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SPTLC3 Gene

protein-coding   GIFtS: 53
GCID: GC20P012938

Serine Palmitoyltransferase, Long Chain Base Subunit 3

(Previous names: chromosome 20 open reading frame 38, serine palmitoyltransferase,...)
(Previous symbols: C20orf38, SPTLC2L)
  Search for SPTLC3
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Serine Palmitoyltransferase, Long Chain Base Subunit 31 2     Chromosome 20 Open Reading Frame 381
SPTLC2L1 2 3 5     LCB2B2
C20orf381 2 3     LCB32
Serine Palmitoyltransferase, Long Chain Base Subunit 2-Like
(Aminotransferase 2)1 2
     SPT32
Long Chain Base Biosynthesis Protein 2b2 3     dJ718P112
Long Chain Base Biosynthesis Protein 32 3     dJ718P11.12
Serine-Palmitoyl-CoA Transferase 32 3     hLCB2b2
LCB 32 3     Serine Palmitoyltransferase 32
SPT 32 3     LCB2b3
EC 2.3.1.503 8     EC 2.3.18

External Ids:    HGNC: 162531   Entrez Gene: 553042   Ensembl: ENSG000001722967   OMIM: 6111205   UniProtKB: Q9NUV73   

Export aliases for SPTLC3 gene to outside databases


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for SPTLC3 Gene:
The SPTLC3 gene encodes an isoform of the third subunit of serine palmitoyltransferase (SPT; EC 2.3.1.50), which
catalyzes the rate-limiting step of the de novo synthesis of sphingolipids (Hornemann et al., 2006 (PubMed
17023427)). SPT contains 2 main subunits: the common SPTLC1 subunit (MIM 605712) and either SPTLC2 (MIM 605713)
or its isoform SPTLC2L (SPTLC3), depending on the tissue in which biosynthesis occurs (Hornemann et al., 2006
(PubMed 17023427)). There are also 2 highly related isoforms of a third subunit, SSSPTA (MIM 613540) and SSSPTB
(MIM 610412), that confer acyl-CoA preference of the SPT enzyme and are essential for maximal enzyme activity
(Han et al., 2009 (PubMed 19416851)).(supplied by OMIM, Nov 2010)

GeneCards Summary for SPTLC3 Gene:
SPTLC3 (serine palmitoyltransferase, long chain base subunit 3) is a protein-coding gene. GO annotations related to this gene include pyridoxal phosphate binding and serine C-palmitoyltransferase activity. An important paralog of this gene is SPTLC2.

UniProtKB/Swiss-Prot: SPTC3_HUMAN, Q9NUV7
Function: Serine palmitoyltransferase (SPT). The heterodimer formed with LCB1/SPTLC1 constitutes the catalytic
core. The composition of the serine palmitoyltransferase (SPT) complex determines the substrate preference. The
SPTLC1-SPTLC3-SPTSSA isozyme uses both C14-CoA and C16-CoA as substrates, while the SPTLC1-SPTLC3-SPTSSB has the
ability to use a broader range of acyl-CoAs without apparent preference




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000020.10  NT_011387.9  NC_018931.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the SPTLC3 gene promoter:
         TBP   AML1a   Pax-6   Nkx2-2   Lmo2   C/EBPalpha   AREB6   SRY   TFIID   Pax-4a   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSPTLC3 promoter sequence
   Search Chromatin IP Primers for SPTLC3

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SPTLC3


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 20p12.1   Ensembl cytogenetic band:  20p12.1   HGNC cytogenetic band: 20p12.1

SPTLC3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SPTLC3 gene location

GeneLoc information about chromosome 20         GeneLoc Exon Structure

GeneLoc location for GC20P012938:  view genomic region     (about GC identifiers)

Start:
12,989,627 bp from pter      End:
13,147,411 bp from pter
Size:
157,785 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: SPTC3_HUMAN, Q9NUV7 (See protein sequence)
Recommended Name: Serine palmitoyltransferase 3  
Size: 552 amino acids; 62049 Da
Cofactor: Pyridoxal phosphate (By similarity)
Subunit: Heterodimer with SPTLC1. Component of the serine palmitoyltransferase (SPT) complex, composed of
LCB1/SPTLC1, LCB2 (SPTLC2 or SPTLC3) and ssPT (SPTSSA and SPTSSB)
Sequence caution: Sequence=AAH05205.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential
poly-A sequence;
Secondary accessions: A2A2I4 B9EK64 Q05DQ8 Q5T1U4 Q9H1L1 Q9H1Z0
Alternative splicing: 2 isoforms:  Q9NUV7-1   Q9NUV7-2   (Variant in position: 149:P->A (in dbSNP:rs934335))

Explore the universe of human proteins at neXtProt for SPTLC3: NX_Q9NUV7

Explore proteomics data for SPTLC3 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus
  • Selected DME Specific Peptides for SPTLC3 (Q9NUV7) (see all 13)
     LYIDEAH  VINMGSYN  LFGYLRDF  YSMEGSIV 


    See SPTLC3 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_060797.2  
    ENSEMBL proteins: 
     ENSP00000389749   ENSP00000381968   ENSP00000409125   ENSP00000409760   ENSP00000367436  
    Reactome Protein details: Q9NUV7

    SPTLC3 Human Recombinant Protein Products:

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    SPTLC3 Assay Products:

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    Cloud-Clone Corp. ELISAs for SPTLC3
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    Search eBioscience for ELISAs for SPTLC3 


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    5 InterPro protein domains:
     IPR004839 Aminotransferase_I/II
     IPR015424 PyrdxlP-dep_Trfase
     IPR001917 Aminotrans_II_pyridoxalP_BS
     IPR015421 PyrdxlP-dep_Trfase_major_sub1
     IPR015422 PyrdxlP-dep_Trfase_major_sub2

    Graphical View of Domain Structure for InterPro Entry Q9NUV7

    ProtoNet protein and cluster: Q9NUV7

    UniProtKB/Swiss-Prot: SPTC3_HUMAN, Q9NUV7
    Similarity: Belongs to the class-II pyridoxal-phosphate-dependent aminotransferase family


    Find genes that share domains with SPTLC3           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: SPTC3_HUMAN, Q9NUV7
    Function: Serine palmitoyltransferase (SPT). The heterodimer formed with LCB1/SPTLC1 constitutes the catalytic
    core. The composition of the serine palmitoyltransferase (SPT) complex determines the substrate preference. The
    SPTLC1-SPTLC3-SPTSSA isozyme uses both C14-CoA and C16-CoA as substrates, while the SPTLC1-SPTLC3-SPTSSB has the
    ability to use a broader range of acyl-CoAs without apparent preference
    Catalytic activity: Palmitoyl-CoA + L-serine = CoA + 3-dehydro-D-sphinganine + CO(2)

         Enzyme Numbers (IUBMB): EC 2.3.1.501 2 EC 2.3.12

         Gene Ontology (GO): 5 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003824catalytic activity ----
    GO:0004758serine C-palmitoyltransferase activity IDA19416851
    GO:0008483transaminase activity ----
    GO:0016829lyase activity ----
    GO:0030170pyridoxal phosphate binding IEA--
         
    Find genes that share ontologies with SPTLC3           About GenesLikeMe


    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for SPTLC3
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    miRNA
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    miRTarBase miRNAs that target SPTLC3:
    hsa-mir-21-5p (MIRT030899)

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    Selected qRT-PCR Assays for microRNAs that regulate SPTLC3 (see all 26):
    hsa-miR-124* hsa-miR-579 hsa-miR-3673 hsa-miR-148b hsa-miR-3616-5p hsa-miR-1285 hsa-miR-197 hsa-miR-511
    SwitchGear 3'UTR luciferase reporter plasmidSPTLC3 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat SPTLC3

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    Clone
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    Browse Sino Biological Human cDNA Clones
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SPTLC3


    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    SPTC3_HUMAN, Q9NUV7: Endoplasmic reticulum membrane; Single-pass membrane protein (By similarity)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    endoplasmic reticulum5
    mitochondrion3
    cytosol2
    nucleus2
    extracellular1

    Gene Ontology (GO): 3 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005789endoplasmic reticulum membrane TAS--
    GO:0016021integral component of membrane IEA--
    GO:0017059serine C-palmitoyltransferase complex IDA17331073

    Find genes that share ontologies with SPTLC3           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    SuperPaths for SPTLC3 About    
    See pathways by source

    SuperPathContained pathways About
    1Sphingolipid metabolism
    Sphingolipid metabolism0.61
    Sphingolipid de novo biosynthesis0.46
    Sphingolipid metabolism0.61
    Sphingolipid Metabolism0.42
    2Metabolism
    Metabolism0.38
    Metabolism of lipids and lipoproteins0.37
    Metabolic pathways0.38


    Find genes that share SuperPaths with SPTLC3           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways


    1 BioSystems Pathway for SPTLC3
        Sphingolipid Metabolism

    1 Reactome Pathway for SPTLC3
        Sphingolipid de novo biosynthesis


    2 Kegg Pathways  (Kegg details for SPTLC3):
        Sphingolipid metabolism
    Metabolic pathways

    UniProtKB/Swiss-Prot: SPTC3_HUMAN, Q9NUV7
    Pathway: Lipid metabolism; sphingolipid metabolism

        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for SPTLC3
    Interactions:

        Search GeneGlobe Interaction Network for SPTLC3

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for SPTLC3 (ENSP000003819684) via UniProtKB, MINT, STRING, and/or I2D (see all 53)

    InteractantInteraction Details
    GeneCardExternal ID(s)
    KDSRENSP000003850834STRING: ENSP00000385083
    SPTLC1ENSP000002625544STRING: ENSP00000262554
    SPTLC2ENSP000002164844STRING: ENSP00000216484
    SPTSSAENSP000002981304STRING: ENSP00000298130
    SPTSSBENSP000003520974STRING: ENSP00000352097
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006520cellular amino acid metabolic process ----
    GO:0006665sphingolipid metabolic process TAS--
    GO:0009058biosynthetic process ----
    GO:0030148sphingolipid biosynthetic process TAS19416851
    GO:0044281small molecule metabolic process TAS--

    Find genes that share ontologies with SPTLC3           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
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      Browse compounds at ApexBio 

    Browse Tocris compounds for SPTLC3 (SPTC3)

    2 HMDB Compounds for SPTLC3    About this table
    CompoundSynonyms CAS #PubMed Ids
    L-Serine(-)-Serine (see all 26)56-45-1--
    Pyridoxal 5'-phosphateApolon B6 (see all 27)54-47-7--

    1 DrugBank Compound for SPTLC3    About this table
    CompoundSynonyms CAS #TypeActionsPubMed Ids
    Pyridoxal PhosphateCodecarboxylase (see all 9)54-47-7targetcofactor17139284 17016423



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for SPTLC3 gene: 
    NM_018327.2  

    Unigene Cluster for SPTLC3:

    Serine palmitoyltransferase, long chain base subunit 3
    Hs.425023  [show with all ESTs]
    Unigene Representative Sequence: NM_018327
    7 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000476791(uc002woc.3) ENST00000434210 ENST00000399002(uc002wod.1)
    ENST00000450297 ENST00000431275 ENST00000485952 ENST00000378194
    miRNA
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    hsa-miR-124* hsa-miR-579 hsa-miR-3673 hsa-miR-148b hsa-miR-3616-5p hsa-miR-1285 hsa-miR-197 hsa-miR-511
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    Additional mRNA sequence: 

    AK001974.1 AK075271.1 AK300184.1 BC005205.1 BC020656.1 BC038248.1 BC150644.1 

    6 DOTS entries:

    DT.97809926  DT.440198  DT.97801764  DT.99959177  DT.95150052  DT.99959144 

    Selected AceView cDNA sequences (see all 36):

    CR600600 BU623697 BQ012499 BM785033 BE866600 BF062908 BX399104 AU137169 
    AK001974 BX283823 CD101710 BX327973 BC005205 AA192413 AI149272 BC020656 
    AI061436 CF994231 AL844430 CF994475 AU138164 AL037465 NM_018327 AU157495 

    GeneLoc Exon Structure

    3 Alternative Splicing Database (ASD) splice patterns (SP) for SPTLC3    About this scheme

    ExUns: 1a · 1b ^ 2 ^ 3 ^ 4
    SP1:                    -         
    SP2:                    -         
    SP3:                              


    ECgene alternative splicing isoforms for SPTLC3

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    SPTLC3 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: AATGTTTACA
    SPTLC3 Expression
    About this image


    SPTLC3 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 5) fully expand
     
     NULL (Uncategorized)    fully expand to see all 2 entries
             Vascular endothelial growth factor-induced embryoid bodies
     
     Thymus (Hematopoietic System)
             Thymus
     
     Bone (Muscoskeletal System)
             TGFbeta3+BMP7-induced chondrocytes
     
     Kidney (Urinary System)
             Ureteric Bud
     
     Cartilage (Muscoskeletal System)
             TGFbeta3+BMP7-induced chondrocytes
    SPTLC3 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    SPTLC3 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.425023

    UniProtKB/Swiss-Prot: SPTC3_HUMAN, Q9NUV7
    Tissue specificity: Expressed in most tissues, except peripheral blood cells and bone marrow, with highest levels
    in heart, kidney, liver, uterus and skin

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    QuantiFast Probe-based Assays in human, mouse, rat SPTLC3
    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SPTLC3

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of animals and fungi.

    Orthologs for SPTLC3 gene from Selected species (see all 15)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Sptlc31 , 5 serine palmitoyltransferase, long chain base subunit more1, 5 76.53(n)1
    70.42(a)1
      2 (68.52 cM)5
    2286771  NM_175467.31  NP_780676.11 
     1394939135 
    chicken
    (Gallus gallus)
    Aves SPTLC31 serine palmitoyltransferase, long chain base subunit more 74(n)
    76.18(a)
      768538  XM_004935231.1  XP_004935288.1 
    lizard
    (Anolis carolinensis)
    Reptilia --
    --
    Uncharacterized protein
    82(a)
    68(a)
    many → 1
    many → 1
    1(128963336-129011098)
    1(128950925-128956490)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia sptlc31 serine palmitoyltransferase, long chain base subunit more 71.61(n)
    76.44(a)
      100487030  XM_002931739.2  XP_002931785.2 
    zebrafish
    (Danio rerio)
    Actinopterygii sptlc31 serine palmitoyltransferase, long chain base subunit more 67.41(n)
    72.04(a)
      445168  NM_001003562.2  NP_001003562.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta lace6
    lace
    44(a)
    1 → many
    2L(15499110-15505018)
    worm
    (Caenorhabditis elegans)
    Secernentea sptl-26
    sptl-36
    Protein SPTL-3, isoform b
    44(a)
    42(a)
    many ↔ many
    many ↔ many
    V(8017947-8021717) WBGene00018398
    V(13893325-13896417) WBGene00011932
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes LCB26
    Component of serine palmitoyltransferase, responsi...
    40(a)
    1 → many
    IV(576474-578159) YDR062W


    ENSEMBL Gene Tree for SPTLC3 (if available)
    TreeFam Gene Tree for SPTLC3 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for SPTLC3 gene
    SPTLC22  
    2 SIMAP similar genes for SPTLC3 using alignment to 5 protein entries:     SPTC3_HUMAN (see all proteins):
    SPTLC2    GCAT

    Find genes that share paralogs with SPTLC3           About GenesLikeMe



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for SPTLC3 (see all 3662)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 20 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs3605361,2
    C,F,A,H--12987644(-) TTGAAG/ATCAGT 1 -- us2k111Minor allele frequency- A:0.25NA EA WA 732
    rs778175481,2
    F--12987716(+) CATACC/AAGCAG 1 -- us2k11Minor allele frequency- A:0.03EA 120
    rs1378918211,2
    --12987786(+) TTCCAA/GTACGG 1 -- us2k10--------
    rs38933921,2
    C,F,A,H--12987789(-) TTACCG/ATATTG 1 -- us2k139Minor allele frequency- A:0.29NS EA NA CSA WA 3702
    rs126259661,2
    C,H--12987868(+) CTAACC/TTTAGC 1 -- us2k14Minor allele frequency- T:0.00NS EA 418
    rs38891561,2
    C,F,A,H--12987877(-) ATTGCA/GATTGC 1 -- us2k118Minor allele frequency- G:0.31NA EA CSA WA 877
    rs1863054951,2
    C--12987883(+) GCAATC/TAGGGG 1 -- us2k10--------
    rs1848561,2
    C,F,O,A,H--12987940(-) AGGTAT/CATATA 1 -- us2k111Minor allele frequency- C:0.27NA WA EA 510
    rs97898271,2
    C--12987983(+) aagaaA/Gaaaaa 1 -- us2k1 trp30--------
    rs1917007581,2
    --12988047(+) AGATGA/GAGAAG 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for SPTLC3 (12989627 - 13147411 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 9 variations for SPTLC3:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2722196CNV Deletion23290073
    esv2017186CNV Deletion18987734
    esv2722198CNV Deletion23290073
    esv2722197CNV Deletion23290073
    nsv912684CNV Loss21882294
    nsv833924CNV Gain17160897
    nsv912685CNV Gain21882294
    nsv518184CNV Gain19592680
    nsv833923CNV Gain+Loss17160897

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing SPTLC3
    DNA2.0 Custom Variant and Variant Library Synthesis for SPTLC3

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 611120    OMIM disorders: --


    Find genes that share disorders with SPTLC3           About GenesLikeMe

    Genetic Association Database (GAD): SPTLC3
    Human Genome Epidemiology (HuGE) Navigator: SPTLC3 (7 documents)

    Export disorders for SPTLC3 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for SPTLC3 gene, integrated from 10 sources (see all 20):
    (articles sorted by number of sources associating them with SPTLC3)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Cloning and initial characterization of a new subunit for mammalian serine-palmitoyltransferase. (PubMed id 17023427)1, 2, 3 Hornemann T.... von Eckardstein A. (J. Biol. Chem. 2006)
    2. Genome-wide association study of personality traits in bipolar patients. (PubMed id 21368711)1, 4 Alliey-Rodriguez N....Gershon E.S. (Psychiatr. Genet. 2011)
    3. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)1, 4 Rose J.E....Uhl G.R. (Mol. Med. 2010)
    4. A genome-wide perspective of genetic variation in human metabolism. (PubMed id 20037589)1, 4 Illig T....Suhre K. (Nat. Genet. 2010)
    5. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PubMed id 20628086)1, 4 Bailey S.D....Anand S. (Diabetes Care 2010)
    6. Genetic determinants of circulating sphingolipid concentrations in European populations. (PubMed id 19798445)1, 4 Hicks A.A....Campbell H. (PLoS Genet. 2009)
    7. Identification of small subunits of mammalian serine palmitoyltransferase that confer distinct acyl-CoA substrate specificities. (PubMed id 19416851)1, 2 Han G.... Dunn T.M. (Proc. Natl. Acad. Sci. U.S.A. 2009)
    8. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    9. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    10. The DNA sequence and comparative analysis of human chromosome 20. (PubMed id 11780052)1, 2 Deloukas P....Rogers J. (Nature 2001)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 55304 HGNC: 16253 AceView: C20orf38 Ensembl:ENSG00000172296 euGenes: HUgn55304
    ECgene: SPTLC3 Kegg: 55304 H-InvDB: SPTLC3

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for SPTLC3 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for SPTLC3 gene:
    Search GeneIP for patents involving SPTLC3

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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