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

Summary

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

Location:: 17p13.2

Exon count:: 6

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	17	NC_000017.11 (5032602..5042414, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	17	NC_060941.1 (4922930..4932848, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	17	NC_000017.10 (4935897..4938721, complement)

Chromosome 17 - NC_000017.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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).
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.
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.
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).
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.
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.
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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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
Ariboflavinosis MedGen: C0035528 OMIM: 615026 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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

GDB:434012 (e-PCR)
- UniSTS:157204

D10S16 (e-PCR)
- UniSTS:155756

PMC164520P2 (e-PCR)
- UniSTS:271493

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

NG_033117.2 RefSeqGene

Range

11988..14812

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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)
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_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000017.11 Reference GRCh38.p14 Primary Assembly

Range

5032602..5042414 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/Swiss-Prot

B5MEV1, B5MEV2, Q6P9E0, Q86UT0, Q9NWF4
XM_047436338.1 → XP_047292294.1 solute carrier family 52, riboflavin transporter, member 1 isoform X1

UniProtKB/Swiss-Prot

B5MEV1, B5MEV2, Q6P9E0, Q86UT0, Q9NWF4
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

NC_060941.1 Alternate T2T-CHM13v2.0

Range

4922930..4932848 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054316597.1 → XP_054172572.1 solute carrier family 52, riboflavin transporter, member 1 isoform X1
XM_054316596.1 → XP_054172571.1 solute carrier family 52, riboflavin transporter, member 1 isoform X1
XM_054316595.1 → XP_054172570.1 solute carrier family 52, riboflavin transporter, member 1 isoform X1