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Q9NQ40 (S52A3_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 108. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (5) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Solute carrier family 52, riboflavin transporter, member 3
Alternative name(s):
Riboflavin transporter 2
Short name=hRFT2
Gene names
Name:SLC52A3
Synonyms:C20orf54, RFT2
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length469 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Riboflavin transporter. Riboflavin transport is Na+-independent but moderately pH-sensitive. Activity is strongly inhibited by riboflavin analogs, such as lumiflavin, flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD), and to a lesser extent by amiloride. Ref.5

Subcellular location

Cell membrane; Multi-pass membrane protein Ref.5.

Tissue specificity

Predominantly expressed in testis. Highly expressed in small intestine and prostate. Ref.5

Involvement in disease

Brown-Vialetto-Van Laere syndrome 1 (BVVLS1) [MIM:211530]: A rare neurologic disorder characterized by sensorineural hearing loss and a variety of cranial nerve palsies, which develop over a relatively short period of time in a previously healthy individual. Sensorineural hearing loss may precede the neurological signs. The course is invariably progressive, but the rate of decline is variable within and between families. With disease evolution, long tract signs, lower motor neuron signs, cerebellar ataxia and lower cranial nerve (III-VI) palsies develop, giving rise to a complex picture resembling amyotrophic lateral sclerosis. Diaphragmatic weakness and respiratory compromise are some of the most distressing features, leading to recurrent chest infections and respiratory failure, which are often the cause of patients' demise.
Note: The disease is caused by mutations affecting the gene represented in this entry. Ref.7

Fazio-Londe disease (FALOND) [MIM:211500]: A rare neurological disease characterized by progressive weakness of the muscles innervated by cranial nerves of the lower brain stem. It may present in childhood with severe neurological deterioration with hypotonia, respiratory insufficiency leading to premature death, or later in life with bulbar weakness which progresses to involve motor neurons throughout the neuroaxis. Clinical manifestations include dysarthria, dysphagia, facial weakness, tongue weakness, and fasciculations of the tongue and facial muscles.
Note: The disease is caused by mutations affecting the gene represented in this entry. Ref.6

Sequence similarities

Belongs to the riboflavin transporter family.

Caution

It is uncertain whether Met-1 or Met-5 is the initiator.

Biophysicochemical properties

Kinetic parameters:

KM=0.98 µM for riboflavin Ref.5

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q9NQ40-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.
Isoform 2 (identifier: Q9NQ40-2)

The sequence of this isoform differs from the canonical sequence as follows:
     401-415: ASWVLFSGCLSYVKV → SIRPVGLLPLRTPHP
     416-469: Missing.
Note: No experimental confirmation available.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 469469Solute carrier family 52, riboflavin transporter, member 3
PRO_0000042636

Regions

Transmembrane3 – 2321Helical; Potential
Transmembrane44 – 6421Helical; Potential
Transmembrane72 – 9221Helical; Potential
Transmembrane98 – 11821Helical; Potential
Transmembrane138 – 15821Helical; Potential
Transmembrane221 – 24121Helical; Potential
Transmembrane293 – 31321Helical; Potential
Transmembrane336 – 35621Helical; Potential
Transmembrane360 – 38021Helical; Potential
Transmembrane382 – 40221Helical; Potential
Transmembrane405 – 42521Helical; Potential
Transmembrane433 – 45321Helical; Potential

Amino acid modifications

Glycosylation941N-linked (GlcNAc...) Potential
Glycosylation1681N-linked (GlcNAc...) Potential

Natural variations

Alternative sequence401 – 41515ASWVL…SYVKV → SIRPVGLLPLRTPHP in isoform 2.
VSP_003814
Alternative sequence416 – 46954Missing in isoform 2.
VSP_003815
Natural variant361E → K in BVVLS1. Ref.7
VAR_063694
Natural variant741I → M.
Corresponds to variant rs35655964 [ dbSNP | Ensembl ].
VAR_053565
Natural variant1321R → W in BVVLS1. Ref.7
VAR_063695
Natural variant1741D → G.
Corresponds to variant rs6054614 [ dbSNP | Ensembl ].
VAR_053566
Natural variant2241F → L in BVVLS1. Ref.7
VAR_063696
Natural variant2671P → L. Ref.3
Corresponds to variant rs3746804 [ dbSNP | Ensembl ].
VAR_053567
Natural variant2781T → M. Ref.3
Corresponds to variant rs3746803 [ dbSNP | Ensembl ].
VAR_053568
Natural variant3031I → V. Ref.3
Corresponds to variant rs3746802 [ dbSNP | Ensembl ].
VAR_053569
Natural variant3501L → M May be a common polymorphism. Ref.7
Corresponds to variant rs76947760 [ dbSNP | Ensembl ].
VAR_063698
Natural variant4111S → R.
Corresponds to variant rs910857 [ dbSNP | Ensembl ].
VAR_063699
Natural variant4131V → A in BVVLS1; may cause a mild form of the disease. Ref.7
VAR_063700
Natural variant4571F → L in BVVLS1. Ref.7
VAR_063701

Experimental info

Sequence conflict111V → D in BAF84395. Ref.1
Sequence conflict1991L → P in BAC11113. Ref.1

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified November 22, 2005. Version 4.
Checksum: 239ED67348C93739

FASTA46950,805
        10         20         30         40         50         60 
MAFLMHLLVC VFGMGSWVTI NGLWVELPLL VMELPEGWYL PSYLTVVIQL ANIGPLLVTL 

        70         80         90        100        110        120 
LHHFRPSCLS EVPIIFTLLG VGTVTCIIFA FLWNMTSWVL DGHHSIAFLV LTFFLALVDC 

       130        140        150        160        170        180 
TSSVTFLPFM SRLPTYYLTT FFVGEGLSGL LPALVALAQG SGLTTCVNVT EISDSVPSPV 

       190        200        210        220        230        240 
PTRETDIAQG VPRALVSALP GMEAPLSHLE SRYLPAHFSP LVFFLLLSIM MACCLVAFFV 

       250        260        270        280        290        300 
LQRQPRCWEA SVEDLLNDQV TLHSIRPREE NDLGPAGTVD SSQGQGYLEE KAAPCCPAHL 

       310        320        330        340        350        360 
AFIYTLVAFV NALTNGMLPS VQTYSCLSYG PVAYHLAATL SIVANPLASL VSMFLPNRSL 

       370        380        390        400        410        420 
LFLGVLSVLG TCFGGYNMAM AVMSPCPLLQ GHWGGEVLIV ASWVLFSGCL SYVKVMLGVV 

       430        440        450        460 
LRDLSRSALL WCGAAVQLGS LLGALLMFPL VNVLRLFSSA DFCNLHCPA 

« Hide

Isoform 2 [UniParc].

Checksum: 8E072208A8998A56
Show »

FASTA41545,043

References

« Hide 'large scale' references
[1]"Complete sequencing and characterization of 21,243 full-length human cDNAs."
Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S. expand/collapse author list , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
Tissue: Mammary gland and Placenta.
[2]"The DNA sequence and comparative analysis of human chromosome 20."
Deloukas P., Matthews L.H., Ashurst J.L., Burton J., Gilbert J.G.R., Jones M., Stavrides G., Almeida J.P., Babbage A.K., Bagguley C.L., Bailey J., Barlow K.F., Bates K.N., Beard L.M., Beare D.M., Beasley O.P., Bird C.P., Blakey S.E. expand/collapse author list , Bridgeman A.M., Brown A.J., Buck D., Burrill W.D., Butler A.P., Carder C., Carter N.P., Chapman J.C., Clamp M., Clark G., Clark L.N., Clark S.Y., Clee C.M., Clegg S., Cobley V.E., Collier R.E., Connor R.E., Corby N.R., Coulson A., Coville G.J., Deadman R., Dhami P.D., Dunn M., Ellington A.G., Frankland J.A., Fraser A., French L., Garner P., Grafham D.V., Griffiths C., Griffiths M.N.D., Gwilliam R., Hall R.E., Hammond S., Harley J.L., Heath P.D., Ho S., Holden J.L., Howden P.J., Huckle E., Hunt A.R., Hunt S.E., Jekosch K., Johnson C.M., Johnson D., Kay M.P., Kimberley A.M., King A., Knights A., Laird G.K., Lawlor S., Lehvaeslaiho M.H., Leversha M.A., Lloyd C., Lloyd D.M., Lovell J.D., Marsh V.L., Martin S.L., McConnachie L.J., McLay K., McMurray A.A., Milne S.A., Mistry D., Moore M.J.F., Mullikin J.C., Nickerson T., Oliver K., Parker A., Patel R., Pearce T.A.V., Peck A.I., Phillimore B.J.C.T., Prathalingam S.R., Plumb R.W., Ramsay H., Rice C.M., Ross M.T., Scott C.E., Sehra H.K., Shownkeen R., Sims S., Skuce C.D., Smith M.L., Soderlund C., Steward C.A., Sulston J.E., Swann R.M., Sycamore N., Taylor R., Tee L., Thomas D.W., Thorpe A., Tracey A., Tromans A.C., Vaudin M., Wall M., Wallis J.M., Whitehead S.L., Whittaker P., Willey D.L., Williams L., Williams S.A., Wilming L., Wray P.W., Hubbard T., Durbin R.M., Bentley D.R., Beck S., Rogers J.
Nature 414:865-871(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[3]"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
The MGC Project Team
Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1), VARIANTS LEU-267; MET-278 AND VAL-303.
Tissue: Pancreas.
[4]"Identification and functional characterization of rat riboflavin transporter 2."
Yamamoto S., Inoue K., Ohta K.Y., Fukatsu R., Maeda J.Y., Yoshida Y., Yuasa H.
J. Biochem. 145:437-443(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION.
[5]"Identification and comparative functional characterization of a new human riboflavin transporter hRFT3 expressed in the brain."
Yao Y., Yonezawa A., Yoshimatsu H., Masuda S., Katsura T., Inui K.
J. Nutr. 140:1220-1226(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, SUBCELLULAR LOCATION, TISSUE SPECIFICITY, BIOPHYSICOCHEMICAL PROPERTIES.
[6]"Brown-Vialetto-Van Laere and Fazio Londe syndrome is associated with a riboflavin transporter defect mimicking mild MADD: a new inborn error of metabolism with potential treatment."
Bosch A.M., Abeling N.G., Ijlst L., Knoester H., van der Pol W.L., Stroomer A.E., Wanders R.J., Visser G., Wijburg F.A., Duran M., Waterham H.R.
J. Inherit. Metab. Dis. 34:159-164(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: INVOLVEMENT IN FALOND.
[7]"Brown-Vialetto-Van Laere syndrome, a ponto-bulbar palsy with deafness, is caused by mutations in c20orf54."
Green P., Wiseman M., Crow Y.J., Houlden H., Riphagen S., Lin J.P., Raymond F.L., Childs A.M., Sheridan E., Edwards S., Josifova D.J.
Am. J. Hum. Genet. 86:485-489(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: VARIANTS BVVLS1 LYS-36; TRP-132; LEU-224; ALA-413 AND LEU-457, VARIANT MET-350.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AK074650 mRNA. Translation: BAC11113.1.
AK291706 mRNA. Translation: BAF84395.1.
AL118502 Genomic DNA. Translation: CAH73077.2.
AL118502 Genomic DNA. Translation: CAH73078.2.
BC009750 mRNA. Translation: AAH09750.2.
RefSeqNP_212134.3. NM_033409.3.
XP_005260712.1. XM_005260655.2.
UniGeneHs.283865.

3D structure databases

ProteinModelPortalQ9NQ40.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING9606.ENSP00000217254.

Protein family/group databases

TCDB9.A.53.1.2. the eukaryotic riboflavin transporter (e-rft) family.

PTM databases

PhosphoSiteQ9NQ40.

Polymorphism databases

DMDM82654931.

Proteomic databases

PRIDEQ9NQ40.

Protocols and materials databases

DNASU113278.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000217254; ENSP00000217254; ENSG00000101276. [Q9NQ40-1]
ENST00000381944; ENSP00000371370; ENSG00000101276. [Q9NQ40-2]
GeneID113278.
KEGGhsa:113278.
UCSCuc002wed.4. human. [Q9NQ40-1]
uc002wee.2. human. [Q9NQ40-2]

Organism-specific databases

CTD113278.
GeneCardsGC20M000741.
H-InvDBHIX0015557.
HGNCHGNC:16187. SLC52A3.
HPAHPA049391.
MIM211500. phenotype.
211530. phenotype.
613350. gene.
neXtProtNX_Q9NQ40.
Orphanet97229. Riboflavin transporter deficiency.
PharmGKBPA25764.
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG326568.
HOGENOMHOG000247012.
HOVERGENHBG051170.
InParanoidQ9NQ40.
KOK14620.
OMAWVLDGHH.
OrthoDBEOG7XDBFX.
PhylomeDBQ9NQ40.
TreeFamTF314820.

Enzyme and pathway databases

ReactomeREACT_111217. Metabolism.
REACT_116125. Disease.

Gene expression databases

ArrayExpressQ9NQ40.
BgeeQ9NQ40.
CleanExHS_C20orf54.
GenevestigatorQ9NQ40.

Family and domain databases

InterProIPR009357. Endogenous_retrovirus_rcpt.
[Graphical view]
PANTHERPTHR12929. PTHR12929. 1 hit.
PfamPF06237. DUF1011. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

GeneWikiC20orf54.
GenomeRNAi113278.
NextBio78824.
PROQ9NQ40.
SOURCESearch...

Entry information

Entry nameS52A3_HUMAN
AccessionPrimary (citable) accession number: Q9NQ40
Secondary accession number(s): A8K6P1 expand/collapse secondary AC list , Q5W1A0, Q5W1A1, Q8NCL7, Q96GD5
Entry history
Integrated into UniProtKB/Swiss-Prot: January 10, 2003
Last sequence update: November 22, 2005
Last modified: April 16, 2014
This is version 108 of the entry and version 4 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Relevant documents

SIMILARITY comments

Index of protein domains and families

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome 20

Human chromosome 20: entries, gene names and cross-references to MIM