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Aliases for NHLH1 Gene

Aliases for NHLH1 Gene

  • Nescient Helix-Loop-Helix 1 2 3 5
  • Class A Basic Helix-Loop-Helix Protein 35 3 4
  • Nescient Helix Loop Helix 1 2 4
  • BHLHa35 3 4
  • NSCL-1 3 4
  • HEN-1 3 4
  • HEN1 3 4
  • Helix-Loop-Helix Protein 1 3
  • NSCL1 3
  • NSCL 3

External Ids for NHLH1 Gene

Previous HGNC Symbols for NHLH1 Gene

  • HEN1

Previous GeneCards Identifiers for NHLH1 Gene

  • GC01P158128
  • GC01P156069
  • GC01P157114
  • GC01P157553
  • GC01P157149
  • GC01P158603
  • GC01P160336
  • GC01P131693
  • GC01P160367

Summaries for NHLH1 Gene

Entrez Gene Summary for NHLH1 Gene

  • The helix-loop-helix (HLH) proteins are a family of putative transcription factors, some of which have been shown to play an important role in growth and development of a wide variety of tissues and species. Four members of this family have been clearly implicated in tumorigenesis via their involvement in chromosomal translocations in lymphoid tumors: MYC (MIM 190080), LYL1 (MIM 151440), E2A (MIM 147141), and SCL (MIM 187040).[supplied by OMIM, Nov 2002]

GeneCards Summary for NHLH1 Gene

NHLH1 (Nescient Helix-Loop-Helix 1) is a Protein Coding gene. Diseases associated with NHLH1 include Cleft Palate, Isolated and Physical Disorder. Gene Ontology (GO) annotations related to this gene include protein dimerization activity and transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific DNA binding. An important paralog of this gene is NHLH2.

UniProtKB/Swiss-Prot for NHLH1 Gene

  • May serve as DNA-binding protein and may be involved in the control of cell-type determination, possibly within the developing nervous system.

Gene Wiki entry for NHLH1 Gene

Additional gene information for NHLH1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for NHLH1 Gene

Genomics for NHLH1 Gene

GeneHancer (GH) Regulatory Elements for NHLH1 Gene

Promoters and enhancers for NHLH1 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
GH01I160283 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 550.8 -1.9 -1938 2.7 HDGF PKNOX1 FOXA2 SMAD1 ARID4B SIN3A DMAP1 YY1 SLC30A9 POLR2B ENSG00000258465 PEX19 NHLH1 DEDD B4GALT3 LINC01133 NCSTN SLAMF8 USP21 COPA
GH01I160368 Promoter/Enhancer 1 EPDnew dbSUPER 550.2 +80.7 80683 0.1 ZNF148 HDAC1 POLR2B POLR2A VEZF1 ZEB2 NHLH1 GC01P160354 RNU4-42P
GH01I159936 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 6.2 -344.9 -344912 10.5 PKNOX1 CLOCK SIN3A ZNF2 ZBTB7B YY1 ZNF143 KLF13 SP3 NFYC IGSF9 ATP1A4 KCNJ10 NHLH1 LINC01133 VSIG8 CFAP45 VANGL2 TAGLN2
GH01I160427 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 10.2 +144.3 144271 6 HDGF HDAC1 PKNOX1 SMAD1 BATF IRF4 RAD21 ZBTB40 ZNF766 ARID2 VANGL2 SLAMF7 SLAMF1 NCSTN ENSG00000228863 NHLH1 ITLN1 CD48 CD244 LY9
GH01I160621 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 9.9 +342.3 342251 13.9 HDGF ATF1 PKNOX1 SMAD1 TCF12 ZNF766 ATF7 RUNX3 JUNB ZNF592 VANGL2 ENSG00000228863 COPA NCSTN SLAMF7 NHLH1 RNU4-42P ITLN1 SLAMF6 SLAMF1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around NHLH1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the NHLH1 gene promoter:

Genomic Locations for NHLH1 Gene

Genomic Locations for NHLH1 Gene
86,480 bases
Plus strand

Genomic View for NHLH1 Gene

Genes around NHLH1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NHLH1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NHLH1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NHLH1 Gene

Proteins for NHLH1 Gene

  • Protein details for NHLH1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Helix-loop-helix protein 1
    Protein Accession:

    Protein attributes for NHLH1 Gene

    133 amino acids
    Molecular mass:
    14618 Da
    Quaternary structure:
    • Efficient DNA binding requires dimerization with another bHLH protein.

neXtProt entry for NHLH1 Gene

Post-translational modifications for NHLH1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for NHLH1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for NHLH1 Gene

Domains & Families for NHLH1 Gene

Gene Families for NHLH1 Gene

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

Protein Domains for NHLH1 Gene

Suggested Antigen Peptide Sequences for NHLH1 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with NHLH1: view

No data available for UniProtKB/Swiss-Prot for NHLH1 Gene

Function for NHLH1 Gene

Molecular function for NHLH1 Gene

GENATLAS Biochemistry:
nescient helix loop helix protein 1,binding the E-box motif,transciently expressed during neuro-genesis,involved in retinal development. Also expressed in neuroblastoma cell line
UniProtKB/Swiss-Prot Function:
May serve as DNA-binding protein and may be involved in the control of cell-type determination, possibly within the developing nervous system.

Phenotypes From GWAS Catalog for NHLH1 Gene

Gene Ontology (GO) - Molecular Function for NHLH1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding IDA 12878195
GO:0001228 transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific DNA binding IDA 12878195
GO:0003677 DNA binding IEA --
GO:0005515 protein binding IPI --
GO:0046983 protein dimerization activity IEA --
genes like me logo Genes that share ontologies with NHLH1: view
genes like me logo Genes that share phenotypes with NHLH1: view

Animal Models for NHLH1 Gene

MGI Knock Outs for NHLH1:

Animal Model Products

CRISPR Products

miRNA for NHLH1 Gene

miRTarBase miRNAs that target NHLH1

Transcription Factor Targets for NHLH1 Gene

Selected GeneGlobe predicted Target genes for NHLH1

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology and HOMER Transcription for NHLH1 Gene

Localization for NHLH1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for NHLH1 Gene

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 NHLH1 gene
Compartment Confidence
nucleus 5
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Golgi apparatus (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for NHLH1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA --
genes like me logo Genes that share ontologies with NHLH1: view

Pathways & Interactions for NHLH1 Gene

SuperPathways for NHLH1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for NHLH1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006366 transcription by RNA polymerase II IEA --
GO:0007275 multicellular organism development IEA --
GO:0007417 central nervous system development TAS 1328219
genes like me logo Genes that share ontologies with NHLH1: view

No data available for Pathways by source and SIGNOR curated interactions for NHLH1 Gene

Drugs & Compounds for NHLH1 Gene

No Compound Related Data Available

Transcripts for NHLH1 Gene

mRNA/cDNA for NHLH1 Gene

(1) REFSEQ mRNAs :
(4) Additional mRNA sequences :
(19) Selected AceView cDNA sequences:
(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for NHLH1 Gene

Nescient helix loop helix 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for NHLH1 Gene

No ASD Table

Relevant External Links for NHLH1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for NHLH1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for NHLH1 Gene

mRNA differential expression in normal tissues according to GTEx for NHLH1 Gene

This gene is overexpressed in Brain - Nucleus accumbens (basal ganglia) (x4.3), Brain - Putamen (basal ganglia) (x4.2), and Brain - Caudate (basal ganglia) (x4.2).

NURSA nuclear receptor signaling pathways regulating expression of NHLH1 Gene:


SOURCE GeneReport for Unigene cluster for NHLH1 Gene:


Evidence on tissue expression from TISSUES for NHLH1 Gene

  • Nervous system(4.4)
  • Eye(4.1)
genes like me logo Genes that share expression patterns with NHLH1: view

Primer Products

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 Phenotype-based relationships between genes and organs from Gene ORGANizer for NHLH1 Gene

Orthologs for NHLH1 Gene

This gene was present in the common ancestor of animals.

Orthologs for NHLH1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia NHLH1 33 34
  • 99.25 (n)
(Monodelphis domestica)
Mammalia NHLH1 34
  • 95 (a)
(Bos Taurus)
Mammalia NHLH1 33 34
  • 90.73 (n)
(Canis familiaris)
Mammalia NHLH1 33 34
  • 89.9 (n)
(Mus musculus)
Mammalia Nhlh1 33 16 34
  • 88.97 (n)
(Rattus norvegicus)
Mammalia Nhlh1 33
  • 88.97 (n)
(Gallus gallus)
Aves NHLH1 33 34
  • 78.46 (n)
(Anolis carolinensis)
Reptilia NHLH1 34
  • 90 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia nhlh1 33
  • 68.75 (n)
(Danio rerio)
Actinopterygii nhlh2 34
  • 68 (a)
fruit fly
(Drosophila melanogaster)
Insecta HLH4C 34
  • 45 (a)
(Caenorhabditis elegans)
Secernentea hlh-15 34
  • 65 (a)
Species where no ortholog for NHLH1 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)
  • 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)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • 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)
  • wheat (Triticum aestivum)

Evolution for NHLH1 Gene

Gene Tree for NHLH1 (if available)
Gene Tree for NHLH1 (if available)

Paralogs for NHLH1 Gene

Paralogs for NHLH1 Gene

(9) SIMAP similar genes for NHLH1 Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with NHLH1: view

Variants for NHLH1 Gene

Sequence variations from dbSNP and Humsavar for NHLH1 Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs1000824034 -- 160,367,810(+) G/T intron_variant
rs1001505943 -- 160,372,224(+) C/A 3_prime_UTR_variant
rs1001820521 -- 160,365,577(+) G/T upstream_transcript_variant
rs1001915294 -- 160,365,652(+) G/A upstream_transcript_variant
rs1001983410 -- 160,367,141(+) G/A 5_prime_UTR_variant

Structural Variations from Database of Genomic Variants (DGV) for NHLH1 Gene

Variant ID Type Subtype PubMed ID
nsv1078290 CNV deletion 25765185
nsv548056 CNV loss 21841781

Variation tolerance for NHLH1 Gene

Residual Variation Intolerance Score: 65.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.52; 11.34% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for NHLH1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NHLH1 Gene

Disorders for NHLH1 Gene

MalaCards: The human disease database

(8) MalaCards diseases for NHLH1 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
cleft palate, isolated
  • cpi
physical disorder
  • physical illness
orofacial cleft
cleft lip/palate-ectodermal dysplasia syndrome
  • clped1
  • neuroblastoma, susceptibility to
- elite association - COSMIC cancer census association via MalaCards
Search NHLH1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for NHLH1

genes like me logo Genes that share disorders with NHLH1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for NHLH1 Gene

Publications for NHLH1 Gene

  1. A comparative structural characterization of the human NSCL-1 and NSCL-2 genes. Two basic helix-loop-helix genes expressed in the developing nervous system. (PMID: 1328219) Lipkowitz S … Kirsch IR (The Journal of biological chemistry 1992) 3 4 22 58
  2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  3. Regulation of neurogenesis by interactions between HEN1 and neuronal LMO proteins. (PMID: 10603358) Bao J … Gautier J (Development (Cambridge, England) 2000) 3 22 58
  4. HEN1 and HEN2: a subgroup of basic helix-loop-helix genes that are coexpressed in a human neuroblastoma. (PMID: 1528853) Brown L … Baer R (Proceedings of the National Academy of Sciences of the United States of America 1992) 3 4 58
  5. Discovery of Genetic Variation on Chromosome 5q22 Associated with Mortality in Heart Failure. (PMID: 27149122) Smith JG … Smith NL (PLoS genetics 2016) 3 58

Products for NHLH1 Gene

Sources for NHLH1 Gene

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