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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:DHX30-LIMD1 (FusionGDB2 ID:HG22907TG8994)

Fusion Gene Summary for DHX30-LIMD1

check button Fusion gene summary
Fusion gene informationFusion gene name: DHX30-LIMD1
Fusion gene ID: hg22907tg8994
HgeneTgene
Gene symbol

DHX30

LIMD1

Gene ID

22907

8994

Gene nameDExH-box helicase 30LIM domains containing 1
SynonymsDDX30|NEDMIAL|RETCOR-
Cytomap('DHX30')('LIMD1')

3p21.31

3p21.31

Type of geneprotein-codingprotein-coding
DescriptionATP-dependent RNA helicase DHX30DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 30DEAH (Asp-Glu-Ala-His) box helicase 30DEAH (Asp-Glu-Ala-His) box polypeptide 30DEAH box protein 30DEAH-box helicase 30putative ATP-dependent RNA helicase DHX30retina co-LIM domain-containing protein 1
Modification date2020032220200313
UniProtAcc.

Q9UGP4

Ensembl transtripts involved in fusion geneENST00000476446, ENST00000348968, 
ENST00000445061, ENST00000446256, 
ENST00000457607, 
Fusion gene scores* DoF score13 X 10 X 8=10407 X 5 X 5=175
# samples 1510
** MAII scorelog2(15/1040*10)=-2.79354912253257
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(10/175*10)=-0.807354922057604
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: DHX30 [Title/Abstract] AND LIMD1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointDHX30(47844702)-LIMD1(45707142), # 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
TgeneLIMD1

GO:0001666

response to hypoxia

22286099

TgeneLIMD1

GO:0016310

phosphorylation

18439753

TgeneLIMD1

GO:0035331

negative regulation of hippo signaling

20303269

TgeneLIMD1

GO:0045892

negative regulation of transcription, DNA-templated

15542589



check button Fusion gene information
* 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
ChimerDB4PRADTCGA-YJ-A8SW-01ADHX30chr3

47844702

-LIMD1chr3

45707142

+
ChimerDB4PRADTCGA-YJ-A8SW-01ADHX30chr3

47844702

+LIMD1chr3

45707142

+
ChimerDB4PRADTCGA-YJ-A8SWDHX30chr3

47844702

+LIMD1chr3

45707141

+
ChimerDB4PRADTCGA-YJ-A8SWDHX30chr3

47844702

+LIMD1chr3

45707142

+


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Fusion Gene ORF analysis for DHX30-LIMD1

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
3UTR-3UTRENST00000476446ENST00000273317DHX30chr3

47844702

+LIMD1chr3

45707142

+
3UTR-3UTRENST00000476446ENST00000273317DHX30chr3

47844702

+LIMD1chr3

45707141

+
3UTR-3UTRENST00000476446ENST00000440097DHX30chr3

47844702

+LIMD1chr3

45707142

+
3UTR-3UTRENST00000476446ENST00000440097DHX30chr3

47844702

+LIMD1chr3

45707141

+
3UTR-3UTRENST00000476446ENST00000465039DHX30chr3

47844702

+LIMD1chr3

45707142

+
3UTR-3UTRENST00000476446ENST00000465039DHX30chr3

47844702

+LIMD1chr3

45707141

+
5UTR-3UTRENST00000348968ENST00000273317DHX30chr3

47844702

+LIMD1chr3

45707142

+
5UTR-3UTRENST00000348968ENST00000273317DHX30chr3

47844702

+LIMD1chr3

45707141

+
5UTR-3UTRENST00000348968ENST00000440097DHX30chr3

47844702

+LIMD1chr3

45707142

+
5UTR-3UTRENST00000348968ENST00000440097DHX30chr3

47844702

+LIMD1chr3

45707141

+
5UTR-3UTRENST00000348968ENST00000465039DHX30chr3

47844702

+LIMD1chr3

45707142

+
5UTR-3UTRENST00000348968ENST00000465039DHX30chr3

47844702

+LIMD1chr3

45707141

+
5UTR-3UTRENST00000445061ENST00000273317DHX30chr3

47844702

+LIMD1chr3

45707142

+
5UTR-3UTRENST00000445061ENST00000273317DHX30chr3

47844702

+LIMD1chr3

45707141

+
5UTR-3UTRENST00000445061ENST00000440097DHX30chr3

47844702

+LIMD1chr3

45707142

+
5UTR-3UTRENST00000445061ENST00000440097DHX30chr3

47844702

+LIMD1chr3

45707141

+
5UTR-3UTRENST00000445061ENST00000465039DHX30chr3

47844702

+LIMD1chr3

45707142

+
5UTR-3UTRENST00000445061ENST00000465039DHX30chr3

47844702

+LIMD1chr3

45707141

+
5UTR-3UTRENST00000446256ENST00000273317DHX30chr3

47844702

+LIMD1chr3

45707142

+
5UTR-3UTRENST00000446256ENST00000273317DHX30chr3

47844702

+LIMD1chr3

45707141

+
5UTR-3UTRENST00000446256ENST00000440097DHX30chr3

47844702

+LIMD1chr3

45707142

+
5UTR-3UTRENST00000446256ENST00000440097DHX30chr3

47844702

+LIMD1chr3

45707141

+
5UTR-3UTRENST00000446256ENST00000465039DHX30chr3

47844702

+LIMD1chr3

45707142

+
5UTR-3UTRENST00000446256ENST00000465039DHX30chr3

47844702

+LIMD1chr3

45707141

+
intron-3UTRENST00000457607ENST00000273317DHX30chr3

47844702

+LIMD1chr3

45707142

+
intron-3UTRENST00000457607ENST00000273317DHX30chr3

47844702

+LIMD1chr3

45707141

+
intron-3UTRENST00000457607ENST00000440097DHX30chr3

47844702

+LIMD1chr3

45707142

+
intron-3UTRENST00000457607ENST00000440097DHX30chr3

47844702

+LIMD1chr3

45707141

+
intron-3UTRENST00000457607ENST00000465039DHX30chr3

47844702

+LIMD1chr3

45707142

+
intron-3UTRENST00000457607ENST00000465039DHX30chr3

47844702

+LIMD1chr3

45707141

+

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 DHX30-LIMD1


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)
DHX30chr347844702+LIMD1chr345707141+0.0020479290.99795204
DHX30chr347844702+LIMD1chr345707141+0.0020479290.99795204
DHX30chr347844702+LIMD1chr345707141+0.0020479290.99795204
DHX30chr347844702+LIMD1chr345707141+0.0020479290.99795204


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.
genomic feature of top 1%

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Fusion Protein Features for DHX30-LIMD1


check button Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:47844702/:45707142)
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
- How to search
1. Put your fusion gene symbol.
2. Press the tab key until there will be shown the breakpoint information filled.
4. Go down and press 'Search' tab twice.
4. Go down to have the hyperlink of the search result.
5. Click the hyperlink.
6. See the FGviewer result for your fusion gene.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
.LIMD1

Q9UGP4

FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.FUNCTION: Adapter or scaffold protein which participates in the assembly of numerous protein complexes and is involved in several cellular processes such as cell fate determination, cytoskeletal organization, repression of gene transcription, cell-cell adhesion, cell differentiation, proliferation and migration. Positively regulates microRNA (miRNA)-mediated gene silencing and is essential for P-body formation and integrity. Acts as a hypoxic regulator by bridging an association between the prolyl hydroxylases and VHL enabling efficient degradation of HIF1A. Acts as a transcriptional corepressor for SNAI1- and SNAI2/SLUG-dependent repression of E-cadherin transcription. Negatively regulates the Hippo signaling pathway and antagonizes phosphorylation of YAP1. Inhibits E2F-mediated transcription, and suppresses the expression of the majority of genes with E2F1-responsive elements. Regulates osteoblast development, function, differentiation and stress osteoclastogenesis. Enhances the ability of TRAF6 to activate adapter protein complex 1 (AP-1) and negatively regulates the canonical Wnt receptor signaling pathway in osteoblasts. May act as a tumor suppressor by inhibiting cell proliferation. {ECO:0000269|PubMed:15542589, ECO:0000269|PubMed:20303269, ECO:0000269|PubMed:20616046, ECO:0000269|PubMed:21834987, ECO:0000269|PubMed:22286099}.

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 DHX30-LIMD1


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 DHX30-LIMD1


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 DHX30-LIMD1


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 DHX30-LIMD1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneDHX30C4540496NEURODEVELOPMENTAL DISORDER WITH SEVERE MOTOR IMPAIRMENT AND ABSENT LANGUAGE2GENOMICS_ENGLAND;UNIPROT
HgeneDHX30C0033578Prostatic Neoplasms1CTD_human
HgeneDHX30C0376358Malignant neoplasm of prostate1CTD_human
HgeneDHX30C1535926Neurodevelopmental Disorders1GENOMICS_ENGLAND