RCAN1

regulator of calcineurin 1

Basic information

Region (hg38): 21:34513141-34615113

Previous symbols: [ "DSCR1" ]

Links

ENSG00000159200 ∙ NCBI:1827 ∙ OMIM:602917 ∙ HGNC:3040 ∙ Uniprot:P53805 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RCAN1 gene.

• Inborn genetic diseases (6 variants)

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			6			6
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	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)
21-34521627-G-A		not specified	Uncertain significance (Jun 18, 2021)
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: gnomAD

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: dbNSFP

• 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