SLC10A6

protein-coding

solute carrier family 10 member 6, the group of Solute carrier family 10

Gene summary

Predicted to enable bile acid:sodium symporter activity. Predicted to be involved in bile acid and bile salt transport. Predicted to be located in plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_197965.3

Inheritance

—

ClinVar variants

U:49B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.98

Max pathogenic AF

—

Genomic locus

chr4:86,823,468-86,849,384

External References & Databases

Ensembl (ENSG00000145283)

Transcript & Mutation Effects

hg38 • Region Span ~25.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SLC10A6 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 54

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_197965.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			49 clinvar	6 clinvar		55
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	49	6	0	55

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 3 of 3 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_197965.3	RefSeq	NP_932069.1	6	MANE Select
ENST00000273905.7	Ensembl	ENSP00000273905.6	6	MANE Select
ENST00001139086.1	Ensembl	ENSP00000804173.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Bile salt and organic anion SLC transporters
Transport of bile salts and organic acids, metal ions and amine compounds
SLC-mediated transmembrane transport
Transport of small molecules

Biological Process

sodium ion transport
bile acid and bile salt transport
sodium-dependent organic anion transport
transmembrane transport

Molecular Function

bile acid:sodium symporter activity
sodium-dependent organic anion transmembrane transporter activity

Cellular Component

plasma membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000273905
Coding exons: 6
Length: 25796
Individuals with no LoFs: 125647
Homozygous LoFs: 2
Heterozygous LoFs: 97
Defined: 125746
p: 0.000394

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.102	201	205	0.980	0.0000101	2439
Missense (PolyPhen)		53	65.132	0.81373		788
Synonymous	0.747	72	80.5	0.894	0.00000442	772
Loss of Function	0.0745	13	13.3	0.978	5.67e-7	152

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0023	0.0023	notable
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00076	0.00071	rare
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.000088	0.000088	rare
South Asian	0.0011	0.0010	notable
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Transports sulfoconjugated steroid hormones, as well as taurolithocholic acid-3-sulfate and sulfoconjugated pyrenes in a sodium-dependent manner. {ECO:0000269|PubMed:17491011}.;

Recessive Scores

pRec: 0.105

Intolerance Scores

LoFtool: 0.854
RVIS EVS: 0.57
RVIS percentile EVS: 82.08

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.223

Gene Damage Prediction

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