NBN nibrin [Homo sapiens (human)] - Gene

Summary

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: mouse all
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Genomic context

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_000008.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

NBS1 lactylation is required for efficient DNA repair and chemotherapy resistance.
Title: NBS1 lactylation is required for efficient DNA repair and chemotherapy resistance.
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.
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.
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.
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.
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.
MRN Complex and Cancer Risk: Old Bottles, New Wine.
Title: MRN Complex and Cancer Risk: Old Bottles, New Wine.
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.
Structure of the human ATM kinase and mechanism of Nbs1 binding.
Title: Structure of the human ATM kinase and mechanism of Nbs1 binding.
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	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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

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

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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

WI-18046 (e-PCR)
- UniSTS:74496

G66922 (e-PCR)
- UniSTS:166957

G66925 (e-PCR)
- UniSTS:166958

G66924 (e-PCR)
- UniSTS:166959

G66926 (e-PCR)
- UniSTS:166960

G66927 (e-PCR)
- UniSTS:166961

G59446 (e-PCR)
- UniSTS:136754

G66920 (e-PCR)
- UniSTS:166962

G66921 (e-PCR)
- UniSTS:166963

G66923 (e-PCR)
- UniSTS:166964

A004N06 (e-PCR)
- UniSTS:70457

RH121752 (e-PCR)
- UniSTS:134496

SHGC-36208 (e-PCR)
- UniSTS:81274

SHGC-84116 (e-PCR)
- UniSTS:104573

PMC96138P1 (e-PCR)
- UniSTS:273625

G59911 (e-PCR)
- UniSTS:137193

RH118942 (e-PCR)
- UniSTS:138228

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 more info	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

NG_008860.1 RefSeqGene

Range

4948..56336

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_158

mRNA and Protein(s)

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]
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

NC_000008.11 Reference GRCh38.p14 Primary Assembly

Range

89933331..89984667 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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]
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]
XM_047421795.1 → XP_047277751.1 nibrin isoform X3
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
XM_047421796.1 → XP_047277752.1 nibrin isoform X4