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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

SCLT1 Gene

protein-coding   GIFtS: 43
GCID: GC04M129805

Sodium Channel And Clathrin Linker 1

  Search for SCLT1
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

Aliases
Sodium Channel And Clathrin Linker 11 2
Sodium Channel-Associated Protein 12 3
CAP-1A2
CAP1A2
hCAP-1A2
SAP13

External Ids:    HGNC: 264061   Entrez Gene: 1323202   Ensembl: ENSG000001514667   OMIM: 6113995   UniProtKB: Q96NL63   

Export aliases for SCLT1 gene to outside databases

Previous GC identifers: GC04M130024 GC04M125535


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Entrez Gene summary for SCLT1 Gene:
SCLT1 acts as a linker protein between the voltage-gated sodium channel Na(v)1.8 (SCN10A; MIM 604427) and clathrin
(see CLTC, MIM 118955) (Liu et al., 2005 (PubMed 15797711)).(supplied by OMIM, Mar 2008)

GeneCards Summary for SCLT1 Gene: 
SCLT1 (sodium channel and clathrin linker 1) is a protein-coding gene. GO annotations related to this gene include clathrin binding and protein C-terminus binding.

UniProtKB/Swiss-Prot: SCLT1_HUMAN, Q96NL6
Function: Adapter protein that links SCN10A to clathrin. Regulates SCN10A channel activity, possibly by promoting
channel internalization (By similarity)




(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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000004.11  NT_016354.19  NC_018915.2  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the SCLT1 gene promoter:
         HFH-3   Sox5   Evi-1   C/EBPalpha   FOXI1   CREB   Pax-3   deltaCREB   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSCLT1 promoter sequence
   Search SABiosciences Chromatin IP Primers for SCLT1

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat SCLT1


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

Entrez Gene cytogenetic band: 4q28.2   Ensembl cytogenetic band:  4q28.2   HGNC cytogenetic band: 4q28.2

SCLT1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SCLT1 gene location

GeneLoc information about chromosome 4         GeneLoc Exon Structure

GeneLoc location for GC04M129805:  view genomic region     (about GC identifiers)

Start:
129,786,076 bp from pter      End:
130,014,764 bp from pter
Size:
228,689 bases      Orientation:
minus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: SCLT1_HUMAN, Q96NL6 (See protein sequence)
Recommended Name: Sodium channel and clathrin linker 1  
Size: 688 amino acids; 80910 Da
Subunit: Interacts with SCN10A and clathrin. Identified in a complex containing SCN10A, clathrin and SCLT1 (By
similarity)
Subcellular location: Cytoplasm, cytoskeleton, microtubule organizing center, centrosome, centriole.
Note=Localizes to the distal appendage region of the centriole, which anchors the mother centriole to the plasma
membrane
Secondary accessions: A4QN04 Q0VAH2 Q6P2M4
Alternative splicing: 4 isoforms:  Q96NL6-1   Q96NL6-2   Q96NL6-3   Q96NL6-4   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for SCLT1: NX_Q96NL6

Explore proteomics data for SCLT1 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q96NL6

  • SCLT1 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    SCLT1 Protein Expression
    REFSEQ proteins: NP_653244.2  
    ENSEMBL proteins: 
     ENSP00000281142   ENSP00000395292   ENSP00000424029   ENSP00000424304   ENSP00000420861  
     ENSP00000425315   ENSP00000401539  

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    Cloud-Clone Corp. Proteins for SCLT1 

    Gene Ontology (GO): 5 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005737cytoplasm IDA--
    GO:0005813centrosome IDA--
    GO:0005814centriole IDA--
    GO:0045111intermediate filament cytoskeleton IDA--
    GO:0071439clathrin complex IEA--

    SCLT1 for ontologies           About GeneDecksing



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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    ProtoNet protein and cluster: Q96NL6


    (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,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: SCLT1_HUMAN, Q96NL6
    Function: Adapter protein that links SCN10A to clathrin. Regulates SCN10A channel activity, possibly by promoting
    channel internalization (By similarity)

         Gene Ontology (GO): 3 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0008022protein C-terminus binding IEA--
    GO:0017080sodium channel regulator activity IEA--
    GO:0030276clathrin binding IEA--
         
    SCLT1 for ontologies           About GeneDecksing


    Phenotypes:
         1 GenomeRNAi human phenotype for SCLT1:
     Proliferating cells 

    Animal Models:
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    (Pathways according to EMD Millipore, 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 SABiosciences, 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 Oct 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for SCLT1

    STRING Interaction Network Preview (showing 3 interactants - click image to see more details)

    5/6 Interacting proteins for SCLT1 (Q96NL63 ENSP000002811424) via UniProtKB, MINT, STRING, and/or I2D (see all 6)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    CALM1P621583I2D: score=1 
    CALM2P621583I2D: score=1 
    CALM3P621583I2D: score=1 
    SCN10AQ9Y5Y93, ENSP000003906004I2D: score=1 STRING: ENSP00000390600
    AMOTQ4VCS53, ENSP000003610274I2D: score=2 STRING: ENSP00000361027
    About this table

    Gene Ontology (GO): 2 biological process terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0042384cilium assembly IMP--
    GO:0045162clustering of voltage-gated sodium channels IEA--

    SCLT1 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for SCLT1

    Search CenterWatch for drugs/clinical trials and news about SCLT1

    (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,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
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    About This Section

    REFSEQ mRNAs for SCLT1 gene: 
    NM_144643.2  

    Unigene Cluster for SCLT1:

    Sodium channel and clathrin linker 1
    Hs.654690  [show with all ESTs]
    Unigene Representative Sequence: AK122852
    10 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000503565 ENST00000281142(uc003igo.2 uc003igp.2) ENST00000506233(uc003ign.2)
    ENST00000439369 ENST00000503215 ENST00000502495 ENST00000506368(uc003igr.2)
    ENST00000511426(uc003igt.4) ENST00000503401 ENST00000434680(uc003igq.2 uc010iob.1)

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    hsa-miR-600 hsa-miR-554 hsa-miR-181a-2* hsa-miR-3647-3p hsa-miR-373* hsa-miR-519e* hsa-miR-515-5p hsa-miR-127-5p
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    Additional mRNA sequence: 

    AK055217.1 AK093361.1 AK122852.1 BC014677.1 BC040258.1 BC064428.1 BC121057.1 BC121058.1 
    BC128051.1 

    8 DOTS entries:

    DT.100008308  DT.101973611  DT.101979600  DT.75175694  DT.97781756  DT.99927598  DT.121221744  DT.95367932 

    24/59 AceView cDNA sequences (see all 59):

    AW083303 AA553518 C01427 BG204665 BC040258 CR593773 NM_144643 AK055217 
    AW513286 BG206279 AW770398 BX374867 AL557810 BM836754 BM924929 BC064428 
    BI496359 AI768586 BU958869 BM986972 BG339994 BM458389 AK093361 BE890996 

    GeneLoc Exon Structure

    4 Alternative Splicing Database (ASD) splice patterns (SP) for SCLT1    About this scheme

    ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10
    SP1:                                -                                             
    SP2:                    -           -                                             
    SP3:                                                                              
    SP4:                                                                              


    ECgene alternative splicing isoforms for SCLT1

    (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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    SCLT1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    SCLT1 Expression
    About this image


    See SCLT1 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for SCLT1

    SOURCE GeneReport for Unigene cluster: Hs.654690
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    In Situ
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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)
    About This Section

    This gene was present in the common ancestor of animals.

    Orthologs for SCLT1 gene from 6/13 species (see all 13)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Sclt11 , 5 sodium channel and clathrin linker 11, 5 82.61(n)1
    75.44(a)1
      3 (19.91 cM)5
    671611  NM_001081411.11  NP_001074880.11 
     416267175 
    chicken
    (Gallus gallus)
    Aves SCLT11 sodium channel and clathrin linker 1 68.43(n)
    60.87(a)
      422486  XM_420451.3  XP_420451.2 
    lizard
    (Anolis carolinensis)
    Reptilia SCLT16
    Uncharacterized protein
    63(a)
    1 ↔ 1
    AAWZ02035000(5652-47670)
    African clawed frog
    (Xenopus laevis)
    Amphibia BJ052961.12   -- 70(n)    BJ052961.1 
    zebrafish
    (Danio rerio)
    Actinopterygii sclt11 sodium channel and clathrin linker 1 56.8(n)
    52.68(a)
      561057  XM_003197632.1  XP_003197680.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG312916
    --
    7(a)
    1 → many
    3R(11736088-11743526)


    ENSEMBL Gene Tree for SCLT1 (if available)
    TreeFam Gene Tree for SCLT1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for SCLT1 gene
    18/19 SIMAP similar genes for SCLT1 using alignment to 4 protein entries:     SCLT1_HUMAN (see all proteins) (see all similar genes):
    THADA    HGSNAT    IFT122    C12orf23    DAPK2    SUN3
    UTY    ATL2    CNOT2    FANCA    LRRC36    FAM3A
    SENP7    BUB1B    GNPTAB    SCIMP    NSD1    SERF1B

    SCLT1 for paralogs           About GeneDecksing



    (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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/3946 SNPs in SCLT1 are shown (see all 3946)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 4 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs709384471,2
    C--125633328(+) ATGAG-/AAAGTGA 1 -- int11Minor allele frequency- AA:0.00NA 2
    rs1120683091,2
    C,F--129804707(+) AAATAC/TGATAA 1 -- ds50011Minor allele frequency- T:0.50CSA 2
    rs3185001,2
    C,F,O,A,H--129804727(+) AAAAAG/AATTCC 1 -- ds50019Minor allele frequency- A:0.31NA CSA WA EA 503
    rs1841218271,2
    C--129804746(+) TCTTAA/TCTGTT 1 -- ds50010--------
    rs1875279271,2
    --129804754(+) GTTAGC/TACCAT 1 -- ds50010--------
    rs1394573421,2
    --129804794(+) CTACAC/TGTGAA 1 -- ds50010--------
    rs1914167991,2
    C--129804815(+) TCACCC/TTCAAC 1 -- ds50010--------
    rs170138981,2
    C,F,H--129804917(+) GGGTGC/TGCTAA 1 -- ds500118Minor allele frequency- T:0.05NA NS EA CSA WA 1953
    rs1839472201,2
    --129804929(+) TTCAAA/GCCAGA 1 -- ds50010--------
    rs771945681,2
    C--129805055(+) ACCTTA/CCAAAT 1 -- ds50010--------

    HapMap Linkage Disequilibrium report for SCLT1 (129786076 - 130014764 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 7 variations for SCLT1:    About this table     
    Variant IDTypeSubtypePubMed ID
    esv2670641CNV Deletion23128226
    esv2656466CNV Deletion23128226
    nsv4505CNV Insertion18451855
    nsv879931CNV Loss21882294
    nsv522694CNV Loss19592680
    nsv517249CNV Gain19592680
    nsv822718CNV Gain20364138

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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section

    SCLT1 for disorders           About MalaCards
    OMIM gene information: 611399    OMIM disorders: --


    SCLT1 for disorders           About GeneDecksing


    Export disorders for SCLT1 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)
    About This Section

    PubMed articles for SCLT1 gene, integrated from 9 sources (see all 12):
    (articles sorted by number of sources associating them with SCLT1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. CAP-1A is a novel linker that binds clathrin and the voltage-gated sodium channel Na(v)1.8. (PubMed id 15797711)1, 3 Liu C....Dib-Hajj S.D. (2005)
    2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    3. Centriole distal appendages promote membrane docking, leading to cilia initiation. (PubMed id 23348840)2 Tanos B.E....Tsou M.F. (2013)
    4. Biochemical and computational analysis of LNX1 interac ting proteins. (PubMed id 22087225)1 Wolting C.D....McGlade C.J. (2011)
    5. Expanding the substantial interactome of NEMO using p rotein microarrays. (PubMed id 20098747)1 Fenner B.J....Prehn J.H. (2010)
    6. Defining the human deubiquitinating enzyme interactio n landscape. (PubMed id 19615732)1 Sowa M.E....Harper J.W. (2009)
    7. Toward a confocal subcellular atlas of the human proteome. (PubMed id 18029348)1 Barbe L....Andersson-Svahn H. (2008)
    8. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. (PubMed id 15815621)2 Hillier L.W....Wilson R.K. (2005)
    9. Scanning the human proteome for calmodulin-binding pr oteins. (PubMed id 15840729)1 Shen X....Liu R. (2005)
    10. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S....Malek J. (2004)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 132320 HGNC: 26406 AceView: FLJ30655 Ensembl:ENSG00000151466 euGenes: HUgn132320
    ECgene: SCLT1 H-InvDB: SCLT1

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for SCLT1 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for SCLT1 gene:
    Search GeneIP for patents involving SCLT1

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



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    GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 4 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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