SLC10A6

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

Basic information

Region (hg38): 4:86823468-86849384

Links

ENSG00000145283 ∙ NCBI:345274 ∙ OMIM:613366 ∙ HGNC:30603 ∙ Uniprot:Q3KNW5 ∙ 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 SLC10A6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC10A6 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			28	4		32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	28	4	0

Variants in SLC10A6

This is a list of pathogenic ClinVar variants found in the SLC10A6 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-86823720-C-T		not specified	Uncertain significance (Sep 30, 2024)
4-86823737-T-G		not specified	Uncertain significance (Feb 12, 2025)
4-86823741-T-C		not specified	Uncertain significance (Feb 12, 2024)
4-86823779-T-C		not specified	Uncertain significance (Jan 17, 2023)
4-86823827-G-A		not specified	Uncertain significance (Aug 08, 2023)
4-86823860-T-C		not specified	Uncertain significance (Nov 15, 2024)
4-86823878-A-C		not specified	Uncertain significance (Feb 01, 2025)
4-86823893-G-A		not specified	Likely benign (Jul 20, 2021)
4-86828107-G-A		not specified	Uncertain significance (Mar 22, 2023)
4-86828119-C-A		not specified	Uncertain significance (Oct 27, 2023)
4-86828147-C-A		not specified	Uncertain significance (Jan 24, 2025)
4-86828162-C-A		not specified	Uncertain significance (Oct 01, 2024)
4-86831835-T-C		not specified	Likely benign (Sep 27, 2024)
4-86833318-A-G		not specified	Uncertain significance (Oct 25, 2023)
4-86833324-T-C		not specified	Uncertain significance (Aug 28, 2023)
4-86833336-G-C		not specified	Uncertain significance (Jun 04, 2024)
4-86833345-T-C		not specified	Uncertain significance (Oct 12, 2021)
4-86833369-T-C		not specified	Uncertain significance (Feb 21, 2024)
4-86833410-G-T		not specified	Uncertain significance (Nov 07, 2022)
4-86848751-T-A		not specified	Uncertain significance (Jan 06, 2023)
4-86848793-C-G		not specified	Uncertain significance (Mar 14, 2025)
4-86848820-G-C		not specified	Uncertain significance (Jan 12, 2024)
4-86848838-T-C		not specified	Uncertain significance (Oct 30, 2024)
4-86848849-G-T		not specified	Uncertain significance (May 23, 2023)
4-86848887-C-T		not specified	Uncertain significance (Sep 20, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC10A6	protein_coding	protein_coding	ENST00000273905	6	25796

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.51e-9	0.114	125647	2	97	125746	0.000394

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.102	201	205	0.980	0.0000101	2439
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00240	0.00239
Ashkenazi Jewish	0.00	0.00
East Asian	0.000761	0.000707
Finnish	0.000139	0.000139
European (Non-Finnish)	0.0000883	0.0000879
Middle Eastern	0.000761	0.000707
South Asian	0.00108	0.00101
Other	0.000163	0.000163

dbNSFP

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}.
• Pathway: 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 (Consensus)

Recessive Scores

• pRec: 0.105

Intolerance Scores

• loftool: 0.854
• rvis_EVS: 0.57
• rvis_percentile_EVS: 82.08

Haploinsufficiency Scores

• pHI: 0.113
• hipred: N
• hipred_score: 0.144
• ghis: 0.467

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.223

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc10a6

Gene ontology

• Biological process: sodium ion transport;bile acid and bile salt transport;sodium-dependent organic anion transport;transmembrane transport
• Cellular component: plasma membrane;integral component of membrane
• Molecular function: bile acid:sodium symporter activity;sodium-dependent organic anion transmembrane transporter activity