Free for academic non-profit institutions. Other users need a Commercial license

Aliases for BNC2 Gene

Aliases for BNC2 Gene

  • Basonuclin 2 2 3 5
  • Zinc Finger Protein Basonuclin-2 3
  • BSN2 3

External Ids for BNC2 Gene

Previous GeneCards Identifiers for BNC2 Gene

  • GC09U900603

Summaries for BNC2 Gene

Entrez Gene Summary for BNC2 Gene

  • This gene encodes a conserved zinc finger protein. The encoded protein functions in skin color saturation. Mutations in this gene are associated with facial pigmented spots. This gene is also associated with susceptibility to adolescent idiopathic scoliosis. [provided by RefSeq, Jul 2016]

GeneCards Summary for BNC2 Gene

BNC2 (Basonuclin 2) is a Protein Coding gene. Diseases associated with BNC2 include Idiopathic Scoliosis and Scoliosis. An important paralog of this gene is BNC1.

UniProtKB/Swiss-Prot for BNC2 Gene

  • Probable transcription factor specific for skin keratinocytes. May play a role in the differentiation of spermatozoa and oocytes.

Gene Wiki entry for BNC2 Gene

Additional gene information for BNC2 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for BNC2 Gene

Genomics for BNC2 Gene

GeneHancer (GH) Regulatory Elements for BNC2 Gene

Promoters and enhancers for BNC2 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
GH09J016702 Promoter/Enhancer 2.7 UCNEbase EPDnew Ensembl ENCODE dbSUPER 650.1 +166.4 166373 4.8 SIN3A FEZF1 ZNF2 GLIS2 DEK REST TSHZ1 MAFF GLIS1 STAT3 GC09P016706 BNC2 GC09P016632
GH09J016725 Promoter/Enhancer 2.4 UCNEbase EPDnew Ensembl ENCODE dbSUPER 650.1 +143.7 143743 2.8 ZSCAN4 MZF1 SIN3A ZNF2 RAD21 RCOR1 ZBTB11 CEBPB REST SP1 BNC2-AS1 BNC2 PIR38257
GH09J016866 Promoter/Enhancer 2.1 EPDnew FANTOM5 Ensembl ENCODE 662.2 +1.4 1355 6.2 PKNOX1 MZF1 SIN3A FEZF1 ZNF335 GLIS2 EGR2 ZNF362 CEBPB ZNF398 BNC2 GC09M016779 LSM1P1
GH09J016824 Enhancer 1.4 UCNEbase Ensembl ENCODE dbSUPER 11.2 +45.1 45061 3.3 CTCF RFX1 MZF1 RAD21 ZNF335 JUND POLR2A SMC3 FOS BNC2 ENSG00000230694 LSM1P1 GC09M016779
GH09J016827 Enhancer 1.2 UCNEbase Ensembl ENCODE 11.6 +42.0 41993 1.8 RFX1 REST ZIC2 NR2F2 GLIS2 CTBP1 POLR2A ZNF341 RCOR1 BNC2 GC09M016779 LSM1P1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around BNC2 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the BNC2 gene promoter:
  • AREB6
  • Olf-1
  • Nkx2-5
  • FOXD3
  • HFH-1
  • Cdc5
  • ISGF-3
  • Sox5
  • RORalpha1
  • RP58

Genomic Locations for BNC2 Gene

Genomic Locations for BNC2 Gene
461,341 bases
Minus strand
461,341 bases
Minus strand

Genomic View for BNC2 Gene

Genes around BNC2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
BNC2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for BNC2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for BNC2 Gene

Proteins for BNC2 Gene

  • Protein details for BNC2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Zinc finger protein basonuclin-2
    Protein Accession:
    Secondary Accessions:
    • B1APG9
    • Q6T3A3
    • Q8NAR2
    • Q9H6J0
    • Q9NXV0

    Protein attributes for BNC2 Gene

    1099 amino acids
    Molecular mass:
    122330 Da
    Quaternary structure:
    No Data Available
    • Sequence=AAR99389.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=BAA90908.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=BAB15269.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=BAC03837.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for BNC2 Gene


neXtProt entry for BNC2 Gene

Post-translational modifications for BNC2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for BNC2 Gene

Domains & Families for BNC2 Gene

Gene Families for BNC2 Gene

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

Protein Domains for BNC2 Gene


Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with BNC2: view

No data available for UniProtKB/Swiss-Prot for BNC2 Gene

Function for BNC2 Gene

Molecular function for BNC2 Gene

UniProtKB/Swiss-Prot Function:
Probable transcription factor specific for skin keratinocytes. May play a role in the differentiation of spermatozoa and oocytes.

Phenotypes From GWAS Catalog for BNC2 Gene

Gene Ontology (GO) - Molecular Function for BNC2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding ISA --
GO:0003676 nucleic acid binding IEA --
GO:0003677 DNA binding IEA --
GO:0008270 zinc ion binding IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with BNC2: view
genes like me logo Genes that share phenotypes with BNC2: view

Animal Model Products

CRISPR Products

miRNA for BNC2 Gene

miRTarBase miRNAs that target BNC2

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for BNC2

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for BNC2 Gene

Localization for BNC2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for BNC2 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 BNC2 gene
Compartment Confidence
plasma membrane 5
nucleus 5
cytosol 5

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for BNC2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm IDA --
genes like me logo Genes that share ontologies with BNC2: view

Pathways & Interactions for BNC2 Gene

No Data Available

Gene Ontology (GO) - Biological Process for BNC2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003416 endochondral bone growth IEA --
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:0043586 tongue development IEA --
genes like me logo Genes that share ontologies with BNC2: view

No data available for Pathways by source and SIGNOR curated interactions for BNC2 Gene

Drugs & Compounds for BNC2 Gene

No Compound Related Data Available

Transcripts for BNC2 Gene

Unigene Clusters for BNC2 Gene

Basonuclin 2:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for BNC2

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for BNC2 Gene

ExUns: 1 ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6a · 6b ^ 7 ^ 8 ^ 9a · 9b · 9c ^ 10 ^ 11 ^ 12
SP1: - - - - - -
SP2: -

Relevant External Links for BNC2 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for BNC2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for BNC2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for BNC2 Gene

This gene is overexpressed in Uterus (x5.6), Ovary (x5.6), and Fallopian Tube (x4.9).

Protein differential expression in normal tissues from HIPED for BNC2 Gene

This gene is overexpressed in Vitreous humor (65.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for BNC2 Gene

Protein tissue co-expression partners for BNC2 Gene

NURSA nuclear receptor signaling pathways regulating expression of BNC2 Gene:


SOURCE GeneReport for Unigene cluster for BNC2 Gene:


mRNA Expression by UniProt/SwissProt for BNC2 Gene:

Tissue specificity: Highly expressed in testis, uterus and small intestine, and weakly expressed in colon and prostate. Also expressed in skin, primary keratinocytes, immortalized keratinocytes, and HeLa and HEK293 cells. Not detected in blood, thymus, spleen or Hep-G2 cells.

Evidence on tissue expression from TISSUES for BNC2 Gene

  • Muscle(2.7)
genes like me logo Genes that share expression patterns with BNC2: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for BNC2 Gene

Orthologs for BNC2 Gene

This gene was present in the common ancestor of animals.

Orthologs for BNC2 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia BNC2 34 33
  • 99.82 (n)
(Canis familiaris)
Mammalia BNC2 34 33
  • 94.29 (n)
(Ornithorhynchus anatinus)
Mammalia BNC2 34
  • 93 (a)
(Monodelphis domestica)
Mammalia BNC2 34
  • 92 (a)
(Bos Taurus)
Mammalia BNC2 34 33
  • 91.96 (n)
(Rattus norvegicus)
Mammalia Bnc2 33
  • 90.99 (n)
(Mus musculus)
Mammalia Bnc2 16 34 33
  • 90.91 (n)
(Gallus gallus)
Aves BNC2 34 33
  • 83.41 (n)
(Anolis carolinensis)
Reptilia BNC2 34
  • 62 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia bnc2 33
  • 76.94 (n)
(Danio rerio)
Actinopterygii bnc2 34
  • 61 (a)
fruit fly
(Drosophila melanogaster)
Insecta disco 34
  • 25 (a)
disco-r 34
  • 13 (a)
(Caenorhabditis elegans)
Secernentea F55C5.11 34
  • 33 (a)
Species where no ortholog for BNC2 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)
  • 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 BNC2 Gene

Gene Tree for BNC2 (if available)
Gene Tree for BNC2 (if available)
Evolutionary constrained regions (ECRs) for BNC2: view image

Paralogs for BNC2 Gene

Paralogs for BNC2 Gene

(7) SIMAP similar genes for BNC2 Gene using alignment to 22 proteins:

  • F5H586_HUMAN
  • H0Y4J1_HUMAN
  • H0Y6W5_HUMAN
  • Q06HB5_HUMAN
  • Q06HB6_HUMAN
  • Q06HB7_HUMAN
  • Q06HB8_HUMAN
  • Q06HB9_HUMAN
  • Q06HC0_HUMAN
  • Q06HC1_HUMAN
  • Q06HC2_HUMAN
  • Q06HC3_HUMAN
  • Q06HC4_HUMAN
  • Q06HC5_HUMAN
  • Q06HC6_HUMAN
  • Q06HC7_HUMAN
  • S4R351_HUMAN
  • S4R3K9_HUMAN
  • S4R3R8_HUMAN
  • S4R3X5_HUMAN
genes like me logo Genes that share paralogs with BNC2: view

Variants for BNC2 Gene

Sequence variations from dbSNP and Humsavar for BNC2 Gene

SNP ID Clin Chr 09 pos Variation AA Info Type
rs114596065 not-provided, benign, Hypotension, not specified 16,436,326(-) G/T coding_sequence_variant, missense_variant
rs114964332 not-provided, Hypotension 16,437,278(-) G/A/C/T coding_sequence_variant, missense_variant
rs117452684 not-provided, conflicting-interpretations-of-pathogenicity, Hypotension, not specified 16,419,521(-) G/A/C 3_prime_UTR_variant, coding_sequence_variant, downstream_transcript_variant, genic_downstream_transcript_variant, missense_variant
rs117470554 not-provided, Hypotension 16,436,649(-) T/A/C coding_sequence_variant, synonymous_variant
rs138187836 not-provided, Hypotension 16,436,143(-) G/A coding_sequence_variant, missense_variant

Structural Variations from Database of Genomic Variants (DGV) for BNC2 Gene

Variant ID Type Subtype PubMed ID
dgv2137e212 CNV loss 25503493
dgv2138e212 CNV gain 25503493
dgv262n6 CNV deletion 16902084
esv1256705 CNV insertion 17803354
esv1359645 CNV insertion 17803354
esv1378850 CNV deletion 17803354
esv1725129 CNV deletion 17803354
esv2675274 CNV deletion 23128226
esv2738238 CNV deletion 23290073
esv2738240 CNV deletion 23290073
esv2738241 CNV deletion 23290073
esv2759673 CNV loss 17122850
esv2761269 CNV loss 21179565
esv3303408 CNV mobile element insertion 20981092
esv3308537 CNV mobile element insertion 20981092
esv3325173 CNV insertion 20981092
esv3344588 CNV insertion 20981092
esv3357139 CNV insertion 20981092
esv3401243 CNV insertion 20981092
esv3409571 CNV insertion 20981092
esv3437436 CNV insertion 20981092
esv3544602 CNV deletion 23714750
esv3573152 CNV loss 25503493
esv3573154 CNV loss 25503493
esv3619815 CNV loss 21293372
esv3619816 CNV loss 21293372
esv3619817 CNV gain 21293372
esv3619818 CNV loss 21293372
esv3619821 CNV loss 21293372
esv3619822 CNV loss 21293372
esv3891623 CNV gain 25118596
esv993349 CNV deletion 20482838
nsv1028923 CNV loss 25217958
nsv1030598 CNV loss 25217958
nsv1075194 CNV deletion 25765185
nsv1077093 CNV deletion 25765185
nsv1124402 CNV deletion 24896259
nsv1137426 CNV deletion 24896259
nsv1145207 CNV deletion 24896259
nsv466265 CNV loss 19166990
nsv476796 CNV novel sequence insertion 20440878
nsv510183 OTHER sequence alteration 20534489
nsv518608 CNV loss 19592680
nsv524264 CNV gain 19592680
nsv524954 CNV loss 19592680
nsv528443 CNV loss 19592680
nsv613670 CNV loss 21841781
nsv613671 CNV loss 21841781
nsv824866 CNV loss 20364138

Variation tolerance for BNC2 Gene

Residual Variation Intolerance Score: 10.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.19; 61.92% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for BNC2 Gene

Human Gene Mutation Database (HGMD)
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 BNC2 Gene

Disorders for BNC2 Gene

MalaCards: The human disease database

(2) MalaCards diseases for BNC2 Gene - From: HGMD, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
idiopathic scoliosis
  • scoliosis idiopathic
- elite association - COSMIC cancer census association via MalaCards
Search BNC2 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for BNC2

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with BNC2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for BNC2 Gene

Publications for BNC2 Gene

  1. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 2 3 4 58
  2. Basonuclin 2: an extremely conserved homolog of the zinc finger protein basonuclin. (PMID: 14988505) Vanhoutteghem A … Djian P (Proceedings of the National Academy of Sciences of the United States of America 2004) 3 4 22 58
  3. A genome-wide association study identifies a novel major locus for glycemic control in type 1 diabetes, as measured by both A1C and glucose. (PMID: 19875614) Paterson AD … Diabetes Control and Complications Trial/Epidemiology of Diabetes Interventions and Complications Research Group (Diabetes 2010) 3 44 58
  4. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 44 58
  5. Web-based, participant-driven studies yield novel genetic associations for common traits. (PMID: 20585627) Eriksson N … Mountain J (PLoS genetics 2010) 3 44 58

Products for BNC2 Gene

Sources for BNC2 Gene

Loading form....