RCN1

reticulocalbin 1, the group of CREC family

Basic information

Region (hg38): 11:32091074-32105722

Previous symbols: [ "RCN" ]

Links

ENSG00000049449NCBI:5954OMIM:602735HGNC:9934Uniprot:Q15293AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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
clinvar
1
missense
28
clinvar
2
clinvar
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)2617242
11-32091236-C-A not specified Uncertain significance (Jan 10, 2023)2475208
11-32091261-T-C not specified Uncertain significance (Apr 14, 2022)2284352
11-32091264-C-A not specified Uncertain significance (Nov 08, 2022)2324685
11-32091288-C-A not specified Uncertain significance (Oct 06, 2021)2409134
11-32091312-T-G not specified Uncertain significance (Aug 12, 2024)3431634
11-32091322-C-G not specified Uncertain significance (Nov 10, 2022)2325928
11-32091327-A-T not specified Uncertain significance (Feb 22, 2023)2487420
11-32091344-C-T not specified Uncertain significance (Jan 23, 2023)2477717
11-32091419-C-G not specified Uncertain significance (Jun 12, 2023)2511024
11-32091433-G-C not specified Uncertain significance (Nov 25, 2024)3431635
11-32097148-A-G not specified Uncertain significance (Dec 06, 2022)2358743
11-32097151-G-T not specified Uncertain significance (Feb 28, 2024)3152723
11-32097163-G-A not specified Uncertain significance (Sep 01, 2021)2276390
11-32097191-C-G not specified Uncertain significance (Jan 10, 2023)2475423
11-32097191-C-T not specified Uncertain significance (Jul 05, 2024)3431630
11-32097231-A-T not specified Uncertain significance (Jul 25, 2024)3431631
11-32098358-G-A Benign (Dec 31, 2019)782955
11-32098409-C-T not specified Uncertain significance (Oct 17, 2023)3152725
11-32098428-A-G not specified Uncertain significance (Sep 27, 2022)2314015
11-32098460-A-G not specified Uncertain significance (Aug 06, 2024)3431633
11-32098463-C-T not specified Uncertain significance (Apr 19, 2023)2538680
11-32098505-C-A not specified Uncertain significance (Jun 08, 2022)2293488
11-32100575-G-A Benign (Aug 03, 2017)784188
11-32103281-C-T not specified Uncertain significance (May 23, 2024)3313427

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RCN1protein_codingprotein_codingENST00000054950 6293363
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.00002880.7951257330141257470.0000557
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.3161621740.9320.000009272188
Missense in Polyphen4753.4320.87962665
Synonymous0.2896568.00.9550.00000367596
Loss of Function1.22913.90.6486.35e-7184

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001780.000178
Ashkenazi Jewish0.00009950.0000992
East Asian0.00005450.0000544
Finnish0.000.00
European (Non-Finnish)0.00003590.0000352
Middle Eastern0.00005450.0000544
South Asian0.00006560.0000653
Other0.0001630.000163

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Rcn1
Phenotype

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