SLC10A1

solute carrier family 10 member 1, the group of Solute carrier family 10

Basic information

Region (hg38): 14:69775415-69797241

Links

ENSG00000100652 ∙ NCBI:6554 ∙ OMIM:182396 ∙ HGNC:10905 ∙ Uniprot:Q14973 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• hypercholanemia, familial, 2 (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC10A1 gene.

• not provided (73 variants)
• Inborn genetic diseases (20 variants)
• SLC10A1-related condition (11 variants)
• Hypercholanemia, familial, 2 (9 variants)
• not specified (3 variants)
• Hepatitis B virus, resistance to (1 variants)
• - (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC10A1 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			11		2	13
missense			65	3	2	70
nonsense		1	1			2
start loss						0
frameshift		3	3			6
inframe indel			1			1
splice donor/acceptor (+/-2bp)			1			1
splice region			1		2	3
non coding						0
Total	0	4	82	3	4

Highest pathogenic variant AF is 0.0000131

Variants in SLC10A1

This is a list of pathogenic ClinVar variants found in the SLC10A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-69776272-A-G		SLC10A1-related disorder	Likely benign (Aug 02, 2023)
14-69776272-AG-A		SLC10A1-related disorder	Likely benign (Jun 15, 2021)
14-69776302-A-T			Uncertain significance (Sep 29, 2017)
14-69776308-C-T		not specified	Uncertain significance (Mar 29, 2023)
14-69776335-C-T		not specified	Uncertain significance (Apr 14, 2022)
14-69776338-C-G		SLC10A1-related disorder	Conflicting classifications of pathogenicity (May 11, 2023)
14-69776371-A-G		not specified	Uncertain significance (Dec 12, 2023)
14-69776375-C-T		SLC10A1-related disorder	Conflicting classifications of pathogenicity (Feb 09, 2022)
14-69776376-A-G		not specified	Uncertain significance (Mar 01, 2023)
14-69778340-A-C		SLC10A1-related disorder	Conflicting classifications of pathogenicity (Jul 03, 2023)
14-69778369-T-C		not specified	Uncertain significance (Dec 07, 2021)
14-69778374-A-G		not specified	Uncertain significance (Jul 12, 2023)
14-69778384-G-A		not specified	Uncertain significance (Jul 17, 2023)
14-69778399-G-C		not specified	Uncertain significance (Jul 06, 2021)
14-69778406-C-T		not specified	Uncertain significance (Nov 21, 2022)
14-69778407-A-C			Uncertain significance (Dec 22, 2017)
14-69778408-T-C			Uncertain significance (May 02, 2017)
14-69778430-A-G			Uncertain significance (May 03, 2018)
14-69778437-C-A		not specified	Uncertain significance (Dec 07, 2021)
14-69778440-A-G			Uncertain significance (Mar 27, 2018)
14-69778455-A-G			Uncertain significance (Oct 12, 2017)
14-69778461-A-C		not specified	Uncertain significance (Nov 08, 2022)
14-69778464-T-C			Uncertain significance (Jun 12, 2018)
14-69778470-A-C		Hypercholanemia, familial, 2	Uncertain significance (Feb 23, 2023)
14-69778476-G-A		not specified • Hypercholanemia, familial, 2 • Hepatitis B virus, resistance to	Benign (Apr 18, 2017)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC10A1	protein_coding	protein_coding	ENST00000216540	5	21873

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.79e-16	0.000247	125519	1	228	125748	0.000911

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.98	279	200	1.39	0.0000104	2274
Missense in Polyphen		92	56.137	1.6388		660
Synonymous	-0.901	86	76.0	1.13	0.00000394	725
Loss of Function	-2.87	18	8.81	2.04	3.68e-7	122

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00225	0.00225
Ashkenazi Jewish	0.00	0.00
East Asian	0.000382	0.000381
Finnish	0.00	0.00
European (Non-Finnish)	0.000684	0.000677
Middle Eastern	0.000382	0.000381
South Asian	0.00243	0.00226
Other	0.000491	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: The hepatic sodium/bile acid uptake system exhibits broad substrate specificity and transports various non-bile acid organic compounds as well. It is strictly dependent on the extracellular presence of sodium.
• Pathway: Bile secretion - Homo sapiens (human);Drug Induction of Bile Acid Pathway;Farnesoid X Receptor Pathway;Nuclear Receptors Meta-Pathway;Metabolism of lipids;Androgen and estrogen biosynthesis and metabolism;Metabolism;Recycling of bile acids and salts;Bile acid and bile salt metabolism;Metabolism of steroids;Bile acid biosynthesis (Consensus)

Recessive Scores

• pRec: 0.348

Intolerance Scores

• loftool: 0.990
• rvis_EVS: -0.89
• rvis_percentile_EVS: 10.37

Haploinsufficiency Scores

• pHI: 0.0949
• hipred: N
• hipred_score: 0.197
• ghis: 0.448

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.266

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc10a1

Gene ontology

• Biological process: sodium ion transport;bile acid and bile salt transport;viral entry into host cell;transmembrane transport
• Cellular component: plasma membrane;integral component of plasma membrane;basolateral plasma membrane
• Molecular function: virus receptor activity;bile acid:sodium symporter activity