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Fusion gene ID: 23533 |
FusionGeneSummary for NBR1_PALB2 |
Fusion gene summary |
Fusion gene information | Fusion gene name: NBR1_PALB2 | Fusion gene ID: 23533 | Hgene | Tgene | Gene symbol | NBR1 | PALB2 | Gene ID | 4077 | 79728 |
Gene name | NBR1, autophagy cargo receptor | partner and localizer of BRCA2 | |
Synonyms | 1A1-3B|IAI3B|M17S2|MIG19 | FANCN|PNCA3 | |
Cytomap | 17q21.31 | 16p12.2 | |
Type of gene | protein-coding | protein-coding | |
Description | next to BRCA1 gene 1 proteinB-box proteincell migration-inducing gene 19 proteinmembrane component, chromosome 17, surface marker 2 (ovarian carcinoma antigen CA125)migration-inducing protein 19neighbor of BRCA1 gene 1 | partner and localizer of BRCA2mutant partner and localizer of BRCA2 | |
Modification date | 20180523 | 20180522 | |
UniProtAcc | Q14596 | Q86YC2 | |
Ensembl transtripts involved in fusion gene | ENST00000341165, ENST00000422280, ENST00000542611, ENST00000590996, ENST00000389312, ENST00000589872, | ENST00000261584, | |
Fusion gene scores | * DoF score | 2 X 2 X 2=8 | 1 X 1 X 1=1 |
# samples | 2 | 1 | |
** MAII score | log2(2/8*10)=1.32192809488736 | log2(1/1*10)=3.32192809488736 | |
Context | PubMed: NBR1 [Title/Abstract] AND PALB2 [Title/Abstract] AND fusion [Title/Abstract] | ||
Functional or gene categories assigned by FusionGDB annotation | DDR (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) |
Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
Partner | Gene | GO ID | GO term | PubMed ID |
Hgene | NBR1 | GO:0016236 | macroautophagy | 19250911 |
Hgene | NBR1 | GO:0051259 | protein complex oligomerization | 19250911 |
Tgene | PALB2 | GO:0000724 | double-strand break repair via homologous recombination | 19369211|19423707 |
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 type | Source | Cancer type | Sample | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand |
TCGA | LD | SKCM | TCGA-ER-A19K-01A | NBR1 | chr17 | 41349123 | + | PALB2 | chr16 | 23625412 | - |
* LD: Li Ding group's fusion gene list RV: Roel Verhaak group's fusion gene list ChiTaRs fusion database |
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. |
ORF | Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand |
Frame-shift | ENST00000341165 | ENST00000261584 | NBR1 | chr17 | 41349123 | + | PALB2 | chr16 | 23625412 | - |
Frame-shift | ENST00000422280 | ENST00000261584 | NBR1 | chr17 | 41349123 | + | PALB2 | chr16 | 23625412 | - |
Frame-shift | ENST00000542611 | ENST00000261584 | NBR1 | chr17 | 41349123 | + | PALB2 | chr16 | 23625412 | - |
Frame-shift | ENST00000590996 | ENST00000261584 | NBR1 | chr17 | 41349123 | + | PALB2 | chr16 | 23625412 | - |
Frame-shift | ENST00000389312 | ENST00000261584 | NBR1 | chr17 | 41349123 | + | PALB2 | chr16 | 23625412 | - |
Frame-shift | ENST00000589872 | ENST00000261584 | NBR1 | chr17 | 41349123 | + | PALB2 | chr16 | 23625412 | - |
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FusionProtFeatures for NBR1_PALB2 |
Main function of each fusion partner protein. (from UniProt) |
Hgene | Tgene |
NBR1 | PALB2 |
Acts probably as a receptor for selective autophagosomaldegradation of ubiquitinated targets.{ECO:0000269|PubMed:19250911}. | Plays a critical role in homologous recombination repair(HRR) through its ability to recruit BRCA2 and RAD51 to DNA breaks(PubMed:16793542, PubMed:19423707, PubMed:19369211,PubMed:22941656, PubMed:24141787, PubMed:28319063). Stronglystimulates the DNA strand-invasion activity of RAD51, stabilizesthe nucleoprotein filament against a disruptive BRC3-BRC4polypeptide and helps RAD51 to overcome the suppressive effect ofreplication protein A (RPA) (PubMed:20871615). Functionallycooperates with RAD51AP1 in promoting of D-loop formation by RAD51(PubMed:20871616). Serves as the molecular scaffold in theformation of the BRCA1-PALB2-BRCA2 complex which is essential forhomologous recombination (PubMed:19369211). Via its WD repeats isproposed to scaffold a HR complex containing RAD51C and BRCA2which is thought to play a role in HR-mediated DNA repair(PubMed:24141787). Essential partner of BRCA2 that promotes thelocalization and stability of BRCA2 (PubMed:16793542). Alsoenables its recombinational repair and checkpoint functions ofBRCA2 (PubMed:16793542). May act by promoting stable associationof BRCA2 with nuclear structures, allowing BRCA2 to escape theeffects of proteasome-mediated degradation (PubMed:16793542).Binds DNA with high affinity for D loop, which comprises single-stranded, double-stranded and branched DNA structures(PubMed:20871616). May play a role in the extension step afterstrand invasion at replication-dependent DNA double-strand breaks;together with BRCA2 is involved in both POLH localization atcollapsed replication forks and DNA polymerization activity(PubMed:24485656). {ECO:0000269|PubMed:16793542,ECO:0000269|PubMed:19369211, ECO:0000269|PubMed:19423707,ECO:0000269|PubMed:20871615, ECO:0000269|PubMed:20871616,ECO:0000269|PubMed:22941656, ECO:0000269|PubMed:24141787,ECO:0000269|PubMed:24485656, ECO:0000269|PubMed:28319063}. |
Retention 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 . * 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. |
Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Protein feature | Protein feature note |
- In-frame and not-retained protein feature among the 13 regional features. |
Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Protein feature | Protein feature note |
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FusionGeneSequence for NBR1_PALB2 |
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 NBR1_PALB2 |
Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in . |
Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160) |
Hgene | Hgene's interactors | Tgene | Tgene's interactors |
NBR1 | VTA1, CIB1, FEZ1, GABARAP, GABARAPL2, CALM1, ITSN2, SQSTM1, MAP1LC3A, USP8, UBC, TTN, NBR1, GABARAPL1, MAP1LC3B, MAP1LC3C, ATXN1L, SPRED2, HTT, GSK3A, CEP55, TNK2, GSK3B, TOLLIP, SYT4, SCGN, LTBR, VAPB, MAP3K3, MAP2K4, CEP135, GTSE1, JUN, SSH3, JUNB, SPPL2B, CORO6, MRPL41, LYPD4 | PALB2 | RAD51, RAD51AP1, CAPN1, MORF4L1, BRCA2, MORF4L2, BRCA1, RBBP8, BACH1, PALB2, ALB, HNRNPC, MOV10, POLH, HIST1H3A, HIST2H2BE, PDS5B, BCAS3, CASZ1, CCL5, CST6, DIRAS3, ERRFI1, FAM84B, GREB1, IL13RA2, IL24, KLK6, LYPD3, MRC2, NAT2, PRDM14, RHOBTB2, SERPINB5, SNAI1, THRSP, HIST1H2BG, CUL3, KEAP1, USP11, USP2, ERCC5, TOP1, TOP2A, TOP3A, RAD51C, XRCC3, POLN, RNF168 |
- Retained PPIs in in-frame fusion. |
Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Still interaction with |
- Lost PPIs in in-frame fusion. |
Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Interaction lost with |
- Retained PPIs, but lost function due to frame-shift fusion. |
Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Interaction lost with |
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RelatedDrugs for NBR1_PALB2 |
Drugs targeting genes involved in this fusion gene. (DrugBank Version 5.1.0 2018-04-02) |
Partner | Gene | UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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RelatedDiseases for NBR1_PALB2 |
Diseases associated with fusion partners. (DisGeNet 4.0) |
Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
Tgene | PALB2 | C0005586 | Bipolar Disorder | 1 | PSYGENET |
Tgene | PALB2 | C0030297 | Pancreatic Neoplasm | 1 | CTD_human |
Tgene | PALB2 | C0036341 | Schizophrenia | 1 | PSYGENET |