SLCO1A2

solute carrier organic anion transporter family member 1A2, the group of Solute carrier organic anion transporter family

Basic information

Region (hg38): 12:21264599-21419594

Previous symbols: [ "SLC21A3" ]

Links

ENSG00000084453 ∙ NCBI:6579 ∙ OMIM:602883 ∙ HGNC:10956 ∙ Uniprot:P46721 ∙ 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 SLCO1A2 gene.

• Inborn genetic diseases (18 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLCO1A2 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
missense			17		1	18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	18	0	2

Variants in SLCO1A2

This is a list of pathogenic ClinVar variants found in the SLCO1A2 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-21269552-A-G		not specified	Uncertain significance (Oct 25, 2023)
12-21269682-G-T		not specified	Uncertain significance (Mar 14, 2023)
12-21269733-C-T		not specified	Uncertain significance (Jan 08, 2024)
12-21274538-C-G		not specified	Uncertain significance (Feb 27, 2023)
12-21274566-A-G		not specified	Uncertain significance (Jan 26, 2023)
12-21274574-G-A		not specified	Uncertain significance (Aug 04, 2021)
12-21274584-C-T		not specified	Uncertain significance (Mar 06, 2023)
12-21292326-T-C		not specified	Uncertain significance (Feb 23, 2023)
12-21293946-A-G		not specified	Uncertain significance (Dec 01, 2022)
12-21293988-C-T		not specified	Uncertain significance (Jan 19, 2022)
12-21295613-T-G		not specified	Uncertain significance (Nov 19, 2022)
12-21295640-A-G		not specified	Uncertain significance (Jan 17, 2023)
12-21295706-C-T		not specified	Uncertain significance (Dec 27, 2023)
12-21295775-G-T		not specified	Uncertain significance (Apr 25, 2023)
12-21300434-A-C		not specified	Uncertain significance (Jun 01, 2023)
12-21300490-G-A			Benign (Jul 13, 2018)
12-21300539-C-T		not specified	Uncertain significance (Mar 29, 2023)
12-21301176-T-C		not specified	Uncertain significance (Jan 30, 2024)
12-21301231-C-T		not specified	Uncertain significance (Jan 17, 2023)
12-21304456-G-A		not specified	Uncertain significance (Jun 12, 2023)
12-21304457-C-G		not specified	Uncertain significance (Oct 16, 2023)
12-21304534-A-G		not specified	Uncertain significance (Feb 16, 2023)
12-21306918-C-T		not specified	Uncertain significance (Dec 11, 2023)
12-21306942-T-A			Benign (Jul 13, 2018)
12-21318838-C-T		not specified	Uncertain significance (Mar 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLCO1A2	protein_coding	protein_coding	ENST00000307378	14	154995

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.06e-16	0.0191	125593	0	154	125747	0.000613

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0668	334	337	0.990	0.0000158	4343
Missense in Polyphen		112	118.7	0.94354		1532
Synonymous	-0.298	121	117	1.04	0.00000573	1263
Loss of Function	0.420	26	28.4	0.915	0.00000120	423

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000565	0.000560
Ashkenazi Jewish	0.00	0.00
East Asian	0.00431	0.00430
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.000385	0.000378
Middle Eastern	0.00431	0.00430
South Asian	0.000446	0.000425
Other	0.000656	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Mediates the Na(+)-independent transport of organic anions such as sulfobromophthalein (BSP) and conjugated (taurocholate) and unconjugated (cholate) bile acids (By similarity). Selectively inhibited by the grapefruit juice component naringin. {ECO:0000250, ECO:0000269|PubMed:17301733}.
• Pathway: Methotrexate Pathway (Brain Cell), Pharmacokinetics;Methotrexate Pathway, Pharmacokinetics;Bile secretion - Homo sapiens (human);Statin Pathway - Generalized, Pharmacokinetics;Metabolism of lipids;Tyrosine metabolism;Androgen and estrogen biosynthesis and metabolism;Metabolism;Recycling of bile acids and salts;Bile acid and bile salt metabolism;Transport of vitamins, nucleosides, and related molecules;SLC-mediated transmembrane transport;Transport of small molecules;Metabolism of steroids;Prostaglandin formation from arachidonate;Bile acid biosynthesis;Transport of organic anions (Consensus)

Recessive Scores

• pRec: 0.0835

Intolerance Scores

• loftool: 0.994
• rvis_EVS: -0.33
• rvis_percentile_EVS: 30.82

Haploinsufficiency Scores

• pHI: 0.309
• hipred: N
• hipred_score: 0.123
• ghis: 0.483

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.338

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slco1a6

Gene ontology

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