SLCO2B1

solute carrier organic anion transporter family member 2B1, the group of Solute carrier organic anion transporter family

Basic information

Region (hg38): 11:75100563-75206549

Previous symbols: [ "SLC21A9" ]

Links

ENSG00000137491 ∙ NCBI:11309 ∙ OMIM:604988 ∙ HGNC:10962 ∙ Uniprot:O94956 ∙ 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 SLCO2B1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLCO2B1 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				2	4	6
missense			34	3		37
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	34	5	4

Variants in SLCO2B1

This is a list of pathogenic ClinVar variants found in the SLCO2B1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-75162667-A-T		not specified	Uncertain significance (Feb 07, 2023)
11-75162756-G-T		not specified	Likely benign (Oct 10, 2023)
11-75163968-C-T			Benign (Jun 01, 2018)
11-75164021-T-C		not specified	Uncertain significance (Nov 09, 2021)
11-75164039-C-T		not specified	Uncertain significance (Jun 12, 2023)
11-75164056-G-C		not specified	Uncertain significance (May 24, 2024)
11-75164072-C-T		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
11-75165804-G-C		not specified	Uncertain significance (Nov 17, 2022)
11-75165854-T-C		not specified	Uncertain significance (Dec 21, 2022)
11-75165860-A-G		not specified	Likely benign (Jan 17, 2024)
11-75165871-C-T		not specified	Uncertain significance (Jun 28, 2023)
11-75165906-G-A			Benign (Jun 18, 2018)
11-75165928-C-T		not specified	Uncertain significance (Jul 30, 2023)
11-75165929-G-A		not specified	Uncertain significance (May 17, 2023)
11-75165931-T-G		not specified	Uncertain significance (Oct 05, 2023)
11-75165941-C-A		not specified	Uncertain significance (Aug 10, 2021)
11-75169217-A-T		not specified	Uncertain significance (Dec 21, 2023)
11-75169283-A-C		not specified	Uncertain significance (Sep 06, 2022)
11-75169299-T-C		not specified	Uncertain significance (Jul 26, 2022)
11-75169669-T-A		not specified	Uncertain significance (Oct 16, 2023)
11-75169695-C-T		not specified	Uncertain significance (May 31, 2023)
11-75169731-C-T		not specified	Uncertain significance (Jul 15, 2021)
11-75169732-G-A		not specified	Uncertain significance (Mar 20, 2023)
11-75172408-C-A			Likely benign (Dec 31, 2019)
11-75172489-C-G		not specified	Uncertain significance (May 31, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLCO2B1	protein_coding	protein_coding	ENST00000289575	14	105987

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000112	1.00	125717	0	30	125747	0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.948	371	426	0.871	0.0000246	4575
Missense in Polyphen		151	178.48	0.84606		1986
Synonymous	-0.0394	188	187	1.00	0.0000120	1501
Loss of Function	3.04	14	32.8	0.427	0.00000190	322

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000178	0.000177
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.0000466	0.0000462
European (Non-Finnish)	0.000141	0.000141
Middle Eastern	0.000163	0.000163
South Asian	0.000163	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Mediates the Na(+)-independent transport of organic anions such as taurocholate, the prostaglandins PGD2, PGE1, PGE2, leukotriene C4, thromboxane B2 and iloprost. {ECO:0000250}.
• Pathway: Statin Pathway - Generalized, Pharmacokinetics;Atorvastatin/Lovastatin/Simvastatin Pathway, Pharmacokinetics;Pravastatin Pathway, Pharmacokinetics;Fluvastatin Pathway, Pharmacokinetics;Rosuvastatin Pathway, Pharmacokinetics;Farnesoid X Receptor Pathway;Nuclear Receptors Meta-Pathway;Androgen and estrogen biosynthesis and metabolism;Transport of vitamins, nucleosides, and related molecules;SLC-mediated transmembrane transport;Transport of small molecules;Transport of organic anions (Consensus)

Recessive Scores

• pRec: 0.178

Intolerance Scores

• loftool: 0.606
• rvis_EVS: -0.48
• rvis_percentile_EVS: 22.78

Haploinsufficiency Scores

• pHI: 0.120
• hipred: N
• hipred_score: 0.306
• ghis: 0.510

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.490

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slco2b1
• Phenotype: growth/size/body region phenotype

Gene ontology

• Biological process: 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