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ZBTB40 zinc finger and BTB domain containing 40 [ Homo sapiens (human) ]

Gene ID: 9923, updated on 3-Apr-2024

Summary

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Official Symbol
ZBTB40provided by HGNC
Official Full Name
zinc finger and BTB domain containing 40provided by HGNC
Primary source
HGNC:HGNC:29045
See related
Ensembl:ENSG00000184677 MIM:612106; AllianceGenome:HGNC:29045
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
ZNF923
Summary
Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in cellular response to DNA damage stimulus. Located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in lymph node (RPKM 6.6), spleen (RPKM 6.6) and 25 other tissues See more
Orthologs
mouse all
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Genomic context

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Location:
1p36.12
Exon count:
22
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (22428909..22531154)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (22252494..22354859)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (22778344..22857647)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:22592955-22593474 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:22613139-22613638 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:22618619-22619118 Neighboring gene microRNA 4418 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:22623785-22624284 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:22651838-22652529 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:22702397-22702897 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:22716534-22717034 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:22717035-22717535 Neighboring gene uncharacterized LOC105376856 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:22743723-22744638 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:22769995-22770614 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:22769377-22769994 Neighboring gene Sharpr-MPRA regulatory region 2075 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:22778273-22778834 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:22791857-22792004 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:22880423-22881056 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:22881753-22882336 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:22882919-22883500 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:22883501-22884082 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:22890520-22891020 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:22898749-22899308 Neighboring gene EPH receptor A8 Neighboring gene Sharpr-MPRA regulatory region 15208 Neighboring gene microRNA 6127

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. Risk Variants in or Near ZBTB40 AND NFATC1 Increase the Risk of Both IBD and Adverse Bone Health Outcomes Highlighting Common Genetic Underpinnings Across Both Diseases. Cushing KC, et al. Inflamm Bowel Dis, 2023 Jun 1. PMID 36680554, Free PMC Article
  2. Opposite associations of osteoprotegerin and ZBTB40 polymorphisms with bone mineral density of the hip in postmenopausal Taiwanese women. Chao TH, et al. J Chin Med Assoc, 2012 Jul. PMID 22824048
  3. Genome-wide association study using extreme truncate selection identifies novel genes affecting bone mineral density and fracture risk. Duncan EL, et al. PLoS Genet, 2011 Apr. PMID 21533022, Free PMC Article
  4. Analysis of recently identified osteoporosis susceptibility genes in Han Chinese women. Liu JM, et al. J Clin Endocrinol Metab, 2010 Sep. PMID 20554715
  5. Multiple genetic loci for bone mineral density and fractures. Styrkarsdottir U, et al. N Engl J Med, 2008 May 29. PMID 18445777

See all (34) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. ZBTB40 is a telomere-associated protein and protects telomeres in human ALT cells.
    Title: ZBTB40 is a telomere-associated protein and protects telomeres in human ALT cells.
  2. Risk Variants in or Near ZBTB40 AND NFATC1 Increase the Risk of Both IBD and Adverse Bone Health Outcomes Highlighting Common Genetic Underpinnings Across Both Diseases.
    Title: Risk Variants in or Near ZBTB40 AND NFATC1 Increase the Risk of Both IBD and Adverse Bone Health Outcomes Highlighting Common Genetic Underpinnings Across Both Diseases.
  3. Opposite associations of osteoprotegerin and ZBTB40 polymorphisms with bone mineral density of the hip in postmenopausal Taiwanese women.
    Title: Opposite associations of osteoprotegerin and ZBTB40 polymorphisms with bone mineral density of the hip in postmenopausal Taiwanese women.
  4. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
  5. Observational study of gene-disease association. (HuGE Navigator)
    Title: Analysis of recently identified osteoporosis susceptibility genes in Han Chinese women.
Submit: New GeneRIF Correction

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

EBI GWAS Catalog

Description
Genome-wide association study link novel loci to endometriosis.
EBI GWAS Catalog
Genome-wide association study using extreme truncate selection identifies novel genes affecting bone mineral density and fracture risk.
EBI GWAS Catalog
Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture.
EBI GWAS Catalog
Multiple genetic loci for bone mineral density and fractures.
EBI GWAS Catalog
Multistage genome-wide association meta-analyses identified two new loci for bone mineral density.
EBI GWAS Catalog
Twenty bone-mineral-density loci identified by large-scale meta-analysis of genome-wide association studies.
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

  • KIAA0478, MGC133098

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 metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables molecular_function ND
No biological Data available
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in DNA damage response IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in bone mineralization NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
zinc finger and BTB domain-containing protein 40

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.

mRNA and Protein(s)

  1. NM_001083621.2 → NP_001077090.1  zinc finger and BTB domain-containing protein 40 isoform a

    See identical proteins and their annotated locations for NP_001077090.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript. Both variants 1 and 2 encode the same isoform (a).
    Source sequence(s)
    AK091019, AL035703, AL358788, BC114607, DA248977
    Consensus CDS
    CCDS224.1
    UniProtKB/Swiss-Prot
    O75066, Q5TFU5, Q8N1R1, Q9NUA8
    UniProtKB/TrEMBL
    Q1RMZ5
    Related
    ENSP00000384527.1, ENST00000404138.5
    Conserved Domains (6) summary
    smart00225
    Location:25 → 113
    BTB; Broad-Complex, Tramtrack and Bric a brac
    COG5048
    Location:794 → 970
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:838 → 858
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00019
    Location:952 → 970
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00651
    Location:19 → 113
    BTB; BTB/POZ domain
    pfam13465
    Location:907 → 932
    zf-H2C2_2; Zinc-finger double domain

  2. NM_001330398.2 → NP_001317327.1  zinc finger and BTB domain-containing protein 40 isoform b

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR and lacks two alternate in-frame exons compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a.
    Source sequence(s)
    AL035703, AL358788
    Consensus CDS
    CCDS81278.1
    UniProtKB/TrEMBL
    F8WAI8, Q1RMZ5
    Related
    ENSP00000363782.4, ENST00000374651.8
    Conserved Domains (6) summary
    COG5048
    Location:682 → 858
    COG5048; FOG: Zn-finger [General function prediction only]
    COG5189
    Location:805 → 919
    SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
    sd00017
    Location:726 → 746
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00019
    Location:840 → 858
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00651
    Location:19 → 113
    BTB; BTB/POZ domain
    cl28408
    Location:150 → 231
    UBQ; Ubiquitin homologues

  3. NM_014870.4 → NP_055685.3  zinc finger and BTB domain-containing protein 40 isoform a

    See identical proteins and their annotated locations for NP_055685.3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Both variants 1 and 2 encode the same isoform (a).
    Source sequence(s)
    AL035703, BC114607, DA248977, DA787818
    Consensus CDS
    CCDS224.1
    UniProtKB/Swiss-Prot
    O75066, Q5TFU5, Q8N1R1, Q9NUA8
    UniProtKB/TrEMBL
    Q1RMZ5
    Related
    ENSP00000364798.4, ENST00000375647.5
    Conserved Domains (6) summary
    smart00225
    Location:25 → 113
    BTB; Broad-Complex, Tramtrack and Bric a brac
    COG5048
    Location:794 → 970
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:838 → 858
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00019
    Location:952 → 970
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00651
    Location:19 → 113
    BTB; BTB/POZ domain
    pfam13465
    Location:907 → 932
    zf-H2C2_2; Zinc-finger double domain

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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    22428909..22531154
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011542499.3 → XP_011540801.1  zinc finger and BTB domain-containing protein 40 isoform X1

    See identical proteins and their annotated locations for XP_011540801.1

    UniProtKB/Swiss-Prot
    O75066, Q5TFU5, Q8N1R1, Q9NUA8
    UniProtKB/TrEMBL
    Q1RMZ5
    Conserved Domains (6) summary
    smart00225
    Location:25 → 113
    BTB; Broad-Complex, Tramtrack and Bric a brac
    COG5048
    Location:794 → 970
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:838 → 858
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00019
    Location:952 → 970
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00651
    Location:19 → 113
    BTB; BTB/POZ domain
    pfam13465
    Location:907 → 932
    zf-H2C2_2; Zinc-finger double domain

  2. XM_047436105.1 → XP_047292061.1  zinc finger and BTB domain-containing protein 40 isoform X2

  3. XM_011542500.3 → XP_011540802.1  zinc finger and BTB domain-containing protein 40 isoform X3

    Conserved Domains (4) summary
    COG5048
    Location:217 → 393
    COG5048; FOG: Zn-finger [General function prediction only]
    COG5189
    Location:340 → 454
    SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
    sd00017
    Location:261 → 281
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00019
    Location:375 → 392
    ZF_C2H2; C2H2 Zn finger [structural motif]

RNA

  1. XR_946804.2 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    22252494..22354859
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054339942.1 → XP_054195917.1  zinc finger and BTB domain-containing protein 40 isoform X1

  2. XM_054339943.1 → XP_054195918.1  zinc finger and BTB domain-containing protein 40 isoform X2

  3. XM_054339944.1 → XP_054195919.1  zinc finger and BTB domain-containing protein 40 isoform X3

RNA

  1. XR_008486221.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9NUA8.4 GenPept UniProtKB/Swiss-Prot:Q9NUA8

Gene LinkOut

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