RSC1A1
Basic information
Region (hg38): 1:15659712-15662033
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
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 | 33 | 38 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region ? | 0 | |||||
non coding ? | 0 | |||||
Total | 0 | 0 | 33 | 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 | not specified | Uncertain significance (Aug 14, 2023) | ||
1-15660053-T-G | not specified | Uncertain significance (Dec 13, 2021) | ||
1-15660092-A-G | not specified | Uncertain significance (Jul 25, 2023) | ||
1-15660106-C-T | not specified | Uncertain significance (Nov 14, 2023) | ||
1-15660179-T-G | not specified | Uncertain significance (Jun 16, 2023) | ||
1-15660197-T-C | not specified | Uncertain significance (Jan 23, 2023) | ||
1-15660215-G-A | not specified | Uncertain significance (May 08, 2023) | ||
1-15660237-T-G | not specified | Uncertain significance (May 23, 2023) | ||
1-15660241-C-T | not specified | Uncertain significance (Jul 21, 2021) | ||
1-15660271-G-A | not specified | Uncertain significance (Apr 09, 2024) | ||
1-15660307-C-G | not specified | Uncertain significance (Jan 29, 2024) | ||
1-15660362-C-G | not specified | Uncertain significance (Oct 12, 2022) | ||
1-15660380-C-T | not specified | Uncertain significance (May 16, 2024) | ||
1-15660419-C-T | not specified | Uncertain significance (Sep 01, 2021) | ||
1-15660436-C-A | not specified | Uncertain significance (Jan 07, 2022) | ||
1-15660482-A-T | not specified | Uncertain significance (Sep 08, 2023) | ||
1-15660539-A-G | not specified | Uncertain significance (Jun 01, 2022) | ||
1-15660582-A-T | not specified | Uncertain significance (Oct 17, 2023) | ||
1-15660596-C-T | not specified | Uncertain significance (Oct 06, 2021) | ||
1-15660628-G-C | not specified | Uncertain significance (Feb 27, 2024) | ||
1-15660640-C-G | not specified | Uncertain significance (Jan 10, 2023) | ||
1-15660675-T-A | not specified | Uncertain significance (Oct 06, 2021) | ||
1-15660692-T-C | not specified | Uncertain significance (May 20, 2024) | ||
1-15660720-T-A | not specified | Uncertain significance (Mar 16, 2022) | ||
1-15660754-C-T | not specified | Uncertain significance (Jan 17, 2024) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
RSC1A1 | protein_coding | protein_coding | ENST00000345034 | 1 | 1854 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
2.35e-13 | 0.0182 | 0 | 0 | 0 | 0 | 0.00 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | -0.243 | 335 | 323 | 1.04 | 0.0000159 | 4017 |
Missense in Polyphen | 64 | 63.423 | 1.0091 | 836 | ||
Synonymous | 0.160 | 118 | 120 | 0.981 | 0.00000616 | 1245 |
Loss of Function | -0.155 | 19 | 18.3 | 1.04 | 8.44e-7 | 254 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00 | 0.00 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.00 | 0.00 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.00 | 0.00 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- 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
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
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