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

Summary

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

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_000008.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

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?

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.
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.
Functional Study of the Human Riboflavin Transporter 2 Using Proteoliposomes System.
Title: Functional Study of the Human Riboflavin Transporter 2 Using Proteoliposomes System.
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.
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.
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.
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.
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.
Eight mutations in SLC52a2 were associated with Brown-Vialetto-Van Laere syndrome.
Title: Clinical, pathological and functional characterization of riboflavin-responsive neuropathy.
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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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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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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

NG_032872.2 RefSeqGene

Range

5057..7716

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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)
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)
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)
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)
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)
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)
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
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

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

NC_000008.11 Reference GRCh38.p14 Primary Assembly

Range

144358552..144361272

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

E9PKE4

Related

ENSP00000501554.1, ENST00000674929.1
XM_047422216.1 → XP_047278172.1 solute carrier family 52, riboflavin transporter, member 2 isoform X2

UniProtKB/TrEMBL

E9PKE4
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
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

NW_018654716.1 Reference GRCh38.p14 PATCHES

Range

89155..91875

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

E9PKE4
XM_054332204.1 → XP_054188179.1 solute carrier family 52, riboflavin transporter, member 2 isoform X1

UniProtKB/Swiss-Prot

A8K6B6, D3DWL8, G1UCY1, Q86UT1, Q9HAB3
XM_054332206.1 → XP_054188181.1 solute carrier family 52, riboflavin transporter, member 2 isoform X2

UniProtKB/TrEMBL

E9PKE4
XM_054332208.1 → XP_054188183.1 solute carrier family 52, riboflavin transporter, member 2 isoform X2

UniProtKB/TrEMBL

E9PKE4
XM_054332207.1 → XP_054188182.1 solute carrier family 52, riboflavin transporter, member 2 isoform X2

UniProtKB/TrEMBL

E9PKE4
XM_054332203.1 → XP_054188178.1 solute carrier family 52, riboflavin transporter, member 2 isoform X1

UniProtKB/Swiss-Prot

A8K6B6, D3DWL8, G1UCY1, Q86UT1, Q9HAB3
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

NC_060932.1 Alternate T2T-CHM13v2.0

Range

145527181..145529901

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

E9PKE4
XM_054361197.1 → XP_054217172.1 solute carrier family 52, riboflavin transporter, member 2 isoform X1

UniProtKB/Swiss-Prot

A8K6B6, D3DWL8, G1UCY1, Q86UT1, Q9HAB3
XM_054361199.1 → XP_054217174.1 solute carrier family 52, riboflavin transporter, member 2 isoform X2

UniProtKB/TrEMBL

E9PKE4
XM_054361201.1 → XP_054217176.1 solute carrier family 52, riboflavin transporter, member 2 isoform X2

UniProtKB/TrEMBL

E9PKE4
XM_054361200.1 → XP_054217175.1 solute carrier family 52, riboflavin transporter, member 2 isoform X2

UniProtKB/TrEMBL

E9PKE4
XM_054361196.1 → XP_054217171.1 solute carrier family 52, riboflavin transporter, member 2 isoform X1

UniProtKB/Swiss-Prot

A8K6B6, D3DWL8, G1UCY1, Q86UT1, Q9HAB3
XM_054361198.1 → XP_054217173.1 solute carrier family 52, riboflavin transporter, member 2 isoform X1

UniProtKB/Swiss-Prot

A8K6B6, D3DWL8, G1UCY1, Q86UT1, Q9HAB3