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

Gene ID: 79581, updated on 11-Apr-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
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Genomic context

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Location:
8q24.3
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (144358552..144361272)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (145527181..145529901)
105.20220307 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. Impact of natural mutations on the riboflavin transporter 2 and their relevance to human riboflavin transporter deficiency 2. Console L, et al. IUBMB Life, 2022 Jul. PMID 34428344
  2. Functional Study of the Human Riboflavin Transporter 2 Using Proteoliposomes System. Console L, et al. Methods Mol Biol, 2021. PMID 33751428
  3. Mitochondrial and Peroxisomal Alterations Contribute to Energy Dysmetabolism in Riboflavin Transporter Deficiency. Colasuonno F, et al. Oxid Med Cell Longev, 2020. PMID 32855765, Free PMC Article
  4. SLC52A2 mutations cause SCABD2 phenotype: A second report. Babanejad M, et al. Int J Pediatr Otorhinolaryngol, 2018 Jan. PMID 29287867
  5. Riboflavin transporter deficiency mimicking mitochondrial myopathy caused by complex II deficiency. Nimmo GAM, et al. Am J Med Genet A, 2018 Feb. PMID 29193829

See all (38) 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
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Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

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
    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_2023_10

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
    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
    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
    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
    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

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
    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

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

    UniProtKB/TrEMBL
    E9PKE4

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

    UniProtKB/TrEMBL
    E9PKE4

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

    UniProtKB/TrEMBL
    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

  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

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
    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

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

    UniProtKB/TrEMBL
    E9PKE4

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

    UniProtKB/TrEMBL
    E9PKE4

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

    UniProtKB/TrEMBL
    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

  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
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9HAB3.1 GenPept UniProtKB/Swiss-Prot:Q9HAB3

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