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SCLT1 sodium channel and clathrin linker 1 [ Homo sapiens (human) ]

Gene ID: 132320, updated on 26-May-2016
Official Symbol
SCLT1provided by HGNC
Official Full Name
sodium channel and clathrin linker 1provided by HGNC
Primary source
HGNC:HGNC:26406
See related
Ensembl:ENSG00000151466 HPRD:08700; MIM:611399; Vega:OTTHUMG00000133346
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CAP1A; CAP-1A
Summary
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]
Orthologs
Location:
4q28.2
Exon count:
27
Annotation release Status Assembly Chr Location
107 current GRCh38.p2 (GCF_000001405.28) 4 NC_000004.12 (128874418..129093607, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (129805148..130014764, complement)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101927259 Neighboring gene uncharacterized LOC102724309 Neighboring gene jade family PHD finger 1 Neighboring gene chromosome 2 open reading frame 27B pseudogene Neighboring gene chromosome 4 open reading frame 33

NHGRI GWAS Catalog

Description
Risk loci for chronic obstructive pulmonary disease: a genome-wide association study and meta-analysis.
NHGRI GWA Catalog
  • Anchoring of the basal body to the plasma membrane, organism-specific biosystem (from REACTOME)
    Anchoring of the basal body to the plasma membrane, organism-specific biosystemThe primary cilium is a microtubule-based organelle that is present on differentiated cells of nearly all eukaryotes. Cilium biogenesis is initiated by the docking of basal bodies, a centriole-derive...
  • Assembly of the primary cilium, organism-specific biosystem (from REACTOME)
    Assembly of the primary cilium, organism-specific biosystemThe primary cilium is one of two main types of cilia present on the surface of many eukaryotic cells (reviewed in Flieghauf et al, 2007). Unlike the motile cilia, which are generally present in large...
  • Organelle biogenesis and maintenance, organism-specific biosystem (from REACTOME)
    Organelle biogenesis and maintenance, organism-specific biosystemThis module describes the biogenesis of organelles. Organelles are subcellular structures of distinctive morphology and function. The organelles of human cells include: mitochondria, endoplasmic reti...
Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Clone Names

  • FLJ30655, FLJ36042, MGC70542

Gene Ontology Provided by GOA

Function Evidence Code Pubs
clathrin binding IEA
Inferred from Electronic Annotation
more info
 
protein C-terminus binding IEA
Inferred from Electronic Annotation
more info
 
sodium channel regulator activity IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
cilium assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
clustering of voltage-gated sodium channels IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
centriole IDA
Inferred from Direct Assay
more info
PubMed 
centrosome IDA
Inferred from Direct Assay
more info
PubMed 
ciliary transition fiber IDA
Inferred from Direct Assay
more info
PubMed 
clathrin complex IEA
Inferred from Electronic Annotation
more info
 
cytosol TAS
Traceable Author Statement
more info
 
extracellular exosome IDA
Inferred from Direct Assay
more info
PubMed 
Preferred Names
sodium channel and clathrin linker 1
Names
sodium channel-associated protein 1

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_034202.1 RefSeqGene

    Range
    5001..214615
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001300897.1NP_001287826.1  sodium channel and clathrin linker 1 isoform 2

    See identical proteins and their annotated locations for NP_001287826.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks several exons and uses an alternate 3'-terminal exon, compared to variant 1. The encoded isoform (2) has a shorter and distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AK055217, AL557810, BC014677, BC064428
    Consensus CDS
    CCDS77958.1
    UniProtKB/Swiss-Prot
    Q96NL6
    Related
    ENSP00000420861, OTTHUMP00000219933, ENST00000511426, OTTHUMT00000364277
  2. NM_001300898.1NP_001287827.1  sodium channel and clathrin linker 1 isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks several exons and uses an alternate 3'-terminal exon, compared to variant 1. The encoded isoform (3) has a shorter and distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AC093826, AK055217, BC040258
    Consensus CDS
    CCDS77957.1
    UniProtKB/Swiss-Prot
    Q96NL6
    UniProtKB/TrEMBL
    D6RBA6
    Related
    ENSP00000424304, OTTHUMP00000219963, ENST00000506368, OTTHUMT00000364358
  3. NM_144643.3NP_653244.2  sodium channel and clathrin linker 1 isoform 1

    See identical proteins and their annotated locations for NP_653244.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AK055217, AK122852, BC128051, BG210856
    Consensus CDS
    CCDS3740.1
    UniProtKB/Swiss-Prot
    Q96NL6
    Related
    ENSP00000281142, OTTHUMP00000164485, ENST00000281142, OTTHUMT00000257176
    Conserved Domains (3) summary
    COG1196
    Location:221549
    Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
    PRK11448
    Location:593685
    hsdR; type I restriction enzyme EcoKI subunit R; Provisional
    TIGR02168
    Location:69360
    SMC_prok_B; chromosome segregation protein SMC, common bacterial type

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 107 details...

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p2 Primary Assembly

Genomic

  1. NC_000004.12 Reference GRCh38.p2 Primary Assembly

    Range
    128874418..129093607 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011531592.1XP_011529894.1  

    Conserved Domains (3) summary
    COG1196
    Location:221549
    Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
    PRK11448
    Location:593675
    hsdR; type I restriction enzyme EcoKI subunit R; Provisional
    TIGR02168
    Location:67363
    SMC_prok_B; chromosome segregation protein SMC, common bacterial type
  2. XM_011531593.1XP_011529895.1  

    Conserved Domains (2) summary
    COG1196
    Location:221549
    Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
    TIGR02168
    Location:67363
    SMC_prok_B; chromosome segregation protein SMC, common bacterial type

RNA

  1. XR_427528.2 RNA Sequence

  2. XR_938689.1 RNA Sequence

  3. XR_938688.1 RNA Sequence

Alternate CHM1_1.1

Genomic

  1. NC_018915.2 Alternate CHM1_1.1

    Range
    129781640..129991617 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)