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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:LSM14A-ACTN4 (FusionGDB2 ID:HG26065TG81)

Fusion Gene Summary for LSM14A-ACTN4

check button Fusion gene summary
Fusion gene informationFusion gene name: LSM14A-ACTN4
Fusion gene ID: hg26065tg81
HgeneTgene
Gene symbol

LSM14A

ACTN4

Gene ID

26065

81

Gene nameLSM14A mRNA processing body assembly factoractinin alpha 4
SynonymsC19orf13|FAM61A|RAP55|RAP55AACTININ-4|FSGS|FSGS1
Cytomap('LSM14A')('ACTN4')

19q13.11

19q13.2

Type of geneprotein-codingprotein-coding
Descriptionprotein LSM14 homolog ALSM14 homolog ALSM14A, SCD6 homolog ARNA-associated protein 55RNA-associated protein 55AalphaSNBPfamily with sequence similarity 61, member AhRAP55hRAP55Aprotein SCD6 homologputative alpha-synuclein-binding proteinalpha-actinin-4focal segmental glomerulosclerosis 1non-muscle alpha-actinin 4
Modification date2020032720200327
UniProtAcc

Q8ND56

O43707

Ensembl transtripts involved in fusion geneENST00000433627, ENST00000540746, 
ENST00000544216, 
Fusion gene scores* DoF score18 X 10 X 10=180027 X 38 X 12=12312
# samples 2448
** MAII scorelog2(24/1800*10)=-2.90689059560852
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(48/12312*10)=-4.68088692071969
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: LSM14A [Title/Abstract] AND ACTN4 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointLSM14A(34663668)-ACTN4(39191240), # samples:3
Anticipated loss of major functional domain due to fusion event.LSM14A-ACTN4 seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF.
* 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
HgeneLSM14A

GO:0033962

cytoplasmic mRNA processing body assembly

16484376

TgeneACTN4

GO:0033209

tumor necrosis factor-mediated signaling pathway

25411248

TgeneACTN4

GO:0035357

peroxisome proliferator activated receptor signaling pathway

22351778

TgeneACTN4

GO:0048384

retinoic acid receptor signaling pathway

22351778

TgeneACTN4

GO:0051272

positive regulation of cellular component movement

9508771



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
ChimerDB4BRCATCGA-AQ-A0Y5-01ALSM14Achr19

34663668

-ACTN4chr19

39191240

+
ChimerDB4BRCATCGA-AQ-A0Y5-01ALSM14Achr19

34663668

+ACTN4chr19

39191240

+
ChimerDB4BRCATCGA-AQ-A0Y5LSM14Achr19

34663668

+ACTN4chr19

39191239

+


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Fusion Gene ORF analysis for LSM14A-ACTN4

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
5CDS-intronENST00000433627ENST00000390009LSM14Achr19

34663668

+ACTN4chr19

39191240

+
5CDS-intronENST00000433627ENST00000390009LSM14Achr19

34663668

+ACTN4chr19

39191239

+
5CDS-intronENST00000433627ENST00000497637LSM14Achr19

34663668

+ACTN4chr19

39191240

+
5CDS-intronENST00000433627ENST00000497637LSM14Achr19

34663668

+ACTN4chr19

39191239

+
5CDS-intronENST00000540746ENST00000390009LSM14Achr19

34663668

+ACTN4chr19

39191240

+
5CDS-intronENST00000540746ENST00000390009LSM14Achr19

34663668

+ACTN4chr19

39191239

+
5CDS-intronENST00000540746ENST00000497637LSM14Achr19

34663668

+ACTN4chr19

39191240

+
5CDS-intronENST00000540746ENST00000497637LSM14Achr19

34663668

+ACTN4chr19

39191239

+
5CDS-intronENST00000544216ENST00000390009LSM14Achr19

34663668

+ACTN4chr19

39191240

+
5CDS-intronENST00000544216ENST00000390009LSM14Achr19

34663668

+ACTN4chr19

39191239

+
5CDS-intronENST00000544216ENST00000497637LSM14Achr19

34663668

+ACTN4chr19

39191240

+
5CDS-intronENST00000544216ENST00000497637LSM14Achr19

34663668

+ACTN4chr19

39191239

+
Frame-shiftENST00000433627ENST00000252699LSM14Achr19

34663668

+ACTN4chr19

39191240

+
Frame-shiftENST00000433627ENST00000252699LSM14Achr19

34663668

+ACTN4chr19

39191239

+
Frame-shiftENST00000433627ENST00000424234LSM14Achr19

34663668

+ACTN4chr19

39191240

+
Frame-shiftENST00000433627ENST00000424234LSM14Achr19

34663668

+ACTN4chr19

39191239

+
Frame-shiftENST00000540746ENST00000252699LSM14Achr19

34663668

+ACTN4chr19

39191240

+
Frame-shiftENST00000540746ENST00000252699LSM14Achr19

34663668

+ACTN4chr19

39191239

+
Frame-shiftENST00000540746ENST00000424234LSM14Achr19

34663668

+ACTN4chr19

39191240

+
Frame-shiftENST00000540746ENST00000424234LSM14Achr19

34663668

+ACTN4chr19

39191239

+
Frame-shiftENST00000544216ENST00000252699LSM14Achr19

34663668

+ACTN4chr19

39191240

+
Frame-shiftENST00000544216ENST00000252699LSM14Achr19

34663668

+ACTN4chr19

39191239

+
Frame-shiftENST00000544216ENST00000424234LSM14Achr19

34663668

+ACTN4chr19

39191240

+
Frame-shiftENST00000544216ENST00000424234LSM14Achr19

34663668

+ACTN4chr19

39191239

+

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 LSM14A-ACTN4


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)
LSM14Achr1934663668+ACTN4chr1939191239+1.35E-111
LSM14Achr1934663668+ACTN4chr1939191239+1.35E-111
LSM14Achr1934663668+ACTN4chr1939191239+1.35E-111
LSM14Achr1934663668+ACTN4chr1939191239+1.35E-111


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 LSM14A-ACTN4


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/:34663668/:39191240)
- 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
LSM14A

Q8ND56

ACTN4

O43707

FUNCTION: Essential for formation of P-bodies, cytoplasmic structures that provide storage sites for translationally inactive mRNAs and protect them from degradation (PubMed:16484376, PubMed:17074753, PubMed:29510985). Acts as a repressor of mRNA translation (PubMed:29510985). May play a role in mitotic spindle assembly (PubMed:26339800). {ECO:0000269|PubMed:16484376, ECO:0000269|PubMed:17074753, ECO:0000269|PubMed:26339800, ECO:0000269|PubMed:29510985}.FUNCTION: F-actin cross-linking protein which is thought to anchor actin to a variety of intracellular structures. This is a bundling protein (Probable). Probably involved in vesicular trafficking via its association with the CART complex. The CART complex is necessary for efficient transferrin receptor recycling but not for EGFR degradation (PubMed:15772161). Involved in tight junction assembly in epithelial cells probably through interaction with MICALL2. Links MICALL2 to the actin cytoskeleton and recruits it to the tight junctions (By similarity). May also function as a transcriptional coactivator, stimulating transcription mediated by the nuclear hormone receptors PPARG and RARA (PubMed:22351778). {ECO:0000250|UniProtKB:P57780, ECO:0000269|PubMed:15772161, ECO:0000269|PubMed:22351778, ECO:0000305|PubMed:9508771}.

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 LSM14A-ACTN4


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 LSM14A-ACTN4


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 LSM14A-ACTN4


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 LSM14A-ACTN4


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneC4551527Focal segmental glomerulosclerosis 19GENOMICS_ENGLAND;UNIPROT
TgeneC0007097Carcinoma1CTD_human
TgeneC0019193Hepatitis, Toxic1CTD_human
TgeneC0024667Animal Mammary Neoplasms1CTD_human
TgeneC0024668Mammary Neoplasms, Experimental1CTD_human
TgeneC0205696Anaplastic carcinoma1CTD_human
TgeneC0205697Carcinoma, Spindle-Cell1CTD_human
TgeneC0205698Undifferentiated carcinoma1CTD_human
TgeneC0205699Carcinomatosis1CTD_human
TgeneC0860207Drug-Induced Liver Disease1CTD_human
TgeneC1257925Mammary Carcinoma, Animal1CTD_human
TgeneC1262760Hepatitis, Drug-Induced1CTD_human
TgeneC1868672NEPHROTIC SYNDROME, STEROID-RESISTANT, AUTOSOMAL RECESSIVE1ORPHANET
TgeneC3658290Drug-Induced Acute Liver Injury1CTD_human
TgeneC4277682Chemical and Drug Induced Liver Injury1CTD_human
TgeneC4279912Chemically-Induced Liver Toxicity1CTD_human