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Aliases for BHLHA9 Gene

Aliases for BHLHA9 Gene

  • Basic Helix-Loop-Helix Family, Member A9 2 3
  • BHLHF42 3 4 6
  • Class F Basic Helix-Loop-Helix Factor 42 3 4
  • Class A Basic Helix-Loop-Helix Protein 9 3
  • Class II Basic Helix-Loop-Helix Protein 3
  • BHLHa9 4

External Ids for BHLHA9 Gene

Previous GeneCards Identifiers for BHLHA9 Gene

  • GC17P001121
  • GC17P001174
  • GC17P001076

Summaries for BHLHA9 Gene

Entrez Gene Summary for BHLHA9 Gene

  • 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]

GeneCards Summary for BHLHA9 Gene

BHLHA9 (Basic Helix-Loop-Helix Family, Member A9) is a Protein Coding gene. Diseases associated with BHLHA9 include split-hand/foot malformation with long bone deficiency 1 and syndactyly, mesoaxial synostotic, with phalangeal reduction. GO annotations related to this gene include protein dimerization activity.

UniProtKB/Swiss-Prot for BHLHA9 Gene

  • Putative transcription factor, which may play a role in limb development.

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for BHLHA9 Gene

Genomics for BHLHA9 Gene

Regulatory Elements for BHLHA9 Gene

Epigenetics Products

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat

Genomic Location for BHLHA9 Gene

1,270,559 bp from pter
1,271,460 bp from pter
902 bases
Plus strand

Genomic View for BHLHA9 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for BHLHA9 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for BHLHA9 Gene

Proteins for BHLHA9 Gene

  • Protein details for BHLHA9 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Class A basic helix-loop-helix protein 9
    Protein Accession:
    Secondary Accessions:
    • A8MSH6

    Protein attributes for BHLHA9 Gene

    235 amino acids
    Molecular mass:
    24132 Da
    Quaternary structure:
    No Data Available
    • Sequence=DAA00302.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

neXtProt entry for BHLHA9 Gene

Proteomics data for BHLHA9 Gene at MOPED

Post-translational modifications for BHLHA9 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for BHLHA9 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for BHLHA9 Gene

Domains for BHLHA9 Gene

Gene Families for BHLHA9 Gene

  • bHLH :Basic helix-loop-helix proteins

Protein Domains for BHLHA9 Gene

Suggested Antigen Peptide Sequences for BHLHA9 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Q7RTU4
  • Contains 1 bHLH (basic helix-loop-helix) domain.
genes like me logo Genes that share domains with BHLHA9: view

Function for BHLHA9 Gene

Molecular function for BHLHA9 Gene

UniProtKB/Swiss-Prot Function: Putative transcription factor, which may play a role in limb development.

Gene Ontology (GO) - Molecular Function for BHLHA9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0005515 protein binding IPI 25466284
GO:0046982 protein heterodimerization activity IDA 25466284
GO:0046983 protein dimerization activity --
genes like me logo Genes that share ontologies with BHLHA9: view

Animal Model Products

CRISPR Products

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for BHLHA9

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes , Animal Models , miRNA , Transcription Factor Targeting and HOMER Transcription for BHLHA9 Gene

Localization for BHLHA9 Gene

Subcellular locations from UniProtKB/Swiss-Prot for BHLHA9 Gene

Subcellular locations from

Jensen Localization Image for BHLHA9 Gene COMPARTMENTS Subcellular localization image for BHLHA9 gene
Compartment Confidence
nucleus 3
cytosol 2
extracellular 1

Gene Ontology (GO) - Cellular Components for BHLHA9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005737 cytoplasm IDA 25466284
genes like me logo Genes that share ontologies with BHLHA9: view

Pathways for BHLHA9 Gene

SuperPathways for BHLHA9 Gene

No Data Available

Interacting Proteins for BHLHA9 Gene

Gene Ontology (GO) - Biological Process for BHLHA9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0007275 multicellular organismal development IEA --
genes like me logo Genes that share ontologies with BHLHA9: view

No data available for Pathways by source for BHLHA9 Gene

Transcripts for BHLHA9 Gene

mRNA/cDNA for BHLHA9 Gene

(0) Additional mRNA sequences :
(1) REFSEQ mRNAs :
(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for BHLHA9 Gene

Basic helix-loop-helix family, member a9:
Representative Sequences:

CRISPR Products

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for BHLHA9

Primer Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for BHLHA9 Gene

No ASD Table

Relevant External Links for BHLHA9 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for BHLHA9 Gene

mRNA expression in normal human tissues for BHLHA9 Gene

mRNA differential expression in normal tissues according to GTEx for BHLHA9 Gene

This gene is overexpressed in Brain - Cortex (9.9), Brain - Frontal Cortex (BA9) (8.8), Brain - Anterior cingulate cortex (BA24) (6.3), Brain - Amygdala (4.8), and Brain - Hypothalamus (4.8).

SOURCE GeneReport for Unigene cluster for BHLHA9 Gene Hs.723790

genes like me logo Genes that share expressions with BHLHA9: view

In Situ Assay Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein expression and mRNA Expression by UniProt/SwissProt for BHLHA9 Gene

Orthologs for BHLHA9 Gene

This gene was present in the common ancestor of mammals.

Orthologs for BHLHA9 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia BHLHA9 35
  • 99.29 (n)
  • 98.72 (a)
  • 99 (a)
(Bos Taurus)
Mammalia BHLHA9 35
  • 81.75 (n)
  • 74.66 (a)
  • 74 (a)
(Canis familiaris)
Mammalia BHLHA9 35
  • 81.57 (n)
  • 73.23 (a)
  • 48 (a)
(Mus musculus)
Mammalia Bhlha9 35
  • 76.11 (n)
  • 68.58 (a)
Bhlha9 16
Bhlha9 36
  • 67 (a)
(Ornithorhynchus anatinus)
Mammalia BHLHA9 36
  • 51 (a)
(Rattus norvegicus)
Mammalia Bhlha9 35
  • 76.44 (n)
  • 71.11 (a)
Species with no ortholog for BHLHA9:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for BHLHA9 Gene

Gene Tree for BHLHA9 (if available)
Gene Tree for BHLHA9 (if available)

Paralogs for BHLHA9 Gene

No data available for Paralogs for BHLHA9 Gene

Variants for BHLHA9 Gene

Sequence variations from dbSNP and Humsavar for BHLHA9 Gene

SNP ID Clin Chr 17 pos Sequence Context AA Info Type MAF
rs2063188 -- 1,270,496(+) GGCCA(A/G)GGCAG upstream-variant-2KB
rs3951819 -- 1,270,800(+) ATCCT(A/G)GACTA reference, synonymous-codon
rs5818793 -- 1,270,192(-) GGGTT(-/C)CACAT upstream-variant-2KB
rs8071123 -- 1,271,512(+) GCCTA(G/T)GGAGG downstream-variant-500B
rs11649945 -- 1,271,489(+) TGGGG(C/T)TGCGC downstream-variant-500B

Structural Variations from Database of Genomic Variants (DGV) for BHLHA9 Gene

Variant ID Type Subtype PubMed ID
nsv907493 CNV Loss 21882294
nsv907496 CNV Loss 21882294
nsv907497 CNV Loss 21882294
nsv509645 CNV Insertion 20534489

Relevant External Links for BHLHA9 Gene

HapMap Linkage Disequilibrium report
Human Gene Mutation Database (HGMD)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for BHLHA9 Gene

Disorders for BHLHA9 Gene


  • Split-hand/foot malformation with long bone deficiency 3 (SHFLD3) [MIM:612576]: A disease characterized by the association of split-hand/foot malformation with long bone deficiency involving the tibia and fibula. Split-hand/foot malformation is a limb malformation involving the central rays of the autopod. Phenotypic expression is extremely variable between and within families, and even between limbs of a single patient, ranging from syndactyly and oligodactyly to the most severe monodactyly with only a single phalanx. Limb features include median clefts of the hands and feet, and aplasia and/or hypoplasia of the phalanges, metacarpals, and metatarsals. {ECO:0000269 PubMed:22147889}. Note=Disease susceptibility may be associated with variations affecting the gene represented in this entry. A copy number variation (CNV) resulting in BHLHA9 duplications is a necessary but not sufficient susceptibility factor for Split-hand/foot malformation with long bone deficiency, a highly variable phenotype with reduced penetrance, particularly in females (PubMed:22147889). {ECO:0000269 PubMed:22147889}.
genes like me logo Genes that share disorders with BHLHA9: view

Publications for BHLHA9 Gene

  1. Exhaustive identification of human class II basic helix-loop-helix proteins by virtual library screening. (PMID: 14516699) McLellan A.S. … Kealey T. (Mech. Dev. 2002) 2 3 4
  2. Phylogenetic and expression analysis of the basic helix-loop-helix transcription factor gene family: genomic approach to cellular differentiation. (PMID: 18557763) Stevens J.D. … Skinner M.K. (Differentiation 2008) 2 3
  3. Duplications of BHLHA9 are associated with ectrodactyly and tibia hemimelia inherited in non-Mendelian fashion. (PMID: 22147889) Klopocki E. … Mundlos S. (J. Med. Genet. 2012) 3 4
  4. Identification of a rare 17p13.3 duplication including the BHLHA9 and YWHAE genes in a family with developmental delay and behavioural problems. (PMID: 23035971) Capra V. … Gimelli G. (BMC Med. Genet. 2012) 3
  5. Split hand/foot malformation with long-bone deficiency and BHLHA9 duplication: report of 13 new families. (PMID: 23790188) Petit F. … Escande F. (Clin. Genet. 2013) 3

Products for BHLHA9 Gene

Sources for BHLHA9 Gene

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