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Center for Computational Systems Medicine level1
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Fusion Gene Summary

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Fusion Gene Sample Information

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Fusion ORF Analysis

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Fusion Amino Acid Sequences

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Fusion Protein Functional Features

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Fusion Protein-Protein Interaction

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Related drugs with this fusion protein

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Related disease with this fusion protein

Fusion Protein:LMNA-IGFBP2

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: LMNA-IGFBP2
FusionPDB ID: 45788
FusionGDB2.0 ID: 45788
HgeneTgene
Gene symbol

LMNA

IGFBP2

Gene ID

4000

3485

Gene namelamin A/Cinsulin like growth factor binding protein 2
SynonymsCDCD1|CDDC|CMD1A|CMT2B1|EMD2|FPL|FPLD|FPLD2|HGPS|IDC|LDP1|LFP|LGMD1B|LMN1|LMNC|LMNL1|MADA|PRO1IBP2|IGF-BP53
Cytomap

1q22

2q35

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-32insulin-like growth factor-binding protein 2IGF-binding protein 2insulin-like growth factor binding protein 2, 36kDa
Modification date2020032920200313
UniProtAcc

P02545

P18065

Ensembl transtripts involved in fusion geneENST idsENST00000347559, ENST00000368300, 
ENST00000368299, ENST00000361308, 
ENST00000368297, ENST00000368301, 
ENST00000392353, ENST00000448611, 
ENST00000473598, ENST00000496738, 
ENST00000233809, ENST00000456764, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score16 X 16 X 9=23044 X 4 X 4=64
# samples 215
** MAII scorelog2(21/2304*10)=-3.45567948377619
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(5/64*10)=-0.356143810225275
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: LMNA [Title/Abstract] AND IGFBP2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)LMNA(156109108)-IGFBP2(217525456), # samples:1
Anticipated loss of major functional domain due to fusion event.LMNA-IGFBP2 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
LMNA-IGFBP2 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
LMNA-IGFBP2 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
LMNA-IGFBP2 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame 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

TgeneIGFBP2

GO:0042104

positive regulation of activated T cell proliferation

15694994


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.
all structure

check buttonFusion gene breakpoints across IGFBP2 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


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Fusion Gene Sample Information

check buttonFusion gene information from FusionGDB2.0.
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
ChimerDB4UCECTCGA-EO-A3AY-01ALMNAchr1

156109108

-IGFBP2chr2

217525456

+


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Fusion ORF Analysis


check buttonFusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)
BP loci
(transcript)
Predicted start
(transcript)
Predicted stop
(transcript)
Seq length
(amino acids)
ENST00000368299LMNAchr1156109108-ENST00000233809IGFBP2chr2217525456+29442253682041657
ENST00000368299LMNAchr1156109108-ENST00000456764IGFBP2chr2217525456+27932253682041657

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
ENST00000368299ENST00000233809LMNAchr1156109108-IGFBP2chr2217525456+0.0204720370.97952795
ENST00000368299ENST00000456764LMNAchr1156109108-IGFBP2chr2217525456+0.0260492270.9739508

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Fusion Amino Acid Sequences


check button For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

>45788_45788_1_LMNA-IGFBP2_LMNA_chr1_156109108_ENST00000368299_IGFBP2_chr2_217525456_ENST00000233809_length(amino acids)=657AA_BP=
MPGASREPAGRRTPTPSSLCPSTRAPRPFRDPCPAGSAANLPAMETPSQRRATRSGAQASSTPLSPTRITRLQEKEDLQELNDRLAVYID
RVRSLETENAGLRLRITESEEVVSREVSGIKAAYEAELGDARKTLDSVAKERARLQLELSKVREEFKELKARNTKKEGDLIAAQARLKDL
EALLNSKEAALSTALSEKRTLEGELHDLRGQVAKLEAALGEAKKQLQDEMLRRVDAENRLQTMKEELDFQKNIYSEELRETKRRHETRLV
EIDNGKQREFESRLADALQELRAQHEDQVEQYKKELEKTYSAKLDNARQSAERNSNLVGAAHEELQQSRIRIDSLSAQLSQLQKQLAAKE
AKLRDLEDSLARERDTSRRLLAEKEREMAEMRARMQQQLDEYQELLDIKLALDMEIHAYRKLLEGEEERLRLSPSPTSQRSRGRASSHSS
QTQGGGSVTKKRKLESTESRSSFSQHARTSGRVAVEEVDEEGKFVRLRNKSNEDQSMGNWQIKRQNGDDPLLTYRFPPKFTLKAGQVVTI
WAAGAGATHSPPTDLVWKAQNTWGCGNSLRTALINSTGEEVAMRKLVRSVTVVEDDEDEDGDDLLHHHHGSHCSSSGDPAEYNLRSRTVL

--------------------------------------------------------------

>45788_45788_2_LMNA-IGFBP2_LMNA_chr1_156109108_ENST00000368299_IGFBP2_chr2_217525456_ENST00000456764_length(amino acids)=657AA_BP=
MPGASREPAGRRTPTPSSLCPSTRAPRPFRDPCPAGSAANLPAMETPSQRRATRSGAQASSTPLSPTRITRLQEKEDLQELNDRLAVYID
RVRSLETENAGLRLRITESEEVVSREVSGIKAAYEAELGDARKTLDSVAKERARLQLELSKVREEFKELKARNTKKEGDLIAAQARLKDL
EALLNSKEAALSTALSEKRTLEGELHDLRGQVAKLEAALGEAKKQLQDEMLRRVDAENRLQTMKEELDFQKNIYSEELRETKRRHETRLV
EIDNGKQREFESRLADALQELRAQHEDQVEQYKKELEKTYSAKLDNARQSAERNSNLVGAAHEELQQSRIRIDSLSAQLSQLQKQLAAKE
AKLRDLEDSLARERDTSRRLLAEKEREMAEMRARMQQQLDEYQELLDIKLALDMEIHAYRKLLEGEEERLRLSPSPTSQRSRGRASSHSS
QTQGGGSVTKKRKLESTESRSSFSQHARTSGRVAVEEVDEEGKFVRLRNKSNEDQSMGNWQIKRQNGDDPLLTYRFPPKFTLKAGQVVTI
WAAGAGATHSPPTDLVWKAQNTWGCGNSLRTALINSTGEEVAMRKLVRSVTVVEDDEDEDGDDLLHHHHGSHCSSSGDPAEYNLRSRTVL

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Fusion Protein Functional Features


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/chr1:156109108/chr2:217525456)
- 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
LMNA

P02545

IGFBP2

P18065

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: Inhibits IGF-mediated growth and developmental rates. IGF-binding proteins prolong the half-life of the IGFs and have been shown to either inhibit or stimulate the growth promoting effects of the IGFs on cell culture. They alter the interaction of IGFs with their cell surface receptors. {ECO:0000269|PubMed:19081843}.

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.
- Retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
TgeneIGFBP2chr1:156109108chr2:217525456ENST0000023380904224_3060326.0DomainThyroglobulin type-1
TgeneIGFBP2chr1:156109108chr2:217525456ENST000002338090438_1340326.0DomainIGFBP N-terminal
TgeneIGFBP2chr1:156109108chr2:217525456ENST0000023380904301_3030326.0MotifNote=Cell attachment site

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneLMNAchr1:156109108chr2:217525456ENST00000347559-11131_3870635.0DomainIF rod
HgeneLMNAchr1:156109108chr2:217525456ENST00000347559-111428_5450635.0DomainLTD
HgeneLMNAchr1:156109108chr2:217525456ENST00000361308-11031_3870573.0DomainIF rod
HgeneLMNAchr1:156109108chr2:217525456ENST00000361308-110428_5450573.0DomainLTD
HgeneLMNAchr1:156109108chr2:217525456ENST00000368300-11231_3870665.0DomainIF rod
HgeneLMNAchr1:156109108chr2:217525456ENST00000368300-112428_5450665.0DomainLTD
HgeneLMNAchr1:156109108chr2:217525456ENST00000368301-11331_3870573.0DomainIF rod
HgeneLMNAchr1:156109108chr2:217525456ENST00000368301-113428_5450573.0DomainLTD
HgeneLMNAchr1:156109108chr2:217525456ENST00000448611-11331_3870575.0DomainIF rod
HgeneLMNAchr1:156109108chr2:217525456ENST00000448611-113428_5450575.0DomainLTD
HgeneLMNAchr1:156109108chr2:217525456ENST00000347559-111417_4220635.0MotifNuclear localization signal
HgeneLMNAchr1:156109108chr2:217525456ENST00000361308-110417_4220573.0MotifNuclear localization signal
HgeneLMNAchr1:156109108chr2:217525456ENST00000368300-112417_4220665.0MotifNuclear localization signal
HgeneLMNAchr1:156109108chr2:217525456ENST00000368301-113417_4220573.0MotifNuclear localization signal
HgeneLMNAchr1:156109108chr2:217525456ENST00000448611-113417_4220575.0MotifNuclear localization signal
HgeneLMNAchr1:156109108chr2:217525456ENST00000347559-1111_330635.0RegionNote=Head
HgeneLMNAchr1:156109108chr2:217525456ENST00000347559-111219_2420635.0RegionNote=Linker 2
HgeneLMNAchr1:156109108chr2:217525456ENST00000347559-111243_3830635.0RegionNote=Coil 2
HgeneLMNAchr1:156109108chr2:217525456ENST00000347559-11134_700635.0RegionNote=Coil 1A
HgeneLMNAchr1:156109108chr2:217525456ENST00000347559-111384_6640635.0RegionNote=Tail
HgeneLMNAchr1:156109108chr2:217525456ENST00000347559-11171_800635.0RegionNote=Linker 1
HgeneLMNAchr1:156109108chr2:217525456ENST00000347559-11181_2180635.0RegionNote=Coil 1B
HgeneLMNAchr1:156109108chr2:217525456ENST00000361308-1101_330573.0RegionNote=Head
HgeneLMNAchr1:156109108chr2:217525456ENST00000361308-110219_2420573.0RegionNote=Linker 2
HgeneLMNAchr1:156109108chr2:217525456ENST00000361308-110243_3830573.0RegionNote=Coil 2
HgeneLMNAchr1:156109108chr2:217525456ENST00000361308-11034_700573.0RegionNote=Coil 1A
HgeneLMNAchr1:156109108chr2:217525456ENST00000361308-110384_6640573.0RegionNote=Tail
HgeneLMNAchr1:156109108chr2:217525456ENST00000361308-11071_800573.0RegionNote=Linker 1
HgeneLMNAchr1:156109108chr2:217525456ENST00000361308-11081_2180573.0RegionNote=Coil 1B
HgeneLMNAchr1:156109108chr2:217525456ENST00000368300-1121_330665.0RegionNote=Head
HgeneLMNAchr1:156109108chr2:217525456ENST00000368300-112219_2420665.0RegionNote=Linker 2
HgeneLMNAchr1:156109108chr2:217525456ENST00000368300-112243_3830665.0RegionNote=Coil 2
HgeneLMNAchr1:156109108chr2:217525456ENST00000368300-11234_700665.0RegionNote=Coil 1A
HgeneLMNAchr1:156109108chr2:217525456ENST00000368300-112384_6640665.0RegionNote=Tail
HgeneLMNAchr1:156109108chr2:217525456ENST00000368300-11271_800665.0RegionNote=Linker 1
HgeneLMNAchr1:156109108chr2:217525456ENST00000368300-11281_2180665.0RegionNote=Coil 1B
HgeneLMNAchr1:156109108chr2:217525456ENST00000368301-1131_330573.0RegionNote=Head
HgeneLMNAchr1:156109108chr2:217525456ENST00000368301-113219_2420573.0RegionNote=Linker 2
HgeneLMNAchr1:156109108chr2:217525456ENST00000368301-113243_3830573.0RegionNote=Coil 2
HgeneLMNAchr1:156109108chr2:217525456ENST00000368301-11334_700573.0RegionNote=Coil 1A
HgeneLMNAchr1:156109108chr2:217525456ENST00000368301-113384_6640573.0RegionNote=Tail
HgeneLMNAchr1:156109108chr2:217525456ENST00000368301-11371_800573.0RegionNote=Linker 1
HgeneLMNAchr1:156109108chr2:217525456ENST00000368301-11381_2180573.0RegionNote=Coil 1B
HgeneLMNAchr1:156109108chr2:217525456ENST00000448611-1131_330575.0RegionNote=Head
HgeneLMNAchr1:156109108chr2:217525456ENST00000448611-113219_2420575.0RegionNote=Linker 2
HgeneLMNAchr1:156109108chr2:217525456ENST00000448611-113243_3830575.0RegionNote=Coil 2
HgeneLMNAchr1:156109108chr2:217525456ENST00000448611-11334_700575.0RegionNote=Coil 1A
HgeneLMNAchr1:156109108chr2:217525456ENST00000448611-113384_6640575.0RegionNote=Tail
HgeneLMNAchr1:156109108chr2:217525456ENST00000448611-11371_800575.0RegionNote=Linker 1
HgeneLMNAchr1:156109108chr2:217525456ENST00000448611-11381_2180575.0RegionNote=Coil 1B


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Fusion Protein-Protein Interaction


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 from validated records (BIOGRID-3.4.160)
GenePPI interactors


check button Protein-protein interactors based on sequence similarity (STRING)
GeneSTRING network
LMNA
IGFBP2


check button - Retained interactions in fusion protein (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost interactions due to fusion (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with
HgeneLMNAchr1:156109108chr2:217525456ENST00000347559-1111_1300635.0MLIP
HgeneLMNAchr1:156109108chr2:217525456ENST00000361308-1101_1300573.0MLIP
HgeneLMNAchr1:156109108chr2:217525456ENST00000368300-1121_1300665.0MLIP
HgeneLMNAchr1:156109108chr2:217525456ENST00000368301-1131_1300573.0MLIP
HgeneLMNAchr1:156109108chr2:217525456ENST00000448611-1131_1300575.0MLIP


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Related Drugs to LMNA-IGFBP2


check button Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDrugSourcePMID

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Related Diseases to LMNA-IGFBP2


check button Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDiseaseSourcePMID

check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource