BHLHA9 (basic helix-loop-helix family member a9)

Gene

• Entrez ID: 727857
• Gene name: Basic helix-loop-helix family member a9
• Gene symbol: BHLHA9
• Synonyms: BHLHF42, CCSPD
• Chromosome: 17
• Chromosome location: 17p13.3
• 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

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs672601337	A>G	Pathogenic	Coding sequence variant, missense variant
rs672601338	G>C	Pathogenic	Coding sequence variant, missense variant
rs672601339	G>T	Pathogenic	Coding sequence variant, missense variant
rs886037856	GA>TT	Likely-pathogenic	Missense variant, coding sequence variant

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000785	Component	Chromatin	ISA
GO:0000977	Function	RNA polymerase II transcription regulatory region sequence-specific DNA binding	IBA	21873635
GO:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	IBA	21873635
GO:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	ISA
GO:0005515	Function	Protein binding	IPI	25466284, 32296183
GO:0005634	Component	Nucleus	IEA
GO:0005737	Component	Cytoplasm	IDA	25466284
GO:0006357	Process	Regulation of transcription by RNA polymerase II	IBA	21873635
GO:0007275	Process	Multicellular organism development	IEA
GO:0032502	Process	Developmental process	IBA	21873635
GO:0046982	Function	Protein heterodimerization activity	IDA	25466284

Other IDs

• MIM: 615416
• HGNC: 35126
• e!Ensembl: ENSG00000205899

Protein

• UniProt ID: Q7RTU4
• Protein name: Class A basic helix-loop-helix protein 9 (bHLHa9) (Class F basic helix-loop-helix factor 42) (bHLHf42)
• Protein function: Transcription factor, which play a role in limb development. Is an essential player in the regulatory network governing transcription of genes implicated in limb morphogenesis.
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00010	HLH	66 → 118	Helix-loop-helix DNA-binding domain	Domain

• Sequence:

  MLRGAPGLGLTARKGAEDSAEDLGGPCPEPGGDSGVLGANGASCSRGEAEEPAGRRRARP
  VRSKARRMAANVRERKRILDYNEAFNALRRALRHDLGGKRLSKIATLRRAIHRIAALSLV
  LRASPAPRGPCGHLECHGPAARGDTGDTGASPPPPAGPSLARPDAARPSVPSAPRCASCP
  PHAPLARPSAVAEGPGLAQASGGSWRRCPGASSAGPPPWPRGYLRSAPGMGHPRS

• Sequence length: 235

Associated diseases

Causal
Disease name	Disease term	dbSNP ID	References
Brachydactyly	Brachydactyly	rs121908949, rs28937580, rs121909082, rs104894122, rs863223289, rs863223290, rs104894121, rs1587657302, rs863223292, rs74315386, rs74315387, rs28936397, rs753691079, rs121909348, rs121917852, rs121917853, rs121917854, rs121917855, rs121917859, rs121917861, rs267606873, rs267606872, rs267606985, rs267606986, rs267606987, rs267606988, rs28933082, rs397514519, rs869025613, rs869025614, rs886039878, rs1553540620, rs1057518333, rs1948841937, rs1948868228, rs1948842030, rs1948842142
Camptosynpolydactyly	Camptosynpolydactyly, Complex	rs886037856	27041388
Ectrodactyly	Ectrodactyly	rs1850314485
Polydactyly	Polydactyly, Polydactyly preaxial type 1	rs1583729398, rs121917709, rs1583734240, rs121917714, rs397507422, rs398122899, rs587776959, rs386833752, rs1057518698, rs1060499558, rs755938967, rs1375768446, rs1309855392, rs1565601979, rs748321474, rs368652620, rs1562587032, rs760694987	22147889
Split-hand-foot malformation with sensorineural hearing loss	Split-Hand-Foot Malformation With Sensorineural Hearing Loss	rs387906737	22147889

Unknown
Disease name	Disease term	dbSNP ID	References
Camptodactyly of fingers	Clinodactyly of the 5th finger
Congenital camptodactyly	Congenital Camptodactyly
Short femur	Congenital hypoplasia of femur
Congenital omphalocele	Congenital omphalocele
Gollop-wolfgang complex	Femur bifid with monodactylous ectrodactyly, Gollop-Wolfgang complex		25351291
Hypoplasia of thumb	Hypoplasia of thumb
Split-hand-foot malformation with long bone deficiency	Split-Hand-Foot Malformation With Long Bone Deficiency 1
Syndactyly, mesoaxial synostotic, with phalangeal reduction	Syndactyly, Mesoaxial Synostotic, with Phalangeal Reduction		25466284, 22147889
Syndactyly of fingers	Syndactyly of fingers
Syndactyly of the toes	Syndactyly of the toes, 2-3 toe syndactyly
Tibial aplasia-ectrodactyly syndrome	Tibial aplasia-ectrodactyly syndrome
Postaxial hand polydactyly	Ulnar polydactyly of fingers