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Aliases for SLC52A3 Gene

Aliases for SLC52A3 Gene

  • Solute Carrier Family 52 Member 3 2 3 5
  • Solute Carrier Family 52 (Riboflavin Transporter), Member 3 2 3
  • Riboflavin Transporter 2 3 4
  • C20orf54 3 4
  • RFVT3 3 4
  • HRFT2 3 4
  • RFT2 3 4
  • Solute Carrier Family 52, Riboflavin Transporter, Member 3 3
  • Chromosome 20 Open Reading Frame 54 2
  • Hypothetical Protein LOC113278 2
  • BA371L19.1 3
  • BVVLS1 3
  • BVVLS 3

External Ids for SLC52A3 Gene

Previous HGNC Symbols for SLC52A3 Gene

  • C20orf54

Summaries for SLC52A3 Gene

Entrez Gene Summary for SLC52A3 Gene

  • 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]

GeneCards Summary for SLC52A3 Gene

SLC52A3 (Solute Carrier Family 52 Member 3) is a Protein Coding gene. Diseases associated with SLC52A3 include Brown-Vialetto-Van Laere Syndrome 1 and Fazio-Londe Disease. Among its related pathways are Vitamin digestion and absorption and Metabolism. GO annotations related to this gene include riboflavin transporter activity. An important paralog of this gene is SLC52A1.

UniProtKB/Swiss-Prot for SLC52A3 Gene

  • Transporter for riboflavin, which must be obtained as a nutrient via intestinal absorption. Riboflavin transport is Na(+)-independent at low pH but significantly reduced by Na(+) depletion under neutral pH conditions. Activity is strongly inhibited by riboflavin analogs, such as lumiflavin, flavin mononucleotide (FMN), flavin adenine dinucleotide (FAD), by methylene blue, and to a lesser extent by amiloride.

Gene Wiki entry for SLC52A3 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SLC52A3 Gene

Genomics for SLC52A3 Gene

Regulatory Elements for SLC52A3 Gene

Enhancers for SLC52A3 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH20F000766 0.5 Ensembl ENCODE 11.5 +7.3 7265 3.5 ATF1 KLF17 RAD21 ETS1 ZNF143 FOS CREM THAP11 ZNF263 ZNF654 SLC52A3 ACTG1P3 RSPO4 ANGPT4 GC20P000743
GH20F000796 0.2 ENCODE 11.4 -21.2 -21202 1.2 SLC52A3 GC20P000795 FAM110A
GH20F000707 0.3 FANTOM5 11.3 +68.3 68304 0.2 SCRT2 SLC52A3 ANGPT4 TMEM74B PIR59185 GC20P000743
GH20F000727 0.8 Ensembl ENCODE 11.2 +47.6 47560 1.3 ARID4B ZNF48 GLIS2 CBX5 ZNF143 ZNF263 SP5 MIER2 REST PPARG SCRT2 SRXN1 SLC52A3 CSNK2A1 ANGPT4 SOX12 GC20P000743 PIR59185
GH20F000567 1.2 Ensembl ENCODE 10.5 +207.5 207450 1.5 ZNF366 GLIS1 ZMYM3 CSNK2A1 TCF15 SLC52A3 NRSN2 NRSN2-AS1 GC20M000594
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around SLC52A3 on UCSC Golden Path with GeneCards custom track

Genomic Location for SLC52A3 Gene

Chromosome:
20
Start:
760,080 bp from pter
End:
776,015 bp from pter
Size:
15,936 bases
Orientation:
Minus strand

Genomic View for SLC52A3 Gene

Genes around SLC52A3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SLC52A3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SLC52A3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SLC52A3 Gene

Proteins for SLC52A3 Gene

  • Protein details for SLC52A3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NQ40-S52A3_HUMAN
    Recommended name:
    Solute carrier family 52, riboflavin transporter, member 3
    Protein Accession:
    Q9NQ40
    Secondary Accessions:
    • A8K6P1
    • Q5W1A0
    • Q5W1A1
    • Q8NCL7
    • Q96GD5

    Protein attributes for SLC52A3 Gene

    Size:
    469 amino acids
    Molecular mass:
    50805 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for SLC52A3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SLC52A3 Gene

Post-translational modifications for SLC52A3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SLC52A3 Gene

No data available for DME Specific Peptides for SLC52A3 Gene

Domains & Families for SLC52A3 Gene

Gene Families for SLC52A3 Gene

Protein Domains for SLC52A3 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for SLC52A3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9NQ40

UniProtKB/Swiss-Prot:

S52A3_HUMAN :
  • Belongs to the riboflavin transporter family.
Family:
  • Belongs to the riboflavin transporter family.
genes like me logo Genes that share domains with SLC52A3: view

Function for SLC52A3 Gene

Molecular function for SLC52A3 Gene

UniProtKB/Swiss-Prot BiophysicochemicalProperties:
Kinetic parameters: KM=0.98 uM for riboflavin {ECO:0000269 PubMed:20463145};
UniProtKB/Swiss-Prot Function:
Transporter for riboflavin, which must be obtained as a nutrient via intestinal absorption. Riboflavin transport is Na(+)-independent at low pH but significantly reduced by Na(+) depletion under neutral pH conditions. Activity is strongly inhibited by riboflavin analogs, such as lumiflavin, flavin mononucleotide (FMN), flavin adenine dinucleotide (FAD), by methylene blue, and to a lesser extent by amiloride.

Gene Ontology (GO) - Molecular Function for SLC52A3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0032217 riboflavin transporter activity TAS --
genes like me logo Genes that share ontologies with SLC52A3: view
genes like me logo Genes that share phenotypes with SLC52A3: view

Human Phenotype Ontology for SLC52A3 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for SLC52A3 Gene

MGI Knock Outs for SLC52A3:

Animal Model Products

miRNA for SLC52A3 Gene

miRTarBase miRNAs that target SLC52A3

Inhibitory RNA Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for SLC52A3 Gene

Localization for SLC52A3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SLC52A3 Gene

Apical cell membrane; Multi-pass membrane protein.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for SLC52A3 Gene COMPARTMENTS Subcellular localization image for SLC52A3 gene
Compartment Confidence
plasma membrane 5

Gene Ontology (GO) - Cellular Components for SLC52A3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane TAS --
GO:0005887 integral component of plasma membrane IDA 20463145
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0016324 apical plasma membrane IEA --
genes like me logo Genes that share ontologies with SLC52A3: view

Pathways & Interactions for SLC52A3 Gene

genes like me logo Genes that share pathways with SLC52A3: view

Pathways by source for SLC52A3 Gene

Interacting Proteins for SLC52A3 Gene

Gene Ontology (GO) - Biological Process for SLC52A3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006771 riboflavin metabolic process TAS --
GO:0006810 transport IEA --
GO:0007605 sensory perception of sound IMP 20206331
GO:0032218 riboflavin transport IDA 20463145
GO:0034605 cellular response to heat IEA --
genes like me logo Genes that share ontologies with SLC52A3: view

No data available for SIGNOR curated interactions for SLC52A3 Gene

Transcripts for SLC52A3 Gene

Unigene Clusters for SLC52A3 Gene

Solute carrier family 52, riboflavin transporter, member 3:
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for SLC52A3 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6
SP1: -
SP2: -
SP3:

Relevant External Links for SLC52A3 Gene

GeneLoc Exon Structure for
SLC52A3
ECgene alternative splicing isoforms for
SLC52A3

Expression for SLC52A3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SLC52A3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SLC52A3 Gene

This gene is overexpressed in Testis (x12.0).

Protein differential expression in normal tissues from HIPED for SLC52A3 Gene

This gene is overexpressed in Testis (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for SLC52A3 Gene



Protein tissue co-expression partners for SLC52A3 Gene

NURSA nuclear receptor signaling pathways regulating expression of SLC52A3 Gene:

SLC52A3

SOURCE GeneReport for Unigene cluster for SLC52A3 Gene:

Hs.283865

mRNA Expression by UniProt/SwissProt for SLC52A3 Gene:

Q9NQ40-S52A3_HUMAN
Tissue specificity: Predominantly expressed in testis. Highly expressed in small intestine and prostate.
genes like me logo Genes that share expression patterns with SLC52A3: view

Primer Products

Orthologs for SLC52A3 Gene

This gene was present in the common ancestor of animals.

Orthologs for SLC52A3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SLC52A3 34 35
  • 98.79 (n)
dog
(Canis familiaris)
Mammalia SLC52A3 34 35
  • 85.5 (n)
cow
(Bos Taurus)
Mammalia SLC52A3 34 35
  • 83.51 (n)
rat
(Rattus norvegicus)
Mammalia Slc52a3 34
  • 77.63 (n)
mouse
(Mus musculus)
Mammalia Slc52a3 34 16 35
  • 77.58 (n)
oppossum
(Monodelphis domestica)
Mammalia -- 35
  • 64 (a)
OneToMany
-- 35
  • 59 (a)
OneToMany
platypus
(Ornithorhynchus anatinus)
Mammalia SLC52A3 35
  • 62 (a)
OneToOne
chicken
(Gallus gallus)
Aves C20H20ORF54 34
  • 67.27 (n)
SLC52A3 35
  • 58 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SLC52A3 35
  • 56 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100486825 34
  • 60.8 (n)
zebrafish
(Danio rerio)
Actinopterygii slc52a3 34 35
  • 60.36 (n)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.2663 34
fruit fly
(Drosophila melanogaster)
Insecta CG11576 34 35
  • 53.22 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP000181 34
  • 52.77 (n)
worm
(Caenorhabditis elegans)
Secernentea Y47D7A.16 34
  • 41.19 (n)
rft-1 35
  • 35 (a)
ManyToMany
rft-2 35
  • 30 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.1348 35
  • 38 (a)
OneToMany
Species where no ortholog for SLC52A3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for SLC52A3 Gene

ENSEMBL:
Gene Tree for SLC52A3 (if available)
TreeFam:
Gene Tree for SLC52A3 (if available)

Paralogs for SLC52A3 Gene

Paralogs for SLC52A3 Gene

(2) SIMAP similar genes for SLC52A3 Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with SLC52A3: view

Variants for SLC52A3 Gene

Sequence variations from dbSNP and Humsavar for SLC52A3 Gene

SNP ID Clin Chr 20 pos Sequence Context AA Info Type
rs267606684 Brown-Vialetto-Van Laere syndrome 1 (BVVLS1) [MIM:211530], Pathogenic 765,381(-) TGAGC(C/T)GGCTG reference, missense
rs267606685 Brown-Vialetto-Van Laere syndrome 1 (BVVLS1) [MIM:211530], Pathogenic 763,901(-) TCTTC(C/T)TCCTC reference, missense
rs267606686 Brown-Vialetto-Van Laere syndrome 1 (BVVLS1) [MIM:211530], Pathogenic 765,669(-) TGCCC(A/G)AGGGC reference, missense
rs267606687 Brown-Vialetto-Van Laere syndrome 1 (BVVLS1) [MIM:211530], Pathogenic 761,198(-) TTACG(C/T)CAAGG reference, missense
rs779750163 Brown-Vialetto-Van Laere syndrome 1 (BVVLS1) [MIM:211530] 761,067(+) CGAGA(A/G)GAGCC reference, missense

Structural Variations from Database of Genomic Variants (DGV) for SLC52A3 Gene

Variant ID Type Subtype PubMed ID
esv3644952 CNV gain 21293372
esv3644961 CNV loss 21293372
nsv1062082 CNV gain 25217958
nsv1067424 CNV gain 25217958
nsv516278 CNV loss 19592680
nsv585191 CNV gain 21841781
nsv585192 CNV loss 21841781

Variation tolerance for SLC52A3 Gene

Residual Variation Intolerance Score: 27.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 8.88; 87.06% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SLC52A3 Gene

Human Gene Mutation Database (HGMD)
SLC52A3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SLC52A3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SLC52A3 Gene

Disorders for SLC52A3 Gene

MalaCards: The human disease database

(12) MalaCards diseases for SLC52A3 Gene - From: OMIM, ClinVar, GeneTests, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
brown-vialetto-van laere syndrome 1
  • brown-vialetto-van laere syndrome
fazio-londe disease
  • progressive bulbar palsy of childhood
brown-vialetto-van laere syndrome
  • bvvls
progressive bulbar palsy
  • progressive bulbar atrophy
gastric cardia adenocarcinoma
  • adenocarcinoma of cardia of stomach
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

S52A3_HUMAN
  • Brown-Vialetto-Van Laere syndrome 1 (BVVLS1) [MIM:211530]: A rare neurologic disorder characterized by sensorineural hearing loss and a variety of cranial nerve palsies, which develop over a relatively short period of time in a previously healthy individual. Sensorineural hearing loss may precede the neurological signs. The course is invariably progressive, but the rate of decline is variable within and between families. With disease evolution, long tract signs, lower motor neuron signs, cerebellar ataxia and lower cranial nerve (III-VI) palsies develop, giving rise to a complex picture resembling amyotrophic lateral sclerosis. Diaphragmatic weakness and respiratory compromise are some of the most distressing features, leading to recurrent chest infections and respiratory failure, which are often the cause of patients demise. {ECO:0000269 PubMed:20206331}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Fazio-Londe disease (FALOND) [MIM:211500]: A rare neurological disease characterized by progressive weakness of the muscles innervated by cranial nerves of the lower brain stem. It may present in childhood with severe neurological deterioration with hypotonia, respiratory insufficiency leading to premature death, or later in life with bulbar weakness which progresses to involve motor neurons throughout the neuroaxis. Clinical manifestations include dysarthria, dysphagia, facial weakness, tongue weakness, and fasciculations of the tongue and facial muscles. {ECO:0000269 PubMed:21110228}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for SLC52A3

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SLC52A3
genes like me logo Genes that share disorders with SLC52A3: view

No data available for Genatlas for SLC52A3 Gene

Publications for SLC52A3 Gene

  1. Identification and functional characterization of rat riboflavin transporter 2. (PMID: 19122205) Yamamoto S. … Yuasa H. (J. Biochem. 2009) 2 3 4 64
  2. The DNA sequence and comparative analysis of human chromosome 20. (PMID: 11780052) Deloukas P. … Rogers J. (Nature 2001) 2 3 4 64
  3. Functional involvement of RFVT3/SLC52A3 in intestinal riboflavin absorption. (PMID: 24264046) Yoshimatsu H. … Matsubara K. (Am. J. Physiol. Gastrointest. Liver Physiol. 2014) 3 4 64
  4. Role of cysteine residues in cell surface expression of the human riboflavin transporter-2 (hRFT2) in intestinal epithelial cells. (PMID: 21512156) Subramanian V.S. … Said H.M. (Am. J. Physiol. Gastrointest. Liver Physiol. 2011) 3 4 64
  5. Brown-Vialetto-Van Laere syndrome, a ponto-bulbar palsy with deafness, is caused by mutations in c20orf54. (PMID: 20206331) Green P. … Josifova D.J. (Am. J. Hum. Genet. 2010) 3 4 64

Products for SLC52A3 Gene

Sources for SLC52A3 Gene

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