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Aliases for SLC52A2 Gene

Aliases for SLC52A2 Gene

  • Solute Carrier Family 52 Member 2 2 3 5
  • Solute Carrier Family 52 (Riboflavin Transporter), Member 2 2 3
  • Porcine Endogenous Retrovirus A Receptor 1 3 4
  • G Protein-Coupled Receptor 172A 2 3
  • Riboflavin Transporter 3 3 4
  • PERV-A Receptor 1 3 4
  • GPR172A 3 4
  • HRFT3 3 4
  • PAR1 3 4
  • RFT3 3 4
  • Solute Carrier Family 52, Riboflavin Transporter, Member 2 3
  • Putative G-Protein Coupled Receptor GPCR41 3
  • Protein GPR172A 4
  • D15Ertd747e 3
  • BVVLS2 3
  • GPCR41 3
  • RFVT2 3

External Ids for SLC52A2 Gene

Previous HGNC Symbols for SLC52A2 Gene

  • GPR172A

Previous GeneCards Identifiers for SLC52A2 Gene

  • GC08P145577

Summaries for SLC52A2 Gene

Entrez Gene Summary for SLC52A2 Gene

  • This gene encodes a membrane protein which belongs to the riboflavin transporter family. In humans, riboflavin must be obtained by intestinal absorption because it cannot be synthesized by the body. The water-soluble vitamin riboflavin is processed to the coenzymes flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD) which then act as intermediaries in many cellular metabolic reactions. Paralogous members of the riboflavin transporter gene family are located on chromosomes 17 and 20. Unlike other members of this family, this gene has higher expression in brain tissue than small intestine. Alternative splicing of this gene results in multiple transcript variants encoding the same protein. Mutations in this gene have been associated with Brown-Vialetto-Van Laere syndrome 2 - an autosomal recessive progressive neurologic disorder characterized by deafness, bulbar dysfunction, and axial and limb hypotonia. [provided by RefSeq, Jul 2012]

GeneCards Summary for SLC52A2 Gene

SLC52A2 (Solute Carrier Family 52 Member 2) is a Protein Coding gene. Diseases associated with SLC52A2 include Brown-Vialetto-Van Laere Syndrome 2 and Spinocerebellar Ataxia, Autosomal Recessive 3. Among its related pathways are Metabolism and Metabolism of water-soluble vitamins and cofactors. Gene Ontology (GO) annotations related to this gene include virus receptor activity and riboflavin transmembrane transporter activity. An important paralog of this gene is SLC52A1.

UniProtKB/Swiss-Prot for SLC52A2 Gene

  • Riboflavin transporter. Riboflavin transport is Na(+)-independent but moderately pH-sensitive. Activity is strongly inhibited by riboflavin analogs, such as lumiflavin. Weakly inhibited by flavin adenine dinucleotide (FAD) and flavin mononucleotide (FMN). In case of infection by retroviruses, acts as a cell receptor to retroviral envelopes similar to the porcine endogenous retrovirus (PERV-A).

Additional gene information for SLC52A2 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SLC52A2 Gene

Genomics for SLC52A2 Gene

GeneHancer (GH) Regulatory Elements for SLC52A2 Gene

Promoters and enhancers for SLC52A2 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
GH08J144353 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE 650.7 +2.4 2377 6.7 PKNOX1 ARID4B SIN3A DMAP1 POLR2B E2F8 ZNF207 ZNF143 SP3 NFYC ENSG00000271698 FBXL6 SLC52A2 TMEM249 CPSF1 VPS28 ZNF7 SHARPIN ZNF623 ZNF250
GH08J144899 Promoter/Enhancer 2.4 EPDnew FANTOM5 Ensembl ENCODE 31.2 +547.5 547456 3.6 HDGF PKNOX1 FOXA2 MLX ARID4B SIN3A DMAP1 ZNF2 ZBTB7B IRF4 ZNF250 ZNF7 CPSF1 VPS28 RPL8 SLC52A2 GPAA1 COMMD5 LRRC14 ZNF16
GH08J144455 Enhancer 1.3 Ensembl ENCODE 47.4 +102.3 102311 1.6 HDGF HNRNPUL1 PKNOX1 FOXA2 ARNT ZFP64 SIN3A ZNF2 YY1 POLR2B ZNF251 ZNF7 ZNF623 LRRC14 ZNF250 CPSF1 ZNF16 VPS28 ZNF517 GPAA1
GH08J143460 Enhancer 1.3 Ensembl ENCODE dbSUPER 39.5 -891.9 -891883 3.6 HDGF PKNOX1 ZNF493 ZNF213 ZNF207 ATF7 RUNX3 ZNF202 JUNB REST ZNF623 CPSF1 VPS28 SLC52A2 JRK GPAA1 TIGD5 ZNF707 ADCK5 ZNF696
GH08J145000 Promoter/Enhancer 1.6 Ensembl ENCODE 31.1 +649.1 649050 5 PKNOX1 SMAD1 MLX ARNT ARID4B SIN3A DMAP1 ZNF2 ZBTB7B YY1 ZNF252P ZNF252P-AS1 VPS28 ADCK5 CPSF1 SLC52A2 COMMD5 ZNF7 ZNF16 C8orf33
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SLC52A2 on UCSC Golden Path with GeneCards custom track

Genomic Locations for SLC52A2 Gene

Genomic Locations for SLC52A2 Gene
chr8:144,354,135-144,361,286
(GRCh38/hg38)
Size:
7,152 bases
Orientation:
Plus strand
chr8:145,577,795-145,584,946
(GRCh37/hg19)
Size:
7,152 bases
Orientation:
Plus strand

Genomic View for SLC52A2 Gene

Genes around SLC52A2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SLC52A2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SLC52A2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SLC52A2 Gene

Proteins for SLC52A2 Gene

  • Protein details for SLC52A2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9HAB3-S52A2_HUMAN
    Recommended name:
    Solute carrier family 52, riboflavin transporter, member 2
    Protein Accession:
    Q9HAB3
    Secondary Accessions:
    • A8K6B6
    • D3DWL8
    • G1UCY1
    • Q86UT1

    Protein attributes for SLC52A2 Gene

    Size:
    445 amino acids
    Molecular mass:
    45777 Da
    Quaternary structure:
    No Data Available

neXtProt entry for SLC52A2 Gene

Post-translational modifications for SLC52A2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for SLC52A2 Gene

Domains & Families for SLC52A2 Gene

Gene Families for SLC52A2 Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • FDA approved drug targets
  • Predicted membrane proteins
  • Predicted secreted proteins
  • Transporters

Protein Domains for SLC52A2 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for SLC52A2 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9HAB3

UniProtKB/Swiss-Prot:

S52A2_HUMAN :
  • Belongs to the riboflavin transporter family.
Family:
  • Belongs to the riboflavin transporter family.
genes like me logo Genes that share domains with SLC52A2: view

Function for SLC52A2 Gene

Molecular function for SLC52A2 Gene

UniProtKB/Swiss-Prot Function:
Riboflavin transporter. Riboflavin transport is Na(+)-independent but moderately pH-sensitive. Activity is strongly inhibited by riboflavin analogs, such as lumiflavin. Weakly inhibited by flavin adenine dinucleotide (FAD) and flavin mononucleotide (FMN). In case of infection by retroviruses, acts as a cell receptor to retroviral envelopes similar to the porcine endogenous retrovirus (PERV-A).
UniProtKB/Swiss-Prot BiophysicochemicalProperties:
Kinetic parameters: KM=0.33 uM for riboflavin {ECO:0000269 PubMed:20463145};

Phenotypes From GWAS Catalog for SLC52A2 Gene

Gene Ontology (GO) - Molecular Function for SLC52A2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001618 virus receptor activity IEA --
GO:0005515 protein binding IPI 25416956
GO:0032217 riboflavin transmembrane transporter activity IEA,TAS --
genes like me logo Genes that share ontologies with SLC52A2: view
genes like me logo Genes that share phenotypes with SLC52A2: view

Human Phenotype Ontology for SLC52A2 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for SLC52A2 Gene

MGI Knock Outs for SLC52A2:

Animal Model Products

  • Taconic Biosciences Mouse Models for SLC52A2

CRISPR Products

miRNA for SLC52A2 Gene

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SLC52A2

Clone Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for SLC52A2 Gene

Localization for SLC52A2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SLC52A2 Gene

Cell membrane; Multi-pass membrane protein.

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 SLC52A2 gene
Compartment Confidence
plasma membrane 5

Gene Ontology (GO) - Cellular Components for SLC52A2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane TAS --
GO:0005887 integral component of plasma membrane IDA,IEA 20463145
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with SLC52A2: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for SLC52A2 Gene

Pathways & Interactions for SLC52A2 Gene

genes like me logo Genes that share pathways with SLC52A2: view

Interacting Proteins for SLC52A2 Gene

Gene Ontology (GO) - Biological Process for SLC52A2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006771 riboflavin metabolic process TAS --
GO:0032218 riboflavin transport IDA,IEA 20463145
GO:0046718 viral entry into host cell IEA --
genes like me logo Genes that share ontologies with SLC52A2: view

No data available for SIGNOR curated interactions for SLC52A2 Gene

Drugs & Compounds for SLC52A2 Gene

(2) Drugs for SLC52A2 Gene - From: DrugBank and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Gamma Hydroxybutyric Acid Approved, Illicit, Investigational Pharma Target, agonist 0
genes like me logo Genes that share compounds with SLC52A2: view

Transcripts for SLC52A2 Gene

Unigene Clusters for SLC52A2 Gene

Solute carrier family 52, riboflavin transporter, member 2:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SLC52A2

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SLC52A2 Gene

ExUns: 1a · 1b · 1c ^ 2a · 2b · 2c ^ 3a · 3b ^ 4 ^ 5a · 5b · 5c · 5d ^ 6a · 6b ^ 7 ^ 8 ^ 9a · 9b · 9c
SP1: - - - - -
SP2: - -
SP3: - - -
SP4: - - -
SP5: - - - - - - - - -
SP6:
SP7: - -
SP8:
SP9:
SP10:

Relevant External Links for SLC52A2 Gene

GeneLoc Exon Structure for
SLC52A2
ECgene alternative splicing isoforms for
SLC52A2

Expression for SLC52A2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SLC52A2 Gene

Protein differential expression in normal tissues from HIPED for SLC52A2 Gene

This gene is overexpressed in Lung (40.6) and Fetal Brain (28.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for SLC52A2 Gene



Protein tissue co-expression partners for SLC52A2 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SLC52A2 Gene:

SLC52A2

SOURCE GeneReport for Unigene cluster for SLC52A2 Gene:

Hs.6459

mRNA Expression by UniProt/SwissProt for SLC52A2 Gene:

Q9HAB3-S52A2_HUMAN
Tissue specificity: Highly expressed in brain, fetal brain and salivary gland. Weakly expressed in other tissues.

Evidence on tissue expression from TISSUES for SLC52A2 Gene

  • Skin(4.2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for SLC52A2 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
  • vertebrae
genes like me logo Genes that share expression patterns with SLC52A2: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues for SLC52A2 Gene

Orthologs for SLC52A2 Gene

This gene was present in the common ancestor of animals.

Orthologs for SLC52A2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia GPR172A 34 33
  • 99.48 (n)
OneToOne
cow
(Bos Taurus)
Mammalia GPR172B 34
  • 85 (a)
OneToMany
GPR172A 33
  • 84.5 (n)
dog
(Canis familiaris)
Mammalia SLC52A1 33
  • 82.55 (n)
-- 34
  • 68 (a)
OneToMany
mouse
(Mus musculus)
Mammalia Slc52a2 16 34 33
  • 80.88 (n)
rat
(Rattus norvegicus)
Mammalia Slc52a2 33
  • 80.27 (n)
oppossum
(Monodelphis domestica)
Mammalia -- 34
  • 63 (a)
OneToMany
platypus
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 50 (a)
OneToMany
lizard
(Anolis carolinensis)
Reptilia -- 34
  • 52 (a)
OneToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia slc52a1 33
  • 59.7 (n)
zebrafish
(Danio rerio)
Actinopterygii slc52a2 33
  • 55.15 (n)
CU571162.1 34
  • 37 (a)
ManyToMany
fruit fly
(Drosophila melanogaster)
Insecta CG11576 34
  • 30 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea rft-1 34
  • 32 (a)
ManyToMany
rft-2 34
  • 27 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.1348 34
  • 31 (a)
OneToMany
Species where no ortholog for SLC52A2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • 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)
  • chicken (Gallus gallus)
  • 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)
  • rainbow trout (Oncorhynchus mykiss)
  • 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 SLC52A2 Gene

ENSEMBL:
Gene Tree for SLC52A2 (if available)
TreeFam:
Gene Tree for SLC52A2 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SLC52A2: view image

Paralogs for SLC52A2 Gene

Paralogs for SLC52A2 Gene

(3) SIMAP similar genes for SLC52A2 Gene using alignment to 7 proteins:

  • S52A2_HUMAN
  • E9PIX2_HUMAN
  • E9PJC1_HUMAN
  • E9PKE4_HUMAN
  • E9PPS0_HUMAN
  • E9PRC3_HUMAN
  • F5GXA8_HUMAN
genes like me logo Genes that share paralogs with SLC52A2: view

Variants for SLC52A2 Gene

Sequence variations from dbSNP and Humsavar for SLC52A2 Gene

SNP ID Clin Chr 08 pos Variation AA Info Type
rs111588500 likely-benign, not specified, Brown-Vialetto-Van Laere syndrome 2 144,359,720(+) C/T 5_prime_UTR_variant, coding_sequence_variant, intron_variant, non_coding_transcript_variant, synonymous_variant
rs117500243 uncertain-significance, benign, not specified, Brown-Vialetto-Van Laere syndrome 2 144,359,845(+) C/A/G/T coding_sequence_variant, intron_variant, missense_variant, non_coding_transcript_variant
rs144290224 likely-benign, not specified, Brown-Vialetto-Van Laere syndrome 2 144,360,710(+) C/T coding_sequence_variant, non_coding_transcript_variant, synonymous_variant
rs144912258 uncertain-significance, Brown-Vialetto-Van Laere syndrome 2 144,360,316(+) G/A/T coding_sequence_variant, missense_variant, non_coding_transcript_variant
rs145502954 uncertain-significance, Brown-Vialetto-Van Laere syndrome 2 144,360,627(+) G/A/T coding_sequence_variant, missense_variant, non_coding_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for SLC52A2 Gene

Variant ID Type Subtype PubMed ID
dgv12434n54 CNV loss 21841781
dgv12437n54 CNV loss 21841781
esv2759652 CNV gain+loss 17122850
nsv428208 CNV gain 18775914
nsv470249 CNV loss 18288195
nsv515809 CNV gain+loss 19592680
nsv612931 CNV loss 21841781
nsv831489 CNV loss 17160897

Variation tolerance for SLC52A2 Gene

Residual Variation Intolerance Score: 22.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.25; 25.00% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SLC52A2 Gene

Human Gene Mutation Database (HGMD)
SLC52A2
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SLC52A2

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SLC52A2 Gene

Disorders for SLC52A2 Gene

MalaCards: The human disease database

(8) MalaCards diseases for SLC52A2 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

S52A2_HUMAN
  • Brown-Vialetto-Van Laere syndrome 2 (BVVLS2) [MIM:614707]: An autosomal recessive progressive neurologic disorder characterized by early childhood onset of sensorineural deafness, bulbar dysfunction, and severe diffuse muscle weakness and wasting resulting in respiratory insufficiency and loss of independent ambulation. Because it results from a defect in riboflavin metabolism, some patients may benefit from high-dose riboflavin supplementation. {ECO:0000269 PubMed:22740598, ECO:0000269 PubMed:22864630, ECO:0000269 PubMed:23243084, ECO:0000269 PubMed:24253200, ECO:0000269 PubMed:27702554}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for SLC52A2

genes like me logo Genes that share disorders with SLC52A2: view

No data available for Genatlas for SLC52A2 Gene

Publications for SLC52A2 Gene

  1. Identification of receptors for pig endogenous retrovirus. (PMID: 12740431) Ericsson TA … Patience C (Proceedings of the National Academy of Sciences of the United States of America 2003) 2 3 4 58
  2. SLC52A2 [p.P141T] and SLC52A3 [p.N21S] causing Brown-Vialetto-Van Laere Syndrome in an Indian patient: First genetically proven case with mutations in two riboflavin transporters. (PMID: 27702554) Udhayabanu T … Ashokkumar B (Clinica chimica acta; international journal of clinical chemistry 2016) 3 4 58
  3. Treatable childhood neuronopathy caused by mutations in riboflavin transporter RFVT2. (PMID: 24253200) Foley AR … Houlden H (Brain : a journal of neurology 2014) 3 4 58
  4. Identification and comparative functional characterization of a new human riboflavin transporter hRFT3 expressed in the brain. (PMID: 20463145) Yao Y … Inui K (The Journal of nutrition 2010) 3 4 58
  5. Single-round selection yields a unique retroviral envelope utilizing GPR172A as its host receptor. (PMID: 19307586) Mazari PM … Roth MJ (Proceedings of the National Academy of Sciences of the United States of America 2009) 4 22 58

Products for SLC52A2 Gene

Sources for SLC52A2 Gene

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