SLC51A

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

Basic information

Region (hg38): 3:196211486-196243178

Links

ENSG00000163959 ∙ NCBI:200931 ∙ OMIM:612084 ∙ HGNC:29955 ∙ Uniprot:Q86UW1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• cholestasis, progressive familial intrahepatic, 6 (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Cholestasis, progressive familial intrahepatic, 6	AR	Gastrointestinal	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	Gastrointestinal	31863603

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC51A gene.

• Inborn genetic diseases (12 variants)
• SLC51A-related condition (2 variants)
• not provided (1 variants)
• Cholestasis, progressive familial intrahepatic, 6 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC51A 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			1		1	2
missense			13	1		14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	1	1

Variants in SLC51A

This is a list of pathogenic ClinVar variants found in the SLC51A region.

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

Position	Type	Phenotype	Significance	ClinVar
3-196216707-G-A		SLC51A-related disorder	Likely benign (Jan 11, 2023)
3-196216712-G-A		SLC51A-related disorder	Likely benign (May 11, 2023)
3-196216719-C-T		SLC51A-related disorder	Likely benign (Jan 27, 2022)
3-196216720-C-G		not specified	Uncertain significance (Feb 16, 2023)
3-196216721-G-A		SLC51A-related disorder	Likely benign (Jan 31, 2023)
3-196216727-G-C		not specified	Uncertain significance (Apr 13, 2022)
3-196217881-C-T		SLC51A-related disorder	Likely benign (Feb 27, 2024)
3-196217893-C-T			Benign (Mar 29, 2018)
3-196217927-C-T		SLC51A-related disorder • not specified	Uncertain significance (Dec 14, 2023)
3-196226952-T-TCTC		SLC51A-related disorder	Likely benign (Jan 09, 2024)
3-196226957-T-C		SLC51A-related disorder	Likely benign (Jul 23, 2023)
3-196226961-C-T		SLC51A-related disorder	Likely benign (Feb 22, 2024)
3-196226965-C-A		not specified	Uncertain significance (Oct 25, 2023)
3-196226966-C-T		SLC51A-related disorder	Likely benign (Dec 03, 2021)
3-196226969-G-T		SLC51A-related disorder	Likely benign (Jul 13, 2021)
3-196226982-C-A		not specified	Likely benign (Dec 06, 2021)
3-196227048-G-A		not specified	Uncertain significance (Sep 29, 2022)
3-196227088-G-C		not specified	Uncertain significance (Jan 06, 2023)
3-196227100-G-C		not specified	Uncertain significance (Oct 29, 2021)
3-196227683-G-C		SLC51A-related disorder	Likely benign (May 16, 2022)
3-196227723-A-T		not specified	Uncertain significance (Feb 22, 2023)
3-196228106-C-T		SLC51A-related disorder	Likely benign (Nov 19, 2021)
3-196228124-C-T		SLC51A-related disorder	Likely benign (Jun 23, 2021)
3-196228125-G-A		not specified	Uncertain significance (Jul 11, 2023)
3-196228172-G-T		SLC51A-related disorder	Uncertain significance (Mar 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC51A	protein_coding	protein_coding	ENST00000296327	9	31692

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0696	0.928	125733	0	15	125748	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.225	184	193	0.954	0.0000105	2161
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000904	0.0000904
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000896	0.0000879
Middle Eastern	0.00	0.00
South Asian	0.0000658	0.0000653
Other	0.000163	0.000163

dbNSFP

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}.
• Pathway: Bile secretion - Homo sapiens (human);Drug Induction of Bile Acid Pathway (Consensus)

Intolerance Scores

• rvis_EVS: -0.4
• rvis_percentile_EVS: 26.73

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.509
• ghis: 0.467

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc51a
• Phenotype: growth/size/body region phenotype; homeostasis/metabolism phenotype; digestive/alimentary phenotype

Gene ontology

• Biological process: bile acid and bile salt transport;bile acid secretion;transmembrane transport
• Cellular component: endoplasmic reticulum membrane;plasma membrane;integral component of membrane;basolateral plasma membrane;protein-containing complex
• Molecular function: bile acid transmembrane transporter activity;protein homodimerization activity;protein heterodimerization activity