Human Gene SLC25A46 (uc003koz.3) Description and Page Index
  Description: Homo sapiens solute carrier family 25, member 46 (SLC25A46), mRNA.
RefSeq Summary (NM_138773): This gene encodes a mitochondrial solute carrier protein family member. It functions in promoting mitochondrial fission, and prevents the formation of hyperfilamentous mitochondria. Mutation of this gene results in neuropathy and optic atrophy. [provided by RefSeq, Aug 2016].
Transcript (Including UTRs)
   Position: hg19 chr5:110,074,754-110,098,484 Size: 23,731 Total Exon Count: 8 Strand: +
Coding Region
   Position: hg19 chr5:110,074,821-110,097,482 Size: 22,662 Coding Exon Count: 8 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesGeneReviewsModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:110,074,754-110,098,484)mRNA (may differ from genome)Protein (418 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedStanford SOURCETreefamUniProtKB

-  Comments and Description Text from UniProtKB
  ID: S2546_HUMAN
DESCRIPTION: RecName: Full=Solute carrier family 25 member 46;
SUBCELLULAR LOCATION: Mitochondrion inner membrane; Multi-pass membrane protein (By similarity).
SIMILARITY: Belongs to the mitochondrial carrier family.
SIMILARITY: Contains 2 Solcar repeats.
SEQUENCE CAUTION: Sequence=AAA03587.1; Type=Erroneous initiation;

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): SLC25A46
CDC HuGE Published Literature: SLC25A46
Positive Disease Associations: Asthma , Cardiac structure and function , Rhinitis, Allergic, Seasonal
Related Studies:
  1. Asthma
    Tomomitsu Hirota et al. Nature genetics 2011, Genome-wide association study identifies three new susceptibility loci for adult asthma in the Japanese population., Nature genetics. [PubMed 21804548]
  2. Asthma
    Dara G Torgerson et al. Nature genetics 2011, Meta-analysis of genome-wide association studies of asthma in ethnically diverse North American populations., Nature genetics. [PubMed 21804549]
  3. Cardiac structure and function
    Vasan ,et al. 2009, Genetic Variants Associated with Cardiac Structure and Function: A Meta-analysis and Replication of Genome-wide Association Data, JAMA 2009 302- 2 : 168-78. [PubMed 19584346]
    We identified 5 genetic loci harboring common variants that were associated with variation in LV diastolic dimensions and aortic root size, but such findings explained a very small proportion of variance.
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: SLC25A46
Diseases sorted by gene-association score: neuropathy, hereditary motor and sensory, type vib* (1300), hereditary motor and sensory neuropathy via* (247), skeletal tuberculosis (16), laryngeal tuberculosis (16), ancylostomiasis (16), neuropathy (11), urogenital tuberculosis (8), laryngeal disease (7), primary bacterial infectious disease (2), leigh syndrome (1), optic atrophy plus syndrome (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 14.73 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 366.39 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -27.9067-0.416 Picture PostScript Text
3' UTR -222.261002-0.222 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR018108 - Mitochondrial_sb/sol_carrier
IPR023395 - Mt_carrier_dom

Pfam Domains:
PF00153 - Mitochondrial carrier protein

SCOP Domains:
103506 - Mitochondrial carrier

ModBase Predicted Comparative 3D Structure on Q96AG3
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserGenome BrowserGenome BrowserGenome BrowserNo ortholog
Gene DetailsGene Details Gene DetailsGene Details 
Gene SorterGene Sorter Gene SorterGene Sorter 
 RGDEnsemblFlyBaseWormBase 
 Protein SequenceProtein SequenceProtein SequenceProtein Sequence 
 AlignmentAlignmentAlignmentAlignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding

Biological Process:
GO:0090149 mitochondrial membrane fission

Cellular Component:
GO:0005739 mitochondrion
GO:0005741 mitochondrial outer membrane
GO:0016020 membrane
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  HQ448268 - Synthetic construct Homo sapiens clone IMAGE:100071670; CCSB000303_01 solute carrier family 25, member 46 (SLC25A46) gene, encodes complete protein.
AK302326 - Homo sapiens cDNA FLJ56268 complete cds.
AK091427 - Homo sapiens cDNA FLJ34108 fis, clone FCBBF3008251, highly similar to Human TB1 gene mRNA.
AK300123 - Homo sapiens cDNA FLJ60882 complete cds.
BC017169 - Homo sapiens solute carrier family 25, member 46, mRNA (cDNA clone MGC:9535 IMAGE:3923005), complete cds.
M74089 - Human TB1 gene mRNA, 3' end.
JD408612 - Sequence 389636 from Patent EP1572962.
JD479027 - Sequence 460051 from Patent EP1572962.
AK290217 - Homo sapiens cDNA FLJ75619 complete cds.
AB529063 - Synthetic construct DNA, clone: pF1KB3906, Homo sapiens SLC25A46 gene for solute carrier family 25, member 46, without stop codon, in Flexi system.
JD021326 - Sequence 2350 from Patent EP1572962.
JD028563 - Sequence 9587 from Patent EP1572962.
AK300116 - Homo sapiens cDNA FLJ58689 complete cds.
JD304341 - Sequence 285365 from Patent EP1572962.
JD344582 - Sequence 325606 from Patent EP1572962.
JD552504 - Sequence 533528 from Patent EP1572962.
JD357084 - Sequence 338108 from Patent EP1572962.
JD376921 - Sequence 357945 from Patent EP1572962.
JD207126 - Sequence 188150 from Patent EP1572962.
JD046552 - Sequence 27576 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: A8K2F2, D3DSZ6, NM_138773, NP_620128, Q04197, Q96AG3, S2546_HUMAN, TB1
UCSC ID: uc003koz.3
RefSeq Accession: NM_138773
Protein: Q96AG3 (aka S2546_HUMAN)
CCDS: CCDS4100.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene SLC25A46:
ataxias (Hereditary Ataxia Overview)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_138773.1
exon count: 8CDS single in 3' UTR: no RNA size: 2358
ORF size: 1257CDS single in intron: no Alignment % ID: 99.96
txCdsPredict score: 2714.00frame shift in genome: no % Coverage: 98.64
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.