SLC47A2

protein-coding

solute carrier family 47 member 2, the group of Solute carrier family 47

Gene summary

This gene encodes a protein belonging to a family of transporters involved in excretion of toxic electrolytes, both endogenous and exogenous, through urine and bile. This transporter family shares homology with the bacterial MATE (multidrug and toxin extrusion) protein family responsible for drug resistance. This gene is one of two members of the MATE transporter family located near each other on chromosome 17. Alternatively spliced transcript variants encoding different isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]

MANE transcript

NM_001099646.3

Inheritance

—

ClinVar variants

U:89B:9

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.81

Max pathogenic AF

—

Genomic locus

chr17:19,678,288-19,718,979

External References & Databases

Ensembl (ENSG00000180638)

Transcript & Mutation Effects

hg38 • Region Span ~40.7 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 SLC47A2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 89

not providedTotal: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001099646.3. 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			3 clinvar	2 clinvar	1 clinvar	6
missense			81 clinvar	5 clinvar	1 clinvar	87
nonsense			1 clinvar			1
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	89	7	2	98

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 26 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001099646.3	RefSeq	NP_001093116.1	17	MANE Select
ENST00000433844.4	Ensembl	ENSP00000391848.3	17	MANE Select
NM_001256663.3	RefSeq	NP_001243592.1	18	Standard
NM_152908.5	RefSeq	NP_690872.2	17	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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

Biological Process

drug transmembrane transport
drug export
transmembrane transport

Molecular Function

drug transmembrane transporter activity
drug:proton antiporter activity

Cellular Component

plasma membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000325411
Coding exons: 17
Length: 40692
Individuals with no LoFs: 125578
Homozygous LoFs: 0
Heterozygous LoFs: 170
Defined: 125748
p: 0.000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.346	326	344	0.948	0.0000192	3850
Missense (PolyPhen)		109	116.3	0.93725		1283
Synonymous	0.189	145	148	0.980	0.00000924	1269
Loss of Function	0.970	25	30.8	0.811	0.00000150	333

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00080	0.00080	rare
Latino/Admixed American	0.00094	0.00087	rare
Ashkenazi Jewish	0.00091	0.00089	rare
East Asian	0.00012	0.00011	rare
Finnish	0.00024	0.00023	rare
European (Non-Finnish)	0.00079	0.00077	rare
South Asian	0.00055	0.00052	rare
Other	0.0012	0.0011	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Solute transporter for tetraethylammonium (TEA), 1- methyl-4-phenylpyridinium (MPP), cimetidine, N-methylnicotinamide, metformin, creatinine, guanidine, procainamide, topotecan, estrone sulfate, acyclovir, and ganciclovir. Responsible for the secretion of cationic drugs across the brush border membranes. {ECO:0000269|PubMed:16807400, ECO:0000269|PubMed:16996621, ECO:0000269|PubMed:17509534}.;

Recessive Scores

pRec: 0.0870

Intolerance Scores

LoFtool: 0.967
RVIS EVS: -0.84
RVIS percentile EVS: 11.28

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.341

Gene Damage Prediction

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