SLC10A2

solute carrier family 10 member 2, the group of Solute carrier family 10

Basic information

Region (hg38): 13:103043997-103066417

Previous symbols: [ "ASBT", "ISBT" ]

Links

ENSG00000125255 ∙ NCBI:6555 ∙ OMIM:601295 ∙ HGNC:10906 ∙ Uniprot:Q12908 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• bile acid malabsorption, primary, 1 (Limited), mode of inheritance: AR
• bile acid malabsorption, primary, 1 (Limited), mode of inheritance: AR
• bile acid malabsorption, primary, 1 (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Bile acid malabsorption, primary 1	AD	Gastrointestinal	Individuals may present with manifestations of diarrhea/steatorrhea such as anasarca and nutritional deficiencies due to fecal loss, and dietary and medical interventions (eg, medium chain triglycerides, bile acid sequestrants) may be beneficial	Gastrointestinal	1017717; 430290; 7106511; 9109432; 9109422; 19823678; 21649730

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC10A2 gene.

• not provided (191 variants)
• Inborn genetic diseases (24 variants)
• Bile acid malabsorption, primary, 1 (11 variants)
• not specified (7 variants)
• SLC10A2-related condition (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC10A2 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			4	18	3	25
missense			117	4	4	125
nonsense			5			5
start loss			2			2
frameshift			3			3
inframe indel			1			1
splice donor/acceptor (+/-2bp)			2			2
splice region			7	3	1	11
non coding			1	9	4	14
Total	0	0	135	31	11

Variants in SLC10A2

This is a list of pathogenic ClinVar variants found in the SLC10A2 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-103046128-G-GA		SLC10A2-related disorder	Likely benign (Jul 12, 2023)
13-103046135-A-G			Uncertain significance (Jan 06, 2024)
13-103046141-C-T			Uncertain significance (Dec 06, 2023)
13-103046142-G-A		SLC10A2-related disorder	Conflicting classifications of pathogenicity (Jan 29, 2024)
13-103046156-C-T		SLC10A2-related disorder	Uncertain significance (Feb 05, 2024)
13-103046160-A-T			Uncertain significance (Aug 17, 2022)
13-103046165-C-T			Uncertain significance (Jul 04, 2023)
13-103046169-A-G			Likely benign (Jul 21, 2022)
13-103046175-C-G			Uncertain significance (May 02, 2017)
13-103046175-C-T			Likely benign (Oct 17, 2023)
13-103046176-G-A			Uncertain significance (Dec 18, 2023)
13-103046178-T-C			Likely benign (Dec 31, 2023)
13-103046190-C-T		SLC10A2-related disorder	Likely benign (Feb 28, 2023)
13-103046198-T-C			Uncertain significance (Dec 20, 2023)
13-103046201-C-T			Uncertain significance (Jun 23, 2022)
13-103046212-G-A			Uncertain significance (Aug 29, 2022)
13-103046248-T-C		not specified	Uncertain significance (May 27, 2023)
13-103046255-C-G			Uncertain significance (Jan 19, 2024)
13-103046258-A-T			Uncertain significance (Jun 09, 2023)
13-103046262-T-C			Uncertain significance (Oct 26, 2022)
13-103046266-AAAC-A			Likely benign (Dec 29, 2023)
13-103046269-C-A			Likely benign (May 29, 2023)
13-103046279-ACAGT-A			Likely benign (Apr 25, 2022)
13-103046280-C-T		Bile acid malabsorption, primary, 1	Benign (Feb 01, 2024)
13-103049291-C-T			Uncertain significance (Dec 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC10A2	protein_coding	protein_coding	ENST00000245312	6	22847

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.58e-17	0.000355	125558	0	190	125748	0.000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.20	292	204	1.43	0.0000116	2266
Missense in Polyphen		80	50.473	1.585		550
Synonymous	-0.982	98	86.4	1.13	0.00000623	708
Loss of Function	-2.02	20	12.4	1.62	6.15e-7	137

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00124	0.00124
Ashkenazi Jewish	0.000794	0.000794
East Asian	0.0000545	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000819	0.000818
Middle Eastern	0.0000545	0.0000544
South Asian	0.00150	0.00150
Other	0.00114	0.00114

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a critical role in the sodium-dependent reabsorption of bile acids from the lumen of the small intestine. Plays a key role in cholesterol metabolism.
• Disease: DISEASE: Primary bile acid malabsorption (PBAM) [MIM:613291]: An intestinal disorder associated with chronic watery diarrhea, excess fecal bile acids, steatorrhea and interruption of the enterohepatic circulation of bile acids. {ECO:0000269|PubMed:9109432}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Bile secretion - Homo sapiens (human);Metabolism of lipids;Metabolism;Recycling of bile acids and salts;Bile acid and bile salt metabolism;Metabolism of steroids;Bile acid biosynthesis (Consensus)

Recessive Scores

• pRec: 0.320

Intolerance Scores

• loftool: 0.966
• rvis_EVS: -0.11
• rvis_percentile_EVS: 45.57

Haploinsufficiency Scores

• pHI: 0.281
• hipred: N
• hipred_score: 0.251

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.767

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc10a2
• Phenotype: digestive/alimentary phenotype; liver/biliary system phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: sodium ion transport;response to bacterium;bile acid and bile salt transport;transmembrane transport
• Cellular component: plasma membrane;integral component of plasma membrane;microvillus;apical plasma membrane
• Molecular function: bile acid:sodium symporter activity