SLC17A1

Chr 6

solute carrier family 17 member 1

Also known as: NAPI-1, NPT-1, NPT1

NCBI Gene: 6568ENSG00000124568UniProt: Q14916

Predicted to enable transmembrane transporter activity. Involved in sodium-dependent phosphate transport; urate metabolic process; and urate transport. Located in apical plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]

209
ClinVar variants
5
Pathogenic / LP
0.00
pLI score
0
Active trials
Clinical Summary— SLC17A1
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
5 Pathogenic / Likely Pathogenic· 187 VUS of 209 total submissions
Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

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.
1.37LOEUF
pLI 0.000
Z-score 0.11
OE 0.98 (0.71–1.37)
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.
0.42Z-score
OE missense 0.93 (0.83–1.03)
235 obs / 253.7 exp
Tolerant

Mild missense constraint

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.0.98 (0.71–1.37)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.93 (0.83–1.03)
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.0.90
0≤1.21.6
LoF obs/exp: 24 / 24.6Missense obs/exp: 235 / 253.7Syn Z: 0.72

ClinVar Variant Classifications

209 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic4
Likely Pathogenic1
VUS187
Likely Benign12
Benign3
Conflicting2
4
Pathogenic
1
Likely Pathogenic
187
VUS
12
Likely Benign
3
Benign
2
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
4
0
4
Likely Pathogenic
0
0
1
0
1
VUS
0
184
3
0
187
Likely Benign
0
11
0
1
12
Benign
0
1
2
0
3
Conflicting
—2
Total0196101209

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

View in ClinVar →

Protein Context — Lollipop Plot

SLC17A1 · protein map & ClinVar variants

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

OMIM — Genotype-Phenotype

OMIM

No OMIM entries found.

Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Polymorphisms in GCKR, SLC17A1 and SLC22A12 were associated with phenotype gout in Han Chinese males: a case-control study.
Zhou ZW et al.·BMC Med Genet
2015
Examining the Association of Rare Allelic Variants in Urate Transporters SLC22A11, SLC22A13, and SLC17A1 with Hyperuricemia and Gout.
Vávra J et al.·Dis Markers
2024
Linkage analysis using whole exome sequencing data implicates SLC17A1, SLC17A3, TATDN2 and TMEM131L in type 1 diabetes in Kuwaiti families.
Hebbar P et al.·Sci Rep
2023
NPT1/SLC17A1 is a renal urate exporter in humans and its common gain-of-function variant decreases the risk of renal underexcretion gout.
Chiba T et al.·Arthritis Rheumatol
2015
Expression of a human NPT1/SLC17A1 missense variant which increases urate export.
Sakiyama M et al.·Nucleosides Nucleotides Nucleic Acids
2016
Robust kernel association testing (RobKAT).
Martinez K et al.·Genet Epidemiol
2020
Serum uric acid and risk of dementia in Parkinson's disease.
González-Aramburu I et al.·Parkinsonism Relat Disord
2014
A systematic review of single nucleotide polymorphisms affecting allopurinol pharmacokinetics and serum uric acid level.
A Zairol Azwan FA et al.·Pharmacogenomics
2024Review
Common genetic variants associated with urinary phthalate levels in children: A genome-wide study.
Bustamante M et al.·Environ Int
2024
Genomewide association study of tenofovir pharmacokinetics and creatinine clearance in AIDS Clinical Trials Group protocol A5202.
Wanga V et al.·Pharmacogenet Genomics
2015Clinical trial
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
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