LOCUS       NM_001294               2470 bp    mRNA    linear   PRI 28-APR-2025
DEFINITION  Homo sapiens CLPTM1 regulator of GABA type A receptor forward
            trafficking (CLPTM1), transcript variant 2, mRNA.
ACCESSION   NM_001294
VERSION     NM_001294.4
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 2470)
  AUTHORS   Liu,N., Li,J., Gao,K., Perszyk,R.E., Zhang,J., Wang,J., Wu,Y.,
            Jenkins,A., Yuan,H., Traynelis,S.F. and Jiang,Y.
  TITLE     De novo CLPTM1 variants with reduced GABAA R current response in
            patients with epilepsy
  JOURNAL   Epilepsia 64 (11), 2968-2981 (2023)
   PUBMED   37577761
  REMARK    GeneRIF: De novo CLPTM1 variants with reduced GABAA R current
            response in patients with epilepsy.
REFERENCE   2  (bases 1 to 2470)
  AUTHORS   Huttlin,E.L., Bruckner,R.J., Navarrete-Perea,J., Cannon,J.R.,
            Baltier,K., Gebreab,F., Gygi,M.P., Thornock,A., Zarraga,G., Tam,S.,
            Szpyt,J., Gassaway,B.M., Panov,A., Parzen,H., Fu,S., Golbazi,A.,
            Maenpaa,E., Stricker,K., Guha Thakurta,S., Zhang,T., Rad,R.,
            Pan,J., Nusinow,D.P., Paulo,J.A., Schweppe,D.K., Vaites,L.P.,
            Harper,J.W. and Gygi,S.P.
  TITLE     Dual proteome-scale networks reveal cell-specific remodeling of the
            human interactome
  JOURNAL   Cell 184 (11), 3022-3040 (2021)
   PUBMED   33961781
REFERENCE   3  (bases 1 to 2470)
  AUTHORS   Christodoulou,E., Visser,M., Potjer,T.P., van der Stoep,N.,
            Rodriguez-Girondo,M., van Doorn,R. and Gruis,N.
  TITLE     Assessing a single SNP located at TERT/CLPTM1L multi-cancer risk
            region as a genetic modifier for risk of pancreatic cancer and
            melanoma in Dutch CDKN2A mutation carriers
  JOURNAL   Fam Cancer 18 (4), 439-444 (2019)
   PUBMED   31203567
  REMARK    GeneRIF: a single SNP located at TERT/CLPTM1L multi-cancer risk
            region as a genetic modifier for risk of pancreatic cancer and
            melanoma in Dutch CDKN2A mutation carriers
REFERENCE   4  (bases 1 to 2470)
  AUTHORS   Hung,R.J., Spitz,M.R., Houlston,R.S., Schwartz,A.G., Field,J.K.,
            Ying,J., Li,Y., Han,Y., Ji,X., Chen,W., Wu,X., Gorlov,I.P., Na,J.,
            de Andrade,M., Liu,G., Brhane,Y., Diao,N., Wenzlaff,A.,
            Davies,M.P.A., Liloglou,T., Timofeeva,M., Muley,T., Rennert,H.,
            Saliba,W., Ryan,B.M., Bowman,E., Barros-Dios,J.M., Perez-Rios,M.,
            Morgenstern,H., Zienolddiny,S., Skaug,V., Ugolini,D., Bonassi,S.,
            van der Heijden,E.H.F.M., Tardon,A., Bojesen,S.E., Landi,M.T.,
            Johansson,M., Bickeboller,H., Arnold,S., Le Marchand,L.,
            Melander,O., Andrew,A., Grankvist,K., Caporaso,N., Teare,M.D.,
            Schabath,M.B., Aldrich,M.C., Kiemeney,L.A., Wichmann,H.E.,
            Lazarus,P., Mayordomo,J., Neri,M., Haugen,A., Zhang,Z.F.,
            Ruano-Ravina,A., Brenner,H., Harris,C.C., Orlow,I., Rennert,G.,
            Risch,A., Brennan,P., Christiani,D.C., Amos,C.I., Yang,P. and
            Gorlova,O.Y.
  TITLE     Lung Cancer Risk in Never-Smokers of European Descent is Associated
            With Genetic Variation in the 5p15.33 TERT-CLPTM1Ll Region
  JOURNAL   J Thorac Oncol 14 (8), 1360-1369 (2019)
   PUBMED   31009812
  REMARK    GeneRIF: Authors detected three genome-wide statistically
            significant single nucleotide polymorphisms mapped to Chromosome 5
            CLPTM1L-TERT region.
REFERENCE   5  (bases 1 to 2470)
  AUTHORS   Inoue,K., Hatano,K., Hanamatsu,Y., Saigo,C., Kito,Y., Bunai,K.,
            Shibata,T. and Takeuchi,T.
  TITLE     Pathobiological role of cleft palate transmembrane protein 1 family
            proteins in oral squamous cell carcinoma
  JOURNAL   J Cancer Res Clin Oncol 145 (4), 851-859 (2019)
   PUBMED   30635792
  REMARK    GeneRIF: Non-tumorous oral squamous cells exhibited vague, weak, or
            little cytoplasmic staining with anti-Clptm1 and CRR9 antibodies.
            By contrast, robust Clptm1 and CRR9 immunoreactivity was found at
            the cancer invasion front in 55 and 54 of the 98 OSCC tissue
            specimens, respectively.
REFERENCE   6  (bases 1 to 2470)
  AUTHORS   Ichikawa,E., Watanabe,A., Nakano,Y., Akita,S., Hirano,A.,
            Kinoshita,A., Kondo,S., Kishino,T., Uchiyama,T., Niikawa,N. and
            Yoshiura,K.I.
  TITLE     PAX9 and TGFB3 are linked to susceptibility to nonsyndromic cleft
            lip with or without cleft palate in the Japanese: population-based
            and family-based candidate gene analyses
  JOURNAL   J Hum Genet 51 (1), 38-46 (2006)
   PUBMED   16247549
  REMARK    GeneRIF: Observational study of gene-disease association. (HuGE
            Navigator)
REFERENCE   7  (bases 1 to 2470)
  AUTHORS   Turhani,D., Item,C.B., Watzinger,E., Sinko,K., Watzinger,F.,
            Lauer,G. and Ewers,R.
  TITLE     Mutation analysis of CLPTM 1 and PVRL 1 genes in patients with
            non-syndromic clefts of lip, alveolus and palate
  JOURNAL   J Craniomaxillofac Surg 33 (5), 301-306 (2005)
   PUBMED   16122939
  REMARK    GeneRIF: Observational study of gene-disease association. (HuGE
            Navigator)
REFERENCE   8  (bases 1 to 2470)
  AUTHORS   Rossi,M.R., Hawthorn,L., Platt,J., Burkhardt,T., Cowell,J.K. and
            Ionov,Y.
  TITLE     Identification of inactivating mutations in the JAK1, SYNJ2, and
            CLPTM1 genes in prostate cancer cells using inhibition of
            nonsense-mediated decay and microarray analysis
  JOURNAL   Cancer Genet Cytogenet 161 (2), 97-103 (2005)
   PUBMED   16102578
  REMARK    GeneRIF: Identification of inactivating mutations in the JAK1,
            SYNJ2, and CLPTM1 genes in prostate cancer cells
REFERENCE   9  (bases 1 to 2470)
  AUTHORS   Yoshiura,K., Machida,J., Daack-Hirsch,S., Patil,S.R.,
            Ashworth,L.K., Hecht,J.T. and Murray,J.C.
  TITLE     Characterization of a novel gene disrupted by a balanced
            chromosomal translocation t(2;19)(q11.2;q13.3) in a family with
            cleft lip and palate
  JOURNAL   Genomics 54 (2), 231-240 (1998)
   PUBMED   9828125
REFERENCE   10 (bases 1 to 2470)
  AUTHORS   Takeuchi,T., Kuro-o,M., Miyazawa,H., Ohtsuki,Y. and Yamamoto,H.
  TITLE     Transgenic expression of a novel thymic epithelial cell antigen
            stimulates abberant development of thymocytes
  JOURNAL   J Immunol 159 (2), 726-733 (1997)
   PUBMED   9218588
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            DB033341.1, BI916245.1, AK074935.1, BC012359.1, BQ574654.1 and
            BM676309.1.
            
            On Nov 23, 2018 this sequence version replaced NM_001294.3.
            
            Transcript Variant: This variant (2) represents the longest
            transcript and encodes the longest isoform (2).
            
            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 :: AF037339.1, AK075262.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1965299, SAMEA1966682
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000337392.10/ ENSP00000336994.4
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-279               DB033341.1         135-413
            280-751             BI916245.1         282-753
            752-1008            AK074935.1         752-1008
            1009-2173           BC012359.1         998-2162
            2174-2466           BQ574654.1         16-308              c
            2467-2470           BM676309.1         24-27               c
FEATURES             Location/Qualifiers
     source          1..2470
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="19"
                     /map="19q13.32"
     gene            1..2470
                     /gene="CLPTM1"
                     /note="CLPTM1 regulator of GABA type A receptor forward
                     trafficking"
                     /db_xref="GeneID:1209"
                     /db_xref="HGNC:HGNC:2087"
                     /db_xref="MIM:604783"
     exon            1..88
                     /gene="CLPTM1"
                     /inference="alignment:Splign:2.1.0"
     CDS             17..2026
                     /gene="CLPTM1"
                     /note="isoform 2 is encoded by transcript variant 2; cleft
                     lip and palate transmembrane protein 1; cleft lip and
                     palate associated transmembrane protein 1; CLPTM1,
                     transmembrane protein; putative lipid scramblase CLPTM1"
                     /codon_start=1
                     /product="putative lipid scramblase CLPTM1 isoform 2"
                     /protein_id="NP_001285.1"
                     /db_xref="CCDS:CCDS12651.1"
                     /db_xref="GeneID:1209"
                     /db_xref="HGNC:HGNC:2087"
                     /db_xref="MIM:604783"
                     /translation="MAAAQEADGARSAVVAAGGGSSGQVTSNGSIGRDPPAETQPQNP
                     PAQPAPNAWQVIKGVLFRIFIIWAISSWFRRGPAPQDQAGPGGAPRVASRNLFPKDTL
                     MNLHVYISEHEHFTDFNATSALFWEQHDLVYGDWTSGENSDGCYEHFAELDIPQSVQQ
                     NGSIYIHVYFTKSGFHPDPRQKALYRRLATVHMSRMINKYKRRRFQKTKNLLTGETEA
                     DPEMIKRAEDYGPVEVISHWHPNITINIVDDHTPWVKGSVPPPLDQYVKFDAVSGDYY
                     PIIYFNDYWNLQKDYYPINESLASLPLRVSFCPLSLWRWQLYAAQSTKSPWNFLGDEL
                     YEQSDEEQDSVKVALLETNPYLLALTIIVSIVHSVFEFLAFKNDIQFWNSRQSLEGLS
                     VRSVFFGVFQSFVVLLYILDNETNFVVQVSVFIGVLIDLWKITKVMDVRLDREHRVAG
                     IFPRLSFKDKSTYIESSTKVYDDMAFRYLSWILFPLLGCYAVYSLLYLEHKGWYSWVL
                     SMLYGFLLTFGFITMTPQLFINYKLKSVAHLPWRMLTYKALNTFIDDLFAFVIKMPVM
                     YRIGCLRDDVVFFIYLYQRWIYRVDPTRVNEFGMSGEDPTAAAPVAEVPTAAGALTPT
                     PAPTTTTATREEASTSLPTKPTQGASSASEPQEAPPKPAEDKKKD"
     exon            89..201
                     /gene="CLPTM1"
                     /inference="alignment:Splign:2.1.0"
     exon            202..325
                     /gene="CLPTM1"
                     /inference="alignment:Splign:2.1.0"
     exon            326..484
                     /gene="CLPTM1"
                     /inference="alignment:Splign:2.1.0"
     exon            485..602
                     /gene="CLPTM1"
                     /inference="alignment:Splign:2.1.0"
     exon            603..688
                     /gene="CLPTM1"
                     /inference="alignment:Splign:2.1.0"
     exon            689..809
                     /gene="CLPTM1"
                     /inference="alignment:Splign:2.1.0"
     exon            810..1054
                     /gene="CLPTM1"
                     /inference="alignment:Splign:2.1.0"
     exon            1055..1148
                     /gene="CLPTM1"
                     /inference="alignment:Splign:2.1.0"
     exon            1149..1339
                     /gene="CLPTM1"
                     /inference="alignment:Splign:2.1.0"
     exon            1340..1435
                     /gene="CLPTM1"
                     /inference="alignment:Splign:2.1.0"
     exon            1436..1571
                     /gene="CLPTM1"
                     /inference="alignment:Splign:2.1.0"
     exon            1572..1739
                     /gene="CLPTM1"
                     /inference="alignment:Splign:2.1.0"
     exon            1740..2470
                     /gene="CLPTM1"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2438..2443
                     /regulatory_class="polyA_signal_sequence"
                     /gene="CLPTM1"
                     /note="hexamer: AATAAA"
     polyA_site      2470
                     /gene="CLPTM1"
                     /note="major polyA site"
ORIGIN      
        1 gacccggagc gggaagatgg cggcggcgca ggaggcggac ggggcccgca gcgccgtggt
       61 ggcggccggg ggaggcagct ccggtcaggt gaccagcaat ggcagcatcg ggagggaccc
      121 gccagcggag acccagcctc agaacccacc ggcccagccg gcacccaatg cctggcaggt
      181 catcaaaggt gtgctgttta ggatcttcat catctgggcc atcagcagtt ggttccgccg
      241 agggccggcc cctcaggacc aggcgggccc cggaggagct ccacgcgtcg ccagccgcaa
      301 cctgttcccc aaagacactt taatgaacct gcatgtgtac atctcagagc acgagcactt
      361 tacagacttc aacgccacgt cggcactctt ctgggaacag cacgatcttg tgtatggcga
      421 ctggactagc ggcgagaact cagacggctg ctacgagcac tttgctgagc tcgatatccc
      481 acagagcgtc cagcagaacg gctccatcta catccacgtt tacttcacca agagtggctt
      541 ccacccagac ccccggcaga aggccctgta ccgccggctt gccacagtcc acatgtcccg
      601 gatgatcaac aaatacaagc gcagacgatt tcagaaaacc aagaacctgc tgacaggaga
      661 gacagaagcg gacccagaaa tgatcaagag ggctgaggac tatgggcctg tggaggtgat
      721 ctcccattgg caccccaaca tcaccatcaa catcgtggac gaccacacgc cgtgggtgaa
      781 gggcagtgtg ccccctcccc tggatcaata tgtgaagttc gacgccgtga gcggtgacta
      841 ctatcccatc atctacttca atgactactg gaacctgcag aaggactact accccatcaa
      901 cgagagcctg gccagcctgc cgctccgcgt ctccttctgc ccactctcgc tttggcgctg
      961 gcagctctat gctgcccaga gcaccaagtc gccctggaac ttcctgggtg atgagttgta
     1021 cgagcagtca gatgaggagc aggactcggt gaaggtggcc ctgctggaga ccaaccccta
     1081 cctgctggcg ctcaccatca tcgtgtctat cgttcacagt gtcttcgagt tcctggcctt
     1141 caagaatgat atccagttct ggaacagccg gcagtccctg gagggcctgt ccgtgcgctc
     1201 cgtcttcttc ggcgttttcc agtcattcgt ggtcctcctc tacatcctgg acaacgagac
     1261 caacttcgtg gtccaggtca gcgtcttcat tggggtcctc atcgacctct ggaagatcac
     1321 caaggtcatg gacgtccggc tggaccgaga gcacagggtg gcaggaatct tcccccgcct
     1381 atccttcaag gacaagtcca cgtatatcga gtcctcgacc aaagtgtatg atgatatggc
     1441 attccggtac ctgtcctgga tcctcttccc gctcctgggc tgctatgccg tctacagtct
     1501 tctgtacctg gagcacaagg gctggtactc ctgggtgctc agcatgctct acggcttcct
     1561 gctgaccttc ggcttcatca ccatgacgcc ccagctcttc atcaactaca agctcaagtc
     1621 tgtggcccac cttccctggc gcatgctcac ctacaaggcc ctcaacacat tcatcgacga
     1681 cctgttcgcc tttgtcatca agatgcccgt tatgtaccgg atcggctgcc tgcgggacga
     1741 tgtggttttc ttcatctacc tctaccaacg gtggatctac cgcgtcgacc ccacccgagt
     1801 caacgagttt ggcatgagtg gagaagaccc cacagctgcc gcccccgtgg ccgaggttcc
     1861 cacagcagca ggggccctca cgcccacacc tgcacccacc acgaccaccg ccaccaggga
     1921 ggaggcctcc acgtccctgc ccaccaagcc cacccagggg gccagctctg ccagcgagcc
     1981 ccaggaagcc cctccaaagc cagcagagga caagaaaaag gattagtcga gactggtcct
     2041 cacctgctcc ggctcctggc gaccactacc cctgcgtccc ggccccctcg cctcccctcc
     2101 ctgtcgccct ttccctggac agatcaggcc ggggcggtgg gaggcccgcc tcaggtcagg
     2161 gcccagcgtg tgatgtaggg gccggggcag gccagggttt gtttgtggag gcgctgtctg
     2221 tccctctgtc cctctgtgtt tccagccatc tcgccctgcc agcccagcac cactgggaat
     2281 catggtgaag ctgatgcagc gttgccgagg gggtgggttg ggcgggggtg gggccgggcc
     2341 cccctacggg atgcccacgg ccgttcatca tcttgtccct cgtcccccta ccacactccc
     2401 cctcctagac cgccgccctt taacacagtc tggatttaat aaattcatat gggtgtttaa
     2461 cttaaactca
//
