RSC1A1

regulator of solute carriers 1

Basic information

Region (hg38): 1:15659712-15662033

Links

ENSG00000215695 ∙ NCBI:6248 ∙ OMIM:601966 ∙ HGNC:10458 ∙ Uniprot:Q92681 ∙ 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 RSC1A1 gene.

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	5		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)
1-15660307-C-G		not specified	Uncertain significance (Jan 29, 2024)
1-15660362-C-G		not specified	Uncertain significance (Oct 12, 2022)
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)
1-15660720-T-A		not specified	Uncertain significance (Mar 16, 2022)
1-15660754-C-T		not specified	Uncertain significance (Jan 17, 2024)
1-15660820-G-A		not specified	Uncertain significance (Dec 17, 2023)
1-15660854-A-G		not specified	Likely benign (Apr 06, 2023)
1-15660871-T-C		not specified	Uncertain significance (Jun 16, 2023)

GnomAD

Source: gnomAD

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: 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

	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