SLC51A

protein-coding

solute carrier family 51 subunit alpha, the group of Solute carrier family 51 subunits

Gene summary

Predicted to enable protein heterodimerization activity; protein homodimerization activity; and transmembrane transporter activity. Involved in bile acid secretion. Located in basolateral plasma membrane. Implicated in progressive familial intrahepatic cholestasis. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_152672.6

Inheritance

ClinVar variants

P:1U:56B:26

Top phenotype

Cholestasis, progressive familial intrahepatic, 6

gnomAD constraint

pLI —, LoF o/e 0.3

Max pathogenic AF

—

Genomic locus

chr3:196,211,487-196,243,178

External References & Databases

Ensembl (ENSG00000163959)

Transcript & Mutation Effects

hg38 • Region Span ~31.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

cholestasis, progressive familial intrahepatic, 6LIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0030360

Submitter: PanelApp Australia

cholestasis, progressive familial intrahepatic, 6LIMITED

Inheritance Pattern: Unknown

Disease ID:MONDO:0030360

Submitter: Labcorp Genetics (formerly Invitae)

Clinical Genomic Database (CGD)

Cholestasis, progressive familial intrahepatic, 6AR

Manifestation: Gastrointestinal

Intervention: Gastrointestinal

Rationale: The condition has been described as involving malabsorptive diarrhea and hepatic dysfunction, and medical management (eg, with ursodiol and cholestyramine) has been described as beneficial

Refs: 31863603

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SLC51A variants in ClinVar

4 Conditions Cataloged

SLC51A-related disorderTotal: 62

not specifiedTotal: 41

Cholestasis, progressive familial intrahepatic, 6Total: 3

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_152672.6. 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			2 clinvar	18 clinvar	1 clinvar	21
missense			54 clinvar	7 clinvar		61
nonsense	1 clinvar					1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	1	0	56	25	1	83

Highest pathogenic variant AF is 0.000006571079

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 15 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_152672.6	RefSeq	NP_689885.4	9	MANE Select
ENST00000296327.10	Ensembl	ENSP00000296327.5	9	MANE Select
ENST00000415111.1	Ensembl	ENSP00000409560.1	2	Standard
ENST00000416660.1	Ensembl	ENSP00000405414.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Bile secretion - Homo sapiens (human)
Drug Induction of Bile Acid Pathway

Biological Process

bile acid and bile salt transport
bile acid secretion
transmembrane transport

Molecular Function

bile acid transmembrane transporter activity
protein homodimerization activity
protein heterodimerization activity

Cellular Component

endoplasmic reticulum membrane
plasma membrane
integral component of membrane
basolateral plasma membrane
protein-containing complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000296327
Coding exons: 9
Length: 31692
Individuals with no LoFs: 125733
Homozygous LoFs: 0
Heterozygous LoFs: 15
Defined: 125748
p: 0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.225	184	193	0.954	0.0000105	2161
Missense (PolyPhen)		59	63.324	0.93171		744
Synonymous	1.32	70	85.5	0.819	0.00000498	737
Loss of Function	2.65	5	16.7	0.300	8.77e-7	178

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000090	0.000088	rare
South Asian	0.000066	0.000065	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Essential component of the Ost-alpha/Ost-beta complex, a heterodimer that acts as the intestinal basolateral transporter responsible for bile acid export from enterocytes into portal blood. Efficiently transports the major species of bile acids. {ECO:0000269|PubMed:16317684}.;

Intolerance Scores

RVIS EVS: -0.4
RVIS percentile EVS: 26.73

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N

Gene Damage Prediction

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