SLCO2B1

protein-coding

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

Gene summary

This locus encodes a member of the organic anion-transporting polypeptide family of membrane proteins. The protein encoded by this locus may function in regulation of placental uptake of sulfated steroids. Alternatively spliced transcript variants have been described. [provided by RefSeq, Nov 2010]

Previous symbols:

SLC21A9

MANE transcript

NM_007256.5

Inheritance

—

ClinVar variants

U:89B:12

Top phenotype

EBV-positive nodal T- and NK-cell lymphoma

gnomAD constraint

pLI —, LoF o/e 0.43

Max pathogenic AF

—

Genomic locus

chr11:75,100,563-75,206,549

External References & Databases

Ensembl (ENSG00000137491)

Transcript & Mutation Effects

hg38 • Region Span ~106.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SLCO2B1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 86

not providedTotal: 6

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_007256.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	2 clinvar	4 clinvar	8
missense			85 clinvar	6 clinvar		91
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	89	8	4	101

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 40 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_007256.5	RefSeq	NP_009187.1	14	MANE Select
ENST00000289575.10	Ensembl	ENSP00000289575.5	14	MANE Select
NM_001145211.3	RefSeq	NP_001138683.1	13	Standard
NM_001145212.3	RefSeq	NP_001138684.1	11	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Statin Pathway - Generalized, Pharmacokinetics
Atorvastatin/Lovastatin/Simvastatin Pathway, Pharmacokinetics
Pravastatin Pathway, Pharmacokinetics
Fluvastatin Pathway, Pharmacokinetics
Rosuvastatin Pathway, Pharmacokinetics

Biological Process

bile acid and bile salt transport
sodium-independent organic anion transport
transmembrane transport

Molecular Function

organic anion transmembrane transporter activity
bile acid transmembrane transporter activity
sodium-independent organic anion transmembrane transporter activity

Cellular Component

plasma membrane
integral component of plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000289575
Coding exons: 14
Length: 105987
Individuals with no LoFs: 125717
Homozygous LoFs: 0
Heterozygous LoFs: 30
Defined: 125747
p: 0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.948	371	426	0.871	0.0000246	4575
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00016	0.00016	rare
Finnish	0.000047	0.000046	rare
European (Non-Finnish)	0.00014	0.00014	rare
South Asian	0.00016	0.00016	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.178

Intolerance Scores

LoFtool: 0.606
RVIS EVS: -0.48
RVIS percentile EVS: 22.78

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.490

Gene Damage Prediction

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