LOCUS       NM_144643               2987 bp    mRNA    linear   PRI 08-OCT-2024
DEFINITION  Homo sapiens sodium channel and clathrin linker 1 (SCLT1),
            transcript variant 1, mRNA.
ACCESSION   NM_144643
VERSION     NM_144643.4
KEYWORDS    RefSeq; MANE Select.
SOURCE      Homo sapiens (human)
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
            Catarrhini; Hominidae; Homo.
REFERENCE   1  (bases 1 to 2987)
  AUTHORS   Grudzinska Pechhacker,M.K., Molnar,A., Pekkola Pacheco,N.,
            Thonberg,H., Querat,L., Birkeldh,U., Nordgren,A. and Lindstrand,A.
  TITLE     Reduced cone photoreceptor function and subtle systemic
            manifestations in two siblings with loss of SCLT1
  JOURNAL   Ophthalmic Genet 45 (1), 95-102 (2024)
   PUBMED   37246745
  REMARK    GeneRIF: Reduced cone photoreceptor function and subtle systemic
            manifestations in two siblings with loss of SCLT1.
REFERENCE   2  (bases 1 to 2987)
  AUTHORS   Haenig,C., Atias,N., Taylor,A.K., Mazza,A., Schaefer,M.H., Russ,J.,
            Riechers,S.P., Jain,S., Coughlin,M., Fontaine,J.F., Freibaum,B.D.,
            Brusendorf,L., Zenkner,M., Porras,P., Stroedicke,M., Schnoegl,S.,
            Arnsburg,K., Boeddrich,A., Pigazzini,L., Heutink,P., Taylor,J.P.,
            Kirstein,J., Andrade-Navarro,M.A., Sharan,R. and Wanker,E.E.
  TITLE     Interactome Mapping Provides a Network of Neurodegenerative Disease
            Proteins and Uncovers Widespread Protein Aggregation in Affected
            Brains
  JOURNAL   Cell Rep 32 (7), 108050 (2020)
   PUBMED   32814053
REFERENCE   3  (bases 1 to 2987)
  AUTHORS   Morisada,N., Hamada,R., Miura,K., Ye,M.J., Nozu,K., Hattori,M. and
            Iijima,K.
  TITLE     Bardet-Biedl syndrome in two unrelated patients with identical
            compound heterozygous SCLT1 mutations
  JOURNAL   CEN Case Rep 9 (3), 260-265 (2020)
   PUBMED   32253632
  REMARK    GeneRIF: Bardet-Biedl syndrome in two unrelated patients with
            identical compound heterozygous SCLT1 mutations.
REFERENCE   4  (bases 1 to 2987)
  AUTHORS   Almli,L.M., Lori,A., Meyers,J.L., Shin,J., Fani,N., Maihofer,A.X.,
            Nievergelt,C.M., Smith,A.K., Mercer,K.B., Kerley,K., Leveille,J.M.,
            Feng,H., Abu-Amara,D., Flory,J.D., Yehuda,R., Marmar,C.R.,
            Baker,D.G., Bradley,B., Koenen,K.C., Conneely,K.N. and Ressler,K.J.
  TITLE     Problematic alcohol use associates with sodium channel and clathrin
            linker 1 (SCLT1) in trauma-exposed populations
  JOURNAL   Addict Biol 23 (5), 1145-1159 (2018)
   PUBMED   29082582
  REMARK    GeneRIF: 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.
REFERENCE   5  (bases 1 to 2987)
  AUTHORS   Adly,N., Alhashem,A., Ammari,A. and Alkuraya,F.S.
  TITLE     Ciliary genes TBC1D32/C6orf170 and SCLT1 are mutated in patients
            with OFD type IX
  JOURNAL   Hum Mutat 35 (1), 36-40 (2014)
   PUBMED   24285566
  REMARK    GeneRIF: 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
REFERENCE   6  (bases 1 to 2987)
  AUTHORS   Tanos,B.E., Yang,H.J., Soni,R., Wang,W.J., Macaluso,F.P.,
            Asara,J.M. and Tsou,M.F.
  TITLE     Centriole distal appendages promote membrane docking, leading to
            cilia initiation
  JOURNAL   Genes Dev 27 (2), 163-168 (2013)
   PUBMED   23348840
REFERENCE   7  (bases 1 to 2987)
  AUTHORS   Liu,C., Cummins,T.R., Tyrrell,L., Black,J.A., Waxman,S.G. and
            Dib-Hajj,S.D.
  TITLE     CAP-1A is a novel linker that binds clathrin and the voltage-gated
            sodium channel Na(v)1.8
  JOURNAL   Mol Cell Neurosci 28 (4), 636-649 (2005)
   PUBMED   15797711
  REMARK    GeneRIF: Functional study in rat suggests that CAP-1A links
            clathrin and a sodium channel.
REFERENCE   8  (bases 1 to 2987)
  AUTHORS   Tomarev,S.I., Wistow,G., Raymond,V., Dubois,S. and Malyukova,I.
  TITLE     Gene expression profile of the human trabecular meshwork: NEIBank
            sequence tag analysis
  JOURNAL   Invest Ophthalmol Vis Sci 44 (6), 2588-2596 (2003)
   PUBMED   12766061
REFERENCE   9  (bases 1 to 2987)
  AUTHORS   Harrington,J.J., Sherf,B., Rundlett,S., Jackson,P.D., Perry,R.,
            Cain,S., Leventhal,C., Thornton,M., Ramachandran,R.,
            Whittington,J., Lerner,L., Costanzo,D., McElligott,K., Boozer,S.,
            Mays,R., Smith,E., Veloso,N., Klika,A., Hess,J., Cothren,K., Lo,K.,
            Offenbacher,J., Danzig,J. and Ducar,M.
  TITLE     Creation of genome-wide protein expression libraries using random
            activation of gene expression
  JOURNAL   Nat Biotechnol 19 (5), 440-445 (2001)
   PUBMED   11329013
REFERENCE   10 (bases 1 to 2987)
  AUTHORS   Forsyth,R. and Gunay-Aygun,M.
  TITLE     Bardet-Biedl Syndrome Overview
  JOURNAL   (in) Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE and
            Amemiya A (Eds.);
            GENEREVIEWS(R);
            (1993)
   PUBMED   20301537
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AK055217.1, BC128051.1,
            AK122852.1 and BG210856.1.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Nov 23, 2018 this sequence version replaced NM_144643.3.
            
            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].
            
            Transcript Variant: This variant (1) represents the longest
            transcript and encodes the longest isoform (1).
            
            Publication Note:  This RefSeq record includes a subset of the
            publications that are available for this gene. Please see the Gene
            record to access additional publications.
            
            ##Evidence-Data-START##
            Transcript exon combination :: SRR1803612.172192.1, AK055217.1
                                           [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMEA1965299,
                                           SAMEA1966682 [ECO:0006172]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000281142.10/ ENSP00000281142.5
            RefSeq Select criteria :: based on conservation, expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-780               AK055217.1         69-848
            781-781             BC128051.1         654-654
            782-1756            AK055217.1         850-1824
            1757-1757           AK122852.1         2448-2448
            1758-2748           AK055217.1         1826-2816
            2749-2987           BG210856.1         314-552
FEATURES             Location/Qualifiers
     source          1..2987
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="4"
                     /map="4q28.2"
     gene            1..2987
                     /gene="SCLT1"
                     /gene_synonym="CAP-1A; CAP1A"
                     /note="sodium channel and clathrin linker 1"
                     /db_xref="GeneID:132320"
                     /db_xref="HGNC:HGNC:26406"
                     /db_xref="MIM:611399"
     exon            1..470
                     /gene="SCLT1"
                     /gene_synonym="CAP-1A; CAP1A"
                     /inference="alignment:Splign:2.1.0"
     CDS             437..2503
                     /gene="SCLT1"
                     /gene_synonym="CAP-1A; CAP1A"
                     /note="isoform 1 is encoded by transcript variant 1;
                     sodium channel-associated protein 1"
                     /codon_start=1
                     /product="sodium channel and clathrin linker 1 isoform 1"
                     /protein_id="NP_653244.2"
                     /db_xref="CCDS:CCDS3740.1"
                     /db_xref="GeneID:132320"
                     /db_xref="HGNC:HGNC:26406"
                     /db_xref="MIM:611399"
                     /translation="MAAEIDFLREQNRRLNEDFRRYQMESFSKYSSVQKAVCQGEGDD
                     TFENLVFDQSFLAPLVTEYDKHLGELNGQLKYYQKQVGEMKLQLENVIKENERLHSEL
                     KDAVEKKLEAFPLGTEVGTDIYADDETVRNLQEQLQLANQEKTQAVELWQTVSQELDR
                     LHKLYQEHMTEAQIHVFESQKQKDQLFDFQQLTKQLHVTNENMEVTNQQFLKTVTEQS
                     VIIEQLRKKLRQAKLELRVAVAKVEELTNVTEDLQGQMKKKEKDVVSAHGREEASDRR
                     LQQLQSSIKQLEIRLCVTIQEANQLRTENTHLEKQTRELQAKCNELENERYEAIVRAR
                     NSMQLLEEANLQKSQALLEEKQKEEDIEKMKETVSRFVQDATIRTKKEVANTKKQCNI
                     QISRLTEELSALQMECAEKQGQIERVIKEKKAVEEELEKIYREGRGNESDYRKLEEMH
                     QRFLVSERSKDDLQLRLTRAENRIKQLETDSSEEISRYQEMIQKLQNVLESERENCGL
                     VSEQRLKLQQENKQLRKETESLRKIALEAQKKAKVKISTMEHEFSIKERGFEVQLREM
                     EDSNRNSIVELRHLLATQQKAANRWKEETKKLTESAEIRINNLKSELSRQKLHTQELL
                     SQLEMANEKVAENEKLILEHQEKANRLQRRLSQAEERAASASQQLSVITVQRRKAASL
                     MNLENI"
     exon            471..538
                     /gene="SCLT1"
                     /gene_synonym="CAP-1A; CAP1A"
                     /inference="alignment:Splign:2.1.0"
     exon            539..597
                     /gene="SCLT1"
                     /gene_synonym="CAP-1A; CAP1A"
                     /inference="alignment:Splign:2.1.0"
     exon            598..670
                     /gene="SCLT1"
                     /gene_synonym="CAP-1A; CAP1A"
                     /inference="alignment:Splign:2.1.0"
     exon            671..726
                     /gene="SCLT1"
                     /gene_synonym="CAP-1A; CAP1A"
                     /inference="alignment:Splign:2.1.0"
     exon            727..862
                     /gene="SCLT1"
                     /gene_synonym="CAP-1A; CAP1A"
                     /inference="alignment:Splign:2.1.0"
     exon            863..985
                     /gene="SCLT1"
                     /gene_synonym="CAP-1A; CAP1A"
                     /inference="alignment:Splign:2.1.0"
     exon            986..1051
                     /gene="SCLT1"
                     /gene_synonym="CAP-1A; CAP1A"
                     /inference="alignment:Splign:2.1.0"
     exon            1052..1122
                     /gene="SCLT1"
                     /gene_synonym="CAP-1A; CAP1A"
                     /inference="alignment:Splign:2.1.0"
     exon            1123..1213
                     /gene="SCLT1"
                     /gene_synonym="CAP-1A; CAP1A"
                     /inference="alignment:Splign:2.1.0"
     exon            1214..1305
                     /gene="SCLT1"
                     /gene_synonym="CAP-1A; CAP1A"
                     /inference="alignment:Splign:2.1.0"
     exon            1306..1483
                     /gene="SCLT1"
                     /gene_synonym="CAP-1A; CAP1A"
                     /inference="alignment:Splign:2.1.0"
     exon            1484..1582
                     /gene="SCLT1"
                     /gene_synonym="CAP-1A; CAP1A"
                     /inference="alignment:Splign:2.1.0"
     exon            1583..1654
                     /gene="SCLT1"
                     /gene_synonym="CAP-1A; CAP1A"
                     /inference="alignment:Splign:2.1.0"
     exon            1655..1729
                     /gene="SCLT1"
                     /gene_synonym="CAP-1A; CAP1A"
                     /inference="alignment:Splign:2.1.0"
     exon            1730..1875
                     /gene="SCLT1"
                     /gene_synonym="CAP-1A; CAP1A"
                     /inference="alignment:Splign:2.1.0"
     exon            1876..2068
                     /gene="SCLT1"
                     /gene_synonym="CAP-1A; CAP1A"
                     /inference="alignment:Splign:2.1.0"
     exon            2069..2265
                     /gene="SCLT1"
                     /gene_synonym="CAP-1A; CAP1A"
                     /inference="alignment:Splign:2.1.0"
     exon            2266..2344
                     /gene="SCLT1"
                     /gene_synonym="CAP-1A; CAP1A"
                     /inference="alignment:Splign:2.1.0"
     exon            2345..2440
                     /gene="SCLT1"
                     /gene_synonym="CAP-1A; CAP1A"
                     /inference="alignment:Splign:2.1.0"
     exon            2441..2987
                     /gene="SCLT1"
                     /gene_synonym="CAP-1A; CAP1A"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2717..2722
                     /regulatory_class="polyA_signal_sequence"
                     /gene="SCLT1"
                     /gene_synonym="CAP-1A; CAP1A"
                     /note="hexamer: AATAAA"
     polyA_site      2736
                     /gene="SCLT1"
                     /gene_synonym="CAP-1A; CAP1A"
                     /note="major polyA site"
     regulatory      2965..2970
                     /regulatory_class="polyA_signal_sequence"
                     /gene="SCLT1"
                     /gene_synonym="CAP-1A; CAP1A"
                     /note="hexamer: AATAAA"
     polyA_site      2987
                     /gene="SCLT1"
                     /gene_synonym="CAP-1A; CAP1A"
                     /note="major polyA site"
ORIGIN      
        1 gacttccgct gctggcctgg ggcttcccag ccgtcttggc gttgtcctct ccaacccccg
       61 ccgctccgcg tagaacgccg ctctcaggct gccgtcaagc tcccgcggca ctctcctagg
      121 tggcccgacg agacccagag tgacccgcgg gacgcctgta tcgaccgcgt cctcttccca
      181 ccagcgtggg attcggttga acgtggagtc cccagcaatc ttcagtctct caccagggcc
      241 agggactcgt ctggggcgcg ggggaaagaa gcgtggcggg gctgtagatg ccgcgtgagt
      301 aggatgcaga ttgcaccgct ggagcgcttg acaaccaacc gagcgttggc ttagttttgt
      361 tttcccgcac agcaagctct ctgtctttca gaggaaggta aaggtggtga aagctctaaa
      421 ctaaaattgt atcgaaatgg ctgcagaaat cgactttctg agagagcaaa atcgaagact
      481 aaatgaagat tttaggcggt atcaaatgga aagtttttcc aaatattcat ctgtacagaa
      541 agctgtctgc caaggagaag gagacgacac atttgaaaac ctagtatttg accaaagctt
      601 tttagctcct cttgttactg agtatgataa acacctagga gaactaaatg ggcagctgaa
      661 atattaccag aaacaggtgg gtgagatgaa attacaactt gaaaatgtca tcaaggaaaa
      721 tgaaaggttg cacagtgaat taaaagatgc tgttgaaaaa aaattggagg cctttcccct
      781 gggcacagag gtaggaactg acatatatgc agatgatgaa acagtcagaa accttcaaga
      841 acaattgcag ctagccaatc aagaaaaaac tcaggctgtg gaactctggc agactgtttc
      901 tcaggagttg gacagactac acaagcttta ccaggaacat atgactgagg cccagattca
      961 tgtatttgaa agtcaaaaac aaaaggatca gctatttgat tttcaacaac tgaccaaaca
     1021 acttcatgtt actaatgaga acatggaagt gactaaccaa cagtttctga aaacagtaac
     1081 tgaacaaagt gtgataatcg aacaactccg aaaaaaactt aggcaagcca aattagagct
     1141 gagagttgct gtagcaaaag tggaagagtt aactaatgtg actgaagatc tgcagggaca
     1201 gatgaaaaag aaggagaagg atgtggtgtc tgcccatgga agagaggaag catcagatag
     1261 gcgtttacag cagttacagt ctagtataaa acaattagaa ataagattat gtgtgacaat
     1321 ccaagaagcc aaccaattaa gaaccgaaaa tacacatctg gaaaaacaga ccagagagct
     1381 acaagcaaag tgcaatgaat tagaaaatga gagatatgag gctattgtaa gagccagaaa
     1441 tagcatgcaa ctcttagaag aagctaacct tcaaaaaagt caggctctac ttgaggagaa
     1501 gcaaaaagaa gaagacatag agaaaatgaa agagacagtt tctcggtttg tacaagatgc
     1561 taccataaga accaagaaag aagttgcaaa caccaaaaaa caatgtaata tacaaatttc
     1621 tcgattaaca gaagaacttt cagcccttca aatggagtgt gctgaaaaac aaggccaaat
     1681 tgaacgagtc attaaggaaa aaaaagcagt ggaagaagaa ctagaaaaga tttaccgtga
     1741 aggcagagga aatgagagtg attacagaaa actggaagaa atgcaccaaa gattcctggt
     1801 ttcagagcgt tcaaaagatg atcttcagct aagacttacg agagcagaaa atagaataaa
     1861 acaacttgaa actgactcct cagaagaaat atcacgttac caagaaatga ttcagaaact
     1921 tcaaaatgta ttggagtctg agagagagaa ctgtgggctt gtcagtgaac aaaggctaaa
     1981 acttcagcaa gaaaataaac agttacggaa agagactgag agtttaagga agattgccct
     2041 ggaggctcaa aaaaaagcca aagtaaagat cagtacaatg gaacatgaat tttcaataaa
     2101 ggaacgtgga tttgaagttc aattgagaga gatggaagac agtaatagaa attccattgt
     2161 tgaactgagg catctcctag cgactcaaca gaaggcagcc aataggtgga aagaagaaac
     2221 gaagaaactt actgaaagtg cagaaattag aatcaataat ctaaagagtg agctgagtcg
     2281 acagaaactt catacccaag agctgctttc tcagctggaa atggcaaatg aaaaggtagc
     2341 tgagaatgaa aagctaattc tagagcatca agaaaaagcc aacagacttc aaaggcgtct
     2401 aagtcaggca gaagagagag ctgcttcagc ttcccagcag ctcagtgtga ttacagtgca
     2461 gagaagaaaa gcagcctccc tgatgaatct ggaaaatatt taaaaatatt catagttcac
     2521 tcacagaact ttagagttgg gaaagcagtt ggactagaag tgtattgaaa tggtaaagcc
     2581 tgcaaagtat aatagttaag gcttgtgtta tttcgcgtaa gcattgttgt tctgttttga
     2641 gggttattgg aaaacagagc agtgaccact tcctgtaagt aaagaaaata taatcctata
     2701 ttgagcttca gtggagaata aaccagctga gaagaactca ttgccttcat caatgtgtct
     2761 gttttttaat tcctcctttt tcccttgaaa ggacataata attttcaaac tatgcaaatt
     2821 tctctttcat aagaaagagt ttttaagaaa attctagaat ttaatatttc agtttccaag
     2881 atttgagaat tttacatcta attgttactt ctaactcatt tttaaagttc ctaagtatcc
     2941 attttattat gaactcataa atgtaataaa ttgtgcactt tctaaaa
//
