XRCC6

gene
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Also known as D22S731D22S671KU70ML8

Summary

XRCC6 (X-ray repair cross complementing 6, HGNC:4055) is a protein-coding gene on chromosome 22q13.2, encoding DNA repair protein Ku70 (P12956). DNA-binding protein critical for the DNA damage response, specifically in repairing double-strand breaks (DSBs) via the classical non-homologous end joining (NHEJ) pathway. It is a common-essential gene (DepMap: required in 99.9% of cancer cell lines).

The p70/p80 autoantigen is a nuclear complex consisting of two subunits with molecular masses of approximately 70 and 80 kDa. The complex functions as a single-stranded DNA-dependent ATP-dependent helicase. The complex may be involved in the repair of nonhomologous DNA ends such as that required for double-strand break repair, transposition, and V(D)J recombination. High levels of autoantibodies to p70 and p80 have been found in some patients with systemic lupus erythematosus.

Source: NCBI Gene 2547 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): autism spectrum disorder (Limited, GenCC)
  • GWAS associations: 6
  • Clinical variants (ClinVar): 66 total
  • Druggable target: yes
  • Cancer dependency (DepMap): dependent in 99.9% of screened cell lines (common-essential)
  • MANE Select transcript: NM_001469

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:4055
Approved symbolXRCC6
NameX-ray repair cross complementing 6
Location22q13.2
Locus typegene with protein product
StatusApproved
AliasesD22S731, D22S671, KU70, ML8
Ensembl geneENSG00000196419
Ensembl biotypeprotein_coding
OMIM152690
Entrez2547

Gene structure

Transcript identifiers

Ensembl transcripts: 38 — 36 protein_coding, 2 retained_intron

ENST00000359308, ENST00000360079, ENST00000402580, ENST00000405506, ENST00000405878, ENST00000428575, ENST00000464116, ENST00000478914, ENST00000892842, ENST00000892843, ENST00000892844, ENST00000892845, ENST00000892846, ENST00000892847, ENST00000892848, ENST00000892849, ENST00000892850, ENST00000892851, ENST00000892852, ENST00000892853, ENST00000938028, ENST00000938029, ENST00000938030, ENST00000938031, ENST00000938032, ENST00000938033, ENST00000938034, ENST00000938035, ENST00000938036, ENST00000938037, ENST00000938038, ENST00000938039, ENST00000938040, ENST00000938041, ENST00000970532, ENST00000970533, ENST00000970534, ENST00000970535

RefSeq mRNA: 4 — MANE Select: NM_001469 NM_001288976, NM_001288977, NM_001288978, NM_001469

CCDS: CCDS14021, CCDS74870, CCDS74871

Canonical transcript exons

ENST00000360079 — 13 exons

ExonStartEnd
ENSE000006560314162811841628230
ENSE000006560534163760841637791
ENSE000006560574164689641647082
ENSE000006560764165690341657032
ENSE000006560944166133141661444
ENSE000008804764165072341650891
ENSE000008804774165352941653690
ENSE000014130634162129541621345
ENSE000035145194162199041622086
ENSE000036725174165825241658352
ENSE000037268324163611341636251
ENSE000037508064163651641636770
ENSE000039010444166362241664041

Expression profiles

Bgee: expression breadth ubiquitous, 288 present calls, max score 99.37.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 169.6383 / max 6138.2634, expressed in 1825 samples.

FANTOM5 promoters (7 alternative TSS)

Promoter IDTPM avgSamples expressed
192491164.45791825
1924902.82431320
1924951.5333881
2094880.316099
1924940.2765127
1924920.117433
1924930.113041

Top tissues by expression

288 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
right testisUBERON:000453499.37gold quality
left testisUBERON:000453399.34gold quality
ventricular zoneUBERON:000305399.22gold quality
islet of LangerhansUBERON:000000699.18gold quality
embryoUBERON:000092299.14gold quality
ganglionic eminenceUBERON:000402399.14gold quality
calcaneal tendonUBERON:000370199.06gold quality
testisUBERON:000047399.05gold quality
adult organismUBERON:000702399.04gold quality
adrenal tissueUBERON:001830398.85gold quality
right adrenal glandUBERON:000123398.79gold quality
thymusUBERON:000237098.74gold quality
type B pancreatic cellCL:000016998.73gold quality
right adrenal gland cortexUBERON:003582798.73gold quality
smooth muscle tissueUBERON:000113598.72gold quality
left adrenal glandUBERON:000123498.70gold quality
left adrenal gland cortexUBERON:003582598.65gold quality
left uterine tubeUBERON:000130398.64gold quality
adrenal glandUBERON:000236998.64gold quality
lymph nodeUBERON:000002998.63gold quality
rectumUBERON:000105298.62gold quality
ectocervixUBERON:001224998.62gold quality
adrenal cortexUBERON:000123598.61gold quality
vermiform appendixUBERON:000115498.60gold quality
cortical plateUBERON:000534398.60gold quality
skin of legUBERON:000151198.59gold quality
endocervixUBERON:000045898.58gold quality
right ovaryUBERON:000211898.58gold quality
ovaryUBERON:000099298.56gold quality
caecumUBERON:000115398.56gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-CURD-95no274.71
E-ANND-3no0.00

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

3 targets.

TargetRegulation
CD40Unknown
ERBB2Unknown
VIM

Upstream regulators (CollecTRI, top): NKX3-1, PRDM1

miRNA regulators (miRDB)

17 targeting XRCC6, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-4692100.0067.322066
HSA-MIR-451499.9967.101870
HSA-MIR-4728-5P99.8569.394718
HSA-MIR-6785-5P99.8268.684428
HSA-MIR-34B-5P99.7867.561175
HSA-MIR-449C-5P99.7867.631168
HSA-MIR-2682-5P99.7367.381055
HSA-MIR-3120-3P99.5470.282669
HSA-MIR-1212399.5271.792990
HSA-MIR-6507-3P99.3567.321059
HSA-MIR-4742-5P98.8968.411542
HSA-MIR-4768-3P98.1666.022330
HSA-MIR-1212098.0568.441768
HSA-MIR-506-5P98.0267.411065
HSA-MIR-892B98.0067.11821
HSA-MIR-5088-5P97.9764.28487
HSA-MIR-7109-3P94.2367.19743

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 99.9% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 40)

  • Studies on the mode of Ku interaction with DNA (PMID:11796732)
  • binding with inositol hexakisphosphate (PMID:11821378)
  • regulates osteocalcin gene expression (PMID:12145306)
  • Ku heterodimer binds to both ends of the Werner protein and functional interaction occurs at the Werner N-terminus (PMID:12177300)
  • role of expression in NF-kappaB activation and COX-2 expression (PMID:12324457)
  • Ku associates with hTERT, and this interaction may function to regulate the access of telomerase to telomeric DNA ends (PMID:12377759)
  • Transcripts of Ku70 and Ku86 genes were detected by RT-PCR and Ku protein was localized in the nucleus of neutrophils as a heterodimer (PMID:12467650)
  • In naevus cell naevi, significant correlations were found between Ku70/80 gene expression and some ploidy-related parameters. (PMID:12494870)
  • The mechanism that regulates for nuclear localization of Ku70 and Ku80 appears to play, at least in part, a key role in regulating the physiological function of Ku in vivo. (PMID:12518983)
  • Coordinated assembly of Ku and p460 subunits of the DNA-dependent protein kinase on DNA ends is necessary for XRCC4-ligase IV recruitment (PMID:12547193)
  • This antigen acts as the transcription factor induced by interleukins (IL)-13 and -4 leading to induction of 15-lipoxygenase (15-LO) in human cells. (PMID:12664628)
  • This autoantigen is induced by a divergence in intracellular signaling between IL-4 and IL-13. (PMID:12664629)
  • DNA repair proteins Ku70 and Ku80 expression is lost in cell nucleus after oxidative stress (PMID:12867423)
  • Ku antigen interacts with RBP-Jkappa and NF-kappaB p50 may act as a positive regulator of p50 expression in gastric cancer AGS cells. (PMID:14570916)
  • DNA-PK can be activated by nucleosomes through the ability of Ku to bind to the ends of nucleosomal DNA, and that the activated DNA-PK is capable of phosphorylating H2AX within the nucleosomes (PMID:14627815)
  • (ADP-ribosyl)ation of Ku70/80 reduces the ability of this factor to stimulate WRN exonuclease, suggesting that covalent modification of Ku70/80 by PARP-1 may play a role in the regulation of the exonucleolytic activity of WRN. (PMID:14734561)
  • Expression of both genes was down-regulated as melanoma progressed. In situ hybridization demonstrated more Ku70- and Ku80-positive cells than immunohistochemical methods, but the correlation between the two methods was highly significant (P <0.01). (PMID:14991539)
  • cell-surface Ku functions as an adhesion receptor for fibronectin; both Ku70 and Ku80 present a structural relationship with integrin I (or A) domains and the A1 and A3 domains of von Willebrand factor, domains known to be involved in Fn binding (PMID:15019772)
  • activity of ESE-1 is positively and negatively modulated by other interacting proteins including Ku70, Ku86, p300, and CBP. (PMID:15075319)
  • Results show that Ku70/Ku80 and DNA-dependent protein kinase catalytic subunit (DNA-PKcs) modulate RAG-mediated cleavage during V(D)J recombination. (PMID:15123719)
  • DNA-binding component of human OF-1 (which binds Herpes simplex virus type 1 origin of replication) contains Ku70 and Ku80 proteins (PMID:15220460)
  • Histone gamma-H2AX promotes binding of nuclear DNA helicase II to transcriptionally stalled sites on chromosomal DNA. (PMID:15613478)
  • Ku70/80 interacts directly with the RNA component of human telomerase, independent of the human telomerase reverse transcriptase protein. (PMID:15824061)
  • Ku70 has a role in human cancer cell sensitization to radiation and etoposide treatments (PMID:15827325)
  • The level of Ku70 in the cytoplasm was decreased, but that of Bax in mitochondria was increased by justicidin A in colorectal cancer cells. (PMID:15905197)
  • Ku70 is a receptor for the rickettsial protein rOmpB. Bacterial internalization is dependent on the presence of cholesterol-enriched microdomains containing Ku70. (PMID:16360032)
  • Ku70 has other antiapoptotic functions in Granzyme A (GzmA)-induced cell death, which are blocked when GzmA proteolyses Ku70 (PMID:16440001)
  • The present study suggests that Ku binds IRES -(internal ribosomal entry site)elements within RNA molecules, and that Ku plays a role in the modulation of IRES- mediated mRNA translation. (PMID:16448389)
  • Dimeric particles are observed in which two DNA-PKcs/Ku70/Ku80 holoenzymes interact through the N-terminal HEAT repeats. (PMID:16713581)
  • Ku-mediated assembly of DNA-PK on DNA ends is responsible for a dissociation of the DNA-PKcs.Artemis complex. (PMID:16857680)
  • Functions in nonhomologous DNA end joining. (PMID:17124166)
  • The three-dimensional structure of the human full-length Ku70-Ku80 dimer at 25 A resolution, alone and in complex with DNA, by using single-particle electron microscopy was reconstructed. (PMID:17159921)
  • poly(ADP-ribose)polymerase-1 and Ku70/Ku80 are transcriptional regulators of S100A9 gene expression (PMID:17187679)
  • maintenance of higher expression of Ku70 and Mre11 may be responsible for keeping longer life span observed in the longevity group (PMID:17202845)
  • SIRT1 modulates DNA repair activity, which could be regulated by the acetylation status of repair protein Ku70 following DNA damage (PMID:17334224)
  • Ku70 protein plays an important role in repair of DNA DSB (double-strand breaks) damage and for maintainance of genome stability. (PMID:17479409)
  • These data support a new role for Ku in the migration of monocytes into tissues, which depends on a tightly regulated pathway of intracellular redistribution. (PMID:17496833)
  • TrkA signaling appears to be proapoptotic in the absence of Ku70. (PMID:17617666)
  • potential relevance of Bin1-Ku interaction to cancer are discussed in light of these findings (PMID:17671430)
  • Genes encoding KU70, MGST1 and BIK show age-related mRNA expression levels in hematopoietic stem cells. (PMID:17714764)

Cross-species orthologs

6 orthologs

OrganismSymbolGene ID
danio_rerioxrcc6ENSDARG00000071551
mus_musculusXrcc6ENSMUSG00000022471
rattus_norvegicusXrcc6ENSRNOG00000006392
drosophila_melanogasterIrbpFBGN0011774
drosophila_melanogasterEndoGIFBGN0028515
caenorhabditis_elegansWBGENE00000519

Paralogs (1): XRCC5 (ENSG00000079246)

Protein

Protein identifiers

DNA repair protein Ku70P12956 (reviewed: P12956)

Alternative names: 5’-deoxyribose-5-phosphate lyase Ku70, 70 kDa subunit of Ku antigen, ATP-dependent DNA helicase 2 subunit 1, ATP-dependent DNA helicase II 70 kDa subunit, CTC box-binding factor 75 kDa subunit, DNA repair protein XRCC6, Lupus Ku autoantigen protein p70, Thyroid-lupus autoantigen, X-ray repair complementing defective repair in Chinese hamster cells 6, X-ray repair cross-complementing protein 6

All UniProt accessions (2): B1AHC9, P12956

UniProt curated annotations — full annotation on UniProt →

Function. DNA-binding protein critical for the DNA damage response, specifically in repairing double-strand breaks (DSBs) via the classical non-homologous end joining (NHEJ) pathway. It forms a heterodimer with XRCC5 (Ku80), creating the Ku70:Ku80 heterodimer (Ku complex), which serves as a DNA end-binding complex. It primarily binds DSBs and recruits essential repair factors, assembling the core long-range NHEJ complex to facilitate the alignment and ligation of broken DNA ends. This pathway ensures the rapid repair of cytotoxic and mutagenic DSBs and contributes to the generation of diversity in T-cell receptors and antibodies through mechanisms such as V(D)J recombination. Likely acts as a 5’-deoxyribose-5-phosphate lyase (5’-dRP lyase), catalyzing the beta-elimination of the 5’-deoxyribose-5-phosphate at abasic sites near DSBs. This activity cleans the termini of abasic sites, a common form of nucleotide damage, preparing broken ends for ligation. It may also possess 3’-5’ DNA helicase activity, although this has not been confirmed in vivo, and its physiological significance remains unclear. Beyond DNA repair, the protein contributes to telomere maintenance. It is also implicated in transcriptional regulation, acting as a cofactor for various transcription factors. It plays a role in the regulation of DNA virus-mediated innate immune response by assembling into the HDP-RNP complex, a complex that serves as a platform for IRF3 phosphorylation and subsequent innate immune response activation through the cGAS-STING pathway. Can also bind RNAs and recruits PRKDC to a wide range of cellular RNAs, including the U3 small nucleolar RNA, playing a role in the biogenesis of ribosomal RNAs. Additionally, it negatively regulates apoptosis by interacting with BAX, sequestering it from the mitochondria, and may possess deubiquitination activity targeting BAX.

Subunit / interactions. Forms a heterodimer with XRCC5/Ku80 to form the Ku70:Ku80 complex (Ku); heterodimerization stabilizes XRCC5 protein. Component of the core long-range non-homologous end joining (NHEJ) complex (also named DNA-PK complex) composed of PRKDC, LIG4, XRCC4, XRCC6/Ku70, XRCC5/Ku86 and NHEJ1/XLF. Additional component of the NHEJ complex includes PAXX. Following autophosphorylation, PRKDC dissociates from DNA, leading to formation of the short-range NHEJ complex, composed of LIG4, XRCC4, XRCC6/Ku70, XRCC5/Ku86 and NHEJ1/XLF. The XRCC5-XRCC6 dimer also associates with NAA15, and this complex binds to the osteocalcin promoter and activates osteocalcin expression. In addition, XRCC6 interacts with the osteoblast-specific transcription factors MSX2, RUNX2 and DLX5. Interacts with ELF3. Interacts with ATP23. The XRCC5-XRRC6 dimer associates in a DNA-dependent manner with APEX1. Binds to CDK9 isoform 2. Identified in a complex with DEAF1 and XRCC5. Interacts with DEAF1 (via the SAND domain); the interaction is direct and may be inhibited by DNA-binding. Interacts with CLU. Interacts with NR4A3; the DNA-dependent protein kinase complex DNA-PK phosphorylates and activates NR4A3 and prevents NR4A3 ubiquitinylation and degradation. Interacts with CYREN isoform 1 (CYREN-1) and isoform 4 (CYREN-2) (via KBM motif). Interacts (via N-terminus) with HSF1 (via N-terminus); this interaction is direct and prevents XRCC5/XRCC6 heterodimeric binding and non-homologous end joining (NHEJ) repair activities induced by ionizing radiation (IR). Part of the HDP-RNP complex composed of at least HEXIM1, PRKDC, XRCC5, XRCC6, paraspeckle proteins (SFPQ, NONO, PSPC1, RBM14, and MATR3) and NEAT1 RNA. Interacts with HMBOX1. Interacts with ATF7; involved in ATF7 lolcaization to telomeres. Interacts with APLF (via KBM motif). Interacts with WRN (via KBM motif). The XRCC5-XRCC6 dimer associates with ALKBH2. Interacts with TPRN; TPRN interacts with a number of DNA damage response proteins, is recruited to sites of DNA damage and may play a role in DNA damage repair. When not acetylated, interacts with BAX. Interacts with ERCC6L2. (Microbial infection) Interacts with human T-cell leukemia virus 1/HTLV-1 protein HBZ.

Subcellular location. Nucleus. Chromosome. Cytoplasm.

Post-translational modifications. Phosphorylation by PRKDC may enhance helicase activity. Phosphorylation of Ser-51 does not affect DNA repair. ADP-ribosylated by PARP3. Methylation by SETD4 leads to accumulation in the cytoplasm and is a prerequisite for acetylation, possibly due to the change of subcellular from the nucleus to the cytosol initiated by methylation, acetylation occurring in the cytosol. Acetylation can be catalyzed in vitro by CREBBP/CBP and KAT2B/PCAF.

Induction. In osteoblasts, by FGF2.

Miscellaneous. Individuals with systemic lupus erythematosus (SLE) and related disorders produce extremely large amounts of autoantibodies to XRCC5 and XRCC6. Existence of a major autoantigenic epitope or epitopes on the C-terminal 190 amino acids of XRCC6 containing the leucine repeat. The majority of autoantibodies to XRCC6 in most sera from patients with SLE seem to be reactive with this region.

Similarity. Belongs to the ku70 family.

Isoforms (2)

UniProt IDNamesCanonical?
P12956-11yes
P12956-22

RefSeq proteins (4): NP_001275905, NP_001275906, NP_001275907, NP_001460* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR003034SAP_domDomain
IPR005160Ku_CDomain
IPR005161Ku_NDomain
IPR006164DNA_bd_Ku70/Ku80Domain
IPR006165Ku70Family
IPR016194SPOC-like_C_dom_sfHomologous_superfamily
IPR027388Ku70_bridge/pillars_dom_sfHomologous_superfamily
IPR036361SAP_dom_sfHomologous_superfamily
IPR036465vWFA_dom_sfHomologous_superfamily
IPR047087KU70_core_domDomain

Pfam: PF02037, PF02735, PF03730, PF03731

Catalyzed reactions (Rhea), 2 shown:

  • ATP + H2O = ADP + phosphate + H(+) (RHEA:13065)
  • 2’-deoxyribonucleotide-(2’-deoxyribose 5’-phosphate)-2’-deoxyribonucleotide-DNA = a 3’-end 2’-deoxyribonucleotide-(2,3-dehydro-2,3-deoxyribose 5’-phosphate)-DNA + a 5’-end 5’-phospho-2’-deoxyribonucleoside-DNA + H(+) (RHEA:66592)

UniProt features (109 total): strand 27, modified residue 22, helix 20, mutagenesis site 12, region of interest 6, sequence conflict 6, turn 6, cross-link 3, domain 2, initiator methionine 1, chain 1, compositionally biased region 1, active site 1, splice variant 1

Structure

Experimental structures (PDB)

59 structures, top 30 by resolution.

PDBMethodResolution (Å)
8AG4ELECTRON MICROSCOPY2.46
1JEYX-RAY DIFFRACTION2.5
3RZXX-RAY DIFFRACTION2.61
7ZYGELECTRON MICROSCOPY2.68
1JEQX-RAY DIFFRACTION2.7
7ZVTELECTRON MICROSCOPY2.74
6ERHX-RAY DIFFRACTION2.8
7ZWAELECTRON MICROSCOPY2.8
9CQ3ELECTRON MICROSCOPY2.8
9GYFELECTRON MICROSCOPY2.8
9N81ELECTRON MICROSCOPY2.8
6ERGX-RAY DIFFRACTION2.9
7Z87ELECTRON MICROSCOPY2.91
9Q8XELECTRON MICROSCOPY2.94
8ASCX-RAY DIFFRACTION2.95
7SGLELECTRON MICROSCOPY3
6ERFX-RAY DIFFRACTION3.01
9CQ6ELECTRON MICROSCOPY3.1
9N83ELECTRON MICROSCOPY3.1
7AXZELECTRON MICROSCOPY3.2
7SU3ELECTRON MICROSCOPY3.3
9N82ELECTRON MICROSCOPY3.3
9IGWELECTRON MICROSCOPY3.32
7Z88ELECTRON MICROSCOPY3.33
9HZGELECTRON MICROSCOPY3.33
9Q80ELECTRON MICROSCOPY3.39
9CQCELECTRON MICROSCOPY3.4
9IOLELECTRON MICROSCOPY3.46
8AG5ELECTRON MICROSCOPY3.47
7ZT6ELECTRON MICROSCOPY3.5

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P12956-F184.430.58

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (1): 31 (schiff-base intermediate with dna; for 5’-deoxyribose-5-phosphate lyase activity)

Post-translational modifications (25): 2, 2, 6, 27, 31, 51, 306, 317, 331, 338, 455, 461, 477, 520, 539, 542, 544, 550, 553, 556 …

Mutagenesis-validated functional residues (12):

PositionPhenotype
31diminishes the ability to form a schiff base. abolishes adduct formation; when associated with a-160 and a-164.
160abolishes adduct formation; when associated with a-31 and a-160.
164abolishes adduct formation; when associated with a-31 and a-164.
539complete loss of suppression of bax-induced apoptosis.
539no effect on suppression of bax-induced apoptosis.
542complete loss of suppression of bax-induced apoptosis.
542no effect on suppression of bax-induced apoptosis.
544no effect on suppression of bax-induced apoptosis.
553partial loss of suppression of bax-induced apoptosis.
553no effect on suppression of bax-induced apoptosis.
556no effect on suppression of bax-induced apoptosis.
570loss of methylation; loss of anti-apoptotic activity; no effect on xrcc5 stabilization.

Function

Pathways and Gene Ontology

Reactome pathways

5 pathways

IDPathway
R-HSA-1648432-LTR circle formation
R-HSA-1834949Cytosolic sensors of pathogen-associated DNA
R-HSA-3270619IRF3-mediated induction of type I IFN
R-HSA-5693571Nonhomologous End-Joining (NHEJ)
R-HSA-6798695Neutrophil degranulation

MSigDB gene sets: 0 (showing top):

GO Biological Process (22): telomere maintenance (GO:0000723), recombinational repair (GO:0000725), activation of innate immune response (GO:0002218), double-strand break repair via nonhomologous end joining (GO:0006303), innate immune response (GO:0045087), positive regulation of lymphocyte differentiation (GO:0045621), negative regulation of DNA-templated transcription (GO:0045892), positive regulation of DNA-templated transcription (GO:0045893), positive regulation of transcription by RNA polymerase II (GO:0045944), regulation of smooth muscle cell proliferation (GO:0048660), cellular hyperosmotic salinity response (GO:0071475), cellular response to gamma radiation (GO:0071480), cellular response to X-ray (GO:0071481), double-strand break repair via classical nonhomologous end joining (GO:0097680), immune system process (GO:0002376), positive regulation of immune system process (GO:0002684), DNA repair (GO:0006281), DNA recombination (GO:0006310), DNA damage response (GO:0006974), response to ionizing radiation (GO:0010212), negative regulation of macromolecule biosynthetic process (GO:0010558), positive regulation of protein kinase activity (GO:0045860)

GO Molecular Function (22): transcription cis-regulatory region binding (GO:0000976), DNA binding (GO:0003677), DNA helicase activity (GO:0003678), damaged DNA binding (GO:0003684), RNA binding (GO:0003723), ATP binding (GO:0005524), ATP-dependent activity, acting on DNA (GO:0008094), ATP hydrolysis activity (GO:0016887), cyclin binding (GO:0030332), telomeric repeat DNA binding (GO:0042162), protein-containing complex binding (GO:0044877), 5’-deoxyribose-5-phosphate lyase activity (GO:0051575), scaffold protein binding (GO:0097110), nucleotide binding (GO:0000166), double-stranded DNA binding (GO:0003690), double-stranded telomeric DNA binding (GO:0003691), catalytic activity (GO:0003824), helicase activity (GO:0004386), protein binding (GO:0005515), hydrolase activity (GO:0016787), lyase activity (GO:0016829), DNA end binding (GO:0045027)

GO Cellular Component (19): chromosome, telomeric region (GO:0000781), nuclear telomere cap complex (GO:0000783), extracellular region (GO:0005576), nucleus (GO:0005634), nucleoplasm (GO:0005654), transcription regulator complex (GO:0005667), nucleolus (GO:0005730), cytosol (GO:0005829), DNA-dependent protein kinase-DNA ligase 4 complex (GO:0005958), membrane (GO:0016020), protein-containing complex (GO:0032991), protein-DNA complex (GO:0032993), secretory granule lumen (GO:0034774), Ku70:Ku80 complex (GO:0043564), DNA-dependent protein kinase complex (GO:0070418), nonhomologous end joining complex (GO:0070419), ficolin-1-rich granule lumen (GO:1904813), chromosome (GO:0005694), cytoplasm (GO:0005737)

Reactome top-level categories

Rollup of top-4 pathways:

CategoryPathways
Innate Immune System2
Integration of provirus1
STING mediated induction of host immune responses1
DNA Double-Strand Break Repair1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure5
nuclear protein-containing complex4
DNA metabolic process3
ATP-dependent activity3
DNA-templated transcription2
regulation of DNA-templated transcription2
cellular response to ionizing radiation2
nucleic acid binding2
DNA binding2
catalytic activity, acting on DNA2
protein binding2
binding2
nuclear lumen2
protein-containing complex2
intracellular membraneless organelle2
telomere organization1
DNA repair1
DNA recombination1
activation of immune response1
positive regulation of innate immune response1
double-strand break repair1
immune response1
defense response to symbiont1
lymphocyte differentiation1
regulation of lymphocyte differentiation1
positive regulation of lymphocyte activation1
positive regulation of leukocyte differentiation1
negative regulation of RNA biosynthetic process1
positive regulation of RNA biosynthetic process1
regulation of transcription by RNA polymerase II1
transcription by RNA polymerase II1
positive regulation of DNA-templated transcription1
regulation of cell population proliferation1
smooth muscle cell proliferation1
hyperosmotic salinity response1
cellular response to salt stress1
cellular hyperosmotic response1
response to gamma radiation1
response to X-ray1
double-strand break repair via nonhomologous end joining1

Protein interactions and networks

STRING

3866 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
XRCC6PRKDCP78527999
XRCC6XRCC5P13010999
XRCC6XRCC4Q13426999
XRCC6NHEJ1Q9H9Q4994
XRCC6PARP1P09874983
XRCC6WRNQ14191982
XRCC6LIG4P49917982
XRCC6PAXXQ9BUH6977
XRCC6LIG3P49916970
XRCC6HOXB7P09629961
XRCC6ATMQ13315931
XRCC6XRCC1P18887914
XRCC6CYRENQ9BWK5905
XRCC6BRCA1P38398902
XRCC6RAD51Q06609902

IntAct

572 interactions, top by confidence:

ABTypeScore
XRCC6XRCC5psi-mi:“MI:0914”(association)0.970
XRCC5XRCC6psi-mi:“MI:0914”(association)0.970
XRCC5XRCC6psi-mi:“MI:0915”(physical association)0.970
XRCC6XRCC5psi-mi:“MI:0915”(physical association)0.970
PRKDCXRCC6psi-mi:“MI:0915”(physical association)0.900
PRKDCXRCC6psi-mi:“MI:0217”(phosphorylation reaction)0.900
PARP1XRCC6psi-mi:“MI:0914”(association)0.850
XRCC6PARP1psi-mi:“MI:0914”(association)0.850
RARANCOR1psi-mi:“MI:0914”(association)0.800
H3C1HAT1psi-mi:“MI:0914”(association)0.770
H2AZ1ZNHIT1psi-mi:“MI:0914”(association)0.770
RECQLPARP1psi-mi:“MI:0914”(association)0.750
H2AXPPM1Gpsi-mi:“MI:0914”(association)0.730
TPT1XRCC6psi-mi:“MI:0915”(physical association)0.710
TPT1XRCC6psi-mi:“MI:0914”(association)0.710
CFTRESYT2psi-mi:“MI:0914”(association)0.710
XRCC6HTTpsi-mi:“MI:0915”(physical association)0.700

BioGRID (1534): XRCC6 (Affinity Capture-MS), XRCC6 (Reconstituted Complex), XRCC6 (Reconstituted Complex), XRCC6 (Affinity Capture-Western), XRCC6 (Affinity Capture-RNA), XRCC6 (Affinity Capture-RNA), XRCC6 (Affinity Capture-RNA), XRCC6 (Affinity Capture-RNA), XRCC5 (Reconstituted Complex), PPARG (Affinity Capture-Western), XRCC6 (Affinity Capture-Western), XRCC6 (Affinity Capture-MS), XRCC6 (Affinity Capture-MS), XRCC6 (Affinity Capture-MS), XRCC6 (Affinity Capture-MS)

ESM2 similar proteins: A2RV18, B5DG51, B8APQ0, D3ZG52, D3ZVK1, E9PY46, I0IUP3, O35654, O48520, O89043, O93257, O93610, P12956, P23475, P33611, P47823, P49004, P49005, Q10QS7, Q13144, Q14181, Q28DV7, Q38899, Q4V7D6, Q566Y1, Q58D13, Q5EBA1, Q5F310, Q5RGJ5, Q63615, Q6AXC6, Q6AXY4, Q6GM65, Q6TH47, Q7ZYP6, Q803A6, Q80YD1, Q8AVL0, Q8C0P5, Q8GWT4

Diamond homologs: O93257, P0CO51, P12956, P23475, Q1DU75, Q26228, Q2MHH4, Q54MA9, Q7F1M0, Q9FQ08, P0CO50, Q0U5F2, Q2MHH3, Q5AVC7, O94395, Q2H0I3, Q6CCK2, Q7SA95

SIGNOR signaling

7 interactions.

AEffectBMechanism
XRCC6up-regulatesPRKDCrelocalization
XRCC6“form complex”DNA-PKbinding
XRCC6“up-regulates activity”UBE2Srelocalization
ATM“up-regulates activity”XRCC6phosphorylation
PRKDC“up-regulates activity”XRCC6phosphorylation

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 119 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Nonhomologous End-Joining (NHEJ)714.5×3e-04
Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks610.8×2e-03
G2/M DNA damage checkpoint710.4×1e-03
DNA Damage/Telomere Stress Induced Senescence510.1×6e-03
Transcriptional regulation of granulopoiesis69.3×3e-03
B-WICH complex positively regulates rRNA expression69.0×3e-03
RNA Polymerase I Promoter Escape69.0×3e-03
Processing of DNA double-strand break ends68.5×4e-03

GO biological processes:

GO termPartnersFoldFDR
double-strand break repair via nonhomologous end joining728.1×3e-06
telomere maintenance717.8×3e-05
intrinsic apoptotic signaling pathway517.1×1e-03
double-strand break repair815.5×1e-05
cellular response to UV514.1×2e-03
heterochromatin formation512.2×3e-03
DNA damage response168.2×1e-07
regulation of cell cycle96.4×1e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

66 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance41
Likely benign5
Benign2

Top pathogenic / likely-pathogenic (0)

SpliceAI

1687 predictions. Top by Δscore:

VariantEffectΔscore
22:41621345:GGT:Gdonor_loss1.0000
22:41621988:A:AGacceptor_gain1.0000
22:41621989:G:GGacceptor_gain1.0000
22:41621989:GT:Gacceptor_gain1.0000
22:41628117:GGA:Gacceptor_gain1.0000
22:41628227:CCAG:Cdonor_loss1.0000
22:41628228:CAGGT:Cdonor_loss1.0000
22:41628230:GGT:Gdonor_loss1.0000
22:41628231:GTAAG:Gdonor_loss1.0000
22:41628232:T:Adonor_loss1.0000
22:41636111:A:AGacceptor_gain1.0000
22:41636112:G:GAacceptor_gain1.0000
22:41636112:GT:Gacceptor_gain1.0000
22:41636112:GTGT:Gacceptor_gain1.0000
22:41636492:A:AGacceptor_gain1.0000
22:41636492:ATTT:Aacceptor_gain1.0000
22:41636493:T:Gacceptor_gain1.0000
22:41636495:T:Aacceptor_gain1.0000
22:41636503:T:TAacceptor_gain1.0000
22:41636515:GGT:Gacceptor_gain1.0000
22:41636769:AGGT:Adonor_loss1.0000
22:41636770:GG:Gdonor_loss1.0000
22:41636771:G:GAdonor_loss1.0000
22:41637590:T:TAacceptor_gain1.0000
22:41637595:A:AGacceptor_gain1.0000
22:41637596:C:Gacceptor_gain1.0000
22:41637603:A:AGacceptor_gain1.0000
22:41637603:AACAG:Aacceptor_gain1.0000
22:41637604:A:Gacceptor_gain1.0000
22:41637605:CAG:Cacceptor_loss1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000039395 (22:41662185 T>C), RS1000044573 (22:41623099 T>A), RS1000142366 (22:41639338 T>C), RS1000305427 (22:41639212 A>G,T), RS1000375614 (22:41650278 A>AT), RS1000387605 (22:41650094 T>G), RS1000442267 (22:41651201 C>G,T), RS1000456841 (22:41650950 C>T), RS1000551701 (22:41626560 T>C,G), RS1000572411 (22:41638974 G>C), RS1000700360 (22:41633408 T>G), RS1000706370 (22:41645151 A>G), RS1000715652 (22:41639723 T>A,C,G), RS1000882199 (22:41654872 G>T), RS1000953475 (22:41655910 C>T)

Disease associations

OMIM: gene MIM:152690 | disease phenotypes:

GenCC curated gene-disease

DiseaseClassificationInheritance
autism spectrum disorderLimitedAutosomal dominant

Mondo (1): autism spectrum disorder (MONDO:0005258)

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

6 associations (top):

StudyTraitp-value
GCST004278_22Pulse pressure3.000000e-11
GCST004988_438Breast cancer2.000000e-09
GCST005232_52Neuroticism3.000000e-18
GCST010002_83Refractive error2.000000e-27
GCST010143_2Meat-related diet4.000000e-08
GCST90014325_73Asthma7.000000e-09

EFO canonical traits (3, from GWAS)

EFO IDTrait name
EFO:0005763pulse pressure measurement
EFO:0007660neuroticism measurement
EFO:0008111diet measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (2): CHEMBL4106136 (PROTEIN COMPLEX), CHEMBL6066958 (SINGLE PROTEIN)

PharmGKB: 1 entry (VIP=true, CPIC=false)

ChEMBL bioactivities

5 potent at pChembl≥5 of 9 total, top 5 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChemblTypeValueUnitMolecule
7.45Kd35.81nMCHEMBL3752910
7.45ED5035.81nMCHEMBL3752910
7.25Kd56.66nMCHEMBL5653589
7.25ED5056.66nMCHEMBL5653589
5.00IC501e+04nMCHEMBL1795743

PubChem BioAssay actives

3 with measured affinity, of 88 total; 3 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

CompoundAssayTypeValueUnit
4-methyl-3-[(1-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide2149792: Binding affinity to human XRCC6 incubated for 45 mins by Kinobead based pull down assaykd0.0358uM
4-methyl-3-[(2-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide2149792: Binding affinity to human XRCC6 incubated for 45 mins by Kinobead based pull down assaykd0.0567uM
2-morpholin-4-ylbenzo[h][1,3]benzoxazin-4-one1325306: Inhibition of human DNA-PK/Ku70/Ku85 using EPPLSQEAFADLWKK as substrate by HTRF assay relative to controlic5010.0000uM

CTD chemical–gene interactions

68 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
4-biphenylaminedecreases expression, decreases reaction2
bisphenol Aaffects expression, decreases expression2
sodium arsenitedecreases expression, increases expression2
Air Pollutantsincreases abundance, increases oxidation, affects expression, affects cotreatment2
Calcitrioldecreases expression2
Cisplatinaffects cotreatment, increases response to substance, decreases expression, increases reaction2
Ozoneaffects cotreatment, increases oxidation, increases abundance, affects expression2
Tetrachlorodibenzodioxindecreases reaction, increases expression, affects binding, increases reaction2
FR900359increases phosphorylation1
bisphenol Fincreases expression1
pradimicin-IRDaffects expression, affects response to substance1
dicrotophosdecreases expression1
alpha-pineneincreases oxidation, increases abundance, affects cotreatment1
1,12-benzoperylenedecreases expression, increases expression1
selenocystinedecreases expression, increases reaction1
pyrogallol 1,3-dimethyl etheraffects cotreatment, decreases expression1
terbufosdecreases expression, increases expression, affects cotreatment1
trichostatin Aincreases acetylation1
arsenitedecreases reaction, affects binding1
3,3’-diindolylmethanedecreases reaction, increases expression1
fludarabinedecreases activity, affects cotreatment, increases acetylation1
sulindac sulfideincreases expression1
coumarinincreases phosphorylation1
2-hydroxyethyl disulfideaffects binding, affects cotreatment, decreases activity1
methacrylaldehydeaffects cotreatment, increases oxidation, increases abundance1
LAQ824decreases activity, increases acetylation, affects cotreatment1
ICG 001increases expression1
bisphenol Bincreases expression1
riccardin Ddecreases expression1
CUDC-907decreases expression1

ChEMBL screening assays

44 unique, capped per target: 44 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL3864780BindingInhibition of human DNA-PK/Ku70/Ku85 at 10 uM using EPPLSQEAFADLWKK as substrate by HTRF assay relative to controlSynthesis of linear and angular aryl-morpholino-naphth-oxazines, their DNA-PK, PI3K, PDE3A and antiplatelet activity. — Bioorg Med Chem Lett

Cellosaurus cell lines

6 cell lines: 3 cancer cell line, 3 spontaneously immortalized cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_1R02HCT116-Ku70(+/-)Cancer cell lineMale
CVCL_C4PEN6-KU70-2-DGCancer cell lineMale
CVCL_HE01HCT 116 XRCC6(+/-)Cancer cell lineMale
CVCL_VU46R70-15Spontaneously immortalized cell lineMale
CVCL_VU47R7080-20Spontaneously immortalized cell lineMale
CVCL_VU48R7080-6Spontaneously immortalized cell lineMale

Clinical trials (associated diseases)

300 trials via MONDO — disease-level, not drug-specific.

TrialPhaseStatusTitle
NCT00391261PHASE4COMPLETEDAn Open-label Trial of Metformin for Weight Control of Pediatric Patients on Antipsychotic Medications.
NCT01028820PHASE4COMPLETEDFMRI Brain Activation of Aripiprazole Treatment in Autism Spectrum Disorders
NCT01333865PHASE4COMPLETEDA Study of Memantine Hydrochloride (Namenda®) for Cognitive and Behavioral Impairment in Adults With Autism Spectrum Disorders
NCT01337700PHASE4COMPLETEDMilnacipran in Autism and the Functional Locus Coeruleus and Noradrenergic Model of Autism
NCT01695200PHASE4COMPLETEDOmega-3 Fatty Acids in Autism Spectrum Disorders
NCT02096952PHASE4COMPLETEDMethylphenidate ER Liquid Formulation in Adults With ASD and ADHD
NCT02235467PHASE4COMPLETEDMultisite Study: Parental Training Using Video Modelling to Develop Social Skills in Children With Autism
NCT02940574PHASE4COMPLETEDNeural and Behavioral Effects of Oxytocin in Autism Spectrum Disorders
NCT03333629PHASE4COMPLETEDPromoting Positive Outcomes for Individuals With ASD: Linking Early Detection, Treatment, and Long-term Outcomes
NCT03337646PHASE4COMPLETEDEvaluation of the Effect and Safety of Lisdexamfetamine in Children Aged 6-12 With ADHD and Autism
NCT03538431PHASE4COMPLETEDImproving Driving in Young People With Autism Spectrum Disorders
NCT03757585PHASE4COMPLETEDNatural Treatments for the Management of Emotional Dysregulation in Youth With Non-verbal Learning Disability (NVLD) and/or Autism Spectrum Disorders (ASD)
NCT04903353PHASE4COMPLETEDPragmatic Trial Comparing Weight Gain in Children With Autism Taking Risperidone Versus Aripiprazole
NCT05063656PHASE4COMPLETEDBiomarker-Driven Pharmacological Treatment of Adolescents With Autism Spectrum Disorder With Gabapentin
NCT05146245PHASE4UNKNOWNSafety and Pharmacokinetics of Antipsychotics in Children 2: Studying TDM in an RCT
NCT05916339PHASE4RECRUITINGAWARE: Management of ADHD in Autism Spectrum Disorder
NCT05954052PHASE4TERMINATEDA Study of Glutathione in Children With Autism Spectrum Disorder
NCT06853665PHASE4RECRUITINGThe TEAM Study - Treatment Efficacy for Autism/Attention Using Mixed Amphetamine
NCT07054697PHASE4COMPLETEDPilot-RCT With Individualized Homeopathic Treatment in the Children With Autism Spectrum Disorder
NCT07161804PHASE4COMPLETEDPilot RCT Using Homeopathic Medicines in ASD
NCT07439042PHASE4NOT_YET_RECRUITINGBuspirone for Anxiety in Autistic Youth
NCT01302964PHASE3COMPLETEDMirtazapine Treatment of Anxiety in Children and Adolescents With Pervasive Developmental Disorders
NCT01706523PHASE3TERMINATEDOpen Label Extension Study of STX209 (Arbaclofen) in Autism Spectrum Disorders
NCT01825798PHASE3COMPLETEDTreatment of Overweight Induced by Antipsychotic Medication in Young People With Autism Spectrum Disorders (ASD)
NCT01972074PHASE3COMPLETEDBehavioral and Neural Response to Memantine in Adolescents With Autism Spectrum Disorder
NCT02985749PHASE3COMPLETEDA Study of Oxytocin for the Treatment of Social Impairment in Individuals With High Functioning Autism Spectrum Disorder
NCT03197922PHASE3COMPLETEDTreatment of Encopresis in Children With Autism Spectrum Disorders
NCT03504917PHASE3TERMINATEDA Study of Balovaptan in Adults With Autism Spectrum Disorder With a 2-Year Open-Label Extension
NCT03553875PHASE3TERMINATEDMemantine for the Treatment of Social Deficits in Youth With Disorders of Impaired Social Interactions
NCT03640156PHASE3COMPLETEDModulating Socially Adaptive Mirror System Functioning in Autism by Oxytocin
NCT03715153PHASE3TERMINATEDEfficacy and Safety of Bumetanide Oral Liquid Formulation in Children Aged From 2 to Less Than 7 Years Old With Autism Spectrum Disorder.
NCT03715166PHASE3TERMINATEDEfficacy and Safety of Bumetanide Oral Liquid Formulation in Children and Adolescents Aged From 7 to Less Than 18 Years Old With Autism Spectrum Disorder
NCT04233502PHASE3WITHDRAWNEfficacy and Safety of Slenyto for Insomnia in Children With ASD
NCT04578756PHASE3COMPLETEDOpen-Label, Flexible-dose Study to Evaluate the Long-Term Safety and Tolerability of Cariprazine in the Treatment of Pediatric Participants With Schizophrenia, Bipolar I Disorder, or Autism Spectrum Disorder
NCT04623398PHASE3COMPLETEDEffect of Lithium in Patients With Autism Spectrum Disorder and Phelan-McDermid Syndrome (SHANK3 Haploinsufficiency)
NCT04725383PHASE3TERMINATEDAmitriptyline for Repetitive Behaviors in Autism Spectrum Disorders
NCT05212493PHASE3COMPLETEDThe Effects of Medical Cannabis in Children With Autistic Spectrum Disorder
NCT05361707PHASE3UNKNOWNEvaluating the Effects of Tasimelteon in Individuals With Autism Spectrum Disorder (ASD) and Sleep Disturbances
NCT05439616PHASE3COMPLETEDStudy of Cariprazine Oral Capsules or Solution to Assess Adverse Events and Change in Irritability Due to Autism Spectrum Disorder (ASD) in Participants Aged 5-17 Years With ASD
NCT06229210PHASE3RECRUITINGSafety and Tolerability Trial of Lumateperone in Pediatric Patients With Schizophrenia, Bipolar Disorder or Autism Spectrum Disorder