SLC47A1

Chr 17

solute carrier family 47 member 1

Also known as: MATE1

NCBI Gene: 55244ENSG00000142494UniProt: Q96FL8

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]

195
ClinVar variants
98
Pathogenic / LP
0.00
pLI score
0
Active trials
Clinical Summary— SLC47A1
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
98 Pathogenic / Likely Pathogenic· 85 VUS of 195 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
1.17LOEUF
pLI 0.000
Z-score 0.85
OE 0.83 (0.60–1.17)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
-0.19Z-score
OE missense 1.03 (0.94–1.13)
334 obs / 324.6 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.83 (0.60–1.17)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.1.03 (0.94–1.13)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.1.04
0≤1.21.6
LoF obs/exp: 24 / 28.9Missense obs/exp: 334 / 324.6Syn Z: -0.39

ClinVar Variant Classifications

195 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic96
Likely Pathogenic2
VUS85
Likely Benign9
Benign3
96
Pathogenic
2
Likely Pathogenic
85
VUS
9
Likely Benign
3
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
96
0
96
Likely Pathogenic
0
0
2
0
2
VUS
0
71
14
0
85
Likely Benign
0
6
2
1
9
Benign
0
1
0
2
3
Total0781143195

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

SLC47A1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Copper metabolism in cell death and autophagy.
Xue Q et al.·Autophagy
2023Review
Association of the SLC47A1 Gene Variant With Responses to Metformin Monotherapy in Drug-naive Patients With Type 2 Diabetes.
Kim H et al.·J Clin Endocrinol Metab
2022Meta-analysis
The influence of metformin transporter gene SLC22A1 and SLC47A1 variants on steady-state pharmacokinetics and glycemic response.
Ningrum VDA et al.·PLoS One
2022
MATE1 Deficiency Exacerbates Dofetilide-Induced Proarrhythmia.
Uddin ME et al.·Int J Mol Sci
2022
Genetic Editing and Pharmacogenetics in Current And Future Therapy Of Neurocognitive Disorders.
Prendecki M et al.·Curr Alzheimer Res
2020Review
Transporter biology in drug approval: regulatory aspects.
Maeda K et al.·Mol Aspects Med
2013Review
The association study between changes in HbA1C with rs2250486 and rs67238751 genetic variants for SLC47A1 in newly diagnosed Iranian patients with type 2 diabetes mellitus: 6 months follow-up study.
Semnani A et al.·Endocrinol Diabetes Metab
2023Cohort
Dual targeting of lipogenesis and PUFAs homeostasis by compound kushen injection suppresses breast cancer bone metastasis.
Dai CL et al.·Phytomedicine
2025
Contributions of pharmacogenetics to personalized precision therapy of diabetes and hypercholesterolemia.
Barrera-Saldaña HA et al.·Gac Med Mex
2025
Identification of clinical and pharmacogenetic factors influencing metformin response in Type 2 diabetes mellitus.
Pérez-Gómez N et al.·Pharmacogenomics
2023
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Frequency of Polymorphisms in SLC47A1 (rs2252281 and rs2289669) and SLC47A2 (rs34834489 and rs12943590) and the Influence of SLC22A1 (rs72552763 and rs622342) on HbA1c Levels in Mexican-Mestizo Patients with DMT2 Treated with Metformin Monotherapy.
Gómez-Hernández MA et al.·Int J Mol Sci
2025🔓 Open AccessCohort
Association of SLC22A1, SLC47A1, and KCNJ11 polymorphisms with efficacy and safety of metformin and sulfonylurea combination therapy in Egyptian patients with type 2 diabetes.
Ahmed A et al.·Res Pharm Sci
2023🔓 Open AccessCohort
Targeting the multidrug and toxin extrusion 1 gene (SLC47A1) sensitizes glioma stem cells to temozolomide.
Batara DC et al.·Am J Cancer Res
2023
Platinum-Acridine Agents with High Activity in Cancers Expressing the Solute Carrier MATE1 (SLC47A1).
Zhang S et al.·ACS Med Chem Lett
2023
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools