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

    Gene ID: 132320, updated on 10-Dec-2024

    Summary

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    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
    mouse all
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    Genomic context

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    See SCLT1 in Genome Data Viewer
    Location:
    4q28.2
    Exon count:
    28
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (128873241..129093539, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (132178615..132397709, complement)
    RS_2024_09 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 long intergenic non-protein coding RNA 3140 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:129535873-129536374 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:129536375-129536874 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:129560764-129561264 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:129565349-129565848 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr4:129569028-129569766 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:129573717-129574216 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21892 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21893 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:129603876-129604400 Neighboring gene Sharpr-MPRA regulatory region 780 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:129605286-129606025 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr4:129606954-129608153 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:129613233-129613734 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_74071 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_74072 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:129654815-129655316 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:129655317-129655816 Neighboring gene small nucleolar RNA U13 Neighboring gene NANOG hESC enhancer GRCh37_chr4:129697052-129697573 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:129723780-129724699 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15686 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21894 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15687 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15688 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15689 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15690 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:129734111-129734692 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:129734693-129735274 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21895 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21896 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21897 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21898 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:129752609-129753288 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr4:129753289-129753968 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:129756920-129757462 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21899 Neighboring gene jade family PHD finger 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21900 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21901 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21902 Neighboring gene chromosome 4 open reading frame 33 Neighboring gene CDRT15 pseudogene 11

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. Reduced cone photoreceptor function and subtle systemic manifestations in two siblings with loss of SCLT1. Grudzinska Pechhacker MK, et al. Ophthalmic Genet, 2024 Feb. PMID 37246745
    2. Bardet-Biedl syndrome in two unrelated patients with identical compound heterozygous SCLT1 mutations. Morisada N, et al. CEN Case Rep, 2020 Aug. PMID 32253632, Free PMC Article
    3. Problematic alcohol use associates with sodium channel and clathrin linker 1 (SCLT1) in trauma-exposed populations. Almli LM, et al. Addict Biol, 2018 Sep. PMID 29082582, Free PMC Article
    4. Identification of submicroscopic genetic changes and precise breakpoint mapping in myelofibrosis using high resolution mate-pair sequencing. Lasho T, et al. Am J Hematol, 2013 Sep. PMID 23733509
    5. Ciliary genes TBC1D32/C6orf170 and SCLT1 are mutated in patients with OFD type IX. Adly N, et al. Hum Mutat, 2014 Jan. PMID 24285566

    See all (35) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Reduced cone photoreceptor function and subtle systemic manifestations in two siblings with loss of SCLT1.
      Title: Reduced cone photoreceptor function and subtle systemic manifestations in two siblings with loss of SCLT1.
    2. Bardet-Biedl syndrome in two unrelated patients with identical compound heterozygous SCLT1 mutations.
      Title: Bardet-Biedl syndrome in two unrelated patients with identical compound heterozygous SCLT1 mutations.
    3. Study results indicate a genome-wide significant association between total alcohol use disorders identification test score in a trauma-exposed cohort and rs1433375, an intergenic single-nucleotide polymorphism located 323 kb upstream of the sodium channel and clathrin linker 1 at 4q28.
      Title: Problematic alcohol use associates with sodium channel and clathrin linker 1 (SCLT1) in trauma-exposed populations.
    4. study identified 2 cases with a severe ciliopathy phenotype consistent with oro-facio-digital syndrome type IX; the autozygome of each index harbored a single truncating variant and the affected genes (SCLT1 and TBC1D32/C6orf170) have roles in centrosomal biology and ciliogenesis; findings suggest a role of SCLT1 and TBC1D32 in ciliopathy pathogenesis
      Title: Ciliary genes TBC1D32/C6orf170 and SCLT1 are mutated in patients with OFD type IX.
    5. Functional study in rat suggests that CAP-1A links clathrin and a sodium channel.
      Title: CAP-1A is a novel linker that binds clathrin and the voltage-gated sodium channel Na(v)1.8.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

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

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    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 binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    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
    		  
    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
    		  
    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

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    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_001300897.2 → NP_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_001300898.2 → NP_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/TrEMBL
      D6RBA6
      Related
      ENSP00000424304.1, ENST00000506368.5

    3. NM_001410807.1 → NP_001397736.1  sodium channel and clathrin linker 1 isoform 4

      Status: REVIEWED

      Source sequence(s)
      AC093783, AC093826
      Consensus CDS
      CCDS93634.1
      UniProtKB/TrEMBL
      A0A494C0G8
      Related
      ENSP00000498519.1, ENST00000651532.1

    4. NM_144643.4 → NP_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
      A4QN04, Q0VAH2, Q6P2M4, Q96NL6
      Related
      ENSP00000281142.5, ENST00000281142.10
      Conserved Domains (3) summary
      COG1196
      Location:221 → 549
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      PRK11448
      Location:593 → 685
      hsdR; type I restriction enzyme EcoKI subunit R; Provisional
      TIGR02168
      Location:69 → 360
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    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_047449590.1 → XP_047305546.1  sodium channel and clathrin linker 1 isoform X3

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

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

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

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

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

    7. XM_047449594.1 → XP_047305550.1  sodium channel and clathrin linker 1 isoform X8

    8. XM_047449593.1 → XP_047305549.1  sodium channel and clathrin linker 1 isoform X7

    9. XM_047449596.1 → XP_047305552.1  sodium channel and clathrin linker 1 isoform X9

    10. XM_047449597.1 → XP_047305553.1  sodium channel and clathrin linker 1 isoform X10

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060928.1 Alternate T2T-CHM13v2.0

      Range
      132178615..132397709 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054348885.1 → XP_054204860.1  sodium channel and clathrin linker 1 isoform X3

    2. XM_054348884.1 → XP_054204859.1  sodium channel and clathrin linker 1 isoform X2

    3. XM_054348883.1 → XP_054204858.1  sodium channel and clathrin linker 1 isoform X1

    4. XM_054348888.1 → XP_054204863.1  sodium channel and clathrin linker 1 isoform X6

    5. XM_054348887.1 → XP_054204862.1  sodium channel and clathrin linker 1 isoform X5

    6. XM_054348886.1 → XP_054204861.1  sodium channel and clathrin linker 1 isoform X4

    7. XM_054348890.1 → XP_054204865.1  sodium channel and clathrin linker 1 isoform X8

    8. XM_054348889.1 → XP_054204864.1  sodium channel and clathrin linker 1 isoform X7

    9. XM_054348891.1 → XP_054204866.1  sodium channel and clathrin linker 1 isoform X9

    10. XM_054348892.1 → XP_054204867.1  sodium channel and clathrin linker 1 isoform X10

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96NL6.2 GenPept UniProtKB/Swiss-Prot:Q96NL6

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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