SLC47A1

protein-coding

solute carrier family 47 member 1, the group of Solute carrier family 47|Small nucleolar RNA protein coding host genes

Gene summary

This gene is located within the Smith-Magenis syndrome region on chromosome 17. It encodes a protein of unknown function. [provided by RefSeq, Jul 2008]

MANE transcript

NM_018242.3

Inheritance

—

ClinVar variants

U:77B:10

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.83

Max pathogenic AF

—

Genomic locus

chr17:19,495,385-19,579,034

External References & Databases

Ensembl (ENSG00000142494)

Transcript & Mutation Effects

hg38 • Region Span ~83.6 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 SLC47A1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 77

not providedTotal: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018242.3. 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			1 clinvar	1 clinvar	2 clinvar	4
missense			76 clinvar	6 clinvar	1 clinvar	83
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	77	7	3	87

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 50 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018242.3	RefSeq	NP_060712.2	17	MANE Select
ENST00000270570.8	Ensembl	ENSP00000270570.4	17	MANE Select
ENST00000395585.5	Ensembl	ENSP00000378951.1	18	Standard
ENST00000395585.6	Ensembl	ENSP00000378951.1	18	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Metformin Pathway, Pharmacokinetics
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
organic cation transport
drug export
transmembrane transport

Molecular Function

drug transmembrane transporter activity
drug:proton antiporter activity

Cellular Component

plasma membrane
integral component of membrane
vesicle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000270570
Coding exons: 17
Length: 83650
Individuals with no LoFs: 125671
Homozygous LoFs: 0
Heterozygous LoFs: 77
Defined: 125748
p: 0.000306

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.186	334	325	1.03	0.0000186	3637
Missense (PolyPhen)		126	123.41	1.021		1473
Synonymous	-0.392	146	140	1.04	0.00000881	1199
Loss of Function	0.851	24	28.9	0.829	0.00000133	323

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00056	0.00055	rare
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00065	0.00065	rare
Finnish	0.00019	0.00018	rare
European (Non-Finnish)	0.00028	0.00028	rare
South Asian	0.00043	0.00042	rare
Other	0.00049	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Solute transporter for tetraethylammonium (TEA), 1- methyl-4-phenylpyridinium (MPP), cimetidine, N-methylnicotinamide (NMN), metformin, creatinine, guanidine, procainamide, topotecan, estrone sulfate, acyclovir, ganciclovir and also the zwitterionic cephalosporin, cephalexin and cephradin. Seems to also play a role in the uptake of oxaliplatin (a new platinum anticancer agent). Able to transport paraquat (PQ or N,N-dimethyl-4-4'-bipiridinium); a widely used herbicid. Responsible for the secretion of cationic drugs across the brush border membranes. {ECO:0000269|PubMed:16330770, ECO:0000269|PubMed:16996621, ECO:0000269|PubMed:17495125, ECO:0000269|PubMed:17509534, ECO:0000269|PubMed:17582384}.;

Recessive Scores

pRec: 0.0902

Intolerance Scores

LoFtool: 0.926
RVIS EVS: -0.22
RVIS percentile EVS: 37.6

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0769

Gene Damage Prediction

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