SLC52A3 solute carrier family 52 member 3 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SLC52A3provided by HGNC
Official Full Name: solute carrier family 52 member 3provided by HGNC
Primary source: HGNC:HGNC:16187
See related: Ensembl:ENSG00000101276 MIM:613350; AllianceGenome:HGNC:16187
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: RFT2; BVVLS; RFVT3; hRFT2; BVVLS1; C20orf54; bA371L19.1
Summary: This gene encodes a riboflavin transporter protein that is strongly expressed in the intestine and likely plays a role in intestinal absorption of riboflavin. The protein is predicted to have eleven transmembrane domains and a cell surface localization signal in the C-terminus. Mutations at this locus have been associated with Brown-Vialetto-Van Laere syndrome and Fazio-Londe disease. [provided by RefSeq, Mar 2012]
Expression: Biased expression in testis (RPKM 24.2), small intestine (RPKM 7.2) and 7 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 20p13

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	20	NC_000020.11 (760080..780033, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	20	NC_060944.1 (804408..824432, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	20	NC_000020.10 (740724..756628, complement)

Chromosome 20 - NC_000020.11 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?

Three cases of adult-onset Brown-Vialetto-Van Laere syndrome: Novel variants in SLC52A3 gene and MRI abnormalities.
Title: Three cases of adult-onset Brown-Vialetto-Van Laere syndrome: Novel variants in SLC52A3 gene and MRI abnormalities.
Promotion of rs3746804 (p. L267P) polymorphism to intracellular SLC52A3a trafficking and riboflavin transportation in esophageal cancer cells.
Title: Promotion of rs3746804 (p. L267P) polymorphism to intracellular SLC52A3a trafficking and riboflavin transportation in esophageal cancer cells.
BVVL/ FL: features caused by SLC52A3 mutations; WDFY4 and TNFSF13B may be novel causative genes.
Title: BVVL/ FL: features caused by SLC52A3 mutations; WDFY4 and TNFSF13B may be novel causative genes.
Functional variation of SLC52A3 rs13042395 predicts survival of Chinese gastric cancer patients.
Title: Functional variation of SLC52A3 rs13042395 predicts survival of Chinese gastric cancer patients.
An Association and Meta-Analysis of Esophageal Squamous Cell Carcinoma Risk Associated with PLCE1 rs2274223, C20orf54 rs13042395 and RUNX1 rs2014300 Polymorphisms.
Title: An Association and Meta-Analysis of Esophageal Squamous Cell Carcinoma Risk Associated with PLCE1 rs2274223, C20orf54 rs13042395 and RUNX1 rs2014300 Polymorphisms.
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.
Justification for screening SLC52A3 included notable clinical similarities between Brown-Vialetto-Van Laere syndrome
Title: Mutation screening of SLC52A3, C19orf12, and TARDBP in Iranian ALS patients.
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).
The riboflavin transporter-3 (SLC52A3) 5'-flanking regions contain NF-kappaB p65/Rel-B-binding sites, which are crucial for mediating SLC52A3 transcriptional activity in esophageal squamous cell carcinoma (ESCC) cells.
Title: SLC52A3 expression is activated by NF-κB p65/Rel-B and serves as a prognostic biomarker in esophageal cancer.
RFVT3 gene and protein expression levels were higher in DLD-1 and HT-29 compared to Caco2 cells. In tumor tissues of patients with CRC, RFVT3 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.

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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 1 MedGen: C0796274 OMIM: 211530 GeneReviews: Riboflavin Transporter Deficiency	Compare labs
Progressive bulbar palsy of childhood MedGen: C0015708 OMIM: 211500 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

RH80917 (e-PCR)
- UniSTS:83736

RH102145 (e-PCR)
- UniSTS:96479

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

Process	Evidence Code	Pubs
involved_in cellular response to heat	IEA Inferred from Electronic Annotation more info
involved_in flavin adenine dinucleotide biosynthetic process	IEA Inferred from Electronic Annotation more info
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 sensory perception of sound	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in apical plasma membrane	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in nuclear membrane	IEA Inferred from Electronic Annotation more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
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 3

Names: SLC52A3a; SLC52A3b; riboflavin transporter 2; solute carrier family 52 (riboflavin transporter), member 3

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_027687.2 RefSeqGene

Range

12486..20906

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_1394

mRNA and Protein(s)

NM_001370085.1 → NP_001357014.1 solute carrier family 52, riboflavin transporter, member 3

Status: REVIEWED

Source sequence(s)

AL118502

Consensus CDS

CCDS13007.1

UniProtKB/Swiss-Prot

A0A2I6BQ49, A8K6P1, K0A6P4, Q5W1A0, Q5W1A1, Q8NCL7, Q96GD5, Q9NQ40

Related

ENSP00000217254.7, ENST00000217254.11

Conserved Domains (1) summary

pfam06237
Location:298 → 395

DUF1011; Protein of unknown function (DUF1011)
NM_001370086.1 → NP_001357015.1 solute carrier family 52, riboflavin transporter, member 3

Status: REVIEWED

Source sequence(s)

AL118502

Consensus CDS

CCDS13007.1

UniProtKB/Swiss-Prot

A0A2I6BQ49, A8K6P1, K0A6P4, Q5W1A0, Q5W1A1, Q8NCL7, Q96GD5, Q9NQ40

Related

ENSP00000494009.1, ENST00000488495.3

Conserved Domains (1) summary

pfam06237
Location:298 → 395

DUF1011; Protein of unknown function (DUF1011)
NM_033409.4 → NP_212134.3 solute carrier family 52, riboflavin transporter, member 3

See identical proteins and their annotated locations for NP_212134.3

Status: REVIEWED

Source sequence(s)

AI244952, AK074650, BC009750, DA302552, DA358731

Consensus CDS

CCDS13007.1

UniProtKB/Swiss-Prot

A0A2I6BQ49, A8K6P1, K0A6P4, Q5W1A0, Q5W1A1, Q8NCL7, Q96GD5, Q9NQ40

Related

ENSP00000494193.1, ENST00000645534.1

Conserved Domains (1) summary

pfam06237
Location:298 → 395

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

NC_000020.11 Reference GRCh38.p14 Primary Assembly

Range

760080..780033 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047439868.1 → XP_047295824.1 solute carrier family 52, riboflavin transporter, member 3 isoform X1

UniProtKB/Swiss-Prot

A0A2I6BQ49, A8K6P1, K0A6P4, Q5W1A0, Q5W1A1, Q8NCL7, Q96GD5, Q9NQ40
XM_024451821.1 → XP_024307589.1 solute carrier family 52, riboflavin transporter, member 3 isoform X1

UniProtKB/Swiss-Prot

A0A2I6BQ49, A8K6P1, K0A6P4, Q5W1A0, Q5W1A1, Q8NCL7, Q96GD5, Q9NQ40

Conserved Domains (1) summary

pfam06237
Location:298 → 395

DUF1011; Protein of unknown function (DUF1011)
XM_047439867.1 → XP_047295823.1 solute carrier family 52, riboflavin transporter, member 3 isoform X1

UniProtKB/Swiss-Prot

A0A2I6BQ49, A8K6P1, K0A6P4, Q5W1A0, Q5W1A1, Q8NCL7, Q96GD5, Q9NQ40