6-46456965-T-G | Benign (Jul 01, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| RCAN2 | protein_coding | protein_coding | ENST00000371374 | 4 | 271235 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.835 | 0.165 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.18 | 102 | 142 | 0.720 | 0.00000822 | 1586 |
| Missense in Polyphen | 30 | 55.676 | 0.53883 | 614 | ||
| Synonymous | 0.517 | 52 | 57.0 | 0.913 | 0.00000358 | 477 |
| Loss of Function | 2.69 | 1 | 10.3 | 0.0971 | 5.20e-7 | 127 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Inhibits calcineurin-dependent transcriptional responses by binding to the catalytic domain of calcineurin A. Could play a role during central nervous system development.;
- Pathway
- Thyroid hormone signaling pathway - Homo sapiens (human);VEGFA-VEGFR2 Signaling Pathway;Role of Calcineurin-dependent NFAT signaling in lymphocytes;Calcium signaling in the CD4+ TCR pathway
(Consensus)
Recessive Scores
- pRec
- 0.124
Intolerance Scores
- loftool
- 0.216
- rvis_EVS
- 0.26
- rvis_percentile_EVS
- 69.83
Haploinsufficiency Scores
- pHI
- 0.502
- hipred
- Y
- hipred_score
- 0.622
- ghis
- 0.404
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.910
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rcan2
- Phenotype
- liver/biliary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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); limbs/digits/tail phenotype; immune system phenotype; skeleton phenotype; growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- calcium-mediated signaling;regulation of phosphoprotein phosphatase activity;regulation of calcineurin-NFAT signaling cascade
- Cellular component
- cellular_component;cytoplasm
- Molecular function
- nucleic acid binding;calcium-dependent protein serine/threonine phosphatase regulator activity