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

Gene ID: 132320, updated on 4-Nov-2022

Summary

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 MIM:611399; AllianceGenome:HGNC:26406
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]
Expression
Ubiquitous expression in ovary (RPKM 5.4), spleen (RPKM 4.9) and 25 other tissues See more
Orthologs
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Genomic context

See SCLT1 in Genome Data Viewer
Location:
4q28.2
Exon count:
28
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (128873241..129093539, complement)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (132188193..132397709, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (129805148..130014694, complement)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 780 Neighboring gene small nucleolar RNA U13 Neighboring gene jade family PHD finger 1 Neighboring gene chromosome 4 open reading frame 33 Neighboring gene CDRT15 pseudogene 11

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

Phenotypes

EBI GWAS Catalog

Description
Risk loci for chronic obstructive pulmonary disease: a genome-wide association study and meta-analysis.
EBI GWAS Catalog

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ30655, FLJ36042, MGC70542

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables clathrin binding IEA
Inferred from Electronic Annotation
more info
 
enables protein C-terminus binding IEA
Inferred from Electronic Annotation
more info
 
enables sodium channel regulator activity IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
involved_in cilium assembly IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
acts_upstream_of_or_within cilium assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in cilium assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in clustering of voltage-gated sodium channels IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
is_active_in centriole IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in centriole IDA
Inferred from Direct Assay
more info
PubMed 
located_in centrosome IDA
Inferred from Direct Assay
more info
PubMed 
part_of ciliary transition fiber IDA
Inferred from Direct Assay
more info
PubMed 
part_of clathrin complex IEA
Inferred from Electronic Annotation
more info
 
located_in cytosol TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
sodium channel and clathrin linker 1
Names
sodium channel-associated protein 1

NCBI Reference Sequences (RefSeq)

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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_034202.2 RefSeqGene

    Range
    5000..214546
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001300897.2NP_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)
    AL557810, BC014677, BC064428
    Consensus CDS
    CCDS77958.1
    UniProtKB/Swiss-Prot
    Q96NL6
    Related
    ENSP00000420861.1, ENST00000511426.5
  2. NM_001300898.2NP_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
    ENSP00000424304.1, ENST00000506368.5
  3. NM_001410807.1NP_001397736.1  sodium channel and clathrin linker 1 isoform 4

    Status: REVIEWED

    Source sequence(s)
    AC093783, AC093826
    Consensus CDS
    CCDS93634.1
    UniProtKB/TrEMBL
    A0A494C0G8
  4. NM_144643.4NP_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
    Q6P2M4, Q96NL6
    Related
    ENSP00000281142.5, ENST00000281142.10
    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 110 details...Open this link in a new tab

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    128873241..129093539 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047449590.1XP_047305546.1  sodium channel and clathrin linker 1 isoform X3

  2. XM_017007717.3XP_016863206.1  sodium channel and clathrin linker 1 isoform X2

  3. XM_017007716.3XP_016863205.1  sodium channel and clathrin linker 1 isoform X1

  4. XM_017007719.2XP_016863208.1  sodium channel and clathrin linker 1 isoform X6

  5. XM_047449592.1XP_047305548.1  sodium channel and clathrin linker 1 isoform X5

  6. XM_017007718.3XP_016863207.1  sodium channel and clathrin linker 1 isoform X4

  7. XM_047449595.1XP_047305551.1  sodium channel and clathrin linker 1 isoform X9

    Related
    ENSP00000498519.1, ENST00000651532.1
  8. XM_047449594.1XP_047305550.1  sodium channel and clathrin linker 1 isoform X8

  9. XM_047449593.1XP_047305549.1  sodium channel and clathrin linker 1 isoform X7

  10. XM_047449596.1XP_047305552.1  sodium channel and clathrin linker 1 isoform X10

  11. XM_047449597.1XP_047305553.1  sodium channel and clathrin linker 1 isoform X11

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    132188193..132397709 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)