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

Gene ID: 54796, updated on 7-Apr-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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Location:
9p22.3-p22.2
Exon count:
17
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (16409503..16870670, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (16421369..16882518, complement)
105.20220307 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
  • 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. An international meta-analysis confirms the association of BNC2 with adolescent idiopathic scoliosis. Ogura Y, et al. Sci Rep, 2018 Mar 16. PMID 29549362, Free PMC Article
  2. Genetic variant of BNC2 gene is functionally associated with adolescent idiopathic scoliosis in Chinese population. Xu L, et al. Mol Genet Genomics, 2017 Aug. PMID 28342042
  3. BNC2 is a putative tumor suppressor gene in high-grade serous ovarian carcinoma and impacts cell survival after oxidative stress. Cesaratto L, et al. Cell Death Dis, 2016 Sep 22. PMID 27899818, Free PMC Article
  4. 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
  5. 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

See all (46) 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
part_of 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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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_2023_10

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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