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Center for Computational Systems Medicine
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Fusion Gene Summary

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Fusion Gene ORF analysis

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Fusion Genomic Features

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Fusion Protein Features

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Fusion Gene Sequence

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Fusion Gene PPI analysis

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Related Drugs

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Related Diseases

Fusion gene:PAFAH1B1-CTDNEP1 (FusionGDB2 ID:61925)

Fusion Gene Summary for PAFAH1B1-CTDNEP1

check button Fusion gene summary
Fusion gene informationFusion gene name: PAFAH1B1-CTDNEP1
Fusion gene ID: 61925
HgeneTgene
Gene symbol

PAFAH1B1

CTDNEP1

Gene ID

5048

23399

Gene nameplatelet activating factor acetylhydrolase 1b regulatory subunit 1CTD nuclear envelope phosphatase 1
SynonymsLIS1|LIS2|MDCR|MDS|NudF|PAFAHDULLARD|HSA011916|NET56
Cytomap

17p13.3

17p13.1

Type of geneprotein-codingprotein-coding
Descriptionplatelet-activating factor acetylhydrolase IB subunit alphalissencephaly 1 proteinplatelet-activating factor acetylhydrolase 1b, regulatory subunit 1 (45kDa)platelet-activating factor acetylhydrolase, isoform Ib, alpha subunit (45kD)platelet-activatinCTD nuclear envelope phosphatase 1C-terminal domain nuclear envelope phosphatase 1dullard homologserine/threonine-protein phosphatase dullard
Modification date2020031320200320
UniProtAcc.

O95476

Ensembl transtripts involved in fusion geneENST00000397195, ENST00000572915, 
ENST00000451360, 		ENST00000574322, 
ENST00000573600, ENST00000318988, 
ENST00000572043, 
Fusion gene scores* DoF score13 X 10 X 4=5207 X 6 X 5=210
# samples 147
** MAII scorelog2(14/520*10)=-1.89308479608349
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(7/210*10)=-1.58496250072116
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: PAFAH1B1 [Title/Abstract] AND CTDNEP1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointPAFAH1B1(2497300)-CTDNEP1(7150662), # samples:3
Anticipated loss of major functional domain due to fusion event.
* 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
HgenePAFAH1B1

GO:0007017

microtubule-based process

11940666

TgeneCTDNEP1

GO:0006470

protein dephosphorylation

17420445|22134922

TgeneCTDNEP1

GO:0006998

nuclear envelope organization

17420445

TgeneCTDNEP1

GO:0034504

protein localization to nucleus

22134922


check buttonFusion gene breakpoints across PAFAH1B1 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check buttonFusion gene breakpoints across CTDNEP1 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check button Fusion gene information from two resources (ChiTars 5.0 and ChimerDB 4.0)
* 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.
SourceDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChimerDB4SKCMTCGA-ER-A197-06APAFAH1B1chr17

2497300

+CTDNEP1chr17

7150662

-
ChimerDB4SKCMTCGA-ER-A197-06APAFAH1B1chr17

2497300

+CTDNEP1chr17

7150662

-
ChimerDB4SKCMTCGA-ER-A197-06APAFAH1B1chr17

2497300

+CTDNEP1chr17

7154920

-
ChimerDB4SKCMTCGA-ER-A197-06APAFAH1B1chr17

2497300

-CTDNEP1chr17

7150662

-


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Fusion Gene ORF analysis for PAFAH1B1-CTDNEP1

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
5UTR-3CDSENST00000397195ENST00000574322PAFAH1B1chr17

2497300

+CTDNEP1chr17

7150662

-
5UTR-3CDSENST00000397195ENST00000573600PAFAH1B1chr17

2497300

+CTDNEP1chr17

7150662

-
5UTR-3CDSENST00000397195ENST00000318988PAFAH1B1chr17

2497300

+CTDNEP1chr17

7150662

-
5UTR-5UTRENST00000397195ENST00000572043PAFAH1B1chr17

2497300

+CTDNEP1chr17

7150662

-
3UTR-3CDSENST00000572915ENST00000574322PAFAH1B1chr17

2497300

+CTDNEP1chr17

7150662

-
3UTR-3CDSENST00000572915ENST00000573600PAFAH1B1chr17

2497300

+CTDNEP1chr17

7150662

-
3UTR-3CDSENST00000572915ENST00000318988PAFAH1B1chr17

2497300

+CTDNEP1chr17

7150662

-
3UTR-5UTRENST00000572915ENST00000572043PAFAH1B1chr17

2497300

+CTDNEP1chr17

7150662

-
intron-3CDSENST00000451360ENST00000574322PAFAH1B1chr17

2497300

+CTDNEP1chr17

7150662

-
intron-3CDSENST00000451360ENST00000573600PAFAH1B1chr17

2497300

+CTDNEP1chr17

7150662

-
intron-3CDSENST00000451360ENST00000318988PAFAH1B1chr17

2497300

+CTDNEP1chr17

7150662

-
intron-5UTRENST00000451360ENST00000572043PAFAH1B1chr17

2497300

+CTDNEP1chr17

7150662

-
5UTR-5UTRENST00000397195ENST00000574322PAFAH1B1chr17

2497300

+CTDNEP1chr17

7154920

-
5UTR-5UTRENST00000397195ENST00000573600PAFAH1B1chr17

2497300

+CTDNEP1chr17

7154920

-
5UTR-5UTRENST00000397195ENST00000318988PAFAH1B1chr17

2497300

+CTDNEP1chr17

7154920

-
5UTR-intronENST00000397195ENST00000572043PAFAH1B1chr17

2497300

+CTDNEP1chr17

7154920

-
3UTR-5UTRENST00000572915ENST00000574322PAFAH1B1chr17

2497300

+CTDNEP1chr17

7154920

-
3UTR-5UTRENST00000572915ENST00000573600PAFAH1B1chr17

2497300

+CTDNEP1chr17

7154920

-
3UTR-5UTRENST00000572915ENST00000318988PAFAH1B1chr17

2497300

+CTDNEP1chr17

7154920

-
3UTR-intronENST00000572915ENST00000572043PAFAH1B1chr17

2497300

+CTDNEP1chr17

7154920

-
intron-5UTRENST00000451360ENST00000574322PAFAH1B1chr17

2497300

+CTDNEP1chr17

7154920

-
intron-5UTRENST00000451360ENST00000573600PAFAH1B1chr17

2497300

+CTDNEP1chr17

7154920

-
intron-5UTRENST00000451360ENST00000318988PAFAH1B1chr17

2497300

+CTDNEP1chr17

7154920

-
intron-intronENST00000451360ENST00000572043PAFAH1B1chr17

2497300

+CTDNEP1chr17

7154920

-

check buttonORFfinder result based on the fusion transcript sequence of in-frame fusion genes.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)

check buttonDeepORF prediction of the coding potential based on the fusion transcript sequence of in-frame fusion genes. DeepORF is a coding potential classifier based on convolutional neural network by comparing the real Ribo-seq data. If the no-coding score < 0.5 and coding score > 0.5, then the in-frame fusion transcript is predicted as being likely translated.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandNo-coding scoreCoding score

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Fusion Genomic Features for PAFAH1B1-CTDNEP1


check buttonFusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints.
HgeneHchrHbpHstrandTgeneTchrTbpTstrand1-pp (fusion gene breakpoint)

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page.

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page.

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Fusion Protein Features for PAFAH1B1-CTDNEP1


check button Go to

FGviewer for the breakpoints of :-:

.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
.CTDNEP1

O95476

FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.FUNCTION: Serine/threonine protein phosphatase forming with CNEP1R1 an active phosphatase complex that dephosphorylates and may activate LPIN1 and LPIN2. LPIN1 and LPIN2 are phosphatidate phosphatases that catalyze the conversion of phosphatidic acid to diacylglycerol and control the metabolism of fatty acids at different levels. May indirectly modulate the lipid composition of nuclear and/or endoplasmic reticulum membranes and be required for proper nuclear membrane morphology and/or dynamics. May also indirectly regulate the production of lipid droplets and triacylglycerol. May antagonize BMP signaling. {ECO:0000269|PubMed:17420445, ECO:0000269|PubMed:22134922}.

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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Fusion Gene Sequence for PAFAH1B1-CTDNEP1


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones.

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Fusion Gene PPI Analysis for PAFAH1B1-CTDNEP1


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


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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Related Drugs for PAFAH1B1-CTDNEP1


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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Related Diseases for PAFAH1B1-CTDNEP1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgenePAFAH1B1C0431375Classical Lissencephaly9GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgenePAFAH1B1C0036341Schizophrenia1PSYGENET
HgenePAFAH1B1C0265219Miller Dieker syndrome1ORPHANET
HgenePAFAH1B1C0596263Carcinogenesis1CTD_human
HgenePAFAH1B1C1848201Subcortical Band Heterotopia1GENOMICS_ENGLAND;ORPHANET
HgenePAFAH1B1C2750748Chromosome 17p13.3 Duplication Syndrome1ORPHANET