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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
  • SLC52A3a 3
  • SLC52A3b 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 Metabolism and Metabolism of water-soluble vitamins and cofactors. Gene Ontology (GO) annotations related to this gene include riboflavin transmembrane 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

Additional gene information for SLC52A3 Gene

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

Genomics for SLC52A3 Gene

GeneHancer (GH) Regulatory Elements for SLC52A3 Gene

Promoters and enhancers for SLC52A3 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH20J000766 Promoter/Enhancer 1.5 EPDnew Ensembl ENCODE 661.5 +7.3 7265 3.5 ATF1 KLF17 ZBTB40 RAD21 ETS1 ZNF143 FOS ATF7 CREM THAP11 SLC52A3 TBC1D20 RBCK1 RSPO4 ANGPT4 GC20P000743
GH20J000775 Enhancer 0.7 Ensembl ENCODE 659.5 +0.1 129 1.1 MAZ LEF1 POLR2A PRDM10 DPF2 KLF4 ZKSCAN1 SLC52A3 RSPO4 ANGPT4 C20orf96 GC20P000743
GH20J000645 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE dbSUPER 10 +129.8 129793 2.3 FOXA2 MLX ARID4B SIN3A DMAP1 ZNF2 SLC30A9 POLR2B ZNF207 ZNF143 SRXN1 TCF15 CSNK2A1 SCRT2 SLC52A3 GC20M000621 GC20M000631 ENSG00000270299
GH20J000727 Enhancer 1.3 Ensembl ENCODE dbSUPER 11.3 +47.5 47530 1.2 ATF1 ARID4B SIN3A ZNF48 GLIS2 CBX5 ARID2 ZNF143 ATF7 NFKBIZ SCRT2 SRXN1 SLC52A3 CSNK2A1 ANGPT4 SOX12 GC20P000743 PIR59185
GH20J000345 Promoter/Enhancer 1.8 Ensembl ENCODE dbSUPER 5.5 +428.3 428329 3.7 MLX ZFP64 FEZF1 DMAP1 YY1 SLC30A9 ZNF213 E2F8 ZNF143 MCM3 NRSN2 NRSN2-AS1 GC20M000344 LOC101929937 ACTG1P3 TBC1D20 ENSG00000272874 DEFB129 DEFB126 DEFB125
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SLC52A3 on UCSC Golden Path with GeneCards custom track

Genomic Locations for SLC52A3 Gene

Genomic Locations for SLC52A3 Gene
chr20:760,080-776,015
(GRCh38/hg38)
Size:
15,936 bases
Orientation:
Minus strand
chr20:740,724-749,228
(GRCh37/hg19)
Size:
8,505 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

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Plasma proteins
  • Potential drug targets
  • Predicted membrane proteins
  • Transporters

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 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.
UniProtKB/Swiss-Prot BiophysicochemicalProperties:
Kinetic parameters: KM=0.98 uM for riboflavin {ECO:0000269 PubMed:20463145};

Phenotypes From GWAS Catalog for SLC52A3 Gene

Gene Ontology (GO) - Molecular Function for SLC52A3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0032217 riboflavin transmembrane transporter activity IEA,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

CRISPR Products

miRNA for SLC52A3 Gene

miRTarBase miRNAs that target SLC52A3

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SLC52A3

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. Cell membrane.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SLC52A3 gene
Compartment Confidence
plasma membrane 5
mitochondrion 1
nucleus 1

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 IEA,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

No data available for Subcellular locations from the Human Protein Atlas (HPA) for SLC52A3 Gene

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:0007605 sensory perception of sound IMP 20206331
GO:0032218 riboflavin transport IDA,IEA 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

Drugs & Compounds for SLC52A3 Gene

No Compound Related Data Available

Transcripts for SLC52A3 Gene

mRNA/cDNA for SLC52A3 Gene

Unigene Clusters for SLC52A3 Gene

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

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SLC52A3

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 CGAP 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.

Evidence on tissue expression from TISSUES for SLC52A3 Gene

  • Pancreas(4)

Phenotype-based relationships between genes and organs from Gene ORGANizer for SLC52A3 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • digestive
  • immune
  • integumentary
  • nervous
  • respiratory
  • skeletal muscle
  • skeleton
Regions:
Head and neck:
  • brain
  • cerebellum
  • cranial nerve
  • epiglottis
  • eye
  • eyelid
  • face
  • head
  • jaw
  • larynx
  • mandible
  • maxilla
  • mouth
  • neck
  • nose
  • pharynx
  • skull
  • tongue
  • vocal cord
Thorax:
  • bronchus
  • diaphragm
  • esophagus
  • lung
  • rib
  • rib cage
  • trachea
Abdomen:
  • stomach
Pelvis:
  • pelvis
Limb:
  • ankle
  • hand
  • knee
  • lower limb
  • upper limb
General:
  • peripheral nerve
  • peripheral nervous system
  • skin
  • spinal column
  • spinal cord
  • vertebrae
genes like me logo Genes that share expression patterns with SLC52A3: view

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 33
  • 98.79 (n)
OneToOne
dog
(Canis familiaris)
Mammalia SLC52A3 34 33
  • 85.5 (n)
OneToOne
cow
(Bos Taurus)
Mammalia SLC52A3 34 33
  • 83.51 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Slc52a3 33
  • 77.63 (n)
mouse
(Mus musculus)
Mammalia Slc52a3 16 34 33
  • 77.58 (n)
oppossum
(Monodelphis domestica)
Mammalia -- 34
  • 64 (a)
OneToMany
-- 34
  • 59 (a)
OneToMany
platypus
(Ornithorhynchus anatinus)
Mammalia SLC52A3 34
  • 62 (a)
OneToOne
chicken
(Gallus gallus)
Aves C20H20ORF54 33
  • 67.27 (n)
SLC52A3 34
  • 58 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SLC52A3 34
  • 56 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100486825 33
  • 60.8 (n)
zebrafish
(Danio rerio)
Actinopterygii slc52a3 34 33
  • 60.36 (n)
OneToOne
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.2663 33
fruit fly
(Drosophila melanogaster)
Insecta CG11576 34 33
  • 53.22 (n)
OneToMany
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP000181 33
  • 52.77 (n)
worm
(Caenorhabditis elegans)
Secernentea Y47D7A.16 33
  • 41.19 (n)
rft-1 34
  • 35 (a)
ManyToMany
rft-2 34
  • 30 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.1348 34
  • 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)
Aminode:
Evolutionary constrained regions (ECRs) for SLC52A3: view image

Paralogs for SLC52A3 Gene

Paralogs for SLC52A3 Gene

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

  • S52A3_HUMAN
  • K0A6P4_HUMAN
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 Variation AA Info Type
rs1060499531 pathogenic, Brown-Vialetto-Van Laere syndrome 1 761,143(-) C/G/T coding_sequence_variant, missense_variant, stop_gained
rs139137879 likely-benign, Brown-Vialetto-Van Laere syndrome 1 761,158(-) G/A coding_sequence_variant, synonymous_variant
rs139430185 likely-benign, Brown-Vialetto-Van Laere syndrome 1 763,626(-) G/A coding_sequence_variant, synonymous_variant
rs139486822 likely-benign, benign, not specified, Brown-Vialetto-Van Laere syndrome 1 765,766(-) G/A coding_sequence_variant, synonymous_variant
rs139965967 likely-benign, Brown-Vialetto-Van Laere syndrome 1 765,229(-) C/A/T coding_sequence_variant, synonymous_variant

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)

Additional Variant Information 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: HGMD, OMIM, ClinVar, GTR, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
brown-vialetto-van laere syndrome 1
  • bvvls1
fazio-londe disease
  • bulbar palsy, progressive, of childhood
brown-vialetto-van laere syndrome
progressive bulbar palsy
  • progressive bulbar atrophy
multiple cranial nerve palsy
  • multiple cranial nerve palsies
- 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, ECO:0000269 PubMed:20920669, ECO:0000269 PubMed:21110228, ECO:0000269 PubMed:22273710, ECO:0000269 PubMed:22633641, ECO:0000269 PubMed:22718020, ECO:0000269 PubMed:22824638, ECO:0000269 PubMed:27702554}. 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.

Additional Disease Information for 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 (Journal of biochemistry 2009) 2 3 4 58
  2. The DNA sequence and comparative analysis of human chromosome 20. (PMID: 11780052) Deloukas P … Rogers J (Nature 2001) 2 3 4 58
  3. Functional involvement of RFVT3/SLC52A3 in intestinal riboflavin absorption. (PMID: 24264046) Yoshimatsu H … Matsubara K (American journal of physiology. Gastrointestinal and liver physiology 2014) 3 4 58
  4. Four novel C20orf54 mutations identified in Brown-Vialetto-Van Laere syndrome patients. (PMID: 22718020) Dezfouli MA … Elahi E (Journal of human genetics 2012) 3 4 58
  5. Effect of clinical mutations on functionality of the human riboflavin transporter-2 (hRFT-2). (PMID: 22273710) Nabokina SM … Said HM (Molecular genetics and metabolism 2012) 3 4 58

Products for SLC52A3 Gene

Sources for SLC52A3 Gene

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