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SLC52A3 solute carrier family 52 member 3 [ Homo sapiens (human) ]

Gene ID: 113278, updated on 2-Nov-2024

Summary

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Official Symbol
SLC52A3provided by HGNC
Official Full Name
solute carrier family 52 member 3provided by HGNC
Primary source
HGNC:HGNC:16187
See related
Ensembl:ENSG00000101276 MIM:613350; AllianceGenome:HGNC:16187
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
RFT2; BVVLS; RFVT3; hRFT2; BVVLS1; C20orf54; bA371L19.1
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 signal in the C-terminus. Mutations at this locus have been associated with Brown-Vialetto-Van Laere syndrome and Fazio-Londe disease. [provided by RefSeq, Mar 2012]
Expression
Biased expression in testis (RPKM 24.2), small intestine (RPKM 7.2) and 7 other tissues See more
Orthologs
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Genomic context

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See SLC52A3 in Genome Data Viewer
Location:
20p13
Exon count:
9
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (760080..780033, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (804408..824432, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (740724..756628, complement)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107985423 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12582 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:642152-642765 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:642766-643378 Neighboring gene sulfiredoxin 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:653674-654187 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12583 Neighboring gene Sharpr-MPRA regulatory region 5118 Neighboring gene scratch family transcriptional repressor 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:669184-669764 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:669765-670343 Neighboring gene MPRA-validated peak4111 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:700539-701043 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:714587-715087 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:749319-749818 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:756400-757102 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr20:771562-772313 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:798226-798402 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:803889-804420 Neighboring gene CRISPRi-validated cis-regulatory element chr20.80 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12584 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17445 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12585 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:822609-823591 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17446 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:825145-825958 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17447 Neighboring gene family with sequence similarity 110 member A Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:836793-837779 Neighboring gene ribosomal protein S10 pseudogene 5 Neighboring gene uncharacterized LOC124904854 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:853162-853662 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:853663-854163 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17448 Neighboring gene angiopoietin 4

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Functional involvement of RFVT3/SLC52A3 in intestinal riboflavin absorption. Yoshimatsu H, et al. Am J Physiol Gastrointest Liver Physiol, 2014 Jan. PMID 24264046
  2. Overexpression of riboflavin transporter 2 contributes toward progression and invasion of glioma. Fu T, et al. Neuroreport, 2016 Oct 19. PMID 27584688
  3. Single nucleotide polymorphism rs13042395 in the SLC52A3 gene as a biomarker for regional lymph node metastasis and relapse-free survival of esophageal squamous cell carcinoma patients. Tan HZ, et al. BMC Cancer, 2016 Jul 29. PMID 27472962, Free PMC Article
  4. Correlation analysis of riboflavin, RFT2 and Helicobater pylori in gastric carcinoma. Matnuri M, et al. Int J Clin Exp Pathol, 2015. PMID 26722538, Free PMC Article
  5. Esophageal Squamous Cell Carcinoma and Gastric Cardia Adenocarcinoma Shared Susceptibility Locus in C20orf54: Evidence from Published Studies. Duan F, et al. Sci Rep, 2015 Jul 8. PMID 26154995, Free PMC Article

See all (54) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Three cases of adult-onset Brown-Vialetto-Van Laere syndrome: Novel variants in SLC52A3 gene and MRI abnormalities.
    Title: Three cases of adult-onset Brown-Vialetto-Van Laere syndrome: Novel variants in SLC52A3 gene and MRI abnormalities.
  2. Promotion of rs3746804 (p. L267P) polymorphism to intracellular SLC52A3a trafficking and riboflavin transportation in esophageal cancer cells.
    Title: Promotion of rs3746804 (p. L267P) polymorphism to intracellular SLC52A3a trafficking and riboflavin transportation in esophageal cancer cells.
  3. BVVL/ FL: features caused by SLC52A3 mutations; WDFY4 and TNFSF13B may be novel causative genes.
    Title: BVVL/ FL: features caused by SLC52A3 mutations; WDFY4 and TNFSF13B may be novel causative genes.
  4. Functional variation of SLC52A3 rs13042395 predicts survival of Chinese gastric cancer patients.
    Title: Functional variation of SLC52A3 rs13042395 predicts survival of Chinese gastric cancer patients.
  5. An Association and Meta-Analysis of Esophageal Squamous Cell Carcinoma Risk Associated with PLCE1 rs2274223, C20orf54 rs13042395 and RUNX1 rs2014300 Polymorphisms.
    Title: An Association and Meta-Analysis of Esophageal Squamous Cell Carcinoma Risk Associated with PLCE1 rs2274223, C20orf54 rs13042395 and RUNX1 rs2014300 Polymorphisms.
  6. Reports on 109 patients with a genetically confirmed diagnosis of riboflavin transporter deficiency are summarized in order to highlight commonly presenting clinical features and possible differences between patients with pathogenic SLC52A2 (RTD2) or SLC52A3 (RTD3) mutations. [review]
    Title: An update on the genetics, clinical presentation, and pathomechanisms of human riboflavin transporter deficiency.
  7. Justification for screening SLC52A3 included notable clinical similarities between Brown-Vialetto-Van Laere syndrome
    Title: Mutation screening of SLC52A3, C19orf12, and TARDBP in Iranian ALS patients.
  8. In the in vitro model, exposing Caco-2 cells to tumor necrosis factor-alpha (TNF-alpha) led to a significant inhibition in RF uptake, an effect that was abrogated upon knocking down TNF receptor 1 (TNFR1). The inhibition in RF uptake was associated with a significant reduction in the expression of hRFVT-3 and -1 protein and mRNA levels, as well as in the activity of the SLC52A3 and SLC52A1 promoters
    Title: Effect of the proinflammatory cytokine TNF-α on intestinal riboflavin uptake: inhibition mediated via transcriptional mechanism(s).
  9. The riboflavin transporter-3 (SLC52A3) 5'-flanking regions contain NF-kappaB p65/Rel-B-binding sites, which are crucial for mediating SLC52A3 transcriptional activity in esophageal squamous cell carcinoma (ESCC) cells.
    Title: SLC52A3 expression is activated by NF-κB p65/Rel-B and serves as a prognostic biomarker in esophageal cancer.
  10. RFVT3 gene and protein expression levels were higher in DLD-1 and HT-29 compared to Caco2 cells. In tumor tissues of patients with CRC, RFVT3 gene expression levels were increased, while protein expression was reduced, with a small reduction in riboflavin amount.
    Title: The Expression of Riboflavin Transporters in Human Colorectal Cancer.
Submit: New GeneRIF Correction See all GeneRIFs (41)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC10698

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables riboflavin transmembrane transporter activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables riboflavin transmembrane transporter activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables riboflavin transmembrane transporter activity TAS
Traceable Author Statement
more info
  
Process Evidence Code Pubs
involved_in cellular response to heat IEA
Inferred from Electronic Annotation
more info
  
involved_in flavin adenine dinucleotide biosynthetic process IEA
Inferred from Electronic Annotation
more info
  
involved_in riboflavin metabolic process TAS
Traceable Author Statement
more info
  
involved_in riboflavin transport IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in riboflavin transport IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in sensory perception of sound IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in apical plasma membrane IEA
Inferred from Electronic Annotation
more info
  
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in nuclear membrane IEA
Inferred from Electronic Annotation
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in plasma membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in plasma membrane TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
solute carrier family 52, riboflavin transporter, member 3
Names
SLC52A3a
SLC52A3b
riboflavin transporter 2
solute carrier family 52 (riboflavin transporter), member 3

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_027687.2 RefSeqGene

    Range
    12486..20906
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_1394

mRNA and Protein(s)

  1. NM_001370085.1 → NP_001357014.1  solute carrier family 52, riboflavin transporter, member 3

    Status: REVIEWED

    Source sequence(s)
    AL118502
    Consensus CDS
    CCDS13007.1
    UniProtKB/Swiss-Prot
    A0A2I6BQ49, A8K6P1, K0A6P4, Q5W1A0, Q5W1A1, Q8NCL7, Q96GD5, Q9NQ40
    Related
    ENSP00000217254.7, ENST00000217254.11
    Conserved Domains (1) summary
    pfam06237
    Location:298 → 395
    DUF1011; Protein of unknown function (DUF1011)

  2. NM_001370086.1 → NP_001357015.1  solute carrier family 52, riboflavin transporter, member 3

    Status: REVIEWED

    Source sequence(s)
    AL118502
    Consensus CDS
    CCDS13007.1
    UniProtKB/Swiss-Prot
    A0A2I6BQ49, A8K6P1, K0A6P4, Q5W1A0, Q5W1A1, Q8NCL7, Q96GD5, Q9NQ40
    Related
    ENSP00000494009.1, ENST00000488495.3
    Conserved Domains (1) summary
    pfam06237
    Location:298 → 395
    DUF1011; Protein of unknown function (DUF1011)

  3. NM_033409.4 → NP_212134.3  solute carrier family 52, riboflavin transporter, member 3

    See identical proteins and their annotated locations for NP_212134.3

    Status: REVIEWED

    Source sequence(s)
    AI244952, AK074650, BC009750, DA302552, DA358731
    Consensus CDS
    CCDS13007.1
    UniProtKB/Swiss-Prot
    A0A2I6BQ49, A8K6P1, K0A6P4, Q5W1A0, Q5W1A1, Q8NCL7, Q96GD5, Q9NQ40
    Related
    ENSP00000494193.1, ENST00000645534.1
    Conserved Domains (1) summary
    pfam06237
    Location:298 → 395
    DUF1011; Protein of unknown function (DUF1011)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    760080..780033 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047439868.1 → XP_047295824.1  solute carrier family 52, riboflavin transporter, member 3 isoform X1

    UniProtKB/Swiss-Prot
    A0A2I6BQ49, A8K6P1, K0A6P4, Q5W1A0, Q5W1A1, Q8NCL7, Q96GD5, Q9NQ40

  2. XM_024451821.1 → XP_024307589.1  solute carrier family 52, riboflavin transporter, member 3 isoform X1

    UniProtKB/Swiss-Prot
    A0A2I6BQ49, A8K6P1, K0A6P4, Q5W1A0, Q5W1A1, Q8NCL7, Q96GD5, Q9NQ40
    Conserved Domains (1) summary
    pfam06237
    Location:298 → 395
    DUF1011; Protein of unknown function (DUF1011)

  3. XM_047439867.1 → XP_047295823.1  solute carrier family 52, riboflavin transporter, member 3 isoform X1

    UniProtKB/Swiss-Prot
    A0A2I6BQ49, A8K6P1, K0A6P4, Q5W1A0, Q5W1A1, Q8NCL7, Q96GD5, Q9NQ40

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    804408..824432 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054322921.1 → XP_054178896.1  solute carrier family 52, riboflavin transporter, member 3 isoform X1

    UniProtKB/Swiss-Prot
    A0A2I6BQ49, A8K6P1, K0A6P4, Q5W1A0, Q5W1A1, Q8NCL7, Q96GD5, Q9NQ40

  2. XM_054322919.1 → XP_054178894.1  solute carrier family 52, riboflavin transporter, member 3 isoform X1

    UniProtKB/Swiss-Prot
    A0A2I6BQ49, A8K6P1, K0A6P4, Q5W1A0, Q5W1A1, Q8NCL7, Q96GD5, Q9NQ40

  3. XM_054322920.1 → XP_054178895.1  solute carrier family 52, riboflavin transporter, member 3 isoform X1

    UniProtKB/Swiss-Prot
    A0A2I6BQ49, A8K6P1, K0A6P4, Q5W1A0, Q5W1A1, Q8NCL7, Q96GD5, Q9NQ40
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9NQ40.4 GenPept UniProtKB/Swiss-Prot:Q9NQ40

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