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

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	113278
Gene name	Solute carrier family 52 member 3
Gene symbol	SLC52A3
Synonyms (NCBI Gene)	BVVLSBVVLS1C20orf54RFT2RFVT3bA371L19.1hRFT2
Chromosome	20
Chromosome location	20p13
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 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

Show/Hide all (1)

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

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

447

Show/Hide Causal Diseases (3)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Auditory neuropathy	Likely pathogenic	rs2514849190	RCV003484505
Brown-Vialetto-van Laere syndrome 1	Pathogenic; Likely pathogenic	rs890871342, rs1986662202, rs1383679424, rs794728004, rs267606683, rs267606685, rs267606688, rs2514849071, rs761042586, rs769740240, rs754753126, rs778363575, rs797045190, rs767263985, rs1486271481 View all (5 more)	RCV001383229 RCV001387225 RCV001957312 RCV000000162 RCV000000163 RCV000000165 RCV000000168 RCV002289053 RCV003598113 RCV003069121 RCV000191970 RCV000191963 RCV000191956 RCV003334445 RCV003598301 RCV003599066 RCV003599067 RCV003598857 RCV000578156 RCV000761355
Progressive bulbar palsy of childhood	Pathogenic	rs754753126, rs778363575, rs1599959574	RCV000024020 RCV002247619 RCV000985191

Show/Hide Unknown Diseases (8)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Cervical cancer	Benign	rs34376836	RCV005894272
Cholangiocarcinoma	Benign	rs8122333	RCV005923286
Madras motor neuron disease	Conflicting classifications of pathogenicity	rs145498634	RCV001095540
Monogenic hearing loss	Conflicting classifications of pathogenicity	rs767263985	RCV005865102
Nonpapillary renal cell carcinoma	Uncertain significance	rs910857	RCV005925381
SLC52A3-related disorder	Likely benign; Conflicting classifications of pathogenicity; Uncertain significance; Benign	rs149534355, rs773916730, rs749668781, rs758570021, rs199588390, rs780735213, rs139486822, rs764568577, rs1986667328, rs139965967, rs147369439, rs62641669, rs6054602, rs151229044, rs546240059, rs199861879, rs145498634, rs774461829 View all (3 more)	RCV003908708 RCV005868343 RCV003395431 RCV005868065 RCV003417696 RCV003926613 RCV003891975 RCV003916828 RCV003936898 RCV003945331 RCV004752948 RCV003952890 RCV003952889 RCV003945681 RCV003918089 RCV003975337 RCV003955741 RCV003405454
Thymoma	Benign	rs8122333	RCV005923285
Uterine corpus endometrial carcinoma	Benign	rs34376836	RCV005894273

Show/Hide Text Mining Associations (34)

Disease Name	Relationship Type	References
Associations from Text MiningDisease 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)