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TP53BP1 tumor protein p53 binding protein 1 [ Homo sapiens (human) ]

Gene ID: 7158, updated on 13-Apr-2024

Summary

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Official Symbol
TP53BP1provided by HGNC
Official Full Name
tumor protein p53 binding protein 1provided by HGNC
Primary source
HGNC:HGNC:11999
See related
Ensembl:ENSG00000067369 MIM:605230; AllianceGenome:HGNC:11999
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
p202; 53BP1; TDRD30; p53BP1
Summary
This gene encodes a protein that functions in the DNA double-strand break repair pathway choice, promoting non-homologous end joining (NHEJ) pathways, and limiting homologous recombination. This protein plays multiple roles in the DNA damage response, including promoting checkpoint signaling following DNA damage, acting as a scaffold for recruitment of DNA damage response proteins to damaged chromatin, and promoting NHEJ pathways by limiting end resection following a double-strand break. These roles are also important during V(D)J recombination, class switch recombination and at unprotected telomeres. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Aug 2017]
Expression
Ubiquitous expression in brain (RPKM 10.8), testis (RPKM 9.9) and 25 other tissues See more
Orthologs
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Genomic context

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See TP53BP1 in Genome Data Viewer
Location:
15q15.3
Exon count:
32
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (43403061..43510640, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (41210396..41317991, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (43695259..43802838, complement)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6385 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9313 Neighboring gene zinc finger and SCAN domain containing 29 Neighboring gene tubulin gamma complex component 4 Neighboring gene RNA, 7SL, cytoplasmic 487, pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:43734212-43734815 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:43769402-43769643 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr15:43784380-43785088 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr15:43785089-43785795 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:43787292-43787792 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9314 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6386 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9315 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:43810281-43810924 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:43819912-43820544 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:43821526-43822026 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:43822027-43822527 Neighboring gene microtubule associated protein 1A Neighboring gene diphosphoinositol pentakisphosphate kinase 1

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. DNA damage-induced cellular senescence is regulated by 53BP1 accumulation in the nuclear foci and phase separation. Oda T, et al. Cell Prolif, 2023 Jun. PMID 36642815, Free PMC Article
  2. Incorporation of 53BP1 into phase-separated bodies in cancer cells during aberrant mitosis. Bleiler M, et al. J Cell Sci, 2023 Jan 1. PMID 36606487, Free PMC Article
  3. 53BP1 regulates heterochromatin through liquid phase separation. Zhang L, et al. Nat Commun, 2022 Jan 18. PMID 35042897, Free PMC Article
  4. The Association of Aging-Related Polymorphisms with Susceptibility to Lung Cancer: A Case-Control Study in a Japanese Population. Furuie H, et al. Asian Pac J Cancer Prev, 2021 Apr 1. PMID 33906323, Free PMC Article
  5. AMPK-mediated phosphorylation on 53BP1 promotes c-NHEJ. Jiang Y, et al. Cell Rep, 2021 Feb 16. PMID 33596428

See all (418) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Control of cell proliferation by memories of mitosis.
    Title: Control of cell proliferation by memories of mitosis.
  2. Extracellular vesicle-derived TP53BP1, CD34, and PBX1 from human peripheral blood serve as potential biomarkers for the assessment and prediction of vascular aging.
    Title: Extracellular vesicle-derived TP53BP1, CD34, and PBX1 from human peripheral blood serve as potential biomarkers for the assessment and prediction of vascular aging.
  3. PLK1 promotes the mitotic surveillance pathway by controlling cytosolic 53BP1 availability.
    Title: PLK1 promotes the mitotic surveillance pathway by controlling cytosolic 53BP1 availability.
  4. DNA repair and antibody diversification: the 53BP1 paradigm.
    Title: DNA repair and antibody diversification: the 53BP1 paradigm.
  5. ATM-ESCO2-SMC3 axis promotes 53BP1 recruitment in response to DNA damage and safeguards genome integrity by stabilizing cohesin complex.
    Title: ATM-ESCO2-SMC3 axis promotes 53BP1 recruitment in response to DNA damage and safeguards genome integrity by stabilizing cohesin complex.
  6. DNA damage-induced cellular senescence is regulated by 53BP1 accumulation in the nuclear foci and phase separation.
    Title: DNA damage-induced cellular senescence is regulated by 53BP1 accumulation in the nuclear foci and phase separation.
  7. HDGFRP3 interaction with 53BP1 promotes DNA double-strand break repair.
    Title: HDGFRP3 interaction with 53BP1 promotes DNA double-strand break repair.
  8. Incorporation of 53BP1 into phase-separated bodies in cancer cells during aberrant mitosis.
    Title: Incorporation of 53BP1 into phase-separated bodies in cancer cells during aberrant mitosis.
  9. Identification of a novel GR-ARID1a-P53BP1 protein complex involved in DNA damage repair and cell cycle regulation.
    Title: Identification of a novel GR-ARID1a-P53BP1 protein complex involved in DNA damage repair and cell cycle regulation.
  10. 53BP1 regulates heterochromatin through liquid phase separation.
    Title: 53BP1 regulates heterochromatin through liquid phase separation.
Submit: New GeneRIF Correction See all GeneRIFs (247)

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

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

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env Knockdown of p53 binding protein-1 causes HIV-1 envelope-induced syncytia to enter abnormal mitoses PubMed
Vpr vpr Soluble HIV-1 Vpr induces a DNA damage response by forming H2AX- and 53BP1-containing DNA repair foci PubMed
vpr HIV-1 Vpr forms nuclear foci containing VPRBP and partially co-localizes with DNA repair foci components 53BP1 and phosphorylated RPA32 PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ41424, MGC138366

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA polymerase II-specific DNA-binding transcription factor binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables damaged DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables histone binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables histone reader activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables methylated histone binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables p53 binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables telomeric DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables transcription coregulator activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables ubiquitin-modified histone reader activity IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in DNA damage checkpoint signaling IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within DNA damage response IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in DNA damage response IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in cellular response to X-ray IEA
Inferred from Electronic Annotation
more info
  
involved_in chromatin organization IEA
Inferred from Electronic Annotation
more info
  
involved_in double-strand break repair via classical nonhomologous end joining IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in double-strand break repair via nonhomologous end joining IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of double-strand break repair via homologous recombination IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of DNA-binding transcription factor activity IC
Inferred by Curator
more info
 PubMed 
involved_in positive regulation of DNA-templated transcription NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in positive regulation of isotype switching IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of isotype switching IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in protein homooligomerization IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein localization to site of double-strand break IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
part_of DNA repair complex IEA
Inferred from Electronic Annotation
more info
  
colocalizes_with chromosome, telomeric region IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in kinetochore IEA
Inferred from Electronic Annotation
more info
  
located_in nuclear body IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in replication fork IEA
Inferred from Electronic Annotation
more info
  
is_active_in site of double-strand break IDA
Inferred from Direct Assay
more info
 PubMed 
located_in site of double-strand break IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
TP53-binding protein 1
Names
p53-binding protein 1
tumor protein 53-binding protein, 1
tumor suppressor p53-binding protein 1

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_001141979.3 → NP_001135451.1  TP53-binding protein 1 isoform 2

    See identical proteins and their annotated locations for NP_001135451.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice junction compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is 2 aa shorter compared to isoform 1.
    Source sequence(s)
    AB210025, AC018924, BM993890, BP228994
    Consensus CDS
    CCDS45251.1
    UniProtKB/TrEMBL
    B7Z3E7
    Related
    ENSP00000393497.2, ENST00000450115.6
    Conserved Domains (3) summary
    smart00292
    Location:1869 → 1954
    BRCT; breast cancer carboxy-terminal domain
    cd00027
    Location:1772 → 1839
    BRCT; Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo ...
    pfam09038
    Location:1488 → 1609
    53-BP1_Tudor; Tumour suppressor p53-binding protein-1 Tudor

  2. NM_001141980.3 → NP_001135452.1  TP53-binding protein 1 isoform 1

    See identical proteins and their annotated locations for NP_001135452.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AC018924, AF078776, BM993890, BP228994, BX537418
    Consensus CDS
    CCDS45250.1
    UniProtKB/TrEMBL
    B7Z3E7
    Related
    ENSP00000371475.5, ENST00000382044.9
    Conserved Domains (3) summary
    smart00292
    Location:1871 → 1956
    BRCT; breast cancer carboxy-terminal domain
    cd00027
    Location:1774 → 1841
    BRCT; Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo ...
    pfam09038
    Location:1488 → 1609
    53-BP1_Tudor; Tumour suppressor p53-binding protein-1 Tudor

  3. NM_001355001.2 → NP_001341930.1  TP53-binding protein 1 isoform 4

    Status: REVIEWED

    Source sequence(s)
    AC018924, AF078776, BM993890, BP228994, BX537418
    Conserved Domains (3) summary
    smart00292
    Location:911 → 996
    BRCT; breast cancer carboxy-terminal domain
    cd00027
    Location:814 → 881
    BRCT; Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo ...
    pfam09038
    Location:528 → 649
    53-BP1_Tudor; tumor suppressor p53-binding protein-1 Tudor

  4. NM_001411050.1 → NP_001397979.1  TP53-binding protein 1 isoform 5

    Status: REVIEWED

    Source sequence(s)
    AC018924
    Consensus CDS
    CCDS91987.1
    UniProtKB/TrEMBL
    A6NNK5
    Related
    ENSP00000371470.3, ENST00000382039.7

  5. NM_005657.4 → NP_005648.1  TP53-binding protein 1 isoform 3

    See identical proteins and their annotated locations for NP_005648.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (3) is shorter at the N-terminus compared to isoform 1.
    Source sequence(s)
    AC018924, AF078776, BM993890, DA003995
    Consensus CDS
    CCDS10096.1
    UniProtKB/Swiss-Prot
    F8VY86, Q12888, Q2M1Z7, Q4LE46, Q5FWZ3, Q7Z3U4
    UniProtKB/TrEMBL
    B7Z3E7
    Related
    ENSP00000263801.3, ENST00000263801.7
    Conserved Domains (3) summary
    smart00292
    Location:1866 → 1951
    BRCT; breast cancer carboxy-terminal domain
    cd00027
    Location:1769 → 1836
    BRCT; Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo ...
    pfam09038
    Location:1483 → 1604
    53-BP1_Tudor; Tumour suppressor p53-binding protein-1 Tudor

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_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    43403061..43510640 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047432994.1 → XP_047288950.1  TP53-binding protein 1 isoform X1

  2. XM_047432995.1 → XP_047288951.1  TP53-binding protein 1 isoform X1

  3. XM_047432998.1 → XP_047288954.1  TP53-binding protein 1 isoform X3

  4. XM_047432997.1 → XP_047288953.1  TP53-binding protein 1 isoform X2

  5. XM_047432999.1 → XP_047288955.1  TP53-binding protein 1 isoform X4

    Related
    ENSP00000388028.1, ENST00000413546.1

RNA

  1. XR_007064488.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    41210396..41317991 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054378735.1 → XP_054234710.1  TP53-binding protein 1 isoform X1

  2. XM_054378736.1 → XP_054234711.1  TP53-binding protein 1 isoform X1

  3. XM_054378738.1 → XP_054234713.1  TP53-binding protein 1 isoform X3

  4. XM_054378737.1 → XP_054234712.1  TP53-binding protein 1 isoform X2

  5. XM_054378739.1 → XP_054234714.1  TP53-binding protein 1 isoform X4

RNA

  1. XR_008489009.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q12888.2 GenPept UniProtKB/Swiss-Prot:Q12888

Gene LinkOut

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