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 (NCBI Gene): 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
GO:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	IBA
GO:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	ISA
GO:0003677	Function	DNA binding	IEA
GO:0005515	Function	Protein binding	IPI	25466284, 32296183
GO:0005634	Component	Nucleus	IEA
GO:0005737	Component	Cytoplasm	IDA	25466284
GO:0005737	Component	Cytoplasm	IEA
GO:0006357	Process	Regulation of transcription by RNA polymerase II	IBA
GO:0032502	Process	Developmental process	IBA
GO:0046982	Function	Protein heterodimerization activity	IDA	25466284
GO:0046983	Function	Protein dimerization activity	IEA

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
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Camptosynpolydactyly, complex	Likely pathogenic	rs886037856	RCV000239477
Mesoaxial synostotic syndactyly with phalangeal reduction	Pathogenic; Likely pathogenic	rs672601337, rs672601338, rs672601339	RCV000149486 RCV000149487 RCV000149488 RCV003990948

Unknown
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
BHLHA9-related disorder	Benign; Uncertain significance; Likely benign	rs3951819, rs1008519083, rs1236657811, rs545441558	RCV003983970 RCV004757466 RCV003899714 RCV003958218

Associations from Text Mining
Disease Name	Relationship Type	References
Adamantinoma	Associate	25351291
Alcohol Related Disorders	Associate	23035971
Alcoholism	Associate	23035971
Autistic Disorder	Associate	23035971
Bipolar Disorder	Associate	23035971
Developmental Disabilities	Associate	23035971
Ectrodactyly	Associate	25351291
Femur bifid with monodactylous ectrodactyly	Associate	25351291
Split hand foot malformation with long bone deficiency	Associate	23813913, 25351291
Split Hand Foot Malformation With Long Bone Deficiency 3	Stimulate	36028842
Syndactyly Mesoaxial Synostotic with Phalangeal Reduction	Associate	25466284