RCN1

reticulocalbin 1, the group of CREC family

Basic information

Region (hg38): 11:32091074-32105722

Previous symbols: [ "RCN" ]

Links

ENSG00000049449 ∙ NCBI:5954 ∙ OMIM:602735 ∙ HGNC:9934 ∙ Uniprot:Q15293 ∙ 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 RCN1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RCN1 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					1	1
missense			28		2	30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	28	0	3

Variants in RCN1

This is a list of pathogenic ClinVar variants found in the RCN1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-32091207-G-C		not specified	Uncertain significance (Aug 08, 2023)
11-32091236-C-A		not specified	Uncertain significance (Jan 10, 2023)
11-32091261-T-C		not specified	Uncertain significance (Apr 14, 2022)
11-32091264-C-A		not specified	Uncertain significance (Nov 08, 2022)
11-32091288-C-A		not specified	Uncertain significance (Oct 06, 2021)
11-32091312-T-G		not specified	Uncertain significance (Aug 12, 2024)
11-32091322-C-G		not specified	Uncertain significance (Nov 10, 2022)
11-32091327-A-T		not specified	Uncertain significance (Feb 22, 2023)
11-32091344-C-T		not specified	Uncertain significance (Jan 23, 2023)
11-32091419-C-G		not specified	Uncertain significance (Jun 12, 2023)
11-32091433-G-C		not specified	Uncertain significance (Nov 25, 2024)
11-32097148-A-G		not specified	Uncertain significance (Dec 06, 2022)
11-32097151-G-T		not specified	Uncertain significance (Feb 28, 2024)
11-32097163-G-A		not specified	Uncertain significance (Sep 01, 2021)
11-32097191-C-G		not specified	Uncertain significance (Jan 10, 2023)
11-32097191-C-T		not specified	Uncertain significance (Jul 05, 2024)
11-32097231-A-T		not specified	Uncertain significance (Jul 25, 2024)
11-32098358-G-A			Benign (Dec 31, 2019)
11-32098409-C-T		not specified	Uncertain significance (Oct 17, 2023)
11-32098428-A-G		not specified	Uncertain significance (Sep 27, 2022)
11-32098460-A-G		not specified	Uncertain significance (Aug 06, 2024)
11-32098463-C-T		not specified	Uncertain significance (Apr 19, 2023)
11-32098505-C-A		not specified	Uncertain significance (Jun 08, 2022)
11-32100575-G-A			Benign (Aug 03, 2017)
11-32103281-C-T		not specified	Uncertain significance (May 23, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RCN1	protein_coding	protein_coding	ENST00000054950	6	293363

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000288	0.795	125733	0	14	125747	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.316	162	174	0.932	0.00000927	2188
Missense in Polyphen		47	53.432	0.87962		665
Synonymous	0.289	65	68.0	0.955	0.00000367	596
Loss of Function	1.22	9	13.9	0.648	6.35e-7	184

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000178	0.000178
Ashkenazi Jewish	0.0000995	0.0000992
East Asian	0.0000545	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000359	0.0000352
Middle Eastern	0.0000545	0.0000544
South Asian	0.0000656	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May regulate calcium-dependent activities in the endoplasmic reticulum lumen or post-ER compartment.
• Pathway: Post-translational protein phosphorylation;Post-translational protein modification;Metabolism of proteins;Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) (Consensus)

Recessive Scores

• pRec: 0.167

Intolerance Scores

• loftool: 0.470
• rvis_EVS: 0.42
• rvis_percentile_EVS: 76.81

Haploinsufficiency Scores

• pHI: 0.175
• hipred: Y
• hipred_score: 0.691
• ghis: 0.436

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.642

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rcn1

Gene ontology

• Biological process: in utero embryonic development;camera-type eye development;post-translational protein modification;cellular protein metabolic process
• Cellular component: endoplasmic reticulum;endoplasmic reticulum lumen
• Molecular function: calcium ion binding;protein binding