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GeneBe

RSC1A1

regulator of solute carriers 1

Basic information

Region (hg38): 1:15659712-15662033

Links

ENSG00000215695NCBI:6248OMIM:601966HGNC:10458Uniprot:Q92681AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RSC1A1 gene.

  • Inborn genetic diseases (26 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RSC1A1 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
21
clinvar
5
clinvar
26
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
?
0
non coding
?
0
Total 0 0 21 5 0

Variants in RSC1A1

This is a list of pathogenic ClinVar variants found in the RSC1A1 region.

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

Position Type Phenotype Significance ClinVar
1-15659984-C-T Inborn genetic diseases Uncertain significance (Aug 14, 2023)2593190
1-15660053-T-G Inborn genetic diseases Uncertain significance (Dec 13, 2021)2266341
1-15660092-A-G Inborn genetic diseases Uncertain significance (Jul 25, 2023)2613767
1-15660179-T-G Inborn genetic diseases Uncertain significance (Jun 16, 2023)2603930
1-15660197-T-C Inborn genetic diseases Uncertain significance (Jan 23, 2023)2477467
1-15660215-G-A Inborn genetic diseases Uncertain significance (May 08, 2023)2511785
1-15660237-T-G Inborn genetic diseases Uncertain significance (May 23, 2023)2568566
1-15660241-C-T Inborn genetic diseases Uncertain significance (Jul 21, 2021)2354047
1-15660362-C-G Inborn genetic diseases Uncertain significance (Oct 12, 2022)2224399
1-15660419-C-T Inborn genetic diseases Uncertain significance (Sep 01, 2021)2247949
1-15660436-C-A Inborn genetic diseases Uncertain significance (Jan 07, 2022)2270891
1-15660482-A-T Inborn genetic diseases Uncertain significance (Sep 08, 2023)2588255
1-15660539-A-G Inborn genetic diseases Uncertain significance (Jun 01, 2022)2286195
1-15660596-C-T Inborn genetic diseases Uncertain significance (Oct 06, 2021)2253986
1-15660640-C-G Inborn genetic diseases Uncertain significance (Jan 10, 2023)2474829
1-15660675-T-A Inborn genetic diseases Uncertain significance (Oct 06, 2021)2320188
1-15660720-T-A Inborn genetic diseases Uncertain significance (Mar 16, 2022)2278687
1-15660854-A-G Inborn genetic diseases Likely benign (Apr 06, 2023)2510190
1-15660871-T-C Inborn genetic diseases Uncertain significance (Jun 16, 2023)2595565
1-15660877-A-T Inborn genetic diseases Uncertain significance (May 31, 2023)2553450
1-15660901-G-A Inborn genetic diseases Likely benign (Dec 06, 2022)2333879
1-15660922-A-G Inborn genetic diseases Likely benign (Nov 10, 2022)2325556
1-15660926-C-T Inborn genetic diseases Uncertain significance (Jul 06, 2021)2355057
1-15661126-A-G Inborn genetic diseases Likely benign (Mar 07, 2023)2464718
1-15661160-G-T Inborn genetic diseases Likely benign (Feb 10, 2023)2461700

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RSC1A1protein_codingprotein_codingENST00000345034 11854
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
2.35e-130.018200000.00
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.2433353231.040.00001594017
Missense in Polyphen6463.4231.0091836
Synonymous0.1601181200.9810.000006161245
Loss of Function-0.1551918.31.048.44e-7254

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.000.00
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Mediates transcriptional and post-transcriptional regulation of SLC5A1. Inhibits a dynamin and PKC-dependent exocytotic pathway of SLC5A1. Also involved in transcriptional regulation of SLC22A2. Exhibits glucose-dependent, short-term inhibition of SLC5A1 and SLC22A2 by inhibiting the release of vesicles from the trans-Golgi network. {ECO:0000269|PubMed:14724758, ECO:0000269|PubMed:16788146, ECO:0000269|PubMed:8836035}.;
Pathway
Transport of bile salts and organic acids, metal ions and amine compounds;SLC-mediated transmembrane transport;Transport of small molecules;Organic cation transport;Organic cation/anion/zwitterion transport;Intestinal hexose absorption;Intestinal absorption;Digestion and absorption (Consensus)

Recessive Scores

pRec
0.230

Intolerance Scores

loftool
0.915
rvis_EVS
1.07
rvis_percentile_EVS
91.67

Haploinsufficiency Scores

pHI
0.416
hipred
N
hipred_score
0.146
ghis
0.416

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.342

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Rsc1a1
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; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); digestive/alimentary phenotype;

Gene ontology

Biological process
regulation of transcription, DNA-templated;negative regulation of glucose transmembrane transport;negative regulation of exocytosis;negative regulation of transport
Cellular component
nucleoplasm;Golgi apparatus;plasma membrane;cell junction
Molecular function
sodium channel inhibitor activity