Free for academic non-profit institutions. Other users need a Commercial license

Aliases for SCLT1 Gene

Aliases for SCLT1 Gene

  • Sodium Channel And Clathrin Linker 1 2 3 5
  • Sodium Channel-Associated Protein 1 3 4
  • CAP-1A 3
  • CAP1A 3
  • SAP1 4

External Ids for SCLT1 Gene

Previous GeneCards Identifiers for SCLT1 Gene

  • GC04M130024
  • GC04M129805
  • GC04M125535

Summaries for SCLT1 Gene

Entrez Gene Summary for SCLT1 Gene

  • This gene encodes an adaptor protein. Studies of a related gene in rat suggest that the encoded protein functions to link clathrin to the sodium channel protein type 10 subunit alpha protein. The encoded protein has also been identified as a component of distal appendages of centrioles that is necessary for ciliogenesis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2014]

GeneCards Summary for SCLT1 Gene

SCLT1 (Sodium Channel And Clathrin Linker 1) is a Protein Coding gene. Diseases associated with SCLT1 include Hypertrophy Of Breast. Among its related pathways are Organelle biogenesis and maintenance and Regulation of PLK1 Activity at G2/M Transition. Gene Ontology (GO) annotations related to this gene include protein C-terminus binding and sodium channel regulator activity.

UniProtKB/Swiss-Prot for SCLT1 Gene

  • Adapter protein that links SCN10A to clathrin. Regulates SCN10A channel activity, possibly by promoting channel internalization (By similarity).

Additional gene information for SCLT1 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SCLT1 Gene

Genomics for SCLT1 Gene

GeneHancer (GH) Regulatory Elements for SCLT1 Gene

Promoters and enhancers for SCLT1 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH04I129091 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 558.7 -0.7 -721 5.3 HDGF PKNOX1 CLOCK SMAD1 ARNT ARID4B SIN3A DMAP1 YY1 POLR2B C4orf33 SCLT1 JADE1 LOC100127912
GH04I128916 Enhancer 1.3 FANTOM5 Ensembl ENCODE 42.9 +176.0 176034 2.5 HDGF CTCF PKNOX1 EBF1 BMI1 BATF IRF4 POLR2A ZNF207 ATF7 SCLT1 C4orf33 JADE1 ENSG00000275647 PIR40738
GH04I128912 Enhancer 0.9 FANTOM5 Ensembl 29.1 +180.3 180306 1.4 SRF EBF1 BMI1 ELF1 ATF2 IRF4 ZNF592 TARDBP IKZF1 NBN SCLT1 JADE1 C4orf33 ENSG00000275647 PIR40738
GH04I128957 Enhancer 1 Ensembl ENCODE 15.1 +135.4 135367 0.9 FOXA2 RARA CREM MIXL1 HMG20B CEBPB ELF1 PPARG NFIL3 RCOR2 C4orf33 SCLT1 ENSG00000275647 ENSG00000281369
GH04I128861 Enhancer 0.9 ENCODE dbSUPER 10.3 +230.8 230795 2.2 HDGF CTCF SIN3A EBF1 ZNF2 RAD21 RELA POLR2A ZNF143 SMC3 JADE1 SCLT1 C4orf33 PIR40738 ENSG00000275647
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SCLT1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SCLT1 gene promoter:

Genomic Locations for SCLT1 Gene

Genomic Locations for SCLT1 Gene
228,687 bases
Minus strand

Genomic View for SCLT1 Gene

Genes around SCLT1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SCLT1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SCLT1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SCLT1 Gene

Proteins for SCLT1 Gene

  • Protein details for SCLT1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Sodium channel and clathrin linker 1
    Protein Accession:
    Secondary Accessions:
    • A4QN04
    • Q0VAH2
    • Q6P2M4

    Protein attributes for SCLT1 Gene

    688 amino acids
    Molecular mass:
    80910 Da
    Quaternary structure:
    • Interacts with SCN10A and clathrin. Identified in a complex containing SCN10A, clathrin and SCLT1 (By similarity).

    Alternative splice isoforms for SCLT1 Gene


neXtProt entry for SCLT1 Gene

Post-translational modifications for SCLT1 Gene

No Post-translational modifications

No data available for DME Specific Peptides for SCLT1 Gene

Domains & Families for SCLT1 Gene

Gene Families for SCLT1 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for SCLT1 Gene


Suggested Antigen Peptide Sequences for SCLT1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with SCLT1: view

No data available for UniProtKB/Swiss-Prot for SCLT1 Gene

Function for SCLT1 Gene

Molecular function for SCLT1 Gene

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

Phenotypes From GWAS Catalog for SCLT1 Gene

Gene Ontology (GO) - Molecular Function for SCLT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008022 protein C-terminus binding IEA --
GO:0017080 sodium channel regulator activity IEA --
GO:0030276 clathrin binding IEA --
genes like me logo Genes that share ontologies with SCLT1: view
genes like me logo Genes that share phenotypes with SCLT1: view

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for SCLT1 Gene

Localization for SCLT1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SCLT1 Gene

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.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SCLT1 gene
Compartment Confidence
extracellular 5
cytoskeleton 5
cytosol 5
nucleus 3
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (3)
  • Microtubules (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SCLT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005813 centrosome IDA 21399614
GO:0005814 centriole IDA,IEA 23348840
GO:0005829 cytosol TAS --
GO:0005856 cytoskeleton IEA --
GO:0070062 extracellular exosome HDA,IDA 23376485
genes like me logo Genes that share ontologies with SCLT1: view

Pathways & Interactions for SCLT1 Gene

genes like me logo Genes that share pathways with SCLT1: view

Pathways by source for SCLT1 Gene

Gene Ontology (GO) - Biological Process for SCLT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0045162 clustering of voltage-gated sodium channels IEA --
GO:0060271 cilium assembly IMP 23348840
GO:0065009 regulation of molecular function IEA --
GO:0097711 ciliary basal body-plasma membrane docking TAS --
genes like me logo Genes that share ontologies with SCLT1: view

No data available for SIGNOR curated interactions for SCLT1 Gene

Drugs & Compounds for SCLT1 Gene

No Compound Related Data Available

Transcripts for SCLT1 Gene

Unigene Clusters for SCLT1 Gene

Sodium channel and clathrin linker 1:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for SCLT1 Gene

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

Relevant External Links for SCLT1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for SCLT1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SCLT1 Gene

mRNA differential expression in normal tissues according to GTEx for SCLT1 Gene

This gene is overexpressed in Whole Blood (x4.0).

Protein differential expression in normal tissues from HIPED for SCLT1 Gene

This gene is overexpressed in Nasal epithelium (44.4) and Uterus (6.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for SCLT1 Gene

NURSA nuclear receptor signaling pathways regulating expression of SCLT1 Gene:


SOURCE GeneReport for Unigene cluster for SCLT1 Gene:


Evidence on tissue expression from TISSUES for SCLT1 Gene

  • Lung(4.3)
  • Nervous system(3.6)
genes like me logo Genes that share expression patterns with SCLT1: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for SCLT1 Gene

Orthologs for SCLT1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for SCLT1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia SCLT1 33 34
  • 99.85 (n)
(Canis familiaris)
Mammalia SCLT1 33 34
  • 89.97 (n)
(Bos Taurus)
Mammalia SCLT1 33 34
  • 88.23 (n)
(Rattus norvegicus)
Mammalia Sclt1 33
  • 83.24 (n)
(Mus musculus)
Mammalia Sclt1 33 16 34
  • 82.61 (n)
(Monodelphis domestica)
Mammalia SCLT1 34
  • 77 (a)
(Ornithorhynchus anatinus)
Mammalia SCLT1 34
  • 56 (a)
(Gallus gallus)
Aves SCLT1 33 34
  • 68.43 (n)
(Anolis carolinensis)
Reptilia SCLT1 34
  • 63 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia sclt1 33
  • 63.69 (n)
Str.17503 33
(Danio rerio)
Actinopterygii sclt1 33 34
  • 56.27 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.7157 34
  • 32 (a)
Species where no ortholog for SCLT1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for SCLT1 Gene

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

Paralogs for SCLT1 Gene

genes like me logo Genes that share paralogs with SCLT1: view

No data available for Paralogs for SCLT1 Gene

Variants for SCLT1 Gene

Sequence variations from dbSNP and Humsavar for SCLT1 Gene

SNP ID Clin Chr 04 pos Variation AA Info Type
rs587777504 uncertain-significance, not provided 129,039,039(-) A/G downstream_transcript_variant, genic_downstream_transcript_variant, genic_upstream_transcript_variant, splice_donor_variant
rs1000000480 -- 128,959,728(-) G/A 5_prime_UTR_variant, coding_sequence_variant, genic_downstream_transcript_variant, missense_variant, non_coding_transcript_variant
rs1000038428 -- 128,883,867(-) G/T downstream_transcript_variant, genic_downstream_transcript_variant, intron_variant
rs1000038978 -- 128,940,217(-) T/C genic_downstream_transcript_variant, intron_variant
rs1000042181 -- 129,079,121(-) C/T genic_upstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for SCLT1 Gene

Variant ID Type Subtype PubMed ID
dgv5386n100 CNV gain 25217958
dgv9261n54 CNV gain 21841781
esv2656466 CNV deletion 23128226
esv2670641 CNV deletion 23128226
esv3564606 CNV deletion 23714750
esv3575771 CNV gain 25503493
esv3602167 CNV gain 21293372
esv3602168 CNV gain 21293372
esv3602169 CNV loss 21293372
esv3602172 CNV loss 21293372
esv3602173 CNV loss 21293372
nsv1020327 CNV loss 25217958
nsv4505 CNV insertion 18451855
nsv517249 CNV gain 19592680
nsv522694 CNV loss 19592680
nsv595399 CNV gain 21841781
nsv822718 CNV gain 20364138

Variation tolerance for SCLT1 Gene

Residual Variation Intolerance Score: 75% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.77; 58.07% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SCLT1 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SCLT1 Gene

Disorders for SCLT1 Gene

MalaCards: The human disease database

(1) MalaCards diseases for SCLT1 Gene - From: HGMD and DISEASES

Disorder Aliases PubMed IDs
hypertrophy of breast
  • breasts enlarged
- elite association - COSMIC cancer census association via MalaCards
Search SCLT1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for SCLT1

genes like me logo Genes that share disorders with SCLT1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SCLT1 Gene

Publications for SCLT1 Gene

  1. Centriole distal appendages promote membrane docking, leading to cilia initiation. (PMID: 23348840) Tanos BE … Tsou MF (Genes & development 2013) 3 4 58
  2. CAP-1A is a novel linker that binds clathrin and the voltage-gated sodium channel Na(v)1.8. (PMID: 15797711) Liu C … Dib-Hajj SD (Molecular and cellular neurosciences 2005) 2 3 58
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  4. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58
  5. Phospho-tyrosine dependent protein-protein interaction network. (PMID: 25814554) Grossmann A … Stelzl U (Molecular systems biology 2015) 3 58

Products for SCLT1 Gene

Sources for SCLT1 Gene

Loading form....