Gene Gene information from NCBI Gene database.
Entrez ID 113278
Gene name Solute carrier family 52 member 3
Gene symbol SLC52A3
Synonyms (NCBI Gene)
BVVLSBVVLS1C20orf54RFT2RFVT3bA371L19.1hRFT2
Chromosome 20
Chromosome location 20p13
Summary This gene encodes a riboflavin transporter protein that is strongly expressed in the intestine and likely plays a role in intestinal absorption of riboflavin. The protein is predicted to have eleven transmembrane domains and a cell surface localization si
SNPs SNP information provided by dbSNP.
27
SNP ID Visualize variation Clinical significance Consequence
rs3833341 ->GTCAATCAG,GTCAG Pathogenic, benign Intron variant
rs267606683 C>A,T Pathogenic Coding sequence variant, missense variant, stop gained
rs267606685 A>G Pathogenic Coding sequence variant, missense variant
rs267606688 G>A,T Pathogenic Coding sequence variant, missense variant
rs754753126 T>C,G Pathogenic Splice acceptor variant
miRNA miRNA information provided by mirtarbase database.
1
miRTarBase ID miRNA Experiments Reference
MIRT044271 hsa-miR-106b-5p CLASH 23622248
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
25
GO ID Ontology Definition Evidence Reference
GO:0005515 Function Protein binding IPI 32814053
GO:0005634 Component Nucleus IDA 29428966
GO:0005634 Component Nucleus IEA
GO:0005737 Component Cytoplasm IDA 29428966
GO:0005737 Component Cytoplasm IEA
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
613350 16187 ENSG00000101276
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
Q9NQ40
Protein name Solute carrier family 52, riboflavin transporter, member 3 (Riboflavin transporter 2) (hRFT2)
Protein function Plasma membrane transporter mediating the uptake by cells of the water soluble vitamin B2/riboflavin that plays a key role in biochemical oxidation-reduction reactions of the carbohydrate, lipid, and amino acid metabolism (PubMed:20463145, PubMe
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF06237 DUF1011 297 395 Protein of unknown function (DUF1011) Family
Tissue specificity TISSUE SPECIFICITY: Predominantly expressed in testis. Highly expressed in small intestine and prostate. {ECO:0000269|PubMed:20463145}.
Sequence
MAFLMHLLVCVFGMGSWVTINGLWVELPLLVMELPEGWYLPSYLTVVIQLANIGPLLVTL
LHHFRPSCLSEVPIIFTLLGVGTVTCIIFAFLWNMTSWVLDGHHSIAFLVLTFFLALVDC
TSSVTFLPFMSRLPTYYLTTFFVGEGLSGLLPALVALAQGSGLTTCVNVTEISDSVPSPV
PTRETDIAQGVPRALVSALPGMEAPLSHLESRYLPAHFSPLVFFLLLSIMMACCLVAFFV
LQRQPRCWEASVEDLLNDQVTLHSIRPREENDLGPAGTVDSSQGQGYLEEKAAPCCPAHL
AFIYTLVAFVNALTNGMLPSVQTYSCLSYGPVAYHLAATLSIVANPLASLVSMFLPNRSL
LFLGVLSVLGTCFGGYNMAMAVMSPCPLLQGHWGG
EVLIVASWVLFSGCLSYVKVMLGVV
LRDLSRSALLWCGAAVQLGSLLGALLMFPLVNVLRLFSSADFCNLHCPA
Sequence length 469
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  KEGG  Reactome
  Vitamin digestion and absorption   Vitamin B2 (riboflavin) metabolism
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
21
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
Auditory neuropathy Likely pathogenic rs2514849190 RCV003484505
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Brown-Vialetto-van Laere syndrome 1 Pathogenic; Likely pathogenic rs890871342, rs1986662202, rs1383679424, rs794728004, rs267606683, rs267606685, rs267606688, rs2514849071, rs761042586, rs769740240, rs754753126, rs778363575, rs797045190, rs767263985, rs1486271481
View all (5 more)
RCV001383229
RCV001387225
RCV001957312
RCV000000162
RCV000000163
View all (15 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Progressive bulbar palsy of childhood Pathogenic rs754753126, rs778363575, rs1599959574 RCV000024020
RCV002247619
RCV000985191
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
ALZHEIMER DISEASE GWAS catalog
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
BROWN-VIALETTO-VAN LAERE SYNDROME CTD
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
BROWN-VIALETTO-VAN LAERE SYNDROME 2 Disgenet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
BULBAR PALSY, PROGRESSIVE CTD
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Adenocarcinoma Of Esophagus Esophageal Cancer BEFREE 23222411
★☆☆☆☆
Found in Text Mining only
Amyotrophic Lateral Sclerosis Amyotrophic Lateral Sclerosis BEFREE 22766032, 30553531
★☆☆☆☆
Found in Text Mining only
Auditory neuropathy Auditory neuropathy Pubtator 32022482 Associate
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Blepharoptosis Ptosis HPO_DG
★☆☆☆☆
Found in Text Mining only
Brown-Vialetto-Van Laere Syndrome 1 Brown-Vialetto-Van Laere Syndrome CLINVAR_DG 20206331, 20920669, 21110228, 22633641, 22718020, 22824638
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Brown-Vialetto-Van Laere Syndrome 1 Brown-Vialetto-Van Laere Syndrome GENOMICS_ENGLAND_DG 20206331, 20920669, 21110228
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Brown-Vialetto-Van Laere Syndrome 1 Brown-Vialetto-Van Laere Syndrome CLINGEN_DG 20206331, 21110228, 22824638, 25462087, 26976849, 27272163, 28637675, 29053833
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Brown-Vialetto-Van Laere Syndrome 1 Brown-Vialetto-Van Laere Syndrome UNIPROT_DG 20206331, 20920669, 21110228, 22273710, 22633641, 22718020, 22824638, 27702554
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Brown-Vialetto-Van Laere Syndrome 1 Brown-Vialetto-Van Laere Syndrome BEFREE 22273710, 22633641, 22718020, 22740598, 22766032, 22864630, 23688382, 24079556, 26444347, 26918385, 26976849, 27702554, 29053833, 30553531, 31064337
View all (1 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Brown-Vialetto-Van Laere Syndrome 1 Brown-Vialetto-Van Laere Syndrome CTD_human_DG
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)