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Aliases for BHLHA9 Gene

Aliases for BHLHA9 Gene

  • Basic Helix-Loop-Helix Family Member A9 2 3 5
  • Basic Helix-Loop-Helix Family, Member A9 2 3
  • Class F Basic Helix-Loop-Helix Factor 42 3 4
  • Fingerin 2 3
  • BHLHF42 3 4
  • Class II Basic Helix-Loop-Helix Protein 3
  • BHLHa9 4

External Ids for BHLHA9 Gene

Previous GeneCards Identifiers for BHLHA9 Gene

  • GC17P001121
  • GC17P001174
  • GC17P001076
  • GC17P001175

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 syndactyly, mesoaxial synostotic, with phalangeal reduction and syndactyly. GO annotations related to this gene include protein heterodimerization activity and protein dimerization activity.

UniProtKB/Swiss-Prot for BHLHA9 Gene

  • 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.

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

Genomic Location for BHLHA9 Gene

Chromosome:
17
Start:
1,270,559 bp from pter
End:
1,271,460 bp from pter
Size:
902 bases
Orientation:
Plus strand

Genomic View for BHLHA9 Gene

Genes around BHLHA9 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
BHLHA9 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
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:
    Q7RTU4-BHA09_HUMAN
    Recommended name:
    Class A basic helix-loop-helix protein 9
    Protein Accession:
    Q7RTU4
    Secondary Accessions:
    • A8MSH6

    Protein attributes for BHLHA9 Gene

    Size:
    235 amino acids
    Molecular mass:
    24132 Da
    Quaternary structure:
    • Heterodimer (PubMed:25466284). Efficient DNA binding requires dimerization with another bHLH protein. Interacts with TCF3, TCF4, and TCF12 (PubMed:25466284).
    SequenceCaution:
    • 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 & Families for BHLHA9 Gene

Gene Families for BHLHA9 Gene

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

UniProtKB/Swiss-Prot:

BHA09_HUMAN :
  • Contains 1 bHLH (basic helix-loop-helix) domain.
Domain:
  • 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:
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.

Gene Ontology (GO) - Molecular Function for BHLHA9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
genes like me logo Genes that share ontologies with BHLHA9: view

Phenotypes for BHLHA9 Gene

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

Human Phenotype Ontology for BHLHA9 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for BHLHA9 Gene

MGI Knock Outs for BHLHA9:

Animal Model Products

CRISPR Products

No data available for Enzyme Numbers (IUBMB) , miRNA , Transcription Factor Targets and HOMER Transcription for BHLHA9 Gene

Localization for BHLHA9 Gene

Subcellular locations from UniProtKB/Swiss-Prot for BHLHA9 Gene

Nucleus. Cytoplasm.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for BHLHA9 Gene COMPARTMENTS Subcellular localization image for BHLHA9 gene
Compartment Confidence
nucleus 5
cytosol 2
extracellular 1

No data available for Gene Ontology (GO) - Cellular Components for BHLHA9 Gene

Pathways & Interactions for BHLHA9 Gene

SuperPathways for BHLHA9 Gene

No Data Available

Interacting Proteins for BHLHA9 Gene

Gene Ontology (GO) - Biological Process for BHLHA9 Gene

None

No data available for Pathways by source and SIGNOR curated interactions for BHLHA9 Gene

Drugs & Compounds for BHLHA9 Gene

No Compound Related Data Available

Transcripts for BHLHA9 Gene

mRNA/cDNA for BHLHA9 Gene

(1) REFSEQ mRNAs :
(0) Additional mRNA sequences :
(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:

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

No ASD Table

Relevant External Links for BHLHA9 Gene

GeneLoc Exon Structure for
BHLHA9
ECgene alternative splicing isoforms for
BHLHA9

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 (x9.9), Brain - Frontal Cortex (BA9) (x8.8), Brain - Anterior cingulate cortex (BA24) (x6.3), Brain - Amygdala (x4.8), and Brain - Hypothalamus (x4.8).

SOURCE GeneReport for Unigene cluster for BHLHA9 Gene Hs.723790

genes like me logo Genes that share expression patterns with BHLHA9: view

In Situ Assay Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein differential expression in normal tissues , Protein expression , mRNA Expression by UniProt/SwissProt and Protein tissue co-expression partners 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
cow
(Bos Taurus)
Mammalia BHLHA9 35
  • 81.75 (n)
  • 74.66 (a)
BHLHA9 36
  • 74 (a)
OneToOne
dog
(Canis familiaris)
Mammalia BHLHA9 35
  • 81.57 (n)
  • 73.23 (a)
BHLHA9 36
  • 48 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Bhlha9 35
  • 76.11 (n)
  • 68.58 (a)
Bhlha9 16
Bhlha9 36
  • 67 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia BHLHA9 35
  • 99.29 (n)
  • 98.72 (a)
BHLHA9 36
  • 99 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Bhlha9 35
  • 76.44 (n)
  • 71.11 (a)
platypus
(Ornithorhynchus anatinus)
Mammalia BHLHA9 36
  • 51 (a)
OneToOne
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

ENSEMBL:
Gene Tree for BHLHA9 (if available)
TreeFam:
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
VAR_073333 Syndactyly, mesoaxial synostotic, with phalangeal reduction (MSSD)
VAR_073334 Syndactyly, mesoaxial synostotic, with phalangeal reduction (MSSD)
VAR_073335 Syndactyly, mesoaxial synostotic, with phalangeal reduction (MSSD)
rs2063188 -- 1,270,496(+) GGCCA(A/G)GGCAG upstream-variant-2KB
rs3951819 -- 1,270,800(+) ATCCT(A/G)GACTA reference, synonymous-codon

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

Variation tolerance for BHLHA9 Gene

Gene Damage Index Score: 0.49; 10.66% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for BHLHA9 Gene

HapMap Linkage Disequilibrium report
BHLHA9
Human Gene Mutation Database (HGMD)
BHLHA9

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

Disorders for BHLHA9 Gene

MalaCards: The human disease database

(8) MalaCards diseases for BHLHA9 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
syndactyly, mesoaxial synostotic, with phalangeal reduction
  • syndactyly type 9
syndactyly
  • chromosome 2q35 duplication syndrome
ectrodactyly with tibial hemimelia
  • split-hand/foot malformation with long bone deficiency
split hand foot malformation
  • ectrodactyly
split hand
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

BHA09_HUMAN
  • 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}.
  • Syndactyly, mesoaxial synostotic, with phalangeal reduction (MSSD) [MIM:609432]: An autosomal recessive, non-syndromic digit anomaly characterized by mesoaxial osseous synostosis at a metacarpal level, reduction of one or more phalanges, hypoplasia of distal phalanges of preaxial and postaxial digits, clinodactyly of fifth fingers, and preaxial fusion of toes. {ECO:0000269 PubMed:25466284}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for BHLHA9

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
BHLHA9
genes like me logo Genes that share disorders with BHLHA9: view

No data available for Genatlas for BHLHA9 Gene

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 67
  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. Severe ipsilateral musculoskeletal involvement in a Cornelia de Lange patient with a novel NIPBL mutation. (PMID: 24874887) Baquero-Montoya C. … PiAc J. (Eur J Med Genet 2014) 3
  4. Japanese founder duplications/triplications involving BHLHA9 are associated with split-hand/foot malformation with or without long bone deficiency and Gollop-Wolfgang complex. (PMID: 25351291) Nagata E. … Ogata T. (Orphanet J Rare Dis 2014) 3
  5. Mutations affecting the BHLHA9 DNA-binding domain cause MSSD, mesoaxial synostotic syndactyly with phalangeal reduction, Malik-Percin type. (PMID: 25466284) Malik S. … Grzeschik K.H. (Am. J. Hum. Genet. 2014) 3

Products for BHLHA9 Gene

Sources for BHLHA9 Gene

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