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Fusion gene ID: 28601 |
FusionGeneSummary for PRDM2_LRRC38 |
Fusion gene summary |
Fusion gene information | Fusion gene name: PRDM2_LRRC38 | Fusion gene ID: 28601 | Hgene | Tgene | Gene symbol | PRDM2 | LRRC38 | Gene ID | 7799 | 126755 |
Gene name | PR/SET domain 2 | leucine rich repeat containing 38 | |
Synonyms | HUMHOXY1|KMT8|KMT8A|MTB-ZF|RIZ|RIZ1|RIZ2 | - | |
Cytomap | 1p36.21 | 1p36.21 | |
Type of gene | protein-coding | protein-coding | |
Description | PR domain zinc finger protein 2GATA-3 binding protein G3BMTE-binding proteinPR domain 2PR domain containing 2, with ZNF domainPR domain-containing protein 2lysine N-methyltransferase 8retinoblastoma protein-binding zinc finger proteinretinoblastom | leucine-rich repeat-containing protein 38BK channel auxiliary gamma subunit LRRC38BK channel auxilliary gamma subunit LRRC38 | |
Modification date | 20180523 | 20180415 | |
UniProtAcc | Q13029 | Q5VT99 | |
Ensembl transtripts involved in fusion gene | ENST00000376048, ENST00000311066, ENST00000235372, ENST00000502727, ENST00000413440, ENST00000343137, ENST00000503842, ENST00000505823, | ENST00000376085, | |
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: PRDM2 [Title/Abstract] AND LRRC38 [Title/Abstract] AND fusion [Title/Abstract] | ||
Functional or gene categories assigned by FusionGDB annotation | Tumor suppressor gene involved fusion gene, retained protein feature but frameshift. DDR (DNA damage repair) gene involved fusion gene, in-frame but not retained their domain. |
* 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 | PRDM2 | GO:0045944 | positive regulation of transcription by RNA polymerase II | 8654390 |
Tgene | LRRC38 | GO:0071805 | potassium ion transmembrane transport | 22547800 |
Tgene | LRRC38 | GO:1903818 | positive regulation of voltage-gated potassium channel activity | 22547800 |
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 | THYM | TCGA-ZB-A969-01A | PRDM2 | chr1 | 14075982 | + | LRRC38 | chr1 | 13802567 | - |
* 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 | ENST00000376048 | ENST00000376085 | PRDM2 | chr1 | 14075982 | + | LRRC38 | chr1 | 13802567 | - |
Frame-shift | ENST00000311066 | ENST00000376085 | PRDM2 | chr1 | 14075982 | + | LRRC38 | chr1 | 13802567 | - |
Frame-shift | ENST00000235372 | ENST00000376085 | PRDM2 | chr1 | 14075982 | + | LRRC38 | chr1 | 13802567 | - |
3UTR-3CDS | ENST00000502727 | ENST00000376085 | PRDM2 | chr1 | 14075982 | + | LRRC38 | chr1 | 13802567 | - |
5UTR-3CDS | ENST00000413440 | ENST00000376085 | PRDM2 | chr1 | 14075982 | + | LRRC38 | chr1 | 13802567 | - |
5UTR-3CDS | ENST00000343137 | ENST00000376085 | PRDM2 | chr1 | 14075982 | + | LRRC38 | chr1 | 13802567 | - |
5UTR-3CDS | ENST00000503842 | ENST00000376085 | PRDM2 | chr1 | 14075982 | + | LRRC38 | chr1 | 13802567 | - |
5UTR-3CDS | ENST00000505823 | ENST00000376085 | PRDM2 | chr1 | 14075982 | + | LRRC38 | chr1 | 13802567 | - |
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FusionProtFeatures for PRDM2_LRRC38 |
Main function of each fusion partner protein. (from UniProt) |
Hgene | Tgene |
PRDM2 | LRRC38 |
S-adenosyl-L-methionine-dependent histonemethyltransferase that specifically methylates 'Lys-9' of histoneH3. May function as a DNA-binding transcription factor. Binds tothe macrophage-specific TPA-responsive element (MTE) of the HMOX1(heme oxygenase 1) gene and may act as a transcriptional activatorof this gene. {ECO:0000269|PubMed:14633678}. | Auxiliary protein of the large-conductance, voltage andcalcium-activated potassium channel (BK alpha). Modulates gatingproperties by producing a marked shift in the BK channel's voltagedependence of activation in the hyperpolarizing direction, and inthe absence of calcium. {ECO:0000269|PubMed:22547800}. |
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 PRDM2_LRRC38 |
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 PRDM2_LRRC38 |
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 |
PRDM2 | ESR1, RB1, PRDM2, PGR, EP300, SRC, TP53, E2F1, HIST3H3, HIST1H3A, CTBP1, MDM2 | LRRC38 |
- 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 PRDM2_LRRC38 |
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 PRDM2_LRRC38 |
Diseases associated with fusion partners. (DisGeNet 4.0) |
Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
Hgene | PRDM2 | C0005695 | Bladder Neoplasm | 1 | CTD_human |
Hgene | PRDM2 | C0040136 | Thyroid Neoplasm | 1 | CTD_human |
Hgene | PRDM2 | C0236733 | Amphetamine-Related Disorders | 1 | CTD_human |