RCAN2

regulator of calcineurin 2

Basic information

Region (hg38): 6:46220735-46491972

Previous symbols: [ "DSCR1L1" ]

Links

ENSG00000172348 ∙ NCBI:10231 ∙ OMIM:604876 ∙ HGNC:3041 ∙ Uniprot:Q14206 ∙ 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 RCAN2 gene.

• Inborn genetic diseases (5 variants)
• not provided (1 variants)

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			5		1	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	5	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)
6-46248849-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: gnomAD

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: dbNSFP

• 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