SLC5A10

Chr 17

solute carrier family 5 member 10

Also known as: SGLT-5, SGLT5

NCBI Gene: 125206ENSG00000154025UniProt: A0PJK1OMIM: 618636

The protein functions as a kidney-specific sodium-dependent transporter that reabsorbs D-mannose and D-fructose from glomerular filtrate across the renal brush border membrane. Mutations in this gene cause autosomal recessive congenital mannose-losing nephropathy, characterized by excessive urinary mannose excretion and associated metabolic complications. The gene shows low constraint against loss-of-function variants (LOEUF 1.039), consistent with the recessive inheritance pattern observed in affected patients.

OMIMResearchSummary from RefSeq, UniProt
MultiplemechanismLOEUF 1.04
Clinical Summary— SLC5A10
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
3 unique Pathogenic / Likely Pathogenic· 165 VUS of 200 total submissions
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
1.04LOEUF
pLI 0.000
Z-score 1.37
OE 0.74 (0.54–1.04)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint
0.82Z-score
OE missense 0.89 (0.81–0.97)
362 obs / 408.7 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.74 (0.54–1.04)
0≤0.351.4
Missense OE0.89 (0.81–0.97)
0≤0.61.4
Synonymous OE1.00
0≤1.21.6
LoF obs/exp: 25 / 33.6Missense obs/exp: 362 / 408.7Syn Z: 0.01
DN
0.79top 25%
GOF
0.80top 10%
LOF
0.2190th %ile

This gene has evidence for multiple mechanisms of pathogenicity (gain-of-function and dominant-negative). Both the Badonyi & Marsh prediction and the broader genomic evidence point to gain-of-function as the predominant mechanism. Different variants in this gene may act through different mechanisms — interpret in context of the specific variant.

GOFprediction above median
DNprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

200 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic3
VUS165
Likely Benign15
3
Pathogenic
165
VUS
15
Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
3
0
3
Likely Pathogenic
0
0
0
0
0
VUS
0
164
1
0
165
Likely Benign
0
15
0
0
15
Benign
0
0
0
0
0
Total017940183

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

View in ClinVar →

Protein Context — Lollipop Plot

SLC5A10 · protein map & ClinVar variants

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

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 4 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC

No open access results found

Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients