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    SLC52A2 solute carrier family 52 member 2 [ Homo sapiens (human) ]

    Gene ID: 79581, updated on 10-Dec-2024

    Summary

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    Official Symbol
    SLC52A2provided by HGNC
    Official Full Name
    solute carrier family 52 member 2provided by HGNC
    Primary source
    HGNC:HGNC:30224
    See related
    Ensembl:ENSG00000185803 MIM:607882; AllianceGenome:HGNC:30224
    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
    PAR1; RFT3; RFVT2; hRFT3; BVVLS2; GPCR41; GPR172A; HuPAR-1; D15Ertd747e
    Summary
    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]
    Expression
    Ubiquitous expression in colon (RPKM 10.9), stomach (RPKM 8.5) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SLC52A2 in Genome Data Viewer
    Location:
    8q24.3
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (144358552..144361272)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (145527181..145529901)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (145582212..145584932)

    Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19675 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:145579988-145580524 Neighboring gene transmembrane protein 249 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19676 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19677 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:145583746-145584281 Neighboring gene F-box and leucine rich repeat protein 6 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:145589246-145589414 Neighboring gene uncharacterized LOC101928902 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr8:145593027-145593528 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:145595436-145595936 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19678 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28096 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19679 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19680 Neighboring gene aarF domain containing kinase 5 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:145613649-145614150 Neighboring gene cleavage and polyadenylation specific factor 1

    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
    • 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. Riboflavin transporter deficiency mimicking mitochondrial myopathy caused by complex II deficiency. Nimmo GAM, et al. Am J Med Genet A, 2018 Feb. PMID 29193829
    2. Mutations in riboflavin transporter present with severe sensory loss and deafness in childhood. Srour M, et al. Muscle Nerve, 2014 Nov. PMID 24616084
    3. Treatable childhood neuronopathy caused by mutations in riboflavin transporter RFVT2. Foley AR, et al. Brain, 2014 Jan. PMID 24253200, Free PMC Article
    4. Auditory neuropathy in Brown-Vialetto-Van Laere syndrome due to riboflavin transporter RFVT2 deficiency. Menezes MP, et al. Dev Med Child Neurol, 2016 Aug. PMID 26918385
    5. Impaired riboflavin transport due to missense mutations in SLC52A2 causes Brown-Vialetto-Van Laere syndrome. Haack TB, et al. J Inherit Metab Dis, 2012 Nov. PMID 22864630, Free PMC Article

    See all (39) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Retrograde response to mitochondrial dysfunctions associated to LOF variations in FLAD1 exon 2: unraveling the importance of RFVT2.
      Title: Retrograde response to mitochondrial dysfunctions associated to LOF variations in FLAD1 exon 2: unraveling the importance of RFVT2.
    2. Impact of natural mutations on the riboflavin transporter 2 and their relevance to human riboflavin transporter deficiency 2.
      Title: Impact of natural mutations on the riboflavin transporter 2 and their relevance to human riboflavin transporter deficiency 2.
    3. Functional Study of the Human Riboflavin Transporter 2 Using Proteoliposomes System.
      Title: Functional Study of the Human Riboflavin Transporter 2 Using Proteoliposomes System.
    4. Mitochondrial and Peroxisomal Alterations Contribute to Energy Dysmetabolism in Riboflavin Transporter Deficiency.
      Title: Mitochondrial and Peroxisomal Alterations Contribute to Energy Dysmetabolism in Riboflavin Transporter Deficiency.
    5. 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.
    6. Whole exome sequencing identified a homozygous likely pathogenic variant in SCL52A3 (c.1223G>A; p.Gly408Asp). We report two new patients with riboflavin transporter deficiency, caused by mutations in two different riboflavin transporter genes.
      Title: Riboflavin transporter deficiency mimicking mitochondrial myopathy caused by complex II deficiency.
    7. RFVT2 gene and protein expression levels were higher in DLD-1 and HT-29 compared to Caco2 cells. In tumor tissues of patients with CRC, RFVT2 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.
    8. This is the second report of the genotype-phenotype correlation between this syndrome named spinocerebellar ataxia with blindness and deafness type 2 (SCABD2) and SLC52A2 gene.
      Title: SLC52A2 mutations cause SCABD2 phenotype: A second report.
    9. Eight mutations in SLC52a2 were associated with Brown-Vialetto-Van Laere syndrome.
      Title: Clinical, pathological and functional characterization of riboflavin-responsive neuropathy.
    10. A novel SLC52A2 mutation identified in a family with spinocerebellar ataxia with blindness and deafness.
      Title: Genes for spinocerebellar ataxia with blindness and deafness (SCABD/SCAR3, MIM# 271250 and SCABD2).
    Submit: New GeneRIF Correction See all GeneRIFs (16)

    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

    Associated conditions

    Description Tests
    Brown-Vialetto-van Laere syndrome 2
    MedGen: C3553538 OMIM: 614707 GeneReviews: Riboflavin Transporter Deficiency
    		Compare labs

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables 4-hydroxybutyrate receptor activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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 2
    Names
    G protein-coupled receptor 172A
    G-protein coupled receptor 41
    PERV-A receptor 1
    human porcine endogenous retrovirus subgroup A receptor 1
    porcine endogenous retrovirus A receptor 1
    putative G-protein coupled receptor GPCR41
    riboflavin transporter 3
    solute carrier family 52 (riboflavin transporter), member 2

    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_032872.2 RefSeqGene

      Range
      5057..7716
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001253815.2 → NP_001240744.1  solute carrier family 52, riboflavin transporter, member 2 isoform 1

      See identical proteins and their annotated locations for NP_001240744.1

      Status: REVIEWED

      Source sequence(s)
      AC233992, AK291581, BQ772207
      Consensus CDS
      CCDS6423.1
      UniProtKB/Swiss-Prot
      A8K6B6, D3DWL8, G1UCY1, Q86UT1, Q9HAB3
      UniProtKB/TrEMBL
      B4E1F8
      Related
      ENSP00000385961.1, ENST00000402965.5
      Conserved Domains (1) summary
      pfam06237
      Location:273 → 371
      DUF1011; Protein of unknown function (DUF1011)

    2. NM_001253816.2 → NP_001240745.1  solute carrier family 52, riboflavin transporter, member 2 isoform 1

      See identical proteins and their annotated locations for NP_001240745.1

      Status: REVIEWED

      Source sequence(s)
      AC233992
      Consensus CDS
      CCDS6423.1
      UniProtKB/Swiss-Prot
      A8K6B6, D3DWL8, G1UCY1, Q86UT1, Q9HAB3
      UniProtKB/TrEMBL
      B4E1F8
      Related
      ENSP00000435820.1, ENST00000530047.5
      Conserved Domains (1) summary
      pfam06237
      Location:273 → 371
      DUF1011; Protein of unknown function (DUF1011)

    3. NM_001363118.2 → NP_001350047.1  solute carrier family 52, riboflavin transporter, member 2 isoform 1

      Status: REVIEWED

      Source sequence(s)
      BC002917, BF984649
      Consensus CDS
      CCDS6423.1
      UniProtKB/Swiss-Prot
      A8K6B6, D3DWL8, G1UCY1, Q86UT1, Q9HAB3
      UniProtKB/TrEMBL
      B4E1F8
      Related
      ENSP00000496184.2, ENST00000643944.2
      Conserved Domains (1) summary
      pfam06237
      Location:273 → 371
      DUF1011; Protein of unknown function (DUF1011)

    4. NM_001363120.2 → NP_001350049.1  solute carrier family 52, riboflavin transporter, member 2 isoform 1

      Status: REVIEWED

      Source sequence(s)
      AU119853, BC002917
      Consensus CDS
      CCDS6423.1
      UniProtKB/Swiss-Prot
      A8K6B6, D3DWL8, G1UCY1, Q86UT1, Q9HAB3
      UniProtKB/TrEMBL
      B4E1F8
      Related
      ENSP00000434728.1, ENST00000527078.6
      Conserved Domains (1) summary
      pfam06237
      Location:273 → 371
      DUF1011; Protein of unknown function (DUF1011)

    5. NM_001363121.2 → NP_001350050.1  solute carrier family 52, riboflavin transporter, member 2 isoform 1

      Status: REVIEWED

      Source sequence(s)
      BC002917, BX462918
      Consensus CDS
      CCDS6423.1
      UniProtKB/Swiss-Prot
      A8K6B6, D3DWL8, G1UCY1, Q86UT1, Q9HAB3
      UniProtKB/TrEMBL
      B4E1F8
      Related
      ENSP00000431965.2, ENST00000534725.6
      Conserved Domains (1) summary
      pfam06237
      Location:273 → 371
      DUF1011; Protein of unknown function (DUF1011)

    6. NM_001363122.2 → NP_001350051.1  solute carrier family 52, riboflavin transporter, member 2 isoform 2

      Status: REVIEWED

      Source sequence(s)
      AC233992, AL560856, BC002917
      Consensus CDS
      CCDS94364.1
      UniProtKB/TrEMBL
      A0A6Q8PG35, E9PKE4
      Conserved Domains (1) summary
      pfam06237
      Location:109 → 207
      DUF1011; Protein of unknown function (DUF1011)

    7. NM_001410949.1 → NP_001397878.1  solute carrier family 52, riboflavin transporter, member 2 isoform 3

      Status: REVIEWED

      Source sequence(s)
      AC233992
      Consensus CDS
      CCDS94365.1
      UniProtKB/TrEMBL
      A0A6Q8PHF8, B4E1F8
      Related
      ENSP00000502670.1, ENST00000526891.2

    8. NM_024531.5 → NP_078807.1  solute carrier family 52, riboflavin transporter, member 2 isoform 1

      See identical proteins and their annotated locations for NP_078807.1

      Status: REVIEWED

      Source sequence(s)
      AC233992, AL560856, BC002917
      Consensus CDS
      CCDS6423.1
      UniProtKB/Swiss-Prot
      A8K6B6, D3DWL8, G1UCY1, Q86UT1, Q9HAB3
      UniProtKB/TrEMBL
      B4E1F8
      Related
      ENSP00000333638.2, ENST00000329994.7
      Conserved Domains (1) summary
      pfam06237
      Location:273 → 371
      DUF1011; Protein of unknown function (DUF1011)

    RNA

    1. NR_045600.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AK303822, CA306391, CN260061, DA289629

    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_000008.11 Reference GRCh38.p14 Primary Assembly

      Range
      144358552..144361272
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017013822.2 → XP_016869311.1  solute carrier family 52, riboflavin transporter, member 2 isoform X2

      UniProtKB/TrEMBL
      A0A6Q8PG35, E9PKE4
      Related
      ENSP00000433583.3, ENST00000526338.7
      Conserved Domains (1) summary
      pfam06237
      Location:109 → 207
      DUF1011; Protein of unknown function (DUF1011)

    2. XM_047422214.1 → XP_047278170.1  solute carrier family 52, riboflavin transporter, member 2 isoform X1

      UniProtKB/Swiss-Prot
      A8K6B6, D3DWL8, G1UCY1, Q86UT1, Q9HAB3
      UniProtKB/TrEMBL
      B4E1F8
      Related
      ENSP00000502406.1, ENST00000674870.1

    3. XM_017013821.2 → XP_016869310.1  solute carrier family 52, riboflavin transporter, member 2 isoform X2

      UniProtKB/TrEMBL
      A0A6Q8PG35, E9PKE4
      Related
      ENSP00000501973.1, ENST00000675597.1
      Conserved Domains (1) summary
      pfam06237
      Location:109 → 207
      DUF1011; Protein of unknown function (DUF1011)

    4. XM_047422217.1 → XP_047278173.1  solute carrier family 52, riboflavin transporter, member 2 isoform X2

      UniProtKB/TrEMBL
      A0A6Q8PG35, E9PKE4
      Related
      ENSP00000501554.1, ENST00000674929.1

    5. XM_047422216.1 → XP_047278172.1  solute carrier family 52, riboflavin transporter, member 2 isoform X2

      UniProtKB/TrEMBL
      A0A6Q8PG35, E9PKE4

    6. XM_047422213.1 → XP_047278169.1  solute carrier family 52, riboflavin transporter, member 2 isoform X1

      UniProtKB/Swiss-Prot
      A8K6B6, D3DWL8, G1UCY1, Q86UT1, Q9HAB3
      UniProtKB/TrEMBL
      B4E1F8
      Related
      ENSP00000502796.1, ENST00000675280.1

    7. XM_047422215.1 → XP_047278171.1  solute carrier family 52, riboflavin transporter, member 2 isoform X1

      UniProtKB/Swiss-Prot
      A8K6B6, D3DWL8, G1UCY1, Q86UT1, Q9HAB3
      UniProtKB/TrEMBL
      B4E1F8

    Reference GRCh38.p14 PATCHES

    Genomic

    1. NW_018654716.1 Reference GRCh38.p14 PATCHES

      Range
      89155..91875
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054332209.1 → XP_054188184.1  solute carrier family 52, riboflavin transporter, member 2 isoform X2

      UniProtKB/TrEMBL
      A0A6Q8PG35, E9PKE4

    2. XM_054332204.1 → XP_054188179.1  solute carrier family 52, riboflavin transporter, member 2 isoform X1

      UniProtKB/Swiss-Prot
      A8K6B6, D3DWL8, G1UCY1, Q86UT1, Q9HAB3
      UniProtKB/TrEMBL
      B4E1F8

    3. XM_054332206.1 → XP_054188181.1  solute carrier family 52, riboflavin transporter, member 2 isoform X2

      UniProtKB/TrEMBL
      A0A6Q8PG35, E9PKE4

    4. XM_054332208.1 → XP_054188183.1  solute carrier family 52, riboflavin transporter, member 2 isoform X2

      UniProtKB/TrEMBL
      A0A6Q8PG35, E9PKE4

    5. XM_054332207.1 → XP_054188182.1  solute carrier family 52, riboflavin transporter, member 2 isoform X2

      UniProtKB/TrEMBL
      A0A6Q8PG35, E9PKE4

    6. XM_054332203.1 → XP_054188178.1  solute carrier family 52, riboflavin transporter, member 2 isoform X1

      UniProtKB/Swiss-Prot
      A8K6B6, D3DWL8, G1UCY1, Q86UT1, Q9HAB3
      UniProtKB/TrEMBL
      B4E1F8

    7. XM_054332205.1 → XP_054188180.1  solute carrier family 52, riboflavin transporter, member 2 isoform X1

      UniProtKB/Swiss-Prot
      A8K6B6, D3DWL8, G1UCY1, Q86UT1, Q9HAB3
      UniProtKB/TrEMBL
      B4E1F8

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060932.1 Alternate T2T-CHM13v2.0

      Range
      145527181..145529901
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054361202.1 → XP_054217177.1  solute carrier family 52, riboflavin transporter, member 2 isoform X2

      UniProtKB/TrEMBL
      A0A6Q8PG35, E9PKE4

    2. XM_054361197.1 → XP_054217172.1  solute carrier family 52, riboflavin transporter, member 2 isoform X1

      UniProtKB/Swiss-Prot
      A8K6B6, D3DWL8, G1UCY1, Q86UT1, Q9HAB3
      UniProtKB/TrEMBL
      B4E1F8

    3. XM_054361199.1 → XP_054217174.1  solute carrier family 52, riboflavin transporter, member 2 isoform X2

      UniProtKB/TrEMBL
      A0A6Q8PG35, E9PKE4

    4. XM_054361201.1 → XP_054217176.1  solute carrier family 52, riboflavin transporter, member 2 isoform X2

      UniProtKB/TrEMBL
      A0A6Q8PG35, E9PKE4

    5. XM_054361200.1 → XP_054217175.1  solute carrier family 52, riboflavin transporter, member 2 isoform X2

      UniProtKB/TrEMBL
      A0A6Q8PG35, E9PKE4

    6. XM_054361196.1 → XP_054217171.1  solute carrier family 52, riboflavin transporter, member 2 isoform X1

      UniProtKB/Swiss-Prot
      A8K6B6, D3DWL8, G1UCY1, Q86UT1, Q9HAB3
      UniProtKB/TrEMBL
      B4E1F8

    7. XM_054361198.1 → XP_054217173.1  solute carrier family 52, riboflavin transporter, member 2 isoform X1

      UniProtKB/Swiss-Prot
      A8K6B6, D3DWL8, G1UCY1, Q86UT1, Q9HAB3
      UniProtKB/TrEMBL
      B4E1F8
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9HAB3.1 GenPept UniProtKB/Swiss-Prot:Q9HAB3

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