RCAN3

RCAN family member 3

Basic information

Region (hg38): 1:24502351-24541040

Previous symbols: [ "DSCR1L2" ]

Links

ENSG00000117602 ∙ NCBI:11123 ∙ OMIM:605860 ∙ HGNC:3042 ∙ Uniprot:Q9UKA8 ∙ 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 RCAN3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RCAN3 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			5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	6	0	0

Variants in RCAN3

This is a list of pathogenic ClinVar variants found in the RCAN3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-24531284-A-G		not specified	Uncertain significance (Mar 06, 2023)
1-24533174-C-T		not specified	Uncertain significance (May 25, 2022)
1-24535117-G-C		not specified	Uncertain significance (Mar 04, 2024)
1-24535123-A-T		not specified	Uncertain significance (Apr 25, 2022)
1-24535192-C-T		not specified	Uncertain significance (Jul 17, 2023)
1-24535218-C-T		not specified	Uncertain significance (Oct 02, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RCAN3	protein_coding	protein_coding	ENST00000374395	4	38144

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000157	0.690	125733	1	12	125746	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.630	109	129	0.844	0.00000704	1590
Missense in Polyphen		43	53.802	0.79922		696
Synonymous	-0.569	58	52.7	1.10	0.00000349	433
Loss of Function	0.877	7	9.99	0.701	6.02e-7	118

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000125	0.000123
Ashkenazi Jewish	0.000104	0.0000992
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000448	0.0000440
Middle Eastern	0.000109	0.000109
South Asian	0.0000985	0.0000653
Other	0.000163	0.000163

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 (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.0921

Intolerance Scores

• loftool: 0.613
• rvis_EVS: -0.14
• rvis_percentile_EVS: 43.29

Haploinsufficiency Scores

• pHI: 0.141
• hipred: N
• hipred_score: 0.352
• ghis: 0.486

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.188

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Rcan3

Gene ontology

• Biological process: anatomical structure morphogenesis;calcium-mediated signaling;regulation of phosphoprotein phosphatase activity;regulation of calcineurin-NFAT signaling cascade
• Cellular component: cytoplasm
• Molecular function: RNA binding;protein binding;calcium-dependent protein serine/threonine phosphatase regulator activity;phosphatase binding;troponin I binding