LOCUS       NM_001164405            1372 bp    mRNA    linear   PRI 19-AUG-2024
DEFINITION  Homo sapiens basic helix-loop-helix family member a9 (BHLHA9),
            mRNA.
ACCESSION   NM_001164405 XM_001125971
VERSION     NM_001164405.2
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 1372)
  AUTHORS   Bukowska-Olech,E., Sowinska-Seidler,A., Wierzba,J. and Jamsheer,A.
  TITLE     SHFLD3 phenotypes caused by 17p13.3 triplication/ duplication
            encompassing Fingerin (BHLHA9) invariably
  JOURNAL   Orphanet J Rare Dis 17 (1), 325 (2022)
   PUBMED   36028842
  REMARK    GeneRIF: SHFLD3 phenotypes caused by 17p13.3 triplication/
            duplication encompassing Fingerin (BHLHA9) invariably.
            Publication Status: Online-Only
REFERENCE   2  (bases 1 to 1372)
  AUTHORS   Sedighzadeh,S.S., Sedaghat,A., Zamani,M., Seifi,T., Shariati,G.,
            Zeighami,J., Mazaheri,N. and Galehdari,H.
  TITLE     Whole exome sequencing identified a novel frameshift variant in the
            BHLHA9 in an Iranian family with mesoaxial synostotic syndactyly
  JOURNAL   Congenit Anom (Kyoto) 61 (6), 220-225 (2021)
   PUBMED   34272776
  REMARK    GeneRIF: Whole exome sequencing identified a novel frameshift
            variant in the BHLHA9 in an Iranian family with mesoaxial
            synostotic syndactyly.
REFERENCE   3  (bases 1 to 1372)
  AUTHORS   Luck,K., Kim,D.K., Lambourne,L., Spirohn,K., Begg,B.E., Bian,W.,
            Brignall,R., Cafarelli,T., Campos-Laborie,F.J., Charloteaux,B.,
            Choi,D., Cote,A.G., Daley,M., Deimling,S., Desbuleux,A., Dricot,A.,
            Gebbia,M., Hardy,M.F., Kishore,N., Knapp,J.J., Kovacs,I.A.,
            Lemmens,I., Mee,M.W., Mellor,J.C., Pollis,C., Pons,C.,
            Richardson,A.D., Schlabach,S., Teeking,B., Yadav,A., Babor,M.,
            Balcha,D., Basha,O., Bowman-Colin,C., Chin,S.F., Choi,S.G.,
            Colabella,C., Coppin,G., D'Amata,C., De Ridder,D., De Rouck,S.,
            Duran-Frigola,M., Ennajdaoui,H., Goebels,F., Goehring,L., Gopal,A.,
            Haddad,G., Hatchi,E., Helmy,M., Jacob,Y., Kassa,Y., Landini,S.,
            Li,R., van Lieshout,N., MacWilliams,A., Markey,D., Paulson,J.N.,
            Rangarajan,S., Rasla,J., Rayhan,A., Rolland,T., San-Miguel,A.,
            Shen,Y., Sheykhkarimli,D., Sheynkman,G.M., Simonovsky,E., Tasan,M.,
            Tejeda,A., Tropepe,V., Twizere,J.C., Wang,Y., Weatheritt,R.J.,
            Weile,J., Xia,Y., Yang,X., Yeger-Lotem,E., Zhong,Q., Aloy,P.,
            Bader,G.D., De Las Rivas,J., Gaudet,S., Hao,T., Rak,J.,
            Tavernier,J., Hill,D.E., Vidal,M., Roth,F.P. and Calderwood,M.A.
  TITLE     A reference map of the human binary protein interactome
  JOURNAL   Nature 580 (7803), 402-408 (2020)
   PUBMED   32296183
REFERENCE   4  (bases 1 to 1372)
  AUTHORS   Khan,F., Arshad,A., Majeed,A.I., Ullah,A. and Ahmad,W.
  TITLE     A novel frameshift variant in BHLHA9 underlies mesoaxial synostotic
            syndactyly associated with postaxial polydactyly
  JOURNAL   Eur J Med Genet 62 (8), 103688 (2019)
   PUBMED   31152918
  REMARK    GeneRIF: This is the second report providing evidence of
            association of polydactyly with Mesoaxial synostotic syndactyly
            caused by frameshift variant in the gene BHLHA9. The present
            molecular investigation will support genetic counselling of the
            local population carrying diseased variants.
REFERENCE   5  (bases 1 to 1372)
  AUTHORS   Paththinige,C.S., Sirisena,N.D., Escande,F., Manouvrier,S.,
            Petit,F. and Dissanayake,V.H.W.
  TITLE     Split hand/foot malformation with long bone deficiency associated
            with BHLHA9 gene duplication: a case report and review of
            literature
  JOURNAL   BMC Med Genet 20 (1), 108 (2019)
   PUBMED   31200655
  REMARK    GeneRIF: BHLHA9 duplication causing split hand/foot malformation
            with long bone deficiency.
            Review article
            Publication Status: Online-Only
REFERENCE   6  (bases 1 to 1372)
  AUTHORS   Capra,V., Mirabelli-Badenier,M., Stagnaro,M., Rossi,A., Tassano,E.,
            Gimelli,S. and Gimelli,G.
  TITLE     Identification of a rare 17p13.3 duplication including the BHLHA9
            and YWHAE genes in a family with developmental delay and
            behavioural problems
  JOURNAL   BMC Med Genet 13, 93 (2012)
   PUBMED   23035971
  REMARK    GeneRIF: BHLHA9 gene contribute to the phenotype of small 17p13.3
            chromosomal duplication in Miller-Dieker syndrome
            Publication Status: Online-Only
REFERENCE   7  (bases 1 to 1372)
  AUTHORS   Klopocki,E., Lohan,S., Doelken,S.C., Stricker,S., Ockeloen,C.W.,
            Soares Thiele de Aguiar,R., Lezirovitz,K., Mingroni Netto,R.C.,
            Jamsheer,A., Shah,H., Kurth,I., Habenicht,R., Warman,M.,
            Devriendt,K., Kordass,U., Hempel,M., Rajab,A., Makitie,O.,
            Naveed,M., Radhakrishna,U., Antonarakis,S.E., Horn,D. and
            Mundlos,S.
  TITLE     Duplications of BHLHA9 are associated with ectrodactyly and tibia
            hemimelia inherited in non-Mendelian fashion
  JOURNAL   J Med Genet 49 (2), 119-125 (2012)
   PUBMED   22147889
  REMARK    GeneRIF: Genomic duplications encompassing BHLHA9 are associated
            with SHFLD and non-Mendelian inheritance characterised by a high
            degree of non-penetrance with sex bias.
REFERENCE   8  (bases 1 to 1372)
  AUTHORS   Vaquerizas,J.M., Kummerfeld,S.K., Teichmann,S.A. and Luscombe,N.M.
  TITLE     A census of human transcription factors: function, expression and
            evolution
  JOURNAL   Nat Rev Genet 10 (4), 252-263 (2009)
   PUBMED   19274049
  REMARK    Review article
REFERENCE   9  (bases 1 to 1372)
  AUTHORS   Stevens,J.D., Roalson,E.H. and Skinner,M.K.
  TITLE     Phylogenetic and expression analysis of the basic helix-loop-helix
            transcription factor gene family: genomic approach to cellular
            differentiation
  JOURNAL   Differentiation 76 (9), 1006-1022 (2008)
   PUBMED   18557763
REFERENCE   10 (bases 1 to 1372)
  AUTHORS   McLellan,A.S., Langlands,K. and Kealey,T.
  TITLE     Exhaustive identification of human class II basic helix-loop-helix
            proteins by virtual library screening
  JOURNAL   Mech Dev 119 Suppl 1, S285-S291 (2002)
   PUBMED   14516699
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AC032044.28.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Dec 19, 2019 this sequence version replaced NM_001164405.1.
            
            Summary: This gene is a member of the basic helix-loop-helix
            family. The encoded protein is a transcription factor involved in
            limb development. Mutations in this gene have been associated with
            mesoaxial synostotic syndactyly Malik-Percin type (MSSD). Copy
            number variation of a locus containing this gene has been linked to
            a form of split-hand/foot malformation with long bone deficiency
            (SHFLD3). [provided by RefSeq, Mar 2015].
            
            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 is intronless :: SRR9304715.411703.1 [ECO:0000345]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000391429.2/ ENSP00000375248.1
            RefSeq Select criteria :: based on single protein-coding transcript
            ##RefSeq-Attributes-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-1372              AC032044.28        177517-178888       c
FEATURES             Location/Qualifiers
     source          1..1372
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="17"
                     /map="17p13.3"
     gene            1..1372
                     /gene="BHLHA9"
                     /gene_synonym="BHLHF42; CCSPD"
                     /note="basic helix-loop-helix family member a9"
                     /db_xref="GeneID:727857"
                     /db_xref="HGNC:HGNC:35126"
                     /db_xref="MIM:615416"
     exon            1..1372
                     /gene="BHLHA9"
                     /gene_synonym="BHLHF42; CCSPD"
                     /inference="alignment:Splign:2.1.0"
     CDS             121..828
                     /gene="BHLHA9"
                     /gene_synonym="BHLHF42; CCSPD"
                     /note="Fingerin; class II basic helix-loop-helix protein;
                     class F basic helix-loop-helix factor 42"
                     /codon_start=1
                     /product="class A basic helix-loop-helix protein 9"
                     /protein_id="NP_001157877.1"
                     /db_xref="CCDS:CCDS45560.1"
                     /db_xref="GeneID:727857"
                     /db_xref="HGNC:HGNC:35126"
                     /db_xref="MIM:615416"
                     /translation="MLRGAPGLGLTARKGAEDSAEDLGGPCPEPGGDSGVLGANGASC
                     SRGEAEEPAGRRRARPVRSKARRMAANVRERKRILDYNEAFNALRRALRHDLGGKRLS
                     KIATLRRAIHRIAALSLVLRASPAPRGPCGHLECHGPAARGDTGDTGASPPPPAGPSL
                     ARPDAARPSVPSAPRCASCPPHAPLARPSAVAEGPGLAQASGGSWRRCPGASSAGPPP
                     WPRGYLRSAPGMGHPRS"
     regulatory      1355..1360
                     /regulatory_class="polyA_signal_sequence"
                     /gene="BHLHA9"
                     /gene_synonym="BHLHF42; CCSPD"
                     /note="hexamer: AATAAA"
     polyA_site      1372
                     /gene="BHLHA9"
                     /gene_synonym="BHLHF42; CCSPD"
                     /note="major polyA site"
ORIGIN      
        1 gggagtgtcc agccccagga gccggggacc gtccgcgtcg cgagccgggc caaggcagtg
       61 ggcagagggc agagggcaga gggccggggc tggggcagag ggcgagtgcc cgggaaggcc
      121 atgctgcggg gcgcgccagg actaggcctc acggcgcgga agggggccga ggactctgcg
      181 gaggacttgg ggggcccctg ccccgagccc gggggcgatt cgggggtgct gggggcgaac
      241 ggcgcttcct gcagccgggg cgaggcggag gagccggcgg gcaggaggcg cgcgcggccg
      301 gtgcggtcca aggcgcggcg catggccgcc aacgtgcggg agcgcaagcg catcctagac
      361 tacaacgagg ccttcaacgc gctgcgccgg gcgctgcggc acgacctggg cggcaagagg
      421 ctctccaaga tcgccacgct gcgcagggcc atccaccgca tcgccgcgct ctccctggtc
      481 ctgcgcgcca gccccgcgcc ccgcgggccc tgcggacacc tggagtgcca cggcccggcc
      541 gcgcgcgggg acaccgggga cacaggcgcc agccccccgc cgcctgcagg gcccagcctc
      601 gcgcgcccag acgccgcccg cccctcggtg ccgtccgcgc cccgctgcgc ctcgtgcccc
      661 ccgcacgcgc ccctggcacg gcccagtgcg gtggccgagg ggccgggcct agcacaggcc
      721 tccgggggaa gctggcgccg ctgtccgggg gcttcctctg ccgggccgcc tccctggccg
      781 cggggctacc tgcgatccgc ccccgggatg ggccatccgc gctcctgacc ggcctcgagg
      841 caccggctgg gctgcaggga ggccgggctg gcagctggac tataaaaccc gggactgcaa
      901 aggcgtcttg gacagagcag aactggaccg gctgagacct ggcgtggaag agaaggagct
      961 cgccagagag aaggagctcc gggacccggg gttgcgcccc cacatcccag cctggggcag
     1021 agagaaggag ctccggggcc tggggctgcg cccccacatc ccagcctagg gaggcagttg
     1081 ccagaaaggc tcaggatcct gaactcatct tggactcgaa ctcgtcttgg aatgccgcct
     1141 tcgcactcct gcgcctccga gccctgtgtg ttctcgatgc ttttaggaga gtgagggctt
     1201 tgaggcagga ggtgtgggag cgtgggaatg cgggtggggc ctgctgtggt ctcgtgggca
     1261 catgagtgcg gagtcccctt ccctgcctgc gctgctgccc aagcctgatc cgggagaggc
     1321 aggatccggg agaggcaggc aggggcagca gccaaataaa aggaaaaact ca
//
