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Aliases for BHLHA9 Gene

Aliases for BHLHA9 Gene

  • Basic Helix-Loop-Helix Family Member A9 2 3 5
  • Class F Basic Helix-Loop-Helix Factor 42 3 4
  • Fingerin 2 3
  • BHLHF42 3 4
  • Class A Basic Helix-Loop-Helix Protein 9 3
  • Basic Helix-Loop-Helix Family, Member A9 2
  • Class II Basic Helix-Loop-Helix Protein 3
  • BHLHf42 4
  • BHLHa9 4
  • CCSPD 3

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 Camptosynpolydactyly, Complex. Gene Ontology (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.

Additional gene information for BHLHA9 Gene

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

Genomics for BHLHA9 Gene

GeneHancer (GH) Regulatory Elements for BHLHA9 Gene

Promoters and enhancers for BHLHA9 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH17J001374 Enhancer 0.9 ENCODE dbSUPER 11.1 +105.5 105489 3.5 PKNOX1 ZNF384 EBF1 FEZF1 ZNF121 ZNF366 ZFP91 ATF7 ZNF600 IKZF2 YWHAE INPP5K MYO1C PITPNA TRARG1 BHLHA9 CRK GC17P001386 ENSG00000280408
GH17J001332 Enhancer 0.7 ENCODE 12.4 +62.2 62173 0.2 HDAC1 MEIS2 CTCF TFAP4 PKNOX1 RB1 RAD21 GLIS2 ARID2 ZSCAN5C TRARG1 BHLHA9 YWHAE INPP5K MYO1C RPA1 SMYD4 GC17P001337 GC17M001298
GH17J001533 Enhancer 0.6 ENCODE 11.3 +263.5 263489 1.6 CTCF ZNF654 RXRA REST ELF1 RAD21 ZBTB33 SPI1 PIR53156 PITPNA TRARG1 BHLHA9 PIR60547 GC17M001526
GH17J001328 Enhancer 0.4 dbSUPER 12.4 +59.1 59086 3 ZSCAN21 NFE2 TRARG1 YWHAE BHLHA9 INPP5K MYO1C RPA1 SMYD4 CRK GC17P001337 GC17M001298
GH17J001102 Enhancer 0.4 dbSUPER 11 -166.6 -166554 2.4 ZNF341 NR2F2 ABR ENSG00000235361 BHLHA9 TRARG1 GLOD4 ENSG00000278794 LOC105371480
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around BHLHA9 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the BHLHA9 gene promoter:
  • PPAR-gamma2
  • PPAR-gamma1
  • C/EBPalpha
  • PPAR-alpha
  • GATA-1
  • CUTL1
  • RFX1
  • deltaCREB
  • CREB
  • AhR

Genomic Locations for BHLHA9 Gene

Genomic Locations for BHLHA9 Gene
902 bases
Plus strand
902 bases
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:
    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:
    • Heterodimer (PubMed:25466284). Efficient DNA binding requires dimerization with another bHLH protein. Interacts with TCF3, TCF4, and TCF12 (PubMed:25466284).
    • Sequence=DAA00302.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

neXtProt entry for BHLHA9 Gene

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

Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins
  • Transcription factors

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

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

No data available for UniProtKB/Swiss-Prot for BHLHA9 Gene

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:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding ISM 19274049
GO:0003677 DNA binding IEA --
GO:0005515 protein binding IPI 25466284
GO:0046982 protein heterodimerization activity IDA 25466284
GO:0046983 protein dimerization activity 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

Clone Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , 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

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for BHLHA9 gene
Compartment Confidence
nucleus 5
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 IEA,IDA 25466284
genes like me logo Genes that share ontologies with BHLHA9: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) 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

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006357 regulation of transcription by RNA polymerase II IEA --
GO:0007275 multicellular organism development IEA --
genes like me logo Genes that share ontologies with BHLHA9: view

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:

Clone 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 from GTEx, Illumina, BioGPS, and CGAP SAGE 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).

NURSA nuclear receptor signaling pathways regulating expression of BHLHA9 Gene:


SOURCE GeneReport for Unigene cluster for BHLHA9 Gene:


Phenotype-based relationships between genes and organs from Gene ORGANizer for BHLHA9 Gene

Germ Layers:
  • ectoderm
  • mesoderm
  • integumentary
  • skeleton
Head and neck:
  • ear
  • head
  • outer ear
  • ankle
  • arm
  • digit
  • elbow
  • finger
  • foot
  • forearm
  • hand
  • hip
  • knee
  • lower limb
  • shin
  • shoulder
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
  • skin
genes like me logo Genes that share expression patterns with BHLHA9: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Evidence on tissue expression from TISSUES 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 34 33
  • 99.29 (n)
(Bos Taurus)
Mammalia BHLHA9 34 33
  • 81.75 (n)
(Canis familiaris)
Mammalia BHLHA9 34 33
  • 81.57 (n)
(Rattus norvegicus)
Mammalia Bhlha9 33
  • 76.44 (n)
(Mus musculus)
Mammalia Bhlha9 16 34 33
  • 76.11 (n)
(Ornithorhynchus anatinus)
Mammalia BHLHA9 34
  • 51 (a)
Species where no ortholog for BHLHA9 was found in the sources mined by GeneCards:
  • 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)
Evolutionary constrained regions (ECRs) for BHLHA9: view image

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 Variation AA Info Type
rs672601337 pathogenic, Syndactyly type 9, Syndactyly, mesoaxial synostotic, with phalangeal reduction (MSSD) [MIM:609432] 1,270,774(+) A/G coding_sequence_variant, missense_variant
rs672601338 pathogenic, Syndactyly type 9, Syndactyly, mesoaxial synostotic, with phalangeal reduction (MSSD) [MIM:609432] 1,270,781(+) G/C coding_sequence_variant, missense_variant
rs672601339 pathogenic, Syndactyly type 9, Syndactyly, mesoaxial synostotic, with phalangeal reduction (MSSD) [MIM:609432] 1,270,787(+) G/T coding_sequence_variant, missense_variant
rs886037856 conflicting-interpretations-of-pathogenicity, Camptosynpolydactyly, complex, Camptosynpolydactyly, complex (CCSPD) [MIM:607539] 1,270,783(+) GA/TT coding_sequence_variant, missense_variant
rs1000204130 -- 1,269,695(+) G/A upstream_transcript_variant

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

Variant ID Type Subtype PubMed ID
dgv3080n100 CNV gain 25217958
dgv3081n100 CNV gain 25217958
esv2761939 CNV loss 21179565
nsv1064006 CNV gain 25217958
nsv509645 CNV insertion 20534489
nsv952097 CNV deletion 24416366

Variation tolerance for BHLHA9 Gene

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

Additional Variant Information for BHLHA9 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

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

Disorders for BHLHA9 Gene

MalaCards: The human disease database

(7) MalaCards diseases for BHLHA9 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
syndactyly, mesoaxial synostotic, with phalangeal reduction
  • mssd
camptosynpolydactyly, complex
  • ccspd
tibial aplasia-ectrodactyly syndrome
  • aplasia of tibia with split-hand/split-foot deformity
split hand-foot malformation
  • split-hand deformity
split-hand/foot malformation 6
  • shfm6
- elite association - COSMIC cancer census association via MalaCards


  • 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.
  • Camptosynpolydactyly, complex (CCSPD) [MIM:607539]: An autosomal recessive disorder characterized by hand and foot deformities consisting of polydactyly with digits arising from the dorsum of hands, syn- and camptodactyly of some fingers, soft tissue syndactyly of first and second toes, and dysplastic nails. {ECO:0000269 PubMed:27041388}. Note=The disease may be caused by mutations affecting the gene represented in this entry.

Additional Disease Information for 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 AS … Kealey T (Mechanisms of development 2002) 2 3 4 58
  2. Mutations affecting the BHLHA9 DNA-binding domain cause MSSD, mesoaxial synostotic syndactyly with phalangeal reduction, Malik-Percin type. (PMID: 25466284) Malik S … Grzeschik KH (American journal of human genetics 2014) 3 4 58
  3. Duplications of BHLHA9 are associated with ectrodactyly and tibia hemimelia inherited in non-Mendelian fashion. (PMID: 22147889) Klopocki E … Mundlos S (Journal of medical genetics 2012) 3 4 58
  4. Phylogenetic and expression analysis of the basic helix-loop-helix transcription factor gene family: genomic approach to cellular differentiation. (PMID: 18557763) Stevens JD … Skinner MK (Differentiation; research in biological diversity 2008) 2 3 58
  5. Complex Camptosynpolydactyly and Mesoaxial synostotic syndactyly with phalangeal reduction are allelic disorders. (PMID: 27041388) Phadke SR … Dalal A (American journal of medical genetics. Part A 2016) 4 58

Products for BHLHA9 Gene

Sources for BHLHA9 Gene

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