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BHLHA9 basic helix-loop-helix family member a9 [ Homo sapiens (human) ]

Gene ID: 727857, updated on 4-Feb-2026
Official Symbol
BHLHA9provided by HGNC
Official Full Name
basic helix-loop-helix family member a9provided by HGNC
Primary source
HGNC:HGNC:35126
See related
Ensembl:ENSG00000205899 MIM:615416; AllianceGenome:HGNC:35126
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CCSPD; BHLHF42
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 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]
Orthologs
all
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See BHLHA9 in Genome Data Viewer
Location:
17p13.3
Exon count:
1
Annotation release Status Assembly Chr Location
RS_2025_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (1270444..1271815)
RS_2025_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (1161409..1162780)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (1173738..1175109)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene ABR activator of RhoGEF and GTPase Neighboring gene mitochondrial ribosomal protein L14 pseudogene 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1083316-1084082 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11443 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11444 Neighboring gene MPRA-validated peak2673 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11446 Neighboring gene ABR antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1119641-1120638 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1123483-1123982 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11447 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:1131887-1132591 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7948 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7949 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11448 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:1167109-1167284 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:1170929-1171732 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:1171733-1172535 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1174140-1174890 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1202102-1202696 Neighboring gene trafficking regulator of GLUT4 (SLC2A4) 1 (gene/pseudogene) Neighboring gene Sharpr-MPRA regulatory region 14526 Neighboring gene tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein epsilon Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:1295206-1295734 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:1302101-1302738 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:1302739-1303376 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:1303377-1304014

Go to nucleotide: Graphics FASTA GenBank

Related articles in PubMed

  1. Whole exome sequencing identified a novel frameshift variant in the BHLHA9 in an Iranian family with mesoaxial synostotic syndactyly. Sedighzadeh SS, et al. Congenit Anom (Kyoto), 2021 Nov. PMID 34272776
  2. Split hand/foot malformation with long-bone deficiency and BHLHA9 duplication: report of 13 new families. Petit F, et al. Clin Genet, 2014 May. PMID 23790188
  3. Severe ipsilateral musculoskeletal involvement in a Cornelia de Lange patient with a novel NIPBL mutation. Baquero-Montoya C, et al. Eur J Med Genet, 2014 Sep. PMID 24874887
  4. Japanese founder duplications/triplications involving BHLHA9 are associated with split-hand/foot malformation with or without long bone deficiency and Gollop-Wolfgang complex. Nagata E, et al. Orphanet J Rare Dis, 2014 Oct 21. PMID 25351291, Free PMC Article
  5. Femoral-tibial-digital malformations in a boy with the Japanese founder triplication of BHLHA9. Nagata E, et al. Am J Med Genet A, 2015 Dec. PMID 26333411

See all (17) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. SHFLD3 phenotypes caused by 17p13.3 triplication/ duplication encompassing Fingerin (BHLHA9) invariably.
    Title: SHFLD3 phenotypes caused by 17p13.3 triplication/ duplication encompassing Fingerin (BHLHA9) invariably.
  2. Whole exome sequencing identified a novel frameshift variant in the BHLHA9 in an Iranian family with mesoaxial synostotic syndactyly.
    Title: Whole exome sequencing identified a novel frameshift variant in the BHLHA9 in an Iranian family with mesoaxial synostotic syndactyly.
  3. This is the second report providing evidence of association of polydactyly with Mesoaxial synostotic syndactyly caused by frameshift variant in the gene BHLHA9. The present molecular investigation will support genetic counselling of the local population carrying diseased variants.
    Title: A novel frameshift variant in BHLHA9 underlies mesoaxial synostotic syndactyly associated with postaxial polydactyly.
  4. BHLHA9 duplication causing split hand/foot malformation with long bone deficiency.
    Title: Split hand/foot malformation with long bone deficiency associated with BHLHA9 gene duplication: a case report and review of literature.
  5. A novel insertion and deletion mutation in the BHLHA9 causes polydactyly and mesoaxial synostotic syndactyly with phalangeal reduction.
    Title: A novel insertion and deletion mutation in the BHLHA9 underlies polydactyly and mesoaxial synostotic syndactyly with phalangeal reduction.
  6. Founder triplication of BHLHA9 is associated with femoral-tibial-digital malformations.
    Title: Femoral-tibial-digital malformations in a boy with the Japanese founder triplication of BHLHA9.
  7. this is the first study revealing the underlying genetic factor for the development of GWC, and demonstrating the presence of triplications involving BHLHA9
    Title: Japanese founder duplications/triplications involving BHLHA9 are associated with split-hand/foot malformation with or without long bone deficiency and Gollop-Wolfgang complex.
  8. BHLHA9 is identified as an essential player in the regulatory network governing limb morphogenesis in humans.
    Title: Mutations affecting the BHLHA9 DNA-binding domain cause MSSD, mesoaxial synostotic syndactyly with phalangeal reduction, Malik-Percin type.
  9. Here, we report on 13 new families presenting with ectrodactyly and harboring a BHLHA9 duplication.
    Title: Split hand/foot malformation with long-bone deficiency and BHLHA9 duplication: report of 13 new families.
  10. BHLHA9 gene contribute to the phenotype of small 17p13.3 chromosomal duplication in Miller-Dieker syndrome
    Title: Identification of a rare 17p13.3 duplication including the BHLHA9 and YWHAE genes in a family with developmental delay and behavioural problems.
Submit: New GeneRIF Correction See all GeneRIFs (11)

Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Camptosynpolydactyly, complex
MedGen: C1843758 OMIM: 607539 GeneReviews: Not available
Compare labs
Mesoaxial synostotic syndactyly with phalangeal reduction
MedGen: C1836206 OMIM: 609432 GeneReviews: Not available
Compare labs

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Products Interactant Other Gene Complex Source Pubs Description

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
  
enables DNA-binding transcription factor activity, RNA polymerase II-specific ISA
Inferred from Sequence Alignment
more info
  
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein dimerization activity IEA
Inferred from Electronic Annotation
more info
  
enables protein heterodimerization activity IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in developmental process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in chromatin ISA
Inferred from Sequence Alignment
more info
  
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  
Preferred Names
class A basic helix-loop-helix protein 9
Names
Fingerin
class F basic helix-loop-helix factor 42
class II basic helix-loop-helix protein

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_042055.1 RefSeqGene

    Range
    4881..6252
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001164405.2 → NP_001157877.1  class A basic helix-loop-helix protein 9

    Status: REVIEWED

    Source sequence(s)
    AC032044
    Consensus CDS
    CCDS45560.1
    UniProtKB/Swiss-Prot
    A8MSH6, Q7RTU4
    Related
    ENSP00000375248.1, ENST00000391429.2
    Conserved Domains (1) summary
    pfam00010
    Location:66 → 117
    HLH; Helix-loop-helix DNA-binding domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2025_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    1270444..1271815
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    1161409..1162780
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q7RTU4.2 GenPept UniProtKB/Swiss-Prot:Q7RTU4

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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