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NBN nibrin [ Homo sapiens (human) ]

Gene ID: 4683, updated on 26-Jul-2021

Summary

Official Symbol
NBNprovided by HGNC
Official Full Name
nibrinprovided by HGNC
Primary source
HGNC:HGNC:7652
See related
Ensembl:ENSG00000104320 MIM:602667
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
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

See NBN in Genome Data Viewer
Location:
8q21.3
Exon count:
20
Annotation release Status Assembly Chr Location
109.20210514 current GRCh38.p13 (GCF_000001405.39) 8 NC_000008.11 (89933331..89984698, complement)
105.20201022 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 cytochrome c oxidase subunit 6B1 pseudogene 6 Neighboring gene RNA, U6 small nuclear 925, pseudogene Neighboring gene oxidative stress induced growth inhibitor family member 2 Neighboring gene Sharpr-MPRA regulatory region 13813 Neighboring gene 2,4-dienoyl-CoA reductase 1

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

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

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated 2020-08-21)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated 2020-08-21)

ClinGen Genome Curation PagePubMed

HIV-1 interactions

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

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 damaged DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
contributes_to damaged DNA binding IC
Inferred by Curator
more info
PubMed 
enables protein N-terminus binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables protein binding IPI
Inferred from Physical Interaction
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 duplex unwinding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in DNA duplex unwinding IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in blastocyst growth IEA
Inferred from Electronic Annotation
more info
 
involved_in cell population proliferation 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 homologous recombination IBA
Inferred from Biological aspect of Ancestor
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
PubMed 
involved_in mitotic G2 DNA damage checkpoint signaling IDA
Inferred from Direct Assay
more info
PubMed 
involved_in negative regulation of telomere capping IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in neuromuscular process controlling balance IEA
Inferred from Electronic Annotation
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 regulation of DNA-dependent 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 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 Mre11 complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
part_of Mre11 complex IDA
Inferred from Direct Assay
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 chromosome, telomeric region HDA 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 TAS
Traceable Author Statement
more info
 
located_in nucleus IDA
Inferred from Direct Assay
more info
PubMed 
located_in replication fork IEA
Inferred from Electronic Annotation
more info
 
located_in site of double-strand break IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

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_001024688.3NP_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/Swiss-Prot
    O60934
    UniProtKB/TrEMBL
    A0A0C4DG07
    Conserved Domains (4) summary
    cd00027
    Location:32100
    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:601663
    Nbs1_C; DNA damage repair protein Nbs1
    pfam16508
    Location:135243
    NIBRIN_BRCT_II; Second BRCT domain on Nijmegen syndrome breakage protein
    cl26761
    Location:420564
    MDN1; Midasin, AAA ATPase with vWA domain, involved in ribosome maturation [Translation, ribosomal structure and biogenesis]
  2. NM_002485.5NP_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
    O60934
    Related
    ENSP00000265433.4, ENST00000265433.8
    Conserved Domains (4) summary
    cd00027
    Location:114182
    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:1109
    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:683745
    Nbs1_C; DNA damage repair protein Nbs1
    pfam16508
    Location:216325
    NIBRIN_BRCT_II; Second BRCT domain on Nijmegen syndrome breakage protein

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000008.11 Reference GRCh38.p13 Primary Assembly

    Range
    89933331..89984698 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017013462.2XP_016868951.1  nibrin isoform X3

    Conserved Domains (2) summary
    pfam08599
    Location:390452
    Nbs1_C; DNA damage repair protein Nbs1
    pfam16508
    Location:132
    NIBRIN_BRCT_II; Second BRCT domain on Nijmegen syndrome breakage protein
  2. XM_024447165.1XP_024302933.1  nibrin isoform X3

    Conserved Domains (2) summary
    pfam08599
    Location:390452
    Nbs1_C; DNA damage repair protein Nbs1
    pfam16508
    Location:132
    NIBRIN_BRCT_II; Second BRCT domain on Nijmegen syndrome breakage protein
  3. XM_017013460.1XP_016868949.1  nibrin isoform X3

    Conserved Domains (2) summary
    pfam08599
    Location:390452
    Nbs1_C; DNA damage repair protein Nbs1
    pfam16508
    Location:132
    NIBRIN_BRCT_II; Second BRCT domain on Nijmegen syndrome breakage protein
  4. XM_024447163.1XP_024302931.1  nibrin isoform X1

    Related
    ENSP00000386924.1, ENST00000409330.5
    Conserved Domains (4) summary
    cd00027
    Location:32100
    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:601663
    Nbs1_C; DNA damage repair protein Nbs1
    pfam16508
    Location:135243
    NIBRIN_BRCT_II; Second BRCT domain on Nijmegen syndrome breakage protein
    cl26761
    Location:420564
    MDN1; Midasin, AAA ATPase with vWA domain, involved in ribosome maturation [Translation, ribosomal structure and biogenesis]
  5. XM_011517045.1XP_011515347.1  nibrin isoform X1

    See identical proteins and their annotated locations for XP_011515347.1

    UniProtKB/Swiss-Prot
    O60934
    UniProtKB/TrEMBL
    A0A0C4DG07
    Conserved Domains (4) summary
    cd00027
    Location:32100
    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:601663
    Nbs1_C; DNA damage repair protein Nbs1
    pfam16508
    Location:135243
    NIBRIN_BRCT_II; Second BRCT domain on Nijmegen syndrome breakage protein
    cl26761
    Location:420564
    MDN1; Midasin, AAA ATPase with vWA domain, involved in ribosome maturation [Translation, ribosomal structure and biogenesis]
  6. XM_024447164.1XP_024302932.1  nibrin isoform X1

    Conserved Domains (4) summary
    cd00027
    Location:32100
    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:601663
    Nbs1_C; DNA damage repair protein Nbs1
    pfam16508
    Location:135243
    NIBRIN_BRCT_II; Second BRCT domain on Nijmegen syndrome breakage protein
    cl26761
    Location:420564
    MDN1; Midasin, AAA ATPase with vWA domain, involved in ribosome maturation [Translation, ribosomal structure and biogenesis]
  7. XM_011517046.1XP_011515348.1  nibrin isoform X2

    Conserved Domains (3) summary
    cd00027
    Location:114182
    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:1109
    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:216325
    NIBRIN_BRCT_II; Second BRCT domain on Nijmegen syndrome breakage protein
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