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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: 28601

FusionGeneSummary for PRDM2_LRRC38

check button Fusion gene summary
Fusion gene informationFusion gene name: PRDM2_LRRC38
Fusion gene ID: 28601
HgeneTgene
Gene symbol

PRDM2

LRRC38

Gene ID

7799

126755

Gene namePR/SET domain 2leucine rich repeat containing 38
SynonymsHUMHOXY1|KMT8|KMT8A|MTB-ZF|RIZ|RIZ1|RIZ2-
Cytomap

1p36.21

1p36.21

Type of geneprotein-codingprotein-coding
DescriptionPR 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 proteinretinoblastomleucine-rich repeat-containing protein 38BK channel auxiliary gamma subunit LRRC38BK channel auxilliary gamma subunit LRRC38
Modification date2018052320180415
UniProtAcc

Q13029

Q5VT99

Ensembl transtripts involved in fusion geneENST00000376048, ENST00000311066, 
ENST00000235372, ENST00000502727, 
ENST00000413440, ENST00000343137, 
ENST00000503842, ENST00000505823, 
ENST00000376085, 
Fusion gene scores* DoF score2 X 2 X 2=81 X 1 X 1=1
# samples 21
** MAII scorelog2(2/8*10)=1.32192809488736log2(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 annotationTumor 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)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
HgenePRDM2

GO:0045944

positive regulation of transcription by RNA polymerase II

8654390

TgeneLRRC38

GO:0071805

potassium ion transmembrane transport

22547800

TgeneLRRC38

GO:1903818

positive regulation of voltage-gated potassium channel activity

22547800


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
TCGALDTHYMTCGA-ZB-A969-01APRDM2chr1

14075982

+LRRC38chr1

13802567

-
* 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-shitENST00000376048ENST00000376085PRDM2chr1

14075982

+LRRC38chr1

13802567

-
Frame-shitENST00000311066ENST00000376085PRDM2chr1

14075982

+LRRC38chr1

13802567

-
Frame-shitENST00000235372ENST00000376085PRDM2chr1

14075982

+LRRC38chr1

13802567

-
3UTR-3CDSENST00000502727ENST00000376085PRDM2chr1

14075982

+LRRC38chr1

13802567

-
5UTR-3CDSENST00000413440ENST00000376085PRDM2chr1

14075982

+LRRC38chr1

13802567

-
5UTR-3CDSENST00000343137ENST00000376085PRDM2chr1

14075982

+LRRC38chr1

13802567

-
5UTR-3CDSENST00000503842ENST00000376085PRDM2chr1

14075982

+LRRC38chr1

13802567

-
5UTR-3CDSENST00000505823ENST00000376085PRDM2chr1

14075982

+LRRC38chr1

13802567

-

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FusionProtFeatures for PRDM2_LRRC38


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
PRDM2

Q13029

LRRC38

Q5VT99

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}.

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 PRDM2_LRRC38


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 PRDM2_LRRC38


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
PRDM2ESR1, RB1, PRDM2, PGR, EP300, SRC, TP53, E2F1, HIST3H3, HIST1H3A, CTBP1, MDM2LRRC38


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 PRDM2_LRRC38


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 PRDM2_LRRC38


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgenePRDM2C0005695Bladder Neoplasm1CTD_human
HgenePRDM2C0040136Thyroid Neoplasm1CTD_human
HgenePRDM2C0236733Amphetamine-Related Disorders1CTD_human