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NBN nibrin [ Homo sapiens (human) ]

Gene ID: 4683, updated on 14-Nov-2024

Summary

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Official Symbol
NBNprovided by HGNC
Official Full Name
nibrinprovided by HGNC
Primary source
HGNC:HGNC:7652
See related
Ensembl:ENSG00000104320 MIM:602667; AllianceGenome:HGNC:7652
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
ATV; NBS; P95; NBS1; AT-V1; AT-V2; hNbs1
Summary
Mutations in this gene are associated with Nijmegen breakage syndrome, an autosomal recessive chromosomal instability syndrome characterized by microcephaly, growth retardation, immunodeficiency, and cancer predisposition. The encoded protein is a member of the MRE11/RAD50 double-strand break repair complex which consists of 5 proteins. This gene product is thought to be involved in DNA double-strand break repair and DNA damage-induced checkpoint activation. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in appendix (RPKM 14.8), thyroid (RPKM 14.2) and 25 other tissues See more
Orthologs
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Genomic context

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See NBN in Genome Data Viewer
Location:
8q21.3
Exon count:
20
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (89933331..89984667, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (91056512..91107848, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (90945559..90996895, complement)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124901974 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:90912677-90913442 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:90913443-90914208 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:90914502-90914800 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19347 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19348 Neighboring gene RNA, U6 small nuclear 925, pseudogene Neighboring gene oxidative stress induced growth inhibitor family member 2 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr8:90959982-90961181 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27608 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:90996459-90997255 Neighboring gene Sharpr-MPRA regulatory region 13813 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19350 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27609 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27610 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27611 Neighboring gene 2,4-dienoyl-CoA reductase 1 Neighboring gene uncharacterized LOC124901976 Neighboring gene calbindin 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 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. NBS1 lactylation is required for efficient DNA repair and chemotherapy resistance.
    Title: NBS1 lactylation is required for efficient DNA repair and chemotherapy resistance.
  2. Suppression of NBS1 Upregulates CyclinB to Induce Olaparib Sensitivity in Ovarian Cancer.
    Title: Suppression of NBS1 Upregulates CyclinB to Induce Olaparib Sensitivity in Ovarian Cancer.
  3. Simultaneous Nbs1 and p53 inactivation in neural progenitors triggers high-grade gliomas.
    Title: Simultaneous Nbs1 and p53 inactivation in neural progenitors triggers high-grade gliomas.
  4. XRCC3 and NBS1 gene polymorphisms modulate the risk of pre-oral cancer and oral cancer in the North Indian population.
    Title: XRCC3 and NBS1 gene polymorphisms modulate the risk of pre-oral cancer and oral cancer in the North Indian population.
  5. The NBN founder mutation-Evidence for a country specific difference in age at cancer manifestation.
    Title: The NBN founder mutation-Evidence for a country specific difference in age at cancer manifestation.
  6. NBN Pathogenic Germline Variants are Associated with Pan-Cancer Susceptibility and In Vitro DNA Damage Response Defects.
    Title: NBN Pathogenic Germline Variants are Associated with Pan-Cancer Susceptibility and In Vitro DNA Damage Response Defects.
  7. MRN Complex and Cancer Risk: Old Bottles, New Wine.
    Title: MRN Complex and Cancer Risk: Old Bottles, New Wine.
  8. Disruption of NBS1/MRN Complex Formation by E4orf3 Supports NF-kappaB That Licenses E1B55K-Deleted Adenovirus-Infected Cells to Accumulate DNA>4n.
    Title: Disruption of NBS1/MRN Complex Formation by E4orf3 Supports NF-κB That Licenses E1B55K-Deleted Adenovirus-Infected Cells to Accumulate DNA>4n.
  9. Structure of the human ATM kinase and mechanism of Nbs1 binding.
    Title: Structure of the human ATM kinase and mechanism of Nbs1 binding.
  10. Association of germline rare pathogenic mutations in guideline-recommended genes with prostate cancer progression: A meta-analysis.
    Title: Association of germline rare pathogenic mutations in guideline-recommended genes with prostate cancer progression: A meta-analysis.
Submit: New GeneRIF Correction See all GeneRIFs (312)

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
Acute lymphoid leukemia
MedGen: C0023449 OMIM: 613065 GeneReviews: Not available
not available
Aplastic anemia
MedGen: C0002874 OMIM: 609135 GeneReviews: Not available
not available
Microcephaly, normal intelligence and immunodeficiency
MedGen: C0398791 OMIM: 251260 GeneReviews: Nijmegen Breakage Syndrome
not available

Variation

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See Variation Viewer (GRCh37.p13)

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp160, precursor env PML, TopBP1, NBS1 or ATM-induced activation of phosphorylation of Chk2 participates in the DNA damage-elicited pro-apoptotic cascade that leads to the demise of Env-elicited syncytia 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

  • FLJ10155, MGC87362

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA-binding transcription factor binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables chromatin-protein adaptor activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables damaged DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
contributes_to damaged DNA binding IC
Inferred by Curator
more info
 PubMed 
enables histone binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables phosphorylation-dependent protein binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein serine/threonine kinase activator activity IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
acts_upstream_of_or_within DNA damage checkpoint signaling IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in DNA damage response, signal transduction by p53 class mediator TAS
Traceable Author Statement
more info
 PubMed 
involved_in DNA double-strand break processing IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in DNA double-strand break processing NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in DNA duplex unwinding IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in DNA duplex unwinding IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in DNA strand resection involved in replication fork processing IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in DNA strand resection involved in replication fork processing NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in R-loop processing IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in blastocyst growth IEA
Inferred from Electronic Annotation
more info
  
involved_in double-strand break repair IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in double-strand break repair via alternative nonhomologous end joining IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in double-strand break repair via homologous recombination IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in double-strand break repair via homologous recombination IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in homologous recombination NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in intrinsic apoptotic signaling pathway IEA
Inferred from Electronic Annotation
more info
  
involved_in isotype switching IEA
Inferred from Electronic Annotation
more info
  
involved_in meiotic cell cycle IEA
Inferred from Electronic Annotation
more info
  
involved_in mitotic G2 DNA damage checkpoint signaling IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in mitotic G2 DNA damage checkpoint signaling IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in mitotic G2/M transition checkpoint NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in negative regulation of telomere capping IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in neuroblast proliferation IEA
Inferred from Electronic Annotation
more info
  
involved_in neuromuscular process controlling balance IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of double-strand break repair via homologous recombination ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of kinase activity IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of protein autophosphorylation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of telomere maintenance IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in protection from non-homologous end joining at telomere IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein K63-linked ubiquitination ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in protein localization to site of double-strand break IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of DNA-templated DNA replication initiation TAS
Traceable Author Statement
more info
 PubMed 
involved_in regulation of cell cycle TAS
Traceable Author Statement
more info
 PubMed 
involved_in t-circle formation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in telomere maintenance IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in telomere maintenance in response to DNA damage IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in telomere maintenance via telomere trimming IGI
Inferred from Genetic Interaction
more info
 PubMed 
involved_in telomeric 3' overhang formation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
part_of BRCA1-C complex IPI
Inferred from Physical Interaction
more info
 PubMed 
located_in Golgi apparatus IDA
Inferred from Direct Assay
more info
  
part_of Mre11 complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of Mre11 complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of Mre11 complex IPI
Inferred from Physical Interaction
more info
 PubMed 
part_of Mre11 complex TAS
Traceable Author Statement
more info
 PubMed 
located_in PML body IDA
Inferred from Direct Assay
more info
 PubMed 
located_in chromosomal region NAS
Non-traceable Author Statement
more info
 PubMed 
located_in chromosome, telomeric region HDA PubMed 
is_active_in chromosome, telomeric region IDA
Inferred from Direct Assay
more info
 PubMed 
located_in chromosome, telomeric region IDA
Inferred from Direct Assay
more info
 PubMed 
colocalizes_with chromosome, telomeric region ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in nuclear inclusion body IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleolus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleus NAS
Non-traceable Author Statement
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
nibrin
Names
Nijmegen breakage syndrome 1 (nibrin)
cell cycle regulatory protein p95
p95 protein of the MRE11/RAD50 complex

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_008860.1 RefSeqGene

    Range
    4948..56336
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_158

mRNA and Protein(s)

  1. NM_001024688.3 → NP_001019859.1  nibrin isoform 2

    See identical proteins and their annotated locations for NP_001019859.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) has an additional exon in the 5' region, as compared to variant 1. This results in translation initiation from a downstream AUG codon and an isoform (2) with a shorter N-terminus compared to isoform 1.
    Source sequence(s)
    AF069291, BC040519, BC136802, BX640816
    Consensus CDS
    CCDS43753.1
    UniProtKB/TrEMBL
    A0A0C4DG07, A6H8Y5, A8K1D3, E5RGN7
    Related
    ENSP00000428252.2, ENST00000523444.2
    Conserved Domains (4) summary
    cd00027
    Location:32 → 100
    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 ...
    pfam08599
    Location:601 → 663
    Nbs1_C; DNA damage repair protein Nbs1
    pfam16508
    Location:135 → 243
    NIBRIN_BRCT_II; Second BRCT domain on Nijmegen syndrome breakage protein
    cl26761
    Location:420 → 564
    MDN1; Midasin, AAA ATPase with vWA domain, involved in ribosome maturation [Translation, ribosomal structure and biogenesis]

  2. NM_002485.5 → NP_002476.2  nibrin isoform 1

    See identical proteins and their annotated locations for NP_002476.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AF069291, BC040519, BC071590, BX640816
    Consensus CDS
    CCDS6249.1
    UniProtKB/Swiss-Prot
    B2R626, B2RNC5, O60672, O60934, Q32NF7, Q53FM6, Q63HR6, Q7LDM2
    UniProtKB/TrEMBL
    A6H8Y5, A8K1D3
    Related
    ENSP00000265433.4, ENST00000265433.8
    Conserved Domains (4) summary
    cd00027
    Location:114 → 182
    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 ...
    cd00060
    Location:1 → 109
    FHA; Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins ...
    pfam08599
    Location:683 → 745
    Nbs1_C; DNA damage repair protein Nbs1
    pfam16508
    Location:216 → 325
    NIBRIN_BRCT_II; Second BRCT domain on Nijmegen syndrome breakage protein

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_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    89933331..89984667 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024447163.2 → XP_024302931.1  nibrin isoform X1

    UniProtKB/TrEMBL
    A0A0C4DG07, A6H8Y5, A8K1D3, E5RGN7
    Related
    ENSP00000386924.1, ENST00000409330.5
    Conserved Domains (4) summary
    cd00027
    Location:32 → 100
    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 ...
    pfam08599
    Location:601 → 663
    Nbs1_C; DNA damage repair protein Nbs1
    pfam16508
    Location:135 → 243
    NIBRIN_BRCT_II; Second BRCT domain on Nijmegen syndrome breakage protein
    cl26761
    Location:420 → 564
    MDN1; Midasin, AAA ATPase with vWA domain, involved in ribosome maturation [Translation, ribosomal structure and biogenesis]

  2. XM_011517045.2 → XP_011515347.1  nibrin isoform X1

    See identical proteins and their annotated locations for XP_011515347.1

    UniProtKB/TrEMBL
    A0A0C4DG07, A6H8Y5, A8K1D3, E5RGN7
    Related
    ENSP00000429971.2, ENST00000517337.2
    Conserved Domains (4) summary
    cd00027
    Location:32 → 100
    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 ...
    pfam08599
    Location:601 → 663
    Nbs1_C; DNA damage repair protein Nbs1
    pfam16508
    Location:135 → 243
    NIBRIN_BRCT_II; Second BRCT domain on Nijmegen syndrome breakage protein
    cl26761
    Location:420 → 564
    MDN1; Midasin, AAA ATPase with vWA domain, involved in ribosome maturation [Translation, ribosomal structure and biogenesis]

  3. XM_047421795.1 → XP_047277751.1  nibrin isoform X3

  4. XM_011517046.2 → XP_011515348.1  nibrin isoform X2

    UniProtKB/TrEMBL
    A0PJ71
    Conserved Domains (3) summary
    cd00027
    Location:114 → 182
    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 ...
    cd00060
    Location:1 → 109
    FHA; Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins ...
    pfam16508
    Location:216 → 325
    NIBRIN_BRCT_II; Second BRCT domain on Nijmegen syndrome breakage protein

  5. XM_047421796.1 → XP_047277752.1  nibrin isoform X4

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    91056512..91107848 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054360508.1 → XP_054216483.1  nibrin isoform X1

    UniProtKB/TrEMBL
    A0A0C4DG07, E5RGN7

  2. XM_054360510.1 → XP_054216485.1  nibrin isoform X3

  3. XM_054360509.1 → XP_054216484.1  nibrin isoform X2

  4. XM_054360511.1 → XP_054216486.1  nibrin isoform X4

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O60934.1 GenPept UniProtKB/Swiss-Prot:O60934

Gene LinkOut

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