HomeAboutRankingsData Sources
Β© 2026 GeneE
🧬
GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
β“˜GeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
SLC52A3
solute carrier family 52 member 3
Chromosome 20 Β· 20p13
NCBI Gene: 113278Ensembl: ENSG00000101276.19HGNC: HGNC:16187UniProt: Q9NQ40
56PubMed Papers
22Diseases
0Drugs
31Pathogenic Variants
FUNCTIONAL ROLE
Transporter
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
protein bindingriboflavin transmembrane transporter activitysensory perception of soundriboflavin transportBrown-Vialetto-van Laere syndrome 1progressive bulbar palsy of childhoodgenetic disorderriboflavin transporter deficiency
✦AI Summary

SLC52A3 encodes a plasma membrane transporter mediating cellular uptake of riboflavin (vitamin B2), an essential water-soluble vitamin critical for oxidation-reduction reactions in carbohydrate, lipid, and amino acid metabolism 1. Since humans cannot synthesize riboflavin endogenously, intestinal absorption via SLC52A3 is essential 1. The SLC52A3 promoter is regulated by Sp1 transcription factor binding in intestinal epithelial cells 2. Loss-of-function SLC52A3 mutations cause autosomal recessive Brown-Vialetto-Van Laere syndrome (BVVLS) and Fazio-Londe disease (FLD), characterized by pontobulbar palsy, progressive muscle weakness, and respiratory insufficiency 34. Early riboflavin supplementation significantly improves neurological outcomes in affected patients, though sensorineural hearing loss may persist 4. Slc52a3 knockout mice exhibit neonatal lethality with severe riboflavin deficiency, hyperlipidemia, and hypoglycemia, demonstrating SLC52A3's critical role in placental riboflavin transport 5. Beyond monogenic disorders, genome-wide association studies identified SLC52A3 as a novel Alzheimer's disease susceptibility locus in Chinese populations 6. The rs13042395 polymorphism is associated with reduced cancer risk and favorable prognosis in esophageal squamous cell carcinoma, with the TT genotype predicting lower lymph node metastasis and longer relapse-free survival 78.

Sources cited
1
SLC52A3 mediates riboflavin uptake essential for oxidation-reduction reactions and humans must obtain riboflavin via intestinal absorption
PMID: 20463145
2
SLC52A3 promoter activity in intestinal epithelial cells is regulated by Sp1 transcription factor binding
PMID: 25394472
3
SLC52A3 mutations cause Brown-Vialetto-Van Laere syndrome with autosomal recessive inheritance
PMID: 33325104
4
SLC52A3 mutations cause Brown-Vialetto-Van Laere syndrome with pontobulbar palsy and respiratory insufficiency, responsive to riboflavin supplementation
PMID: 28856173
5
Slc52a3 knockout mice show neonatal lethality with riboflavin deficiency and impaired placental riboflavin transport
PMID: 27272163
6
SLC52A3 identified as novel Alzheimer's disease susceptibility locus in Chinese populations
PMID: 39023044
7
SLC52A3 rs13042395 polymorphism associated with decreased cancer risk
PMID: 27600099
8
SLC52A3 rs13042395 TT genotype associated with reduced lymph node metastasis and longer relapse-free survival in esophageal squamous cell carcinoma
PMID: 27472962
Disease Associationsβ“˜22
Brown-Vialetto-van Laere syndrome 1Open Targets
0.84Strong
progressive bulbar palsy of childhoodOpen Targets
0.71Strong
genetic disorderOpen Targets
0.52Moderate
riboflavin transporter deficiencyOpen Targets
0.46Moderate
progressive bulbar palsyOpen Targets
0.46Moderate
distal hereditary motor neuropathyOpen Targets
0.46Moderate
obstructive sleep apneaOpen Targets
0.34Weak
auditory neuropathyOpen Targets
0.33Weak
Alzheimer diseaseOpen Targets
0.31Weak
response to xenobiotic stimulusOpen Targets
0.28Weak
appendicitisOpen Targets
0.27Weak
poisoningOpen Targets
0.27Weak
Madras motor neuron diseaseOpen Targets
0.27Weak
diabetic ketoacidosisOpen Targets
0.16Weak
intestinal impactionOpen Targets
0.15Weak
hypertrophic cardiomyopathyOpen Targets
0.11Weak
esophageal squamous cell carcinomaOpen Targets
0.10Suggestive
gastric cancerOpen Targets
0.08Suggestive
gastritisOpen Targets
0.08Suggestive
pancreatic adenocarcinomaOpen Targets
0.05Suggestive
Brown-Vialetto-Van Laere syndrome 1UniProt
Fazio-Londe diseaseUniProt
Pathogenic Variants31
NM_033409.4(SLC52A3):c.935C>T (p.Ala312Val)Pathogenic
Brown-Vialetto-van Laere syndrome 1|not provided
β˜…β˜…β˜†β˜†2026β†’ Residue 312
NM_033409.4(SLC52A3):c.639C>G (p.Tyr213Ter)Pathogenic
Brown-Vialetto-van Laere syndrome 1|Progressive bulbar palsy of childhood|Inborn genetic diseases|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 213
NM_033409.4(SLC52A3):c.550G>T (p.Glu184Ter)Pathogenic
Brown-Vialetto-van Laere syndrome 1|Inborn genetic diseases
β˜…β˜…β˜†β˜†2025β†’ Residue 184
NM_033409.4(SLC52A3):c.753del (p.Val252fs)Pathogenic
Brown-Vialetto-van Laere syndrome 1|Inborn genetic diseases
β˜…β˜…β˜†β˜†2025β†’ Residue 252
NM_033409.4(SLC52A3):c.775C>T (p.Gln259Ter)Pathogenic
Inborn genetic diseases|Brown-Vialetto-van Laere syndrome 1
β˜…β˜…β˜†β˜†2023β†’ Residue 259
NM_033409.4(SLC52A3):c.1325_1326del (p.Leu442fs)Likely pathogenic
Brown-Vialetto-van Laere syndrome 1|not provided
β˜…β˜…β˜†β˜†2023β†’ Residue 442
NM_033409.4(SLC52A3):c.71G>A (p.Trp24Ter)Pathogenic
Progressive bulbar palsy of childhood|not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 24
NM_033409.4(SLC52A3):c.745G>T (p.Glu249Ter)Pathogenic
Brown-Vialetto-van Laere syndrome 1
β˜…β˜†β˜†β˜†2025β†’ Residue 249
NM_033409.4(SLC52A3):c.317dup (p.Ala107fs)Pathogenic
Brown-Vialetto-van Laere syndrome 1
β˜…β˜†β˜†β˜†2025β†’ Residue 107
NM_033409.4(SLC52A3):c.662del (p.Leu221fs)Likely pathogenic
Brown-Vialetto-van Laere syndrome 1
β˜…β˜†β˜†β˜†2024β†’ Residue 221
NM_033409.4(SLC52A3):c.1292G>A (p.Trp431Ter)Likely pathogenic
not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 431
NM_033409.4(SLC52A3):c.704T>C (p.Leu235Pro)Likely pathogenic
Auditory neuropathy
β˜…β˜†β˜†β˜†2023β†’ Residue 235
NM_033409.4(SLC52A3):c.853C>T (p.Gln285Ter)Pathogenic
Brown-Vialetto-van Laere syndrome 1
β˜…β˜†β˜†β˜†2023β†’ Residue 285
NM_033409.4(SLC52A3):c.293G>A (p.Trp98Ter)Pathogenic
Brown-Vialetto-van Laere syndrome 1
β˜…β˜†β˜†β˜†2023β†’ Residue 98
NM_033409.4(SLC52A3):c.51G>A (p.Trp17Ter)Pathogenic
Brown-Vialetto-van Laere syndrome 1
β˜…β˜†β˜†β˜†2022β†’ Residue 17
NM_033409.4(SLC52A3):c.790_791del (p.Ser264fs)Pathogenic
Brown-Vialetto-van Laere syndrome 1
β˜…β˜†β˜†β˜†2022β†’ Residue 264
NM_033409.4(SLC52A3):c.408C>G (p.Tyr136Ter)Pathogenic
Brown-Vialetto-van Laere syndrome 1
β˜…β˜†β˜†β˜†2022β†’ Residue 136
NM_033409.4(SLC52A3):c.742del (p.Trp248fs)Likely pathogenic
Brown-Vialetto-van Laere syndrome 1
β˜…β˜†β˜†β˜†2022β†’ Residue 248
NM_033409.4(SLC52A3):c.481_484dup (p.Gly162fs)Pathogenic
Brown-Vialetto-van Laere syndrome 1
β˜…β˜†β˜†β˜†2021β†’ Residue 162
NM_033409.4(SLC52A3):c.1203dup (p.Ser402fs)Likely pathogenic
Inborn genetic diseases
β˜…β˜†β˜†β˜†2021β†’ Residue 402
View on ClinVar β†—
Related Genes
PLCE1Protein interaction86%DLEC1Protein interaction72%SLC52A1Shared pathway67%SLC52A2Shared pathway67%SLC22A14Shared pathway33%RTBDNShared pathway33%
Tissue Expression6 tissues
Heart
100%
Brain
99%
Ovary
39%
Lung
16%
Liver
7%
Bone Marrow
2%
Gene Interaction Network
Click a node to explore
SLC52A3PLCE1DLEC1SLC52A1SLC52A2SLC22A14RTBDN
PROTEIN STRUCTURE
Preparing viewer…
PDB8XSN Β· 3.29 Γ… Β· EM
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
1.01LoF Tolerant
pLIβ“˜
0.00Tolerant
Observed/Expected LoF0.71 [0.51–1.01]
RankingsWhere SLC52A3 stands among ~20K protein-coding genes
  • #8,138of 20,598
    Most Researched56
  • #1,782of 5,498
    Most Pathogenic Variants31
  • #9,865of 17,882
    Most Constrained (LOEUF)1.01
Genes detectedSLC52A3
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
Genome-wide meta-analysis identifies ancestry-specific loci for Alzheimer's disease.
PMID: 39023044
Alzheimers Dement Β· 2024
1.00
2
SLC gene mutations and pediatric neurological disorders: diverse clinical phenotypes in a Saudi Arabian population.
PMID: 34797406
Hum Genet Β· 2022
0.90
3
Decreased risk of developing cancer in subjects carrying SLC52A3 rs13042395 polymorphism: proof from a meta-analysis.
PMID: 27600099
Biomark Med Β· 2016
0.80
4
Identification and characterization of the minimal 5'-regulatory region of the human riboflavin transporter-3 (SLC52A3) in intestinal epithelial cells.
PMID: 25394472
Am J Physiol Cell Physiol Β· 2015
0.70
5
Brown-Vialetto-Van Laere and Fazio-Londe syndromes: SLC52A3 mutations with puzzling phenotypes and inheritance.
PMID: 33325104
Eur J Neurol Β· 2021
0.60