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    BNC2 basonuclin zinc finger protein 2 [ Homo sapiens (human) ]

    Gene ID: 54796, updated on 2-Nov-2024

    Summary

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    Official Symbol
    BNC2provided by HGNC
    Official Full Name
    basonuclin zinc finger protein 2provided by HGNC
    Primary source
    HGNC:HGNC:30988
    See related
    Ensembl:ENSG00000173068 MIM:608669; AllianceGenome:HGNC:30988
    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
    bn2; BSN2; LUTO
    Summary
    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]
    Expression
    Biased expression in endometrium (RPKM 6.6), ovary (RPKM 5.5) and 13 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See BNC2 in Genome Data Viewer
    Location:
    9p22.3-p22.2
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (16409503..16870670, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (16421369..16882518, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (16409501..16870668, complement)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene coiled-coil domain containing 171 Neighboring gene uncharacterized LOC107987049 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr9:16030074-16031273 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:16036253-16036508 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:16060174-16061373 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:16179471-16179971 Neighboring gene NANOG hESC enhancer GRCh37_chr9:16243838-16244339 Neighboring gene long intergenic non-protein coding RNA 3041 Neighboring gene uncharacterized LOC124902124 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:16322644-16323144 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:16329447-16330006 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19788 Neighboring gene uncharacterized LOC124902125 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr9:16435259-16436458 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28216 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr9:16485208-16485860 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr9:16485861-16486512 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:16515916-16516476 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:16515335-16515901 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:16514088-16514670 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:16514766-16515334 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:16626962-16627495 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:16653272-16653772 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:16704398-16705152 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:16706560-16707060 Neighboring gene VISTA enhancer hs307 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:16726395-16726896 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:16730147-16730694 Neighboring gene Sharpr-MPRA regulatory region 7975 Neighboring gene NANOG hESC enhancer GRCh37_chr9:16795834-16796335 Neighboring gene Sharpr-MPRA regulatory region 8712 Neighboring gene BNC2 antisense RNA 1 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr9:16809986-16810513 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:16810514-16811042 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_107116 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr9:16867432-16868631 Neighboring gene LSM1 homolog, mRNA degradation associated pseudogene 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:16921666-16922273 Neighboring gene uncharacterized LOC124902126 Neighboring gene uncharacterized LOC105375983 Neighboring gene RNA, 7SL, cytoplasmic 720, pseudogene

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Genome-wide investigation of regional blood-based DNA methylation adjusted for complete blood counts implicates BNC2 in ovarian cancer. Winham SJ, et al. Genet Epidemiol, 2014 Jul. PMID 24853948, Free PMC Article
    2. Human skin color is influenced by an intergenic DNA polymorphism regulating transcription of the nearby BNC2 pigmentation gene. Visser M, et al. Hum Mol Genet, 2014 Nov 1. PMID 24916375
    3. Basonuclin-2 regulates extracellular matrix production and degradation. Orang A, et al. Life Sci Alliance, 2023 Oct. PMID 37536977, Free PMC Article
    4. Chromosomal abnormalities and novel disease-related regions in progression from Barrett's esophagus to esophageal adenocarcinoma. Akagi T, et al. Int J Cancer, 2009 Nov 15. PMID 19670330, Free PMC Article
    5. Genetic variation on 9p22 is associated with abnormal ovarian ultrasound results in the Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial. Wentzensen N, et al. PLoS One, 2011. PMID 21750727, Free PMC Article

    See all (48) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Basonuclin-2 regulates extracellular matrix production and degradation.
      Title: Basonuclin-2 regulates extracellular matrix production and degradation.
    2. Functional genomics uncovers the transcription factor BNC2 as required for myofibroblastic activation in fibrosis.
      Title: Functional genomics uncovers the transcription factor BNC2 as required for myofibroblastic activation in fibrosis.
    3. Genomic characterization of the adolescent idiopathic scoliosis-associated transcriptome and regulome.
      Title: Genomic characterization of the adolescent idiopathic scoliosis-associated transcriptome and regulome.
    4. BNC2 Mutation is associated with Autosomal-Dominant Congenital Lower Urinary-Tract Obstruction.
      Title: Rare Variants in BNC2 Are Implicated in Autosomal-Dominant Congenital Lower Urinary-Tract Obstruction.
    5. The BNC2 locus is related to risk of adolescent idiopathic scoliosis globally.
      Title: An international meta-analysis confirms the association of BNC2 with adolescent idiopathic scoliosis.
    6. the intergenic region located around rs3814113 regulates BNC2 expression, which in turn affects cell survival after oxidative stress response.
      Title: BNC2 is a putative tumor suppressor gene in high-grade serous ovarian carcinoma and impacts cell survival after oxidative stress.
    7. This study suggests a functional role of BNC2 in the development and progression of the spinal deformity in adolescent idiopathic scoliosis.
      Title: Genetic variant of BNC2 gene is functionally associated with adolescent idiopathic scoliosis in Chinese population.
    8. Study indicates that BNC2 expression was down-regulated in hepatocellular tumors and cell lines showing a frequent gene deletion.
      Title: Decreased Expression of BNC1 and BNC2 Is Associated with Genetic or Epigenetic Regulation in Hepatocellular Carcinoma.
    9. A functional SNP leading to increased expression in BNC2 is implicated in the etiology of Adolescent Idiopathic Scoliosis.
      Title: A Functional SNP in BNC2 Is Associated with Adolescent Idiopathic Scoliosis.
    10. BNC2 gene mutation influencing facial pigmented spots.
      Title: A Genome-Wide Association Study Identifies the Skin Color Genes IRF4, MC1R, ASIP, and BNC2 Influencing Facial Pigmented Spots.
    Submit: New GeneRIF Correction See all GeneRIFs (28)

    Phenotypes

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    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
    Lower urinary tract obstruction, congenital
    MedGen: C5231427 OMIM: 618612 GeneReviews: Not available
    		Compare labs

    EBI GWAS Catalog

    Description
    A genome-wide association study identifies a new ovarian cancer susceptibility locus on 9p22.2.
    EBI GWAS Catalog
    A genome-wide search for quantitative trait loci affecting the cortical surface area and thickness of Heschl's gyrus.
    EBI GWAS Catalog
    Genome-wide association study of a heart failure related metabolomic profile among African Americans in the Atherosclerosis Risk in Communities (ARIC) study.
    EBI GWAS Catalog
    Hundreds of variants clustered in genomic loci and biological pathways affect human height.
    EBI GWAS Catalog
    Web-based, participant-driven studies yield novel genetic associations for common traits.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ20043, FLJ34928, DKFZp686A01127

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables rDNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in endochondral bone growth IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in mesenchyme development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of DNA-templated transcription IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in roof of mouth development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in tongue development IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in chromatin IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    zinc finger protein basonuclin-2
    Names
    basonuclin 2

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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_051226.1 RefSeqGene

      Range
      5051..466336
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001317939.2 → NP_001304868.1  zinc finger protein basonuclin-2 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 5' coding region, contains an alternate penultimate exon and uses an alternate splice site in the 3' terminal exon, compared to variant 1. It encodes isoform 2 which is shorter and has a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AL449983, CR933649
      UniProtKB/TrEMBL
      H0Y6W5
      Related
      ENSP00000408370.1, ENST00000418777.5
      Conserved Domains (1) summary
      sd00017
      Location:401 → 422
      ZF_C2H2; C2H2 Zn finger [structural motif]

    2. NM_001317940.2 → NP_001304869.1  zinc finger protein basonuclin-2 isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) has multiple differences, compared to variant 1. These differences result in a distinct 5' UTR and cause translation initiation at an alternate start codon, compared to variant 1. The encoded protein (isoform 3) is shorter and has a distinct N-terminus, compared to isoform 1.
      Source sequence(s)
      AK299073, AL449983
      UniProtKB/TrEMBL
      B4DR27
      Conserved Domains (1) summary
      sd00017
      Location:942 → 963
      ZF_C2H2; C2H2 Zn finger [structural motif]

    3. NM_017637.6 → NP_060107.3  zinc finger protein basonuclin-2 isoform 1

      See identical proteins and their annotated locations for NP_060107.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AK131398, AL449983, AY438376, DA494074
      Consensus CDS
      CCDS6482.2
      UniProtKB/Swiss-Prot
      B1APG9, Q6T3A3, Q6ZN30, Q8NAR2, Q9H6J0, Q9NXV0
      UniProtKB/TrEMBL
      B1APH0
      Related
      ENSP00000370047.3, ENST00000380672.9
      Conserved Domains (1) summary
      sd00017
      Location:1037 → 1058
      ZF_C2H2; C2H2 Zn finger [structural motif]

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000009.12 Reference GRCh38.p14 Primary Assembly

      Range
      16409503..16870670 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047423506.1 → XP_047279462.1  zinc finger protein basonuclin-2 isoform X26

    2. XM_047423501.1 → XP_047279457.1  zinc finger protein basonuclin-2 isoform X21

      Related
      ENSP00000515060.1, ENST00000700553.1

    3. XM_047423494.1 → XP_047279450.1  zinc finger protein basonuclin-2 isoform X15

    4. XM_047423514.1 → XP_047279470.1  zinc finger protein basonuclin-2 isoform X34

    5. XM_047423513.1 → XP_047279469.1  zinc finger protein basonuclin-2 isoform X33

    6. XM_047423493.1 → XP_047279449.1  zinc finger protein basonuclin-2 isoform X14

    7. XM_047423512.1 → XP_047279468.1  zinc finger protein basonuclin-2 isoform X32

      Related
      ENSP00000431516.1, ENST00000484726.5

    8. XM_047423488.1 → XP_047279444.1  zinc finger protein basonuclin-2 isoform X9

    9. XM_047423487.1 → XP_047279443.1  zinc finger protein basonuclin-2 isoform X8

    10. XM_047423515.1 → XP_047279471.1  zinc finger protein basonuclin-2 isoform X35

    11. XM_047423481.1 → XP_047279437.1  zinc finger protein basonuclin-2 isoform X2

    12. XM_047423486.1 → XP_047279442.1  zinc finger protein basonuclin-2 isoform X7

    13. XM_047423484.1 → XP_047279440.1  zinc finger protein basonuclin-2 isoform X5

    14. XM_047423489.1 → XP_047279445.1  zinc finger protein basonuclin-2 isoform X10

    15. XM_047423510.1 → XP_047279466.1  zinc finger protein basonuclin-2 isoform X30

    16. XM_047423511.1 → XP_047279467.1  zinc finger protein basonuclin-2 isoform X31

    17. XM_047423505.1 → XP_047279461.1  zinc finger protein basonuclin-2 isoform X25

    18. XM_047423517.1 → XP_047279473.1  zinc finger protein basonuclin-2 isoform X37

    19. XM_047423500.1 → XP_047279456.1  zinc finger protein basonuclin-2 isoform X20

    20. XM_047423503.1 → XP_047279459.1  zinc finger protein basonuclin-2 isoform X23

    21. XM_047423516.1 → XP_047279472.1  zinc finger protein basonuclin-2 isoform X36

    22. XM_047423502.1 → XP_047279458.1  zinc finger protein basonuclin-2 isoform X22

    23. XM_047423498.1 → XP_047279454.1  zinc finger protein basonuclin-2 isoform X19

    24. XM_047423508.1 → XP_047279464.1  zinc finger protein basonuclin-2 isoform X28

    25. XM_047423495.1 → XP_047279451.1  zinc finger protein basonuclin-2 isoform X16

    26. XM_047423491.1 → XP_047279447.1  zinc finger protein basonuclin-2 isoform X12

    27. XM_047423492.1 → XP_047279448.1  zinc finger protein basonuclin-2 isoform X13

      Related
      ENSP00000370042.1, ENST00000380667.6

    28. XM_047423483.1 → XP_047279439.1  zinc finger protein basonuclin-2 isoform X4

    29. XM_047423480.1 → XP_047279436.1  zinc finger protein basonuclin-2 isoform X1

    30. XM_047423482.1 → XP_047279438.1  zinc finger protein basonuclin-2 isoform X3

    31. XM_047423485.1 → XP_047279441.1  zinc finger protein basonuclin-2 isoform X6

    32. XM_047423490.1 → XP_047279446.1  zinc finger protein basonuclin-2 isoform X11

    33. XM_047423507.1 → XP_047279463.1  zinc finger protein basonuclin-2 isoform X27

    34. XM_047423496.1 → XP_047279452.1  zinc finger protein basonuclin-2 isoform X17

    35. XM_047423504.1 → XP_047279460.1  zinc finger protein basonuclin-2 isoform X24

    36. XM_047423497.1 → XP_047279453.1  zinc finger protein basonuclin-2 isoform X18

    37. XM_047423509.1 → XP_047279465.1  zinc finger protein basonuclin-2 isoform X29

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060933.1 Alternate T2T-CHM13v2.0

      Range
      16421369..16882518 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6ZN30.1 GenPept UniProtKB/Swiss-Prot:Q6ZN30

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