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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:LMNA-SYT11 (FusionGDB2 ID:45554)

Fusion Gene Summary for LMNA-SYT11

check button Fusion gene summary
Fusion gene informationFusion gene name: LMNA-SYT11
Fusion gene ID: 45554
HgeneTgene
Gene symbol

LMNA

SYT11

Gene ID

4000

91683

Gene namelamin A/Csynaptotagmin 12
SynonymsCDCD1|CDDC|CMD1A|CMT2B1|EMD2|FPL|FPLD|FPLD2|HGPS|IDC|LDP1|LFP|LGMD1B|LMN1|LMNC|LMNL1|MADA|PRO1SYT11|sytXII
Cytomap

1q22

11q13.2

Type of geneprotein-codingprotein-coding
Descriptionlamin70 kDa laminepididymis secretory sperm binding proteinlamin A/C-like 1mandibuloacral dysplasia type Aprelamin-A/Crenal carcinoma antigen NY-REN-32synaptotagmin-12synaptotagmin-XII
Modification date2020032920200313
UniProtAcc

P02545

.
Ensembl transtripts involved in fusion geneENST00000368301, ENST00000361308, 
ENST00000347559, ENST00000368300, 
ENST00000368299, ENST00000448611, 
ENST00000368297, ENST00000473598, 
ENST00000392353, ENST00000496738, 
ENST00000368324, ENST00000539162, 
Fusion gene scores* DoF score16 X 16 X 9=23046 X 3 X 5=90
# samples 216
** MAII scorelog2(21/2304*10)=-3.45567948377619
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(6/90*10)=-0.584962500721156
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: LMNA [Title/Abstract] AND SYT11 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointLMNA(156085065)-SYT11(155850291), # samples:2
Anticipated loss of major functional domain due to fusion event.LMNA-SYT11 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
HgeneLMNA

GO:0090343

positive regulation of cell aging

20458013


check buttonFusion gene breakpoints across LMNA (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 SYT11 (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
ChimerDB4BRCATCGA-AQ-A54N-01ALMNAchr1

156085065

+SYT11chr1

155850291

+
ChimerDB4BRCATCGA-AQ-A54N-01ALMNAchr1

156085065

-SYT11chr1

155850291

+


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Fusion Gene ORF analysis for LMNA-SYT11

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-shiftENST00000368301ENST00000368324LMNAchr1

156085065

+SYT11chr1

155850291

+
5CDS-5UTRENST00000368301ENST00000539162LMNAchr1

156085065

+SYT11chr1

155850291

+
Frame-shiftENST00000361308ENST00000368324LMNAchr1

156085065

+SYT11chr1

155850291

+
5CDS-5UTRENST00000361308ENST00000539162LMNAchr1

156085065

+SYT11chr1

155850291

+
Frame-shiftENST00000347559ENST00000368324LMNAchr1

156085065

+SYT11chr1

155850291

+
5CDS-5UTRENST00000347559ENST00000539162LMNAchr1

156085065

+SYT11chr1

155850291

+
Frame-shiftENST00000368300ENST00000368324LMNAchr1

156085065

+SYT11chr1

155850291

+
5CDS-5UTRENST00000368300ENST00000539162LMNAchr1

156085065

+SYT11chr1

155850291

+
Frame-shiftENST00000368299ENST00000368324LMNAchr1

156085065

+SYT11chr1

155850291

+
5CDS-5UTRENST00000368299ENST00000539162LMNAchr1

156085065

+SYT11chr1

155850291

+
intron-3CDSENST00000448611ENST00000368324LMNAchr1

156085065

+SYT11chr1

155850291

+
intron-5UTRENST00000448611ENST00000539162LMNAchr1

156085065

+SYT11chr1

155850291

+
intron-3CDSENST00000368297ENST00000368324LMNAchr1

156085065

+SYT11chr1

155850291

+
intron-5UTRENST00000368297ENST00000539162LMNAchr1

156085065

+SYT11chr1

155850291

+
intron-3CDSENST00000473598ENST00000368324LMNAchr1

156085065

+SYT11chr1

155850291

+
intron-5UTRENST00000473598ENST00000539162LMNAchr1

156085065

+SYT11chr1

155850291

+
intron-3CDSENST00000392353ENST00000368324LMNAchr1

156085065

+SYT11chr1

155850291

+
intron-5UTRENST00000392353ENST00000539162LMNAchr1

156085065

+SYT11chr1

155850291

+
intron-3CDSENST00000496738ENST00000368324LMNAchr1

156085065

+SYT11chr1

155850291

+
intron-5UTRENST00000496738ENST00000539162LMNAchr1

156085065

+SYT11chr1

155850291

+

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 LMNA-SYT11


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)
LMNAchr1156085065+SYT11chr1155850290+1.58E-060.99999845
LMNAchr1156085065+SYT11chr1155850290+1.58E-060.99999845

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 LMNA-SYT11


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
LMNA

P02545

.
FUNCTION: Lamins are components of the nuclear lamina, a fibrous layer on the nucleoplasmic side of the inner nuclear membrane, which is thought to provide a framework for the nuclear envelope and may also interact with chromatin. Lamin A and C are present in equal amounts in the lamina of mammals. Recruited by DNA repair proteins XRCC4 and IFFO1 to the DNA double-strand breaks (DSBs) to prevent chromosome translocation by immobilizing broken DNA ends (PubMed:31548606). Plays an important role in nuclear assembly, chromatin organization, nuclear membrane and telomere dynamics. Required for normal development of peripheral nervous system and skeletal muscle and for muscle satellite cell proliferation (PubMed:10080180, PubMed:22431096, PubMed:10814726, PubMed:11799477, PubMed:18551513). Required for osteoblastogenesis and bone formation (PubMed:12075506, PubMed:15317753, PubMed:18611980). Also prevents fat infiltration of muscle and bone marrow, helping to maintain the volume and strength of skeletal muscle and bone (PubMed:10587585). Required for cardiac homeostasis (PubMed:10580070, PubMed:12927431, PubMed:18611980, PubMed:23666920). {ECO:0000269|PubMed:10080180, ECO:0000269|PubMed:10580070, ECO:0000269|PubMed:10587585, ECO:0000269|PubMed:10814726, ECO:0000269|PubMed:11799477, ECO:0000269|PubMed:12075506, ECO:0000269|PubMed:12927431, ECO:0000269|PubMed:15317753, ECO:0000269|PubMed:18551513, ECO:0000269|PubMed:18611980, ECO:0000269|PubMed:22431096, ECO:0000269|PubMed:23666920, ECO:0000269|PubMed:31548606}.; FUNCTION: Prelamin-A/C can accelerate smooth muscle cell senescence. It acts to disrupt mitosis and induce DNA damage in vascular smooth muscle cells (VSMCs), leading to mitotic failure, genomic instability, and premature senescence.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.

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 LMNA-SYT11


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 LMNA-SYT11


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 LMNA-SYT11


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 LMNA-SYT11


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneLMNAC1449563Cardiomyopathy, Familial Idiopathic24CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneLMNAC1720860Familial Partial Lipodystrophy, Type 219CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneLMNAC0033300Progeria16CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneLMNAC0410190Autosomal Dominant Emery-Dreifuss Muscular Dystrophy (disorder)10CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneLMNAC0432291Mandibuloacral dysostosis9CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneLMNAC1720859Familial Partial Lipodystrophy, Type 16CTD_human;ORPHANET
HgeneLMNAC0271694Familial partial lipodystrophy5CTD_human;GENOMICS_ENGLAND
HgeneLMNAC0406585Lethal tight skin contracture syndrome (disorder)5CTD_human;GENOMICS_ENGLAND;ORPHANET
HgeneLMNAC0796031Malouf syndrome5CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneLMNAC0007193Cardiomyopathy, Dilated4CTD_human
HgeneLMNAC1720861Familial Partial Lipodystrophy, Type 34CTD_human
HgeneLMNAC2750035Emery-Dreifuss Muscular Dystrophy 34GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneLMNAC2750785MUSCULAR DYSTROPHY, CONGENITAL, LMNA-RELATED (disorder)4CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneLMNAC0410189Muscular Dystrophy, Emery-Dreifuss3CTD_human
HgeneLMNAC0686353Muscular Dystrophies, Limb-Girdle3CTD_human;GENOMICS_ENGLAND
HgeneLMNAC0751337X-Linked Emery-Dreifuss Muscular Dystrophy3CTD_human
HgeneLMNAC1450051Autosomal Recessive Emery-Dreifuss Muscular Dystrophy3CTD_human;ORPHANET
HgeneLMNAC1854154Charcot-Marie-Tooth disease, Type 2B13CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneLMNAC1857829Heart-hand syndrome, Slovenian type3CTD_human;GENOMICS_ENGLAND;ORPHANET
HgeneLMNAC1832931ARRHYTHMOGENIC RIGHT VENTRICULAR DYSPLASIA, FAMILIAL, 22ORPHANET
HgeneLMNAC4275075Atypical Werner syndrome2ORPHANET
HgeneLMNAC0004245Atrioventricular Block1CTD_human
HgeneLMNAC0004331Auriculo-Ventricular Dissociation1CTD_human
HgeneLMNAC0011644Scleroderma1CTD_human
HgeneLMNAC0016508Congenital Foot Deformity1CTD_human
HgeneLMNAC0017668Focal glomerulosclerosis1GENOMICS_ENGLAND
HgeneLMNAC0018566Congenital Hand Deformities1CTD_human
HgeneLMNAC0018794Heart Block1CTD_human
HgeneLMNAC0032460Polycystic Ovary Syndrome1CTD_human
HgeneLMNAC0036420Localized scleroderma1CTD_human
HgeneLMNAC0037188Sinoatrial Block1CTD_human
HgeneLMNAC0042514Tachycardia, Ventricular1CTD_human
HgeneLMNAC0085298Sudden Cardiac Death1CTD_human
HgeneLMNAC0152013Adenocarcinoma of lung (disorder)1CTD_human
HgeneLMNAC0263409Linear Scleroderma1CTD_human
HgeneLMNAC0376634Craniofacial Abnormalities1CTD_human
HgeneLMNAC0546264Congenital Fiber Type Disproportion1GENOMICS_ENGLAND
HgeneLMNAC0796083Najjar syndrome1ORPHANET
HgeneLMNAC1136321HIV-Associated Lipodystrophy Syndrome1CTD_human
HgeneLMNAC1136382Sclerocystic Ovaries1CTD_human
HgeneLMNAC1527383Morphea1CTD_human
HgeneLMNAC1720824Sudden Cardiac Arrest1CTD_human
HgeneLMNAC4049702Focal Segmental Glomerulosclerosis, Not Otherwise Specified1GENOMICS_ENGLAND
HgeneLMNAC4750858LMNA-related cardiocutaneous progeria syndrome1ORPHANET
TgeneSYT11C0036341Schizophrenia1PSYGENET