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SLC52A1 solute carrier family 52 member 1 [ Homo sapiens (human) ]

Gene ID: 55065, updated on 2-Nov-2024

Summary

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Official Symbol
SLC52A1provided by HGNC
Official Full Name
solute carrier family 52 member 1provided by HGNC
Primary source
HGNC:HGNC:30225
See related
Ensembl:ENSG00000132517 MIM:607883; AllianceGenome:HGNC:30225
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
PAR2; RFT1; RBFVD; RFVT1; hRFT1; GPCR42; GPR172B; huPAR-2
Summary
Biological redox reactions require electron donors and acceptor. Vitamin B2 is the source for the flavin in flavin adenine dinucleotide (FAD) and flavin mononucleotide (FMN) which are common redox reagents. This gene encodes a member of the riboflavin (vitamin B2) transporter family. Haploinsufficiency of this protein can cause maternal riboflavin deficiency. Multiple alternatively spliced variants, encoding the same protein, have been identified. [provided by RefSeq, Jan 2013]
Expression
Biased expression in duodenum (RPKM 20.9), placenta (RPKM 16.1) and 2 other tissues See more
Orthologs
all
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Genomic context

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See SLC52A1 in Genome Data Viewer
Location:
17p13.2
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (5032602..5042414, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (4922930..4932848, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (4935897..4938721, complement)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene CAMTA2 antisense RNA 1 Neighboring gene inhibitor of CDK, cyclin A1 interacting protein 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8060 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8061 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8062 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:4902950-4903561 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:4903562-4904172 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:4906716-4907915 Neighboring gene kinesin family member 1C Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8063 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:4923264-4924463 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:4925730-4926294 Neighboring gene KIF1C antisense RNA 1 Neighboring gene uncharacterized LOC105371501 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8064 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11564 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:4946945-4947093 Neighboring gene Sharpr-MPRA regulatory region 9431 Neighboring gene zinc finger with KRAB and SCAN domains 1 pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:4965616-4966376 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:4981230-4982101 Neighboring gene ZFP3 divergent transcript

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Riboflavin 1 Transporter Deficiency: Novel SLC52A1 Variants and Expansion of the Phenotypic Spectrum.
    Title: Riboflavin 1 Transporter Deficiency: Novel SLC52A1 Variants and Expansion of the Phenotypic Spectrum.
  2. Whole-exome Sequencing Identifies SLC52A1 and ZNF106 Variants as Novel Genetic Risk Factors for (Early) Multiple-organ Failure in Acute Pancreatitis.
    Title: Whole-exome Sequencing Identifies SLC52A1 and ZNF106 Variants as Novel Genetic Risk Factors for (Early) Multiple-organ Failure in Acute Pancreatitis.
  3. Riboflavin transporter SLC52A1, a target of p53, suppresses cellular senescence by activating mitochondrial complex II.
    Title: Riboflavin transporter SLC52A1, a target of p53, suppresses cellular senescence by activating mitochondrial complex II.
  4. 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).
  5. We here report a case of transient MADD, caused by a heterozygous intronic variation, c.1134+11G>A, in the SLC52A1 gene encoding RFVT1. This variation creates a binding site for the splice inhibitory hnRNP A1 protein and causes exon 4 skipping. Riboflavin deficiency and maternal malnutrition during pregnancy might have been the determining factor in the outcome of this case.
    Title: An intronic variation in SLC52A1 causes exon skipping and transient riboflavin-responsive multiple acyl-CoA dehydrogenation deficiency.
  6. In HT-29 cells, the RFVT1 protein level was drastically lower. In tumor tissues of patients with CRC, RFVT1 content was reduced at both protein and mRNA levels compared to normal mucosa.
    Title: The Expression of Riboflavin Transporters in Human Colorectal Cancer.
  7. results are the first to reveal the identity of the minimal SLC52A1 promoter and to establish an important role for Sp-1 in its activity
    Title: Identification and characterization of 5'-flanking region of the human riboflavin transporter 1 gene (SLC52A1).
  8. data suggest that MMND is a distinct clinical subgroup of childhood onset MND patients where the known genetic defects are so far negative.
    Title: Madras motor neuron disease (MMND) is distinct from the riboflavin transporter genetic defects that cause Brown-Vialetto-Van Laere syndrome.
  9. summary of recent findings on the cloning, nomenclature, functional characterization and genetic diseases of RFVT1/SLC52A1, RFVT2/SLC52A2 and RFVT3/SLC52A3 [review]
    Title: Novel riboflavin transporter family RFVT/SLC52: identification, nomenclature, functional characterization and genetic diseases of RFVT/SLC52.
  10. Intestinal riboflavin uptake process undergoes differentiation-dependent upregulation and suggest that this is mediated (at least in part) via transcriptional mechanisms of SLC52A1 and SLC52A3.
    Title: Differentiation-dependent regulation of intestinal vitamin B(2) uptake: studies utilizing human-derived intestinal epithelial Caco-2 cells and native rat intestine.
Submit: New GeneRIF Correction See all GeneRIFs (12)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Ariboflavinosis
MedGen: C0035528 OMIM: 615026 GeneReviews: Riboflavin Transporter Deficiency
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Variation

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See Variation Viewer (GRCh37.p13)

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ10060

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
  
enables virus receptor activity IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
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 symbiont entry into host cell IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
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 1
Names
G protein-coupled receptor 172B
G-protein coupled receptor GPCR42
PERV-A receptor 2
porcine endogenous retrovirus A receptor 2
solute carrier family 52 (riboflavin transporter), member 1

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_033117.2 RefSeqGene

    Range
    11988..14812
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001104577.2 → NP_001098047.1  solute carrier family 52, riboflavin transporter, member 1 precursor

    See identical proteins and their annotated locations for NP_001098047.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript. Both variants 1 and 2 encode the same protein.
    Source sequence(s)
    AK000922, AY070775, BC092473, BU752646, DA383729
    Consensus CDS
    CCDS11066.1
    UniProtKB/Swiss-Prot
    B5MEV1, B5MEV2, Q6P9E0, Q86UT0, Q9NWF4
    Related
    ENSP00000399979.1, ENST00000424747.1
    Conserved Domains (1) summary
    pfam06237
    Location:280 → 374
    DUF1011; Protein of unknown function (DUF1011)

  2. NM_017986.4 → NP_060456.3  solute carrier family 52, riboflavin transporter, member 1 precursor

    See identical proteins and their annotated locations for NP_060456.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Both variants 1 and 2 encode the same protein.
    Source sequence(s)
    AK000922, AY070775, BC092473, BU752646, DA383729
    Consensus CDS
    CCDS11066.1
    UniProtKB/Swiss-Prot
    B5MEV1, B5MEV2, Q6P9E0, Q86UT0, Q9NWF4
    Related
    ENSP00000254853.5, ENST00000254853.10
    Conserved Domains (1) summary
    pfam06237
    Location:280 → 374
    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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    5032602..5042414 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047436339.1 → XP_047292295.1  solute carrier family 52, riboflavin transporter, member 1 isoform X1

    UniProtKB/Swiss-Prot
    B5MEV1, B5MEV2, Q6P9E0, Q86UT0, Q9NWF4

  2. XM_047436338.1 → XP_047292294.1  solute carrier family 52, riboflavin transporter, member 1 isoform X1

    UniProtKB/Swiss-Prot
    B5MEV1, B5MEV2, Q6P9E0, Q86UT0, Q9NWF4

  3. XM_011523951.3 → XP_011522253.1  solute carrier family 52, riboflavin transporter, member 1 isoform X1

    See identical proteins and their annotated locations for XP_011522253.1

    UniProtKB/Swiss-Prot
    B5MEV1, B5MEV2, Q6P9E0, Q86UT0, Q9NWF4
    Conserved Domains (1) summary
    pfam06237
    Location:280 → 374
    DUF1011; Protein of unknown function (DUF1011)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    4922930..4932848 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054316597.1 → XP_054172572.1  solute carrier family 52, riboflavin transporter, member 1 isoform X1

  2. XM_054316596.1 → XP_054172571.1  solute carrier family 52, riboflavin transporter, member 1 isoform X1

  3. XM_054316595.1 → XP_054172570.1  solute carrier family 52, riboflavin transporter, member 1 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9NWF4.2 GenPept UniProtKB/Swiss-Prot:Q9NWF4

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