Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	113278
Gene name Gene Name - the full gene name approved by the HGNC.	Solute carrier family 52 member 3
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	SLC52A3
Synonyms (NCBI Gene) Gene synonyms aliases	BVVLS, BVVLS1, C20orf54, RFT2, RFVT3, bA371L19.1, hRFT2
Chromosome Chromosome number	20
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	20p13
Summary Summary of gene provided in NCBI Entrez Gene.	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 si

Show/Hide all(27)

SNP ID	Visualize variation	Clinical significance	Consequence
rs3833341	->GTCAATCAG,GTCAG	Pathogenic, benign	Intron variant
rs267606683	C>A,T	Pathogenic	Coding sequence variant, missense variant, stop gained
rs267606685	A>G	Pathogenic	Coding sequence variant, missense variant
rs267606688	G>A,T	Pathogenic	Coding sequence variant, missense variant
rs754753126	T>C,G	Pathogenic	Splice acceptor variant
rs758570021	G>A,T	Pathogenic	Coding sequence variant, stop gained, synonymous variant
rs761224042	A>C,G	Uncertain-significance, likely-pathogenic	Coding sequence variant, missense variant
rs767263985	G>T	Pathogenic	Missense variant, coding sequence variant
rs778363575	G>A,C	Pathogenic	Coding sequence variant, synonymous variant, stop gained
rs778479139	G>A	Pathogenic	Missense variant, coding sequence variant
rs794728004	AG>-	Likely-pathogenic, pathogenic	Coding sequence variant, frameshift variant
rs797045190	A>G	Pathogenic	Missense variant, coding sequence variant
rs797045191	C>T	Pathogenic	Missense variant, coding sequence variant
rs797045192	A>T	Pathogenic	Missense variant, coding sequence variant
rs797045193	A>G	Pathogenic	Missense variant, coding sequence variant
rs797045194	G>T	Pathogenic	Missense variant, coding sequence variant
rs797045195	G>A	Pathogenic	Missense variant, coding sequence variant
rs797045196	C>A	Pathogenic	Missense variant, coding sequence variant
rs797045197	A>C	Pathogenic	Missense variant, coding sequence variant
rs797045198	C>T	Pathogenic	Missense variant, coding sequence variant
rs1057524605	C>T	Likely-pathogenic	Coding sequence variant, missense variant
rs1060499531	C>G,T	Pathogenic	Stop gained, coding sequence variant, missense variant
rs1167512470	A>G	Likely-pathogenic	Coding sequence variant, missense variant
rs1555783467	C>T	Likely-pathogenic	Coding sequence variant, missense variant
rs1555783543	A>G	Likely-pathogenic	Coding sequence variant, missense variant
rs1568721373	G>-	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1599959574	C>T	Likely-pathogenic	Stop gained, coding sequence variant

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miRTarBase ID	miRNA	Experiments	Reference
MIRT044271	hsa-miR-106b-5p	CLASH	23622248

Show/Hide all(25)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005515	Function	Protein binding	IPI	32814053
GO:0005634	Component	Nucleus	IDA	29428966
GO:0005634	Component	Nucleus	IEA
GO:0005737	Component	Cytoplasm	IDA	29428966
GO:0005737	Component	Cytoplasm	IEA
GO:0005886	Component	Plasma membrane	IBA
GO:0005886	Component	Plasma membrane	IDA	20463145, 22273710, 29428966
GO:0005886	Component	Plasma membrane	IEA
GO:0005886	Component	Plasma membrane	IEA
GO:0005886	Component	Plasma membrane	TAS
GO:0006771	Process	Riboflavin metabolic process	IEA
GO:0006771	Process	Riboflavin metabolic process	TAS
GO:0007605	Process	Sensory perception of sound	IMP	20206331
GO:0016020	Component	Membrane	IEA
GO:0016324	Component	Apical plasma membrane	IEA
GO:0031965	Component	Nuclear membrane	IEA
GO:0032217	Function	Riboflavin transmembrane transporter activity	IBA
GO:0032217	Function	Riboflavin transmembrane transporter activity	IDA	20463145
GO:0032217	Function	Riboflavin transmembrane transporter activity	IEA
GO:0032217	Function	Riboflavin transmembrane transporter activity	TAS
GO:0032218	Process	Riboflavin transport	IBA
GO:0032218	Process	Riboflavin transport	IDA	20463145, 22273710
GO:0032218	Process	Riboflavin transport	IEA
GO:0034605	Process	Cellular response to heat	IEA
GO:0072388	Process	Flavin adenine dinucleotide biosynthetic process	IEA

MIM	HGNC	e!Ensembl
613350	16187	ENSG00000101276

Protein

UniProt ID

Q9NQ40

Protein name

Solute carrier family 52, riboflavin transporter, member 3 (Riboflavin transporter 2) (hRFT2)

Protein function

Plasma membrane transporter mediating the uptake by cells of the water soluble vitamin B2/riboflavin that plays a key role in biochemical oxidation-reduction reactions of the carbohydrate, lipid, and amino acid metabolism (PubMed:20463145, PubMe

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF06237	DUF1011	297 → 395	Protein of unknown function (DUF1011)	Family

Tissue specificity

TISSUE SPECIFICITY: Predominantly expressed in testis. Highly expressed in small intestine and prostate. {ECO:0000269|PubMed:20463145}.

Sequence

MAFLMHLLVCVFGMGSWVTINGLWVELPLLVMELPEGWYLPSYLTVVIQLANIGPLLVTL
LHHFRPSCLSEVPIIFTLLGVGTVTCIIFAFLWNMTSWVLDGHHSIAFLVLTFFLALVDC
TSSVTFLPFMSRLPTYYLTTFFVGEGLSGLLPALVALAQGSGLTTCVNVTEISDSVPSPV
PTRETDIAQGVPRALVSALPGMEAPLSHLESRYLPAHFSPLVFFLLLSIMMACCLVAFFV
LQRQPRCWEASVEDLLNDQVTLHSIRPREENDLGPAGTVDSSQGQGYLEEKAAPCCPAHL
AFIYTLVAFVNALTNGMLPSVQTYSCLSYGPVAYHLAATLSIVANPLASLVSMFLPNRSL
LFLGVLSVLGTCFGGYNMAMAVMSPCPLLQGHWGGEVLIVASWVLFSGCLSYVKVMLGVV
LRDLSRSALLWCGAAVQLGSLLGALLMFPLVNVLRLFSSADFCNLHCPA

Sequence length

469

Interactions

View interactions

	KEGG		Reactome
	Vitamin digestion and absorption		Vitamin B2 (riboflavin) metabolism

Show/Hide Causal Diseases (1)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Brown-Vialetto-Van Laere Syndrome	brown-vialetto-van laere syndrome 1	rs754753126, rs778363575, rs797045190, rs1555783467, rs1568721373, rs794728004, rs267606683, rs267606685, rs267606688	N/A

Show/Hide Unknown Diseases (4)

Disease merge term	Disease name	Evidence	References	Source
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Auditory Neuropathy	auditory neuropathy	N/A	N/A	ClinVar
Bulbar palsy	progressive bulbar palsy	N/A	N/A	GenCC
Oligodendroglioma	Oligodendroglioma	N/A	N/A	GWAS
Prostate cancer	Prostate cancer	N/A	N/A	GWAS

Show/Hide Text Mining Associations (34)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Auditory neuropathy	Associate	32022482
Brown Vialetto Van Laere syndrome	Associate	20206331, 21110228, 22273710, 22740598, 24139842, 26918385, 27702554, 27777325, 28382968, 29950502, 31500345, 33109881, 35418370
Brown Vialetto Van Laere syndrome	Stimulate	22098162
Bulbar Palsy Progressive	Associate	20206331
Carcinogenesis	Associate	22471455, 24761851, 26722538
Carcinogenesis	Inhibit	24260322
Carcinoma Squamous Cell	Stimulate	24260322
Carcinoma Squamous Cell	Associate	24761851
Cardiovascular Diseases	Associate	31500345
Cerebellar Ataxia	Associate	35418370
Deafness	Associate	20206331
Esophageal Neoplasms	Associate	29428966, 35549728
Esophageal Squamous Cell Carcinoma	Associate	22471455, 22865593, 27472962, 29428966, 35549728
Esophagitis	Associate	35549728
Gastrointestinal Neoplasms	Associate	22805490
Hearing Loss	Associate	33109881, 35418370
Hearing Loss Sensorineural	Associate	35418370
Lung Neoplasms	Associate	26176862
Lymphatic Metastasis	Associate	27472962, 35549728
Motor Neuron Disease	Associate	24139842
Multiple Acyl Coenzyme A Dehydrogenase Deficiency	Associate	21110228
Neoplasm Metastasis	Associate	35549728
Neoplasms	Inhibit	22791947
Neoplasms	Associate	24260322, 26176862, 27472962, 29428966, 31500345, 35549728
Nerve Degeneration	Associate	28382968
Neurodegenerative Diseases	Associate	26918385, 31500345
Optic Atrophy	Associate	33109881
Precancerous Conditions	Associate	35549728
Precursor T Cell Lymphoblastic Leukemia Lymphoma	Associate	3535926
Respiratory Insufficiency	Associate	21110228
Riboflavin Deficiency	Associate	32022482, 34428344
Stomach Neoplasms	Associate	21427165, 22791947, 26176862, 26722538, 28220687, 32685482, 32888389
Uterine Cervical Neoplasms	Associate	24761851
Uterine Cervicitis	Associate	24260322

SLC52A3 (solute carrier family 52 member 3)