SLC23A1

Chr 5

solute carrier family 23 member 1

Also known as: SLC23A2, SVCT1, YSPL3

NCBI Gene: 9963ENSG00000170482UniProt: Q9UHI7

The absorption of vitamin C into the body and its distribution to organs requires two sodium-dependent vitamin C transporters. This gene encodes one of the two transporters. The encoded protein is active in bulk vitamin C transport involving epithelial surfaces. Previously, this gene had an official symbol of SLC23A2. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2008]

0
Active trials
14
Pathogenic / LP
109
ClinVar variants
5
Pubs (1 yr)
2.0
Missense Z
0.54
LOEUF
Clinical Summary— SLC23A1
⚡
Population Constraint (gnomAD)
Constrained for loss-of-function variants (OE-LoF 0.30) despite low pLI — interpret in context.
📋
ClinVar Variants
14 Pathogenic / Likely Pathogenic· 83 VUS of 109 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Moderate LoF intolerance
LoF Constraint
0.54LOEUF
pLI 0.024
Z-score 3.37
OE 0.30 (0.17–0.54)
Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint
1.99Z-score
OE missense 0.71 (0.64–0.78)
254 obs / 360.1 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.30 (0.17–0.54)
0≤0.351.4
Missense OE0.71 (0.64–0.78)
0≤0.61.4
Synonymous OE0.82
0≤1.21.6
LoF obs/exp: 8 / 26.9Missense obs/exp: 254 / 360.1Syn Z: 1.71
DNGOF
DN
0.77top 25%
GOF
0.77top 25%
LOF
0.2287th %ile

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

DNprediction above median
GOFprediction 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

109 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic13
Likely Pathogenic1
VUS83
Likely Benign7
Benign5
13
Pathogenic
1
Likely Pathogenic
83
VUS
7
Likely Benign
5
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
13
0
13
Likely Pathogenic
0
0
1
0
1
VUS
0
70
13
0
83
Likely Benign
0
4
1
2
7
Benign
0
2
1
2
5
Total076294109

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

View in ClinVar →

SLC23A1 · protein map & ClinVar variants

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

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Landmark / reviewRecent case evidence
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 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Impact of SLC23A1 and SLC23A2 Polymorphisms on the Risk for Preeclampsia in a Chinese Han Population.
Hou H et al.·J Nutr Sci Vitaminol (Tokyo)
2022
Temporo-spacial microanatomical distribution of the murine sodium-dependent ascorbic acid transporters Slc23a1 and Slc23a2 in the kidney throughout development.
Eck PK et al.·Biochem Cell Biol
2017
Variation in the SLC23A1 gene does not influence cardiometabolic outcomes to the extent expected given its association with L-ascorbic acid.
Wade KH et al.·Am J Clin Nutr
2015Open Access
SLC23A1 polymorphism rs6596473 in the vitamin C transporter SVCT1 is associated with aggressive periodontitis.
de Jong TM et al.·J Clin Periodontol
2014
Polymorphisms in the sodium-dependent ascorbate transporter gene SLC23A1 are associated with susceptibility to Crohn disease.
Amir Shaghaghi M et al.·Am J Clin Nutr
2014
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