LOCUS       NM_006415               2783 bp    mRNA    linear   PRI 08-OCT-2024
DEFINITION  Homo sapiens serine palmitoyltransferase long chain base subunit 1
            (SPTLC1), transcript variant 1, mRNA.
ACCESSION   NM_006415
VERSION     NM_006415.4
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 2783)
  AUTHORS   Rochat,J., Blavier,A., Ruet,S., Vasseur,S., Puma,A., Desnous,B.,
            Chan,V., Delmont,E., Attarian,S., Juntas Morales,R., Quadrio,I.,
            Vidoni,L., Bonello-Palot,N. and Cheillan,D.
  TITLE     Functional and Molecular Characterization of New SPTLC1 Missense
            Variants in Patients with Hereditary Sensory and Autonomic
            Neuropathy Type 1 (HSAN1)
  JOURNAL   Genes (Basel) 15 (6), 692 (2024)
   PUBMED   38927628
  REMARK    GeneRIF: Functional and Molecular Characterization of New SPTLC1
            Missense Variants in Patients with Hereditary Sensory and Autonomic
            Neuropathy Type 1 (HSAN1).
            Publication Status: Online-Only
REFERENCE   2  (bases 1 to 2783)
  AUTHORS   Li,C., Hou,Y., Wei,Q., Lin,J., Jiang,Z., Jiang,Q., Yang,T.,
            Xiao,Y., Huang,J., Cheng,Y., Ou,R., Liu,K., Chen,X., Song,W.,
            Zhao,B., Wu,Y., Cao,B., Chen,Y. and Shang,H.
  TITLE     Mutation screening of SPTLC1 and SPTLC2 in amyotrophic lateral
            sclerosis
  JOURNAL   Hum Genomics 17 (1), 28 (2023)
   PUBMED   36966328
  REMARK    GeneRIF: Mutation screening of SPTLC1 and SPTLC2 in amyotrophic
            lateral sclerosis.
            Publication Status: Online-Only
REFERENCE   3  (bases 1 to 2783)
  AUTHORS   Jagle,S., Hsu,H.H., Juratli,H.A., Zimmer,A.D., Prieschl,A.,
            Alter,S., Wiedenhofer,B., Metze,D., Emmert,S. and Fischer,J.
  TITLE     Pathogenic variants in the SPTLC1 gene cause hyperkeratosis
            lenticularis perstans
  JOURNAL   Br J Dermatol 188 (1), 94-99 (2023)
   PUBMED   36689507
  REMARK    GeneRIF: Pathogenic variants in the SPTLC1 gene cause
            hyperkeratosis lenticularis perstans.
REFERENCE   4  (bases 1 to 2783)
  AUTHORS   Wang,P., Wei,Q., Li,H. and Wu,Z.Y.
  TITLE     Clinical feature difference between juvenile amyotrophic lateral
            sclerosis with SPTLC1 and FUS mutations
  JOURNAL   Chin Med J (Engl) 136 (2), 176-183 (2023)
   PUBMED   36801857
  REMARK    GeneRIF: Clinical feature difference between juvenile amyotrophic
            lateral sclerosis with SPTLC1 and FUS mutations.
            Review article
            Publication Status: Online-Only
REFERENCE   5  (bases 1 to 2783)
  AUTHORS   Fiorillo,C., Capodivento,G., Geroldi,A., Tozza,S., Moroni,I.,
            Mohassel,P., Cataldi,M., Campana,C., Morando,S., Panicucci,C.,
            Pedemonte,M., Brolatti,N., Siliquini,S., Traverso,M., Baratto,S.,
            Debellis,D., Magri,S., Prada,V., Bellone,E., Salpietro,V.,
            Donkervoort,S., Gable,K., Gupta,S.D., Dunn,T.M., Bonnemann,C.G.,
            Taroni,F., Bruno,C., Schenone,A., Mandich,P., Nobbio,L. and
            Nolano,M.
  TITLE     The SPTLC1 p.S331 mutation bridges sensory neuropathy and motor
            neuron disease and has implications for treatment
  JOURNAL   Neuropathol Appl Neurobiol 48 (7), e12842 (2022)
   PUBMED   35904184
  REMARK    GeneRIF: The SPTLC1 p.S331 mutation bridges sensory neuropathy and
            motor neuron disease and has implications for treatment.
REFERENCE   6  (bases 1 to 2783)
  AUTHORS   Perry,D.K., Carton,J., Shah,A.K., Meredith,F., Uhlinger,D.J. and
            Hannun,Y.A.
  TITLE     Serine palmitoyltransferase regulates de novo ceramide generation
            during etoposide-induced apoptosis
  JOURNAL   J Biol Chem 275 (12), 9078-9084 (2000)
   PUBMED   10722759
REFERENCE   7  (bases 1 to 2783)
  AUTHORS   Hanada,K., Hara,T. and Nishijima,M.
  TITLE     Purification of the serine palmitoyltransferase complex responsible
            for sphingoid base synthesis by using affinity peptide
            chromatography techniques
  JOURNAL   J Biol Chem 275 (12), 8409-8415 (2000)
   PUBMED   10722674
REFERENCE   8  (bases 1 to 2783)
  AUTHORS   Gable,K., Slife,H., Bacikova,D., Monaghan,E. and Dunn,T.M.
  TITLE     Tsc3p is an 80-amino acid protein associated with serine
            palmitoyltransferase and required for optimal enzyme activity
  JOURNAL   J Biol Chem 275 (11), 7597-7603 (2000)
   PUBMED   10713067
REFERENCE   9  (bases 1 to 2783)
  AUTHORS   Weiss,B. and Stoffel,W.
  TITLE     Human and murine serine-palmitoyl-CoA transferase--cloning,
            expression and characterization of the key enzyme in sphingolipid
            synthesis
  JOURNAL   Eur J Biochem 249 (1), 239-247 (1997)
   PUBMED   9363775
REFERENCE   10 (bases 1 to 2783)
  AUTHORS   Nicholson,G.A.
  TITLE     SPTLC1-Related Hereditary Sensory Neuropathy
  JOURNAL   (in) Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE and
            Amemiya A (Eds.);
            GENEREVIEWS(R);
            (1993)
   PUBMED   20301564
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from DA305642.1, AK291546.1 and
            BC068537.1.
            
            On Nov 23, 2018 this sequence version replaced NM_006415.3.
            
            Summary: This gene encodes a member of the class-II
            pyridoxal-phosphate-dependent aminotransferase family. The encoded
            protein is the long chain base subunit 1 of serine
            palmitoyltransferase. Serine palmitoyltransferase converts L-serine
            and palmitoyl-CoA to 3-oxosphinganine with pyridoxal 5'-phosphate
            and is the key enzyme in sphingolipid biosynthesis. Mutations in
            this gene were identified in patients with hereditary sensory
            neuropathy type 1. Alternatively spliced variants encoding
            different isoforms have been identified. Pseudogenes of this gene
            have been defined on chromosomes 1, 6, 10, and 13. [provided by
            RefSeq, Jul 2013].
            
            Transcript Variant: This variant (1) represents the longest
            transcript, and encodes isoform a.
            
            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 :: SRR1660805.171411.1,
                                           SRR1660809.106592.1 [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMEA1965299,
                                           SAMEA1966682 [ECO:0006172]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000262554.7/ ENSP00000262554.2
            RefSeq Select criteria :: based on conservation, expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-39                DA305642.1         62-100
            40-1523             AK291546.1         1-1484
            1524-2783           BC068537.1         1457-2716
FEATURES             Location/Qualifiers
     source          1..2783
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="9"
                     /map="9q22.31"
     gene            1..2783
                     /gene="SPTLC1"
                     /gene_synonym="ALS27; HSAN1; HSN1; LBC1; LCB1; SPT1; SPTI"
                     /note="serine palmitoyltransferase long chain base subunit
                     1"
                     /db_xref="GeneID:10558"
                     /db_xref="HGNC:HGNC:11277"
                     /db_xref="MIM:605712"
     exon            1..100
                     /gene="SPTLC1"
                     /gene_synonym="ALS27; HSAN1; HSN1; LBC1; LCB1; SPT1; SPTI"
                     /inference="alignment:Splign:2.1.0"
     CDS             44..1465
                     /gene="SPTLC1"
                     /gene_synonym="ALS27; HSAN1; HSN1; LBC1; LCB1; SPT1; SPTI"
                     /EC_number="2.3.1.50"
                     /note="isoform a is encoded by transcript variant 1; long
                     chain base biosynthesis protein 1; serine-palmitoyl-CoA
                     transferase 1; serine C-palmitoyltransferase"
                     /codon_start=1
                     /product="serine palmitoyltransferase 1 isoform a"
                     /protein_id="NP_006406.1"
                     /db_xref="CCDS:CCDS6692.1"
                     /db_xref="GeneID:10558"
                     /db_xref="HGNC:HGNC:11277"
                     /db_xref="MIM:605712"
                     /translation="MATATEQWVLVEMVQALYEAPAYHLILEGILILWIIRLLFSKTY
                     KLQERSDLTVKEKEELIEEWQPEPLVPPVPKDHPALNYNIVSGPPSHKTVVNGKECIN
                     FASFNFLGLLDNPRVKAAALASLKKYGVGTCGPRGFYGTFDVHLDLEDRLAKFMKTEE
                     AIIYSYGFATIASAIPAYSKRGDIVFVDRAACFAIQKGLQASRSDIKLFKHNDMADLE
                     RLLKEQEIEDQKNPRKARVTRRFIVVEGLYMNTGTICPLPELVKLKYKYKARIFLEES
                     LSFGVLGEHGRGVTEHYGINIDDIDLISANMENALASIGGFCCGRSFVIDHQRLSGQG
                     YCFSASLPPLLAAAAIEALNIMEENPGIFAVLKEKCGQIHKALQGISGLKVVGESLSP
                     AFHLQLEESTGSREQDVRLLQEIVDQCMNRSIALTQARYLEKEEKCLPPPSIRVVVTV
                     EQTEEELERAASTIKEVAQAVLL"
     exon            101..208
                     /gene="SPTLC1"
                     /gene_synonym="ALS27; HSAN1; HSN1; LBC1; LCB1; SPT1; SPTI"
                     /inference="alignment:Splign:2.1.0"
     exon            209..303
                     /gene="SPTLC1"
                     /gene_synonym="ALS27; HSAN1; HSN1; LBC1; LCB1; SPT1; SPTI"
                     /inference="alignment:Splign:2.1.0"
     exon            304..397
                     /gene="SPTLC1"
                     /gene_synonym="ALS27; HSAN1; HSN1; LBC1; LCB1; SPT1; SPTI"
                     /inference="alignment:Splign:2.1.0"
     exon            398..470
                     /gene="SPTLC1"
                     /gene_synonym="ALS27; HSAN1; HSN1; LBC1; LCB1; SPT1; SPTI"
                     /inference="alignment:Splign:2.1.0"
     exon            471..603
                     /gene="SPTLC1"
                     /gene_synonym="ALS27; HSAN1; HSN1; LBC1; LCB1; SPT1; SPTI"
                     /inference="alignment:Splign:2.1.0"
     exon            604..733
                     /gene="SPTLC1"
                     /gene_synonym="ALS27; HSAN1; HSN1; LBC1; LCB1; SPT1; SPTI"
                     /inference="alignment:Splign:2.1.0"
     exon            734..823
                     /gene="SPTLC1"
                     /gene_synonym="ALS27; HSAN1; HSN1; LBC1; LCB1; SPT1; SPTI"
                     /inference="alignment:Splign:2.1.0"
     exon            824..931
                     /gene="SPTLC1"
                     /gene_synonym="ALS27; HSAN1; HSN1; LBC1; LCB1; SPT1; SPTI"
                     /inference="alignment:Splign:2.1.0"
     exon            932..1027
                     /gene="SPTLC1"
                     /gene_synonym="ALS27; HSAN1; HSN1; LBC1; LCB1; SPT1; SPTI"
                     /inference="alignment:Splign:2.1.0"
     exon            1028..1124
                     /gene="SPTLC1"
                     /gene_synonym="ALS27; HSAN1; HSN1; LBC1; LCB1; SPT1; SPTI"
                     /inference="alignment:Splign:2.1.0"
     exon            1125..1179
                     /gene="SPTLC1"
                     /gene_synonym="ALS27; HSAN1; HSN1; LBC1; LCB1; SPT1; SPTI"
                     /inference="alignment:Splign:2.1.0"
     exon            1180..1297
                     /gene="SPTLC1"
                     /gene_synonym="ALS27; HSAN1; HSN1; LBC1; LCB1; SPT1; SPTI"
                     /inference="alignment:Splign:2.1.0"
     exon            1298..1371
                     /gene="SPTLC1"
                     /gene_synonym="ALS27; HSAN1; HSN1; LBC1; LCB1; SPT1; SPTI"
                     /inference="alignment:Splign:2.1.0"
     exon            1372..2783
                     /gene="SPTLC1"
                     /gene_synonym="ALS27; HSAN1; HSN1; LBC1; LCB1; SPT1; SPTI"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2710..2715
                     /regulatory_class="polyA_signal_sequence"
                     /gene="SPTLC1"
                     /gene_synonym="ALS27; HSAN1; HSN1; LBC1; LCB1; SPT1; SPTI"
                     /note="hexamer: GATAAA"
     polyA_site      2730
                     /gene="SPTLC1"
                     /gene_synonym="ALS27; HSAN1; HSN1; LBC1; LCB1; SPT1; SPTI"
     regulatory      2765..2770
                     /regulatory_class="polyA_signal_sequence"
                     /gene="SPTLC1"
                     /gene_synonym="ALS27; HSAN1; HSN1; LBC1; LCB1; SPT1; SPTI"
                     /note="hexamer: AATAAA"
     polyA_site      2783
                     /gene="SPTLC1"
                     /gene_synonym="ALS27; HSAN1; HSN1; LBC1; LCB1; SPT1; SPTI"
                     /note="major polyA site"
ORIGIN      
        1 gggacgcgct tgtgacccgc cttccggaag gaagcggcta actatggcga ccgccacgga
       61 gcagtgggtt ctggtggaga tggtacaggc gctttacgag gctcctgctt accatcttat
      121 tttggaaggg attctgatcc tctggataat cagacttctt ttctctaaga cttacaaatt
      181 acaagaacga tctgatctta cagtcaagga aaaagaagaa ctgattgaag agtggcaacc
      241 agaacctctt gttcctcctg tcccaaaaga ccatcctgct ctcaactaca acatcgtttc
      301 aggccctcca agccacaaaa ctgtggtgaa tggaaaagaa tgtataaact tcgcctcatt
      361 taattttctt ggattgttgg ataaccctag ggttaaggca gcagctttag catctctaaa
      421 gaagtatggc gtggggactt gtggacccag aggattttat ggcacatttg atgttcattt
      481 ggatttggaa gaccgcctgg caaaatttat gaagacagaa gaagccatta tatactcata
      541 tggatttgcc accatagcca gtgctattcc tgcttactct aaaagagggg acattgtttt
      601 tgtagataga gctgcctgct ttgctattca gaaaggatta caggcatccc gtagtgacat
      661 taagttattt aagcataatg acatggctga cctcgagcga ctactaaaag aacaagagat
      721 cgaagatcaa aagaatcctc gcaaggctcg tgtaactcgg cgtttcattg tagtagaagg
      781 attgtatatg aatactggaa ctatttgtcc tcttccagaa ttggttaagt taaaatacaa
      841 atacaaagca agaatcttcc tggaggaaag cctttcattt ggagtcctag gagagcatgg
      901 ccgaggagtc actgaacact atggaatcaa tattgatgat attgatctta tcagtgccaa
      961 catggagaat gcacttgctt ctattggagg tttctgctgt ggcaggtctt ttgtaattga
     1021 ccatcagcga ctttccggcc agggatactg cttttcagct tcgttacctc ccctgttagc
     1081 tgctgcagca attgaggccc tcaacatcat ggaagagaat ccaggtattt ttgcagtgtt
     1141 gaaggaaaag tgcggacaaa ttcataaagc tttacaaggc atttctggat taaaagtggt
     1201 gggggagtcc ctttctccag cctttcacct acaactggaa gagagcactg ggtctcgcga
     1261 gcaagatgtc agactgcttc aggaaattgt agatcaatgc atgaacagaa gtattgcatt
     1321 aactcaggcg cgctacttgg agaaagaaga gaagtgtctc cctcctccca gcattcgggt
     1381 tgtggtcacg gtggaacaaa cagaggaaga actggagaga gctgcgtcca ccatcaagga
     1441 ggtagcccag gccgtcctgc tctaggcaga gtcccgggac catggcctcc tgccacacaa
     1501 cacgcagaga ggactcaaga ctcccgctgg ccatggagtg gcctgaaaga gagcaagaac
     1561 atgtggatct ttgataggat tgttaccaaa tggtgtcagt atggaccaat tgtgtgacca
     1621 tgagaaggat gcttattttt tttaaaaaga aaacacatct aaaagcccag gaactgattt
     1681 ttttaagagg aaaactaatg acagtgtata actgatgttt aaattgtgca tttagtacta
     1741 tttaaatgtt ttcttatact agtattttat attcttttgt tgtcgtttaa aactggagct
     1801 tcagtgtctc ttccctccct ctaatagtaa tggttcagta agcactcctt aactccttag
     1861 tatttcatag aaaaatgact gcaacattaa agctaagagg aacacttcaa catatgtggt
     1921 acaaatttat attgaagatc taaataaacc acgtattttc cagtcttcgt tgtgtgaagc
     1981 taaatggtgg ctaaaaggaa cactttttgt gtgattatta taaactttgc attgtatttg
     2041 aatcttagaa cttttgtaca cactaaatat tgatgtcaca ccatttctaa tctgagcatc
     2101 cttagccaga gaatattcat tatacttcct aagtgagcaa taatttaaat cagaagctat
     2161 tttattttaa tgtaattaac ctttctttac atttcttatg tgttcacctc taatctgttt
     2221 taggaagaga gttggttatt atgttgatcc cataatataa atcatatcct ttatatttta
     2281 gaatatctca aatgtattcc ttttttgtat ggtgggtttg cctagggacg tgtaactaca
     2341 ggcttttact aagccaagga aaaagagaat ttttcttttc atcttacaaa ttccagatat
     2401 ctacaaaaga tgtgaaagca ctaaaaatac catttttaag cagtacttta cctgtttttt
     2461 ctttagcaaa ccaggttatg tggtgtaaag gtttgttata cgtgccacaa tatagcatat
     2521 aaatattatg ccatcattcc ttctcttgtt aaaggtagaa gaataaaatt gtgattttta
     2581 taacctgtgc ttattactca aatggtcttc aacatctttt taaacaacac atactttttg
     2641 aatgttcagt ttctattttg cttgaggtat tttgtacata tgtgccttgt gattgctgct
     2701 gctttaaagg ataaagtact ctttggggga tgagtctggt ttgttttgtt ttatttttta
     2761 atgaaataaa cctatattcc tga
//
