RCN2

reticulocalbin 2, the group of CREC family

Basic information

Region (hg38): 15:76931737-76954393

Links

ENSG00000117906 ∙ NCBI:5955 ∙ OMIM:602584 ∙ HGNC:9935 ∙ Uniprot:Q14257 ∙ 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 RCN2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RCN2 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			16			16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	16	0	0

Variants in RCN2

This is a list of pathogenic ClinVar variants found in the RCN2 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-76931855-C-T		not specified	Uncertain significance (Jan 24, 2024)
15-76931872-G-T		not specified	Uncertain significance (Nov 09, 2022)
15-76931950-A-G		not specified	Uncertain significance (Jul 05, 2023)
15-76931981-T-C		not specified	Uncertain significance (Mar 19, 2024)
15-76932388-G-A		not specified	Uncertain significance (Aug 04, 2023)
15-76935531-C-T		not specified	Uncertain significance (Jul 14, 2023)
15-76935548-G-T		not specified	Uncertain significance (Mar 29, 2022)
15-76935570-A-G		not specified	Uncertain significance (Jan 09, 2024)
15-76935661-G-A		not specified	Uncertain significance (Dec 08, 2023)
15-76943762-A-G		not specified	Uncertain significance (Nov 09, 2021)
15-76943780-G-A		not specified	Uncertain significance (Apr 24, 2024)
15-76943836-G-A		not specified	Uncertain significance (Oct 05, 2023)
15-76948412-G-T		not specified	Uncertain significance (Apr 18, 2023)
15-76948421-G-T		not specified	Uncertain significance (May 04, 2022)
15-76948545-A-T		not specified	Uncertain significance (Nov 30, 2022)
15-76949072-G-A			Likely benign (Mar 01, 2022)
15-76949143-C-T		not specified	Uncertain significance (Dec 20, 2023)
15-76949167-C-T		not specified	Uncertain significance (Jun 17, 2022)
15-76949205-T-C		not specified	Uncertain significance (Jul 27, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RCN2	protein_coding	protein_coding	ENST00000394885	7	18642

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0294	0.961	125738	0	10	125748	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.841	112	140	0.800	0.00000667	2109
Missense in Polyphen		36	53.724	0.67009		807
Synonymous	0.693	42	48.1	0.873	0.00000244	534
Loss of Function	2.27	5	14.3	0.350	6.85e-7	198

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000299	0.0000299
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000565	0.0000544
Finnish	0.0000465	0.0000462
European (Non-Finnish)	0.0000617	0.0000615
Middle Eastern	0.0000565	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Not known. Binds calcium.
• Pathway: miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase (Consensus)

Recessive Scores

• pRec: 0.126

Intolerance Scores

• loftool: 0.564
• rvis_EVS: -0.14
• rvis_percentile_EVS: 42.88

Haploinsufficiency Scores

• pHI: 0.530
• hipred: Y
• hipred_score: 0.654
• ghis: 0.676

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.625

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rcn2

Gene ontology

• Cellular component: nucleolus;endoplasmic reticulum;endoplasmic reticulum lumen
• Molecular function: calcium ion binding;protein binding