LOCUS       NM_001128126            4060 bp    mRNA    linear   PRI 12-FEB-2025
DEFINITION  Homo sapiens adaptor related protein complex 4 subunit sigma 1
            (AP4S1), transcript variant 2, mRNA.
ACCESSION   NM_001128126
VERSION     NM_001128126.3
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 4060)
  AUTHORS   D'Amore,A., Tessa,A., Naef,V., Bassi,M.T., Citterio,A.,
            Romaniello,R., Fichi,G., Galatolo,D., Mero,S., Battini,R.,
            Bertocci,G., Baldacci,J., Sicca,F., Gemignani,F., Ricca,I.,
            Rubegni,A., Hirst,J., Marchese,M., Sahin,M., Ebrahimi-Fakhari,D.
            and Santorelli,F.M.
  TITLE     Loss of ap4s1 in zebrafish leads to neurodevelopmental defects
            resembling spastic paraplegia 52
  JOURNAL   Ann Clin Transl Neurol 7 (4), 584-589 (2020)
   PUBMED   32216065
  REMARK    GeneRIF: Loss of ap4s1 in zebrafish leads to neurodevelopmental
            defects resembling spastic paraplegia 52.
REFERENCE   2  (bases 1 to 4060)
  AUTHORS   McCullough,C.G., Szelinger,S., Belnap,N., Ramsey,K., Schrauwen,I.,
            Claasen,A.M., Burke,L.W., Siniard,A.L., Huentelman,M.J.,
            Narayanan,V. and Craig,D.W.
  TITLE     Utilizing RNA and outlier analysis to identify an intronic
            splice-altering variant in AP4S1 in a sibling pair with progressive
            spastic paraplegia
  JOURNAL   Hum Mutat 41 (2), 412-419 (2020)
   PUBMED   31660686
  REMARK    GeneRIF: Utilizing RNA and outlier analysis to identify an intronic
            splice-altering variant in AP4S1 in a sibling pair with progressive
            spastic paraplegia.
REFERENCE   3  (bases 1 to 4060)
  AUTHORS   Tessa,A., Battini,R., Rubegni,A., Storti,E., Marini,C.,
            Galatolo,D., Pasquariello,R. and Santorelli,F.M.
  TITLE     Identification of mutations in AP4S1/SPG52 through next generation
            sequencing in three families
  JOURNAL   Eur J Neurol 23 (10), 1580-1587 (2016)
   PUBMED   27444738
  REMARK    GeneRIF: Identification of mutations in AP4S1/SPG52 in hereditary
            spastic paraplegia.
REFERENCE   4  (bases 1 to 4060)
  AUTHORS   Hardies,K., May,P., Djemie,T., Tarta-Arsene,O., Deconinck,T.,
            Craiu,D., Helbig,I., Suls,A., Balling,R., Weckhuysen,S., De
            Jonghe,P. and Hirst,J.
  CONSRTM   AR working group of the EuroEPINOMICS RES Consortium
  TITLE     Recessive loss-of-function mutations in AP4S1 cause mild
            fever-sensitive seizures, developmental delay and spastic
            paraplegia through loss of AP-4 complex assembly
  JOURNAL   Hum Mol Genet 24 (8), 2218-2227 (2015)
   PUBMED   25552650
  REMARK    GeneRIF: Premature stop mutations in AP4S1 result in loss of AP-4
            complex assembly and cause fever-sensitive seizures, developmental
            delay and spastic paraplegia.
REFERENCE   5  (bases 1 to 4060)
  AUTHORS   Abou Jamra,R., Philippe,O., Raas-Rothschild,A., Eck,S.H., Graf,E.,
            Buchert,R., Borck,G., Ekici,A., Brockschmidt,F.F., Nothen,M.M.,
            Munnich,A., Strom,T.M., Reis,A. and Colleaux,L.
  TITLE     Adaptor protein complex 4 deficiency causes severe
            autosomal-recessive intellectual disability, progressive spastic
            paraplegia, shy character, and short stature
  JOURNAL   Am J Hum Genet 88 (6), 788-795 (2011)
   PUBMED   21620353
REFERENCE   6  (bases 1 to 4060)
  AUTHORS   Hirst,J., Bright,N.A., Rous,B. and Robinson,M.S.
  TITLE     Characterization of a fourth adaptor-related protein complex
  JOURNAL   Mol Biol Cell 10 (8), 2787-2802 (1999)
   PUBMED   10436028
REFERENCE   7  (bases 1 to 4060)
  AUTHORS   Dell'Angelica,E.C., Mullins,C. and Bonifacino,J.S.
  TITLE     AP-4, a novel protein complex related to clathrin adaptors
  JOURNAL   J Biol Chem 274 (11), 7278-7285 (1999)
   PUBMED   10066790
REFERENCE   8  (bases 1 to 4060)
  AUTHORS   Alecu,J., Schierbaum,L. and Ebrahimi-Fakhari,D.
  TITLE     AP-4-Associated Hereditary Spastic Paraplegia
  JOURNAL   (in) Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE and
            Amemiya A (Eds.);
            GENEREVIEWS(R);
            (1993)
   PUBMED   30543385
REFERENCE   9  (bases 1 to 4060)
  AUTHORS   Hedera,P.
  TITLE     Hereditary Spastic Paraplegia Overview
  JOURNAL   (in) Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE and
            Amemiya A (Eds.);
            GENEREVIEWS(R);
            (1993)
   PUBMED   20301682
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AK304115.1, AL121808.4,
            AI570549.1 and R46468.1.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Apr 22, 2019 this sequence version replaced NM_001128126.2.
            
            Summary: This gene encodes a member of the adaptor complexes small
            subunit protein family. These proteins are components of the
            heterotetrameric adaptor protein complexes, which play important
            roles in the secretory and endocytic pathways by mediating vesicle
            formation and sorting of integral membrane proteins. The encoded
            protein is the small subunit of adaptor protein complex-4, which is
            associated with both clathrin- and nonclathrin-coated vesicles.
            Mutations in this gene are associated with spastic quadriplegic
            cerebral palsy-6. Alternatively spliced transcript variants
            encoding multiple isoforms have been observed for this gene, and a
            pseudogene of this gene is located on the long arm of chromosome 6.
            [provided by RefSeq, Dec 2011].
            
            Transcript Variant: This variant (2) uses an alternate splice site
            in the 3' coding region and has an alternate terminal exon,
            compared to variant 1. Variants 2, 5 and 6 encode the same isoform
            (2), which is shorter and has a distinct C-terminus, compared to
            isoform 1.
            
            Sequence Note: This RefSeq record was created from transcript and
            genomic sequence data to make the sequence consistent with the
            reference genome assembly. The genomic coordinates used for the
            transcript record were based on transcript alignments.
            
            ##Evidence-Data-START##
            Transcript exon combination :: SRR1660803.15016.1, AK304115.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1965299, SAMEA1966682
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000542754.7/ ENSP00000438170.2
            RefSeq Select criteria :: based on manual assertion, conservation,
                                      expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-1088              AK304115.1         1-1088
            1089-3624           AL121808.4         28420-30955         c
            3625-4054           AI570549.1         1-430               c
            4055-4060           R46468.1           22-27               c
FEATURES             Location/Qualifiers
     source          1..4060
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="14"
                     /map="14q12"
     gene            1..4060
                     /gene="AP4S1"
                     /gene_synonym="AP47B; CLA20; CLAPS4; CPSQ6; SPG52"
                     /note="adaptor related protein complex 4 subunit sigma 1"
                     /db_xref="GeneID:11154"
                     /db_xref="HGNC:HGNC:575"
                     /db_xref="MIM:607243"
     exon            1..139
                     /gene="AP4S1"
                     /gene_synonym="AP47B; CLA20; CLAPS4; CPSQ6; SPG52"
                     /inference="alignment:Splign:2.1.0"
     exon            140..348
                     /gene="AP4S1"
                     /gene_synonym="AP47B; CLA20; CLAPS4; CPSQ6; SPG52"
                     /inference="alignment:Splign:2.1.0"
     CDS             211..645
                     /gene="AP4S1"
                     /gene_synonym="AP47B; CLA20; CLAPS4; CPSQ6; SPG52"
                     /note="isoform 2 is encoded by transcript variant 2;
                     clathrin-associated/assembly/adaptor protein, sigma 4;
                     AP-4 adaptor complex subunit sigma-1; sigma-4-adaptin;
                     AP-4 adapter complex subunit sigma-1; adaptor related
                     protein complex 4 sigma 1 subunit"
                     /codon_start=1
                     /product="AP-4 complex subunit sigma-1 isoform 2"
                     /protein_id="NP_001121598.1"
                     /db_xref="CCDS:CCDS45093.1"
                     /db_xref="GeneID:11154"
                     /db_xref="HGNC:HGNC:575"
                     /db_xref="MIM:607243"
                     /translation="MIKFFLMVNKQGQTRLSKYYEHVDINKRTLLETEVIKSCLSRSN
                     EQCSFIEYKDFKLIYRQYAALFIVVGVNDTENEMAIYEFIHNFVEVLDEYFSRVSELD
                     IMFNLDKVHIILDEMVLNGCIVETNRARILAPLLILDKMSES"
     exon            349..435
                     /gene="AP4S1"
                     /gene_synonym="AP47B; CLA20; CLAPS4; CPSQ6; SPG52"
                     /inference="alignment:Splign:2.1.0"
     exon            436..504
                     /gene="AP4S1"
                     /gene_synonym="AP47B; CLA20; CLAPS4; CPSQ6; SPG52"
                     /inference="alignment:Splign:2.1.0"
     exon            505..516
                     /gene="AP4S1"
                     /gene_synonym="AP47B; CLA20; CLAPS4; CPSQ6; SPG52"
                     /inference="alignment:Splign:2.1.0"
     exon            517..4060
                     /gene="AP4S1"
                     /gene_synonym="AP47B; CLA20; CLAPS4; CPSQ6; SPG52"
                     /inference="alignment:Splign:2.1.0"
     regulatory      1017..1022
                     /regulatory_class="polyA_signal_sequence"
                     /gene="AP4S1"
                     /gene_synonym="AP47B; CLA20; CLAPS4; CPSQ6; SPG52"
                     /note="hexamer: AATAAA"
     polyA_site      1042
                     /gene="AP4S1"
                     /gene_synonym="AP47B; CLA20; CLAPS4; CPSQ6; SPG52"
                     /note="major polyA site"
     regulatory      4032..4037
                     /regulatory_class="polyA_signal_sequence"
                     /gene="AP4S1"
                     /gene_synonym="AP47B; CLA20; CLAPS4; CPSQ6; SPG52"
                     /note="hexamer: AATAAA"
     polyA_site      4060
                     /gene="AP4S1"
                     /gene_synonym="AP47B; CLA20; CLAPS4; CPSQ6; SPG52"
ORIGIN      
        1 actaaaagcc aaaatggctg ccccgaggag gcccgcaccg cgtagccagt gaaggttggg
       61 gagcaagctt atgcgggaaa gagggagggg gactccagga aaagccgttg agaggaccat
      121 cacaacctga gcagcacagg ttccagttac agccatccct tgtcataact tttgaactgt
      181 atttggaaaa atactggcca ggaaagaaaa atgataaaat ttttcctcat ggtgaataaa
      241 caagggcaga ctcgactttc taagtactat gaacatgtgg atattaataa gcgtacactt
      301 ctggaaacag aagtcataaa gagctgtctc tctcgatcca atgaacaatg ctctttcatt
      361 gaatataagg attttaagct gatatatcgg cagtatgcag ctctcttcat tgtggttgga
      421 gttaatgaca ctgagaacga gatggctatt tatgaattca ttcataactt tgtggaagtt
      481 ttagatgagt atttcagccg agtgagtgaa ttagatataa tgtttaattt ggataaagta
      541 cacatcattt tggatgagat ggtgttaaat ggctgcattg tggaaactaa cagggcaaga
      601 attcttgccc ctctactaat tcttgataag atgtcagaaa gctgaaagga agtctcttcg
      661 agacaatatg gatttatcag aaatgcgagt accgtggaat acatctcaac atgttaaccc
      721 agaagaatct ggaagaccac aattacaaaa tggggtatcc ttccaaagac attataaata
      781 ggcattttcc acagttccta aaaagaaaac acaactgtac tttaaaatat gtacaaagaa
      841 aaaaatttct ttaaactgag agagaagttt tattttctaa ttgtaaacat atctgtcgca
      901 ctttaaattc tgttgagcac ctaaggaacc cttcttggtc tatgcttctt ttgcaaattg
      961 aattcaggaa tagcaggatg gtagtgggaa gaaagtatgg cagttttccg tcagccaata
     1021 aagttttaaa atttaaacac aaggcatttt gagtaacgct gttttctgaa agctattttt
     1081 ttttttttga gacggagtct agtctagctg tgtcacctgg cacattctcg gctcactgca
     1141 acctccactt ccggggttca agcgattctc ctgcctcagc ctccgagctg ggactacagg
     1201 catgcaccac cacacctggc taatttttgt atttttagta gagacagggt ttcaccatgt
     1261 tggccaggct gtctcaaact cctgacctca ggtgatctgc ctgcctcagc ctcccagaac
     1321 gctgggatta cagatgagcc acagtgcctg acttctgaag gctgtcttat tcctttaaaa
     1381 ggcttagtaa aattaacttt ttaagaggtg tttttttgtt tgtttttttg ttttgttttt
     1441 taagacggag tcttgctctg tcacccaagc tggagtgcag tggtgtgatc tcagctcact
     1501 gcaacctcca cctctgggtt taagcaattc tcctgcctca gcctcctgag tagctgcgac
     1561 tacaggcatg tagtccccag gagactgagc tgtgattaca gatgtgagcc accatgccct
     1621 gcccggtttt atgtaaagcc cagctaattt ttgtattttt agtagagata gggtttcacc
     1681 atgttggcca ggctgttctt gaactcctga cctcaagtga tccacctgct tcagcctccc
     1741 aaagtgctgg gattacaagc atgagccacc atgcccagcc aagaggtgtt ttttgtttgt
     1801 ttgtttttaa gagaagcagg tcttgctgtg ttgtccaggc tggactgcag tggcttttca
     1861 caagcatgat catgttgtac tacaaccttg aaccttcctg gcctggctct aaaagctttg
     1921 taatgtgggg ctggtgcagt gcctcacacc tgtaacccct gcactttggg aggctgagga
     1981 aggaggatcg cttgaggcca gaaattcaag accagcctgg gcaacataga cctcatctct
     2041 acaaaaaatg caaaaatcag ccgggtgtgg tggcacatac ctgtagtctc aactactcgg
     2101 gagtctgagg cagaagattt cttgagccca ggagttcgag tctgcagtga gctatgatcg
     2161 tgtcactgca ctccagcctg ggtgacagag tgaaaccctg tctcaaaaat aaaaaagtcc
     2221 gagtgcggtg gctcaggcct gtaatcccaa cattttgggg ggccaagcca ggaggattgg
     2281 ttgagcccat tagttcaaga ccagcctggg caacacagca agaccatatc tctacaaaaa
     2341 ataaataggt gtgatggctc atgcctgtaa tcctagtact ttgggaggcc gaggcaggca
     2401 gatcacttga ggtcaggagt ttgaaaccag cctggccaac atggcaaaac cttgtctcta
     2461 ctaaaaatac aaaaagttag ccaggcatgg tggcaagcac ctctaatctc agctactcag
     2521 gaggctgagg cagtagaatt gcttgaaccc gggaggcaga ggttgcagtg agccgagatc
     2581 atgccactgc actccagcct gggcgacaga gtgagaccct gtctctaaaa ataagtaaat
     2641 aactaattaa aaagttagcc agctgtggtg gtgagcacct gtactcctaa ctactcaaga
     2701 ggctgagatg ggagaattga tcaagcctag gagtttgagg ctgcagtgaa ctatgatcac
     2761 aacactgtac tccaacctgg gtaatggagt gaggccctgc ctcaaaaaca caaaaacaaa
     2821 acaaaaaaac ttttataaca tgtacctaac aaagatgcag agttaaattt tatttgccag
     2881 tttgtaaaag cctttgatac tcattttaag ggcacttagt aattacaatg ccattatgta
     2941 attaactcta tagagaacat tactttcaaa taatggatgg tcagacatta agacagcccc
     3001 agagagcccc tacagctatc ctttatcccg ttttttgttt gttttttgga gacagcatct
     3061 ccgtctccta ggctggagtg cagtggtgtg atcatgcctc actacagcct gtacctcctg
     3121 ggctcaggtg ctcctcccac ctcagcctcc tgagtaactg ggaccacagg tgcgcacccc
     3181 ctccacccag ctaatttttg tattttgttg tagagatagg gtttcactat gttgcccaga
     3241 ctggtctcga attcctgcag tcacatgatc catctgcctt cgccttccaa agtgttggga
     3301 ttacaggcct gagccactgt gcccagtctt tttatgccac attttaaaag gtttgcttat
     3361 taataagctt actgttaatg aaatttagtt caaagtttaa aagtagaatg cagccaggca
     3421 tggtggctta cgcctataat cccagcactt tgggacgcca aggtgggtag atcatttgag
     3481 gtcaggagtt caagaccagc ttggccaaca tggtgagacc ctgtctctac taaaactacg
     3541 aaaaattagc cgggcatggt ggcacgcgcc tataatccca actacttggg aggctgtggt
     3601 aggaggatca cttgaaccca ggagacagag gttgcagtga gttgagatcg agattgtgcc
     3661 actgcactcc agcctgggca cagagtgaga ttccgtctca aaaaaaaaaa aaaaaaaaaa
     3721 agtagaaagc aagaaagtgt ctctgtacag gtaggcatga aatgaatcct tctcttcctc
     3781 ccctttactc ctttaacccc ttctcctgca atgtcttgaa gtaaattact gtcattacag
     3841 aagagcaatg cactgcatcc ccccaaaacc tttctatatg cttttgctac cccgttaaca
     3901 gaagaatata cagaactgtc ttaggcgaaa gtatgtacag tagtccctct cttatccact
     3961 gtttcgcatt ctgtggtttg tgttactcat ggtcaactga ggtcccaaaa tattaaacag
     4021 aaaattccag aaataaacaa tgtataagtt ttaaactgca
//
