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Center for Computational Systems Medicine
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FusionGeneSummary

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FusionProtFeature

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FusionGeneSequence

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FusionGenePPI

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RelatedDrugs

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RelatedDiseases

Fusion gene ID: 42227

FusionGeneSummary for XRCC6_L3MBTL2

check button Fusion gene summary
Fusion gene informationFusion gene name: XRCC6_L3MBTL2
Fusion gene ID: 42227
HgeneTgene
Gene symbol

XRCC6

L3MBTL2

Gene ID

2547

83746

Gene nameX-ray repair cross complementing 6L3MBTL2, polycomb repressive complex 1 subunit
SynonymsCTC75|CTCBF|G22P1|KU70|ML8|TLAAH-l(3)mbt-l|L3MBT
Cytomap

22q13.2

22q13.2

Type of geneprotein-codingprotein-coding
DescriptionX-ray repair cross-complementing protein 65'-dRP lyase Ku705'-deoxyribose-5-phosphate lyase Ku7070 kDa subunit of Ku antigenATP-dependent DNA helicase 2 subunit 1ATP-dependent DNA helicase II, 70 kDa subunitCTC box binding factor 75 kDa subunitDNA lethal(3)malignant brain tumor-like protein 2H-l(3)mbt-like protein 2L(3)mbt-like protein 2l(3)mbt-like 2
Modification date2018052320180522
UniProtAcc

P12956

Q969R5

Ensembl transtripts involved in fusion geneENST00000360079, ENST00000402580, 
ENST00000428575, ENST00000359308, 
ENST00000405878, ENST00000405506, 
ENST00000216237, ENST00000489136, 
Fusion gene scores* DoF score7 X 5 X 7=2453 X 5 X 4=60
# samples 76
** MAII scorelog2(7/245*10)=-1.8073549220576
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(6/60*10)=0
Context

PubMed: XRCC6 [Title/Abstract] AND L3MBTL2 [Title/Abstract] AND fusion [Title/Abstract]

Functional or gene categories assigned by FusionGDB annotationDDR (DNA damage repair) gene involved fusion gene, retained protein feature but frameshift.
* DoF score (Degree of Frequency) = # partners X # break points X # cancer types
** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
HgeneXRCC6

GO:0002218

activation of innate immune response

28712728

HgeneXRCC6

GO:0045860

positive regulation of protein kinase activity

22504299

HgeneXRCC6

GO:0045893

positive regulation of transcription, DNA-templated

12145306

HgeneXRCC6

GO:0051290

protein heterotetramerization

24095731

HgeneXRCC6

GO:0071480

cellular response to gamma radiation

26359349

HgeneXRCC6

GO:0097680

double-strand break repair via classical nonhomologous end joining

24095731


check button Fusion gene information from three resources
(ChiTars (NAR, 2018), tumorfusions (NAR, 2018), Gao et al. (Cell, 2018))
* All genome coordinats were lifted-over on hg19.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
Data typeSourceCancer typeSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
TCGALDOVTCGA-13-A5FT-01AXRCC6chr22

42054356

+L3MBTL2chr22

41621798

+
* LD: Li Ding group's fusion gene list
  RV: Roel Verhaak group's fusion gene list
  ChiTaRs fusion database

check button Open reading frame (ORF) analsis of fusion genes based on Ensembl gene isoform structure.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
ORFHenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrand
Frame-shitENST00000360079ENST00000216237XRCC6chr22

42054356

+L3MBTL2chr22

41621798

+
5CDS-intronENST00000360079ENST00000489136XRCC6chr22

42054356

+L3MBTL2chr22

41621798

+
Frame-shitENST00000402580ENST00000216237XRCC6chr22

42054356

+L3MBTL2chr22

41621798

+
5CDS-intronENST00000402580ENST00000489136XRCC6chr22

42054356

+L3MBTL2chr22

41621798

+
Frame-shitENST00000428575ENST00000216237XRCC6chr22

42054356

+L3MBTL2chr22

41621798

+
5CDS-intronENST00000428575ENST00000489136XRCC6chr22

42054356

+L3MBTL2chr22

41621798

+
Frame-shitENST00000359308ENST00000216237XRCC6chr22

42054356

+L3MBTL2chr22

41621798

+
5CDS-intronENST00000359308ENST00000489136XRCC6chr22

42054356

+L3MBTL2chr22

41621798

+
Frame-shitENST00000405878ENST00000216237XRCC6chr22

42054356

+L3MBTL2chr22

41621798

+
5CDS-intronENST00000405878ENST00000489136XRCC6chr22

42054356

+L3MBTL2chr22

41621798

+
Frame-shitENST00000405506ENST00000216237XRCC6chr22

42054356

+L3MBTL2chr22

41621798

+
5CDS-intronENST00000405506ENST00000489136XRCC6chr22

42054356

+L3MBTL2chr22

41621798

+

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FusionProtFeatures for XRCC6_L3MBTL2


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
XRCC6

P12956

L3MBTL2

Q969R5

Single-stranded DNA-dependent ATP-dependent helicase.Has a role in chromosome translocation. The DNA helicase IIcomplex binds preferentially to fork-like ends of double-strandedDNA in a cell cycle-dependent manner. It works in the 3'-5'direction. Binding to DNA may be mediated by XRCC6. Involved inDNA non-homologous end joining (NHEJ) required for double-strandbreak repair and V(D)J recombination. The XRCC5/6 dimer acts asregulatory subunit of the DNA-dependent protein kinase complexDNA-PK by increasing the affinity of the catalytic subunit PRKDCto DNA by 100-fold. The XRCC5/6 dimer is probably involved instabilizing broken DNA ends and bringing them together. Theassembly of the DNA-PK complex to DNA ends is required for theNHEJ ligation step. Required for osteocalcin gene expression.Probably also acts as a 5'-deoxyribose-5-phosphate lyase (5'-dRPlyase), by catalyzing the beta-elimination of the 5' deoxyribose-5-phosphate at an abasic site near double-strand breaks. 5'-dRPlyase activity allows to 'clean' the termini of abasic sites, aclass of nucleotide damage commonly associated with strand breaks,before such broken ends can be joined. The XRCC5/6 dimer togetherwith APEX1 acts as a negative regulator of transcription. Plays arole in the regulation of DNA virus-mediated innate immuneresponse by assembling into the HDP-RNP complex, a complex thatserves as a platform for IRF3 phosphorylation and subsequentinnate immune response activation through the cGAS-STING pathway.{ECO:0000269|PubMed:12145306, ECO:0000269|PubMed:20383123,ECO:0000269|PubMed:20493174, ECO:0000269|PubMed:2466842,ECO:0000269|PubMed:28712728, ECO:0000269|PubMed:7957065,ECO:0000269|PubMed:8621488, ECO:0000269|PubMed:9742108}. Putative Polycomb group (PcG) protein. PcG proteinsmaintain the transcriptionally repressive state of genes, probablyvia a modification of chromatin, rendering it heritably changed inits expressibility. Its association with a chromatin-remodelingcomplex suggests that it may contribute to prevent expression ofgenes that trigger the cell into mitosis. Binds to monomethylatedand dimethylated 'Lys-20' on histone H4. Binds histone H3 peptidesthat are monomethylated or dimethylated on 'Lys-4', 'Lys-9' or'Lys-27'. {ECO:0000269|PubMed:19233876}.

check buttonRetention analysis result of each fusion partner protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at

download page

.

* Minus value of BPloci means that the break pointn is located before the CDS.
- In-frame and retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note


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FusionGeneSequence for XRCC6_L3MBTL2


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences.
(nt: nucleotides, aa: amino acids)

* Fusion amino acid sequences.

* Fusion transcript sequences (only coding sequence (CDS) region).

* Fusion transcript sequences (Full-length transcript).

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FusionGenePPI for XRCC6_L3MBTL2


check button Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in

ChiPPI page

.

check button Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160)
HgeneHgene's interactorsTgeneTgene's interactors
XRCC6VAV1, NCF4, XRCC5, MRE11A, CBX5, AR, CCNA1, CDK2, TERF2IP, CHEK1, NCOA6, KAT2A, CREBBP, ACD, CDCA5, ARAP1, FMNL1, GAL3ST4, ILVBL, NOTCH1, PGAM1, RBBP4, TBCD, ABCD4, PLGRKT, GSE1, NHP2L1, NIT1, PECAM1, RRAS2, SNTA1, ATP6V1E1, PAEP, PAFAH1B3, RPLP1, SERPINB9, YWHAZ, XRCC6BP1, CLU, PRKDC, RPA2, TERT, DNTT, HOXC4, HOXD4, DLX2, POU2F2, POU2F1, TAL1, TERF2, WRN, BIN1, PTTG1, CD40, PCNA, HSF1, ABL1, DHX9, FCHSD1, SIRT6, NR1H4, CHD1L, TP53, BARD1, ESR1, PARP1, SIRT3, MGMT, PDX1, SRRM2, MSX2, RUNX2, NAA15, H2AFX, PHF1, XRCC4, LIG4, KAT2B, EP300, ATXN3, ILF2, THRA, THRB, BIRC5, CHAF1A, HIST1H3A, HIST1H3E, H3F3A, BAZ1A, MYC, USF1, HDAC5, UBE3A, RBM39, MDM2, BAX, DDB2, PSMA3, CMTM6, RPS10, RASA1, EFNA1, TAC1, PDK1, CENPU, KIAA0408, EID1, VBP1, SDHC, PDPK1, ANXA1, BTG1, PNRC2, QRSL1, RGS2, MAP4K2, HERPUD1, SEP15, SPARC, COIL, LIG3, HOXB7, YY1, RNF146, SMARCAD1, ORC3, ORC2, ORC6, ORC4, TCF7L2, NDRG1, HDGF, ILF3, MSH6, MSH2, CBX1, CBX3, CEBPA, ARRB2, SIRT7, HNRNPA1, CFLAR, HDAC6, ERG, ISG15, TONSL, CUL5, COPS5, CAND1, HTT, CLTC, TADA3, CCT3, KCND3, ARHGAP5, EEF2, SDHA, HSPA5, KIF23, PGR, XRCC6, BRCA1, ECT2, PAXIP1, TP53BP1, NCL, CSNK2A1, SMURF1, PNKP, FN1, VCAM1, GZMA, GZMB, SMAD7, SKIL, SMAD3, ZNF512B, ITGA4, PPID, IGSF8, ICAM1, HMGA1, HMGA2, LMNA, CTBP2, COPB1, ADCY7, EPS8, MAP2K5, CAPN11, SERPINA2, TARDBP, PARK2, PRPF40A, WBP4, PIN1, CTNNA1, CUL2, CSDE1, FARSB, GANAB, GART, IMPDH1, JUP, DPYSL3, PLOD2, RANBP3, SAMHD1, SET, ST13, SUPT5H, SWAP70, ATP6V1B2, HYOU1, RPSA, NARS, RPA1, RPA3, ATRX, EMD, ELF3, EHF, ENO1, SHMT2, MOV10, NXF1, PPARG, CUL7, OBSL1, CCDC8, EED, SUMO2, MAST3, WDR76, APLF, PHRF1, NTRK1, DYNC1LI1, GTF2I, HNRNPK, NAE1, PDIA3, RFC1, TKT, TMOD3, SCARNA22, CSNK1A1, DNM2, BAG2, ANKRD28, POT1, TINF2, TNRC18, CCDC57, C9orf142, BANP, CRY2, MACROD1, MCM2, NF2, SNW1, TFAP2A, UHRF2, U2AF2, RC3H1, FOXL2, NFATC1, NFATC2, AHSA1, RNF126, PARP2, XPC, SUPT16H, XRCC1, H2AFY, CDK5RAP1, SSRP1, SPTA1, COX15, DLD, DLST, DNM1L, HSD17B10, SOD1, VDAC1, TRIM25, UBE2S, YAP1L3MBTL2MEAF6, PHF10, STAM2, RB1, CBX3, HDAC3, HIST1H4A, E2F6, RNF2, HIST3H3, HIST4H4, PCGF6, SMARCAD1, RYBP, YAF2, MPP3, PIAS1, HIST1H3A, AES, PAICS, TBC1D9B, STAC3, TRIM42, PSME3, WDR5, PSMC3, MIER2, XPO1, MYO19, MAX, FOXJ2, FOXR1, HDAC1, SSFA2, SERPINF1, TFDP1, TFDP2, CIZ1, MGA, LIN54, ITPR2, RING1, ZNF296, ITPR3, MTA1, MTA2, KBTBD7, MBD3, UBE2O, ASB6, CDH19, GATAD2B, HDAC2, TRIM25


check button - Retained PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


check button - Retained PPIs, but lost function due to frame-shift fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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RelatedDrugs for XRCC6_L3MBTL2


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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RelatedDiseases for XRCC6_L3MBTL2


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneL3MBTL2C0025149Medulloblastoma1CTD_human