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SPTLC1 Gene

protein-coding   GIFtS: 67
GCID: GC09M094793

Serine Palmitoyltransferase, Long Chain Base Subunit 1

(Previous names: hereditary sensory neuropathy, type 1)
(Previous symbol: HSN1)
  See SPTLC1-related diseases
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 11 2     EC 2.3.1.503 8
HSN11 2 5     LBC12 5
SPT12 3 5     Hereditary Sensory Neuropathy, Type 11
Long Chain Base Biosynthesis Protein 12 3     HSAN12
Serine-Palmitoyl-CoA Transferase 12 3     SPTI2
LCB12 3     Serine C-Palmitoyltransferase2
LCB 12 3     Serine Palmitoyltransferase 12
SPT 12 3     HSAN5

External Ids:    HGNC: 112771   Entrez Gene: 105582   Ensembl: ENSG000000900547   OMIM: 6057125   UniProtKB: O152693   

Export aliases for SPTLC1 gene to outside databases

Previous GC identifers: GC09M085621 GC09M086522 GC09M088092 GC09M090134 GC09M091873 GC09M093833 GC09M064471


(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 SPTLC1 Gene:
This gene encodes a member of the class-II pyridoxal-phosphate-dependent aminotransferase family. The encoded
protein is the long chain base subunit 1 of serine palmitoyltransferase. Serine palmitoyltransferase converts
L-serine and palmitoyl-CoA to 3-oxosphinganine with pyridoxal 5'-phosphate and is the key enzyme in sphingolipid
biosynthesis. Mutations in this gene were identified in patients with hereditary sensory neuropathy type 1.
Alternatively spliced variants encoding different isoforms have been identified. Pseudogenes of this gene have
been defined on chromosomes 1, 6, 10, and 13. (provided by RefSeq, Jul 2013)

GeneCards Summary for SPTLC1 Gene:
SPTLC1 (serine palmitoyltransferase, long chain base subunit 1) is a protein-coding gene. Diseases associated with SPTLC1 include hereditary sensory neuropathy type ia, and hereditary sensory neuropathy type 1. GO annotations related to this gene include pyridoxal phosphate binding and serine C-palmitoyltransferase activity.

UniProtKB/Swiss-Prot: SPTC1_HUMAN, O15269
Function: Serine palmitoyltransferase (SPT). The heterodimer formed with SPTLC2 or SPTLC3 constitutes the
catalytic core. The composition of the serine palmitoyltransferase (SPT) complex determines the substrate
preference. The SPTLC1-SPTLC2-SPTSSA complex shows a strong preference for C16-CoA substrate, while the
SPTLC1-SPTLC3-SPTSSA isozyme uses both C14-CoA and C16-CoA as substrates, with a slight preference for C14-CoA.
The SPTLC1-SPTLC2-SPTSSB complex shows a strong preference for C18-CoA substrate, while the SPTLC1-SPTLC3-SPTSSB
isozyme displays an ability to use a broader range of acyl-CoAs, without apparent preference

Gene Wiki entry for SPTLC1 Gene


(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_000009.11  NT_008470.20  NC_018920.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the SPTLC1 gene promoter:
         Max1   AML1a   HSF1 (long)   E47   MEF-2A   COMP1   HSF1short   aMEF-2   c-Myc   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSPTLC1 promoter sequence
   Search Chromatin IP Primers for SPTLC1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SPTLC1


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

Entrez Gene cytogenetic band: 9q22.2   Ensembl cytogenetic band:  9q22.31   HGNC cytogenetic band: 9q22.31

SPTLC1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SPTLC1 gene location

GeneLoc information about chromosome 9         GeneLoc Exon Structure

GeneLoc location for GC09M094793:  view genomic region     (about GC identifiers)

Start:
94,793,427 bp from pter      End:
94,877,690 bp from pter
Size:
84,264 bases      Orientation:
minus 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., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: SPTC1_HUMAN, O15269 (See protein sequence)
Recommended Name: Serine palmitoyltransferase 1  
Size: 473 amino acids; 52744 Da
Cofactor: Pyridoxal phosphate (By similarity)
Subunit: Heterodimer with SPTLC2 or SPTLC3. Component of the serine palmitoyltransferase (SPT) complex, composed
of SPTLC1, either SPTLC2 or SPTLC3, and either SPTSSA or SPTSSB. Interacts with SPTSSA and SPTSSB; the
interaction is direct. Interacts with ORMDL3
Caution: Variant Ala-387 has been originally thought to cause HSAN1A (PubMed:15037712). Subsequently, it has been
shown to be a rare, benign polymorphism found in homozygous state in a healthy individual (PubMed:19132419)
Secondary accessions: A8K681 Q5VWB4 Q96IX6
Alternative splicing: 2 isoforms:  O15269-1   O15269-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for SPTLC1: NX_O15269

Explore proteomics data for SPTLC1 at MOPED

Post-translational modifications: 

  • Phosphorylation at Tyr-164 inhibits activity and promotes cell survival1
  • Ubiquitination2 at Lys57, Lys197, Lys375
  • Modification sites at PhosphoSitePlus
  • Selected DME Specific Peptides for SPTLC1 (O15269) (see all 13)
     DVHLDLE  NFASFNFL  NPRVKAAA  CGPRGFYGT 


    See SPTLC1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (3 alternative transcripts): 
    NP_001268232.1  NP_006406.1  NP_847894.1  

    ENSEMBL proteins: 
     ENSP00000262554   ENSP00000337635  
    Reactome Protein details: O15269

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

    Graphical View of Domain Structure for InterPro Entry O15269

    ProtoNet protein and cluster: O15269

    2 Blocks protein domains:
    IPB001917 Aminotransferase
    IPB004839 Aminotransferase


    UniProtKB/Swiss-Prot: SPTC1_HUMAN, O15269
    Similarity: Belongs to the class-II pyridoxal-phosphate-dependent aminotransferase family


    Find genes that share domains with SPTLC1           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, 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: SPTC1_HUMAN, O15269
    Function: Serine palmitoyltransferase (SPT). The heterodimer formed with SPTLC2 or SPTLC3 constitutes the
    catalytic core. The composition of the serine palmitoyltransferase (SPT) complex determines the substrate
    preference. The SPTLC1-SPTLC2-SPTSSA complex shows a strong preference for C16-CoA substrate, while the
    SPTLC1-SPTLC3-SPTSSA isozyme uses both C14-CoA and C16-CoA as substrates, with a slight preference for C14-CoA.
    The SPTLC1-SPTLC2-SPTSSB complex shows a strong preference for C18-CoA substrate, while the SPTLC1-SPTLC3-SPTSSB
    isozyme displays an 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)
    Biophysicochemical properties: Kinetic parameters: KM=0.75 mM for serine; Vmax=1350 pmol/min/mg enzyme;

         Enzyme Number (IUBMB): EC 2.3.1.501 2

         Gene Ontology (GO): 3 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0004758serine C-palmitoyltransferase activity IDA19416851
    GO:0005515protein binding IPI19416851
    GO:0030170pyridoxal phosphate binding IEA--
         
    Find genes that share ontologies with SPTLC1           About GenesLikeMe


    Phenotypes:
         5 MGI mutant phenotypes (inferred from 2 alleles(MGI details for Sptlc1):
     behavior/neurological  homeostasis/metabolism  mortality/aging  nervous system  reproductive system 

    Find genes that share phenotypes with SPTLC1           About GenesLikeMe

    Animal Models:
         MGI mouse knock-out Sptlc1tm1Jia for SPTLC1

       genOway: Develop your customized and physiologically relevant rodent model for SPTLC1

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    Selected qRT-PCR Assays for microRNAs that regulate SPTLC1 (see all 21):
    hsa-miR-1178 hsa-miR-16-2* hsa-miR-137 hsa-miR-15a hsa-miR-944 hsa-miR-374a hsa-miR-424 hsa-miR-124
    SwitchGear 3'UTR luciferase reporter plasmidSPTLC1 3' UTR sequence
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    (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
    SPTC1_HUMAN, O15269: Endoplasmic reticulum membrane; Single-pass membrane protein (By similarity)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    endoplasmic reticulum5
    cytosol2
    extracellular1
    golgi apparatus1
    mitochondrion1
    nucleus1
    plasma membrane1

    Gene Ontology (GO): 4 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 IDA19416851
    GO:0035339SPOTS complex IDA--

    Find genes that share ontologies with SPTLC1           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 SPTLC1 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
    3ceramide de novo biosynthesis
    ceramide de novo biosynthesis


    Find genes that share SuperPaths with SPTLC1           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways


    2 BioSystems Pathways for SPTLC1
        Sphingolipid Metabolism
    ceramide de novo biosynthesis

    1 Reactome Pathway for SPTLC1
        Sphingolipid de novo biosynthesis


    2 Kegg Pathways  (Kegg details for SPTLC1):
        Sphingolipid metabolism
    Metabolic pathways

    UniProtKB/Swiss-Prot: SPTC1_HUMAN, O15269
    Pathway: Lipid metabolism; sphingolipid metabolism

        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for SPTLC1
    Interactions:

        GeneGlobe Interaction Network for SPTLC1

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

    Selected Interacting proteins for SPTLC1 (O152693 ENSP000002625544) via UniProtKB, MINT, STRING, and/or I2D (see all 139)

    InteractantInteraction Details
    GeneCardExternal ID(s)
    ENSG00000206324Q999433, ENSP000003827234I2D: score=1 STRING: ENSP00000382723
    ENSG00000226467Q999433, ENSP000004058644I2D: score=1 STRING: ENSP00000405864
    ENSG00000227642Q999433, ENSP000003895164I2D: score=1 STRING: ENSP00000389516
    ENSG00000228892Q999433, ENSP000004128054I2D: score=1 STRING: ENSP00000412805
    ENSG00000235758Q999433, ENSP000004012874I2D: score=1 STRING: ENSP00000401287
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 8):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006665sphingolipid metabolic process TAS--
    GO:0006686sphingomyelin biosynthetic process IEA--
    GO:0009058biosynthetic process ----
    GO:0030148sphingolipid biosynthetic process TAS19416851
    GO:0044281small molecule metabolic process TAS--

    Find genes that share ontologies with SPTLC1           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 Tocris compounds for SPTLC1 (SPTC1)

    8 HMDB Compounds for SPTLC1    About this table
    CompoundSynonyms CAS #PubMed Ids
    3-Dehydrosphinganine1-Hydroxy-2-amino-3-oxo-octadecane (see all 9)16105-69-4--
    Alpha-TocopherolVitamin Ea (see all 22)59-02-9--
    Carbon dioxideCarbon oxide (see all 5)124-38-9--
    Coenzyme AAcetoacetyl coenzyme A sodium salt (see all 21)85-61-0--
    L-Serine(-)-Serine (see all 26)56-45-1--
    Palmityl-CoAPalmityl-CoA (see all 13)1763-10-6--
    Pyridoxal 5'-phosphateApolon B6 (see all 27)54-47-7--
    Squalene(E,E,E,E)-Squalene (see all 10)111-02-4--

    2 DrugBank Compounds for SPTLC1    About this table
    CompoundSynonyms CAS #TypeActionsPubMed Ids
    Pyridoxal PhosphateCodecarboxylase (see all 9)54-47-7targetcofactor12782147 11781309 11279212
    L-Serine(-)-Serine (see all 11)56-45-1target--17559874

    3 Novoseek inferred chemical compound relationships for SPTLC1 gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    serine 72.4 19 11781309 (3), 11242114 (2), 16311270 (1), 18515784 (1) (see all 13)
    ceramide 63.6 5 18515784 (1), 19592499 (1), 20208441 (1)
    cholesterol 2 4 18484747 (2), 9761725 (1)



    Find genes that share compounds with SPTLC1           About GenesLikeMe



    (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 SPTLC1 gene (3 alternative transcripts): 
    NM_001281303.1  NM_006415.3  NM_178324.2  

    Unigene Cluster for SPTLC1:

    Serine palmitoyltransferase, long chain base subunit 1
    Hs.90458  [show with all ESTs]
    Unigene Representative Sequence: AB209757
    7 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000262554(uc011ltv.1 uc004arl.1 uc004arm.1) ENST00000469778
    ENST00000482632 ENST00000337841(uc004arn.1) ENST00000477888 ENST00000488921
    ENST00000461132
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    Additional mRNA sequence: 

    AB209757.1 AF116613.1 AF147304.1 AK098344.1 AK291546.1 AK299153.1 AK309775.1 BC007085.1 
    BC068537.1 Y08685.1 

    22 DOTS entries:

    DT.444903  DT.92458220  DT.102820  DT.95312939  DT.100681874  DT.121208736  DT.91724848  DT.95225508 
    DT.95312943  DT.100743822  DT.121208704  DT.92458222  DT.97816127  DT.100813818  DT.121208779  DT.92023316 
    DT.99981543  DT.121208741  DT.91871110  DT.92004418  DT.92458221  DT.97801742 

    Selected AceView cDNA sequences (see all 300):

    BU579723 AI985480 AA627479 BM454934 BM999986 CD622626 CB216099 AA973574 
    T39656 AA864603 AF147304 AW673758 T39740 AU138413 AU138619 AU141494 
    BQ576284 AW513973 AI269059 AI370330 AA304528 BI258416 BF110128 CR615416 

    GeneLoc Exon Structure


    (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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    SPTLC1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: AGAAGGATGC
    SPTLC1 Expression
    About this image


    SPTLC1 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 8) fully expand
     
     Brain (Nervous System)    fully expand to see all 4 entries
             Myelinating Oligodendrocyte Cells Forebrain White Matter
             Cerebral Cortex
     
     Trophoblast (Extraembryonic Tissues)
             Trophoblast Cells Trophoblast
     
     Testis (Reproductive System)
             Leydig Cells Testis Interstitium
     
     Ovary (Reproductive System)
             Oviduct
     
     Liver (Hepatobiliary System)
             Hepatocytes Liver Lobule
    SPTLC1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    SPTLC1 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.90458

    UniProtKB/Swiss-Prot: SPTC1_HUMAN, O15269
    Tissue specificity: Widely expressed. Not detected in small intestine

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    (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 eukaryotes.

    Orthologs for SPTLC1 gene from Selected species (see all 24)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Sptlc11 , 5 serine palmitoyltransferase, long chain base subunit more1, 5 84.57(n)1
    91.75(a)1
      13 (27.68 cM)5
    2686561  NM_009269.21  NP_033295.21 
     533327485 
    chicken
    (Gallus gallus)
    Aves SPTLC11 serine palmitoyltransferase, long chain base subunit more 79.8(n)
    87.5(a)
      426145  XM_004949252.1  XP_004949309.1 
    lizard
    (Anolis carolinensis)
    Reptilia SPTLC16
    serine palmitoyltransferase, long chain base subun...
    87(a)
    1 ↔ 1
    2(31523293-31555342)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.73642 Xenopus laevis transcribed sequence with moderate similarity more 78.21(n)    BU911419.1 
    zebrafish
    (Danio rerio)
    Actinopterygii CA474602.12   -- 72.87(n)   386944  CA474602.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta Spt-I1 , 3 serine C-palmitoyltransferase3
    Serine palmitoyltransferase subunit I1
    52(a)3
    54.4(n)1
    52.59(a)1
      49F43
    364481  NM_136998.21  NP_610842.11 
    worm
    (Caenorhabditis elegans)
    Secernentea C23H3.43
    sptl-11
    aminotransferase3
    sptl-11
    49(a)3
    57.06(n)1
    53.27(a)1
      II(51538-52611)3
    1733891  NM_001026807.21  NP_001021978.11 
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes LCB1(YMR296C)4
    LCB11
    Component of serine palmitoyltransferase, responsible more4
    LCB11
    47.12(n)1
    37.98(a)1
      13(860891-859215)4
    8553421, 4  NP_014025.11, 4 
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons LCB11 LCB1 52.49(n)
    45.02(a)
      829800  NM_001036719.1  NP_001031796.1 
    rice
    (Oryza sativa)
    Liliopsida Os02g08069001 Os02g0806900 53.75(n)
    48.55(a)
      4331075  NM_001054986.1  NP_001048451.2 


    ENSEMBL Gene Tree for SPTLC1 (if available)
    TreeFam Gene Tree for SPTLC1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for SPTLC1 gene

    Find genes that share paralogs with SPTLC1           About GenesLikeMe


    Selected Pseudogenes.org Pseudogenes for SPTLC1 (see all 10)
    PGOHUM00000238713 PGOHUM00000248637 PGOHUM00000249153 PGOHUM00000245003 PGOHUM00000240671


    (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 SPTLC1 (see all 1815)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 9 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0113944
    Neuropathy, hereditary sensory and autonomic, 1A (HSAN1A)4--see VAR_0113942 V D mis40--------
    VAR_0662454
    Neuropathy, hereditary sensory and autonomic, 1A (HSAN1A)4--see VAR_0662452 S F mis40--------
    VAR_0662464
    Neuropathy, hereditary sensory and autonomic, 1A (HSAN1A)4--see VAR_0662462 A V mis40--------
    VAR_0113934
    Neuropathy, hereditary sensory and autonomic, 1A (HSAN1A)4--see VAR_0113932 C Y mis40--------
    VAR_0113924
    Neuropathy, hereditary sensory and autonomic, 1A (HSAN1A)4--see VAR_0113922 C W mis40--------
    VAR_0366104
    A breast cancer sample4--see VAR_0366102 R W mis40--------
    rs1194820841,2,,4
    Cpathogenic194818681(-) GGTGGG/CGGAGT 2 /A /G mis11Minor allele frequency- C:0.00NA 4552
    rs1194820831,2
    Cpathogenic194848434(-) AGATGA/TTCATT 2 D V mis10--------
    rs1194820821,2
    Cpathogenic194860385(-) ACTTGG/TGGACC 4 W C mis10--------
    rs1194820811,2
    Cpathogenic194860386(-) GACTTA/GTGGAC 4 Y C mis10--------

    HapMap Linkage Disequilibrium report for SPTLC1 (94793427 - 94877690 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 1 variation for SPTLC1:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv831653CNV Gain17160897

    Human Gene Mutation Database (HGMD): SPTLC1
    Locus Specific Mutation Databases (LSDB): SPTLC1

    Site Specific Mutation Identification with PCR Assays
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 605712   
    OMIM disorders: 162400  
    UniProtKB/Swiss-Prot: SPTC1_HUMAN, O15269
  • Neuropathy, hereditary sensory and autonomic, 1A (HSAN1A) [MIM:162400]: A form of hereditary sensory and
    autonomic neuropathy, a genetically and clinically heterogeneous group of disorders characterized by degeneration
    of dorsal root and autonomic ganglion cells, and by prominent sensory abnormalities with a variable degree of
    motor and autonomic dysfunction. The neurological phenotype is often complicated by severe infections,
    osteomyelitis, and amputations. HSAN1A is an autosomal dominant axonal form with onset in the second or third
    decades. Initial symptoms are loss of pain, touch, heat, and cold sensation over the feet, followed by distal
    muscle wasting and weakness. Loss of pain sensation leads to chronic skin ulcers and distal amputations. Note=The
    disease is caused by mutations affecting the gene represented in this entry

  • 8 diseases for SPTLC1:    
    About MalaCards
    hereditary sensory neuropathy type ia    hereditary sensory neuropathy type 1    neuropathy, hereditary sensory and autonomic, type ia    sensory neuropathy type 1
    alcoholic neuropathy    tabes dorsalis    neuropathy    hereditary sensory neuropathy

    3 diseases from the University of Copenhagen DISEASES database for SPTLC1:
    Peripheral neuropathy     Tabes dorsalis     Alcoholic neuropathy

    Find genes that share disorders with SPTLC1           About GenesLikeMe

    5 Novoseek inferred disease relationships for SPTLC1 gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    neuropathy, hereditary sensory, type i 97.5 9 16364956 (3), 18018475 (2), 11242114 (1), 15037712 (1) (see all 5)
    sensory neuropathy hereditary 92.6 1 16311270 (1)
    sensory neuropathy 69.6 1 16364956 (1)
    charcot-marie-tooth disease 66.3 2 16364956 (1)
    neurodegeneration 34.7 2 15467453 (1)

    GeneTests: SPTLC1
    GeneReviews: SPTLC1
    Genetic Association Database (GAD): SPTLC1
    Human Genome Epidemiology (HuGE) Navigator: SPTLC1 (2 documents)

    Export disorders for SPTLC1 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 SPTLC1 gene, integrated from 10 sources (see all 80):
    (articles sorted by number of sources associating them with SPTLC1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Human and murine serine-palmitoyl-CoA transferase. Cloning, expression and characterization of the key enzyme in sphingolipid synthesis. (PubMed id 9363775)1, 2, 3, 9 Weiss B. and Stoffel W. (Eur. J. Biochem. 1997)
    2. Genes for hereditary sensory and autonomic neuropathies: a genotype- phenotype correlation. (PubMed id 19651702)1, 2, 4, 9 Rotthier A.... Timmerman V. (Brain 2009)
    3. SPTLC1 mutation in twin sisters with hereditary sensory neuropathy type I. (PubMed id 15037712)1, 2, 9 Verhoeven K.... De Jonghe P. (Neurology 2004)
    4. Mutations in SPTLC1, encoding serine palmitoyltransferase, long chain base subunit-1, cause hereditary sensory neuropathy type I. (PubMed id 11242114)1, 2, 9 Dawkins J.L....Nicholson G.A. (Nat. Genet. 2001)
    5. Phosphorylation of serine palmitoyltransferase long chain-1 (SPTLC1) on tyrosine 164 inhibits its activity and promotes cell survival. (PubMed id 23629659)1, 2 Taouji S....Chevet E. (J. Biol. Chem. 2013)
    6. Frequency of mutations in the genes associated with hereditary sensory and autonomic neuropathy in a UK cohort. (PubMed id 22302274)1, 2 Davidson G.L.... Reilly M.M. (J. Neurol. 2012)
    7. Characterization of two mutations in the SPTLC1 subunit of serine palmitoyltransferase associated with hereditary sensory and autonomic neuropathy type I. (PubMed id 21618344)1, 2 Rotthier A.... Janssens K. (Hum. Mutat. 2011)
    8. Orm family proteins mediate sphingolipid homeostasis. (PubMed id 20182505)1, 2 Breslow D.K.... Weissman J.S. (Nature 2010)
    9. Maternal genes and facial clefts in offspring: a comprehensive search for genetic associations in two population-based cleft studies from Scandinavia. (PubMed id 20634891)1, 4 Jugessur A....Murray J.C. (PLoS ONE 2010)
    10. A systematic comparison of all mutations in hereditary sensory neuropathy type I (HSAN I) reveals that the G387A mutation is not disease associated. (PubMed id 19132419)1, 2 Hornemann T.... von Eckardstein A. (Neurogenetics 2009)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Disorders
    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: 10558 HGNC: 11277 AceView: SPTLC1 Ensembl:ENSG00000090054 euGenes: HUgn10558
    ECgene: SPTLC1 Kegg: 10558 H-InvDB: SPTLC1

    (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 SPTLC1 Pharmacogenomics, SNPs, Pathways
    GeneReviewshttp://www.ncbi.nlm.nih.gov/books/NBK1116/?term=SPTLC1[genesymbol]

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for SPTLC1 gene:
    Search GeneIP for patents involving SPTLC1

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



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