SLC47A1

Chr 17

solute carrier family 47 member 1

Also known as: MATE1

NCBI Gene: 55244 ENSG00000142494 UniProt: Q96FL8 OMIM: 609832

The protein functions as a multidrug efflux pump that transports cationic compounds including endogenous metabolites, drugs, and toxins through the kidney and liver for excretion in urine and bile. This gene shows extremely low constraint against loss-of-function variants (pLI ~0), and no clear disease associations have been established from mutations in SLC47A1. The gene is located within the Smith-Magenis syndrome region on chromosome 17, but deletions causing this syndrome typically involve multiple genes.

OMIM ResearchSummary from RefSeq, UniProt

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]

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.17

LOEUF

Multiple*

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

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?

-0.19Z-score

OE missense 1.03 (0.94–1.13)

334 obs / 324.6 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?0.83 (0.60–1.17)

0≤0.351.4

Missense OE?1.03 (0.94–1.13)

0≤0.61.4

Synonymous OE?1.04

0≤1.21.6

LoF obs/exp: 24 / 28.9Missense obs/exp: 334 / 324.6Syn Z: -0.39

Background carrier burden — how many people carry a rare variant somewhere in SLC47A1?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 63

840 rare PASS variants

Rare truncating (LoF)

1 in 490

167 rare PASS variants

Rare synonymous (reference)

1 in 130

314 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for SLC47A1. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 84	1 in 490
South Asian	~43k	1 in 49	1 in 380
Remaining (unassigned)	~30k	1 in 78	1 in 620
European (Finnish)	~27k	1 in 160	1 in 4,300
Admixed American	~22k	1 in 67	1 in 860
African / African American	~21k	1 in 70	1 in 230
East Asian	~20k	1 in 60	1 in 580
Ashkenazi Jewish	~13k	1 in 220	≈ 1 in 3,300
Middle Eastern	~2,884	1 in 53	1 in 480

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.