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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:LRRFIP2-RAP1A

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: LRRFIP2-RAP1A
FusionPDB ID: 50098
FusionGDB2.0 ID: 50098
HgeneTgene
Gene symbol

LRRFIP2

RAP1A

Gene ID

9209

5906

Gene nameLRR binding FLII interacting protein 2RAP1A, member of RAS oncogene family
SynonymsHUFI-2C21KG|G-22K|KREV-1|KREV1|RAP1|SMGP21
Cytomap

3p22.2

1p13.2

Type of geneprotein-codingprotein-coding
Descriptionleucine-rich repeat flightless-interacting protein 2LRR FLII-interacting protein 2leucine rich repeat (in FLII) interacting protein 2ras-related protein Rap-1AGTP-binding protein smg p21ARas-related protein Krev-1
Modification date2020031320200329
UniProtAcc

Q9Y608

.
Ensembl transtripts involved in fusion geneENST idsENST00000336686, ENST00000354379, 
ENST00000396428, ENST00000421276, 
ENST00000421307, ENST00000440230, 
ENST00000490597, 		ENST00000494982, 
ENST00000356415, ENST00000369709, 
ENST00000436150, ENST00000545460, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score15 X 15 X 8=180010 X 9 X 4=360
# samples 1710
** MAII scorelog2(17/1800*10)=-3.40439025507934
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(10/360*10)=-1.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: LRRFIP2 [Title/Abstract] AND RAP1A [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)LRRFIP2(37170553)-RAP1A(112245957), # samples:1
Anticipated loss of major functional domain due to fusion event.LRRFIP2-RAP1A 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.
LRRFIP2-RAP1A 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.
LRRFIP2-RAP1A seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
LRRFIP2-RAP1A seems lost the major protein functional domain in Tgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
LRRFIP2-RAP1A seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF.
LRRFIP2-RAP1A seems lost the major protein functional domain in Tgene partner, which is a tumor suppressor 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
TgeneRAP1A

GO:0071320

cellular response to cAMP

21840392

TgeneRAP1A

GO:0072659

protein localization to plasma membrane

17916086

TgeneRAP1A

GO:0098696

regulation of neurotransmitter receptor localization to postsynaptic specialization membrane

12202034


check buttonFusion gene breakpoints across LRRFIP2 (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 RAP1A (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
ChimerDB4Non-CancerTCGA-AF-3400-11ALRRFIP2chr3

37170553

-RAP1Achr1

112245957

+


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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)
ENST00000336686LRRFIP2chr337170553-ENST00000356415RAP1Achr1112245957+134225881629182
ENST00000336686LRRFIP2chr337170553-ENST00000436150RAP1Achr1112245957+170825881629182
ENST00000336686LRRFIP2chr337170553-ENST00000369709RAP1Achr1112245957+492025881629182
ENST00000336686LRRFIP2chr337170553-ENST00000545460RAP1Achr1112245957+71625881629182
ENST00000440230LRRFIP2chr337170553-ENST00000356415RAP1Achr1112245957+18747906131161182
ENST00000440230LRRFIP2chr337170553-ENST00000436150RAP1Achr1112245957+22407906131161182
ENST00000440230LRRFIP2chr337170553-ENST00000369709RAP1Achr1112245957+54527906131161182
ENST00000440230LRRFIP2chr337170553-ENST00000545460RAP1Achr1112245957+12487906131161182

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
ENST00000336686ENST00000356415LRRFIP2chr337170553-RAP1Achr1112245957+0.0019383530.9980616
ENST00000336686ENST00000436150LRRFIP2chr337170553-RAP1Achr1112245957+0.0018217450.99817824
ENST00000336686ENST00000369709LRRFIP2chr337170553-RAP1Achr1112245957+0.0020598770.9979401
ENST00000336686ENST00000545460LRRFIP2chr337170553-RAP1Achr1112245957+0.0039157050.99608433
ENST00000440230ENST00000356415LRRFIP2chr337170553-RAP1Achr1112245957+0.0020913650.9979087
ENST00000440230ENST00000436150LRRFIP2chr337170553-RAP1Achr1112245957+0.0016096860.9983903
ENST00000440230ENST00000369709LRRFIP2chr337170553-RAP1Achr1112245957+0.0020862120.9979138
ENST00000440230ENST00000545460LRRFIP2chr337170553-RAP1Achr1112245957+0.0048110830.99518895

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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

>50098_50098_1_LRRFIP2-RAP1A_LRRFIP2_chr3_37170553_ENST00000336686_RAP1A_chr1_112245957_ENST00000356415_length(amino acids)=182AA_BP=59
MGTPASGRKRTPVKDRFSAEDEALSNIAREAEARLAAKRAARAEARDIRMRELERQQKEEQFTAMRDLYMKNGQGFALVYSITAQSTFND
LQDLREQILRVKDTEDVPMILVGNKCDLEDERVVGKEQGQNLARQWCNCAFLESSAKSKINVNEIFYDLVRQINRKTPVEKKKPKKKSCL

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

>50098_50098_2_LRRFIP2-RAP1A_LRRFIP2_chr3_37170553_ENST00000336686_RAP1A_chr1_112245957_ENST00000369709_length(amino acids)=182AA_BP=59
MGTPASGRKRTPVKDRFSAEDEALSNIAREAEARLAAKRAARAEARDIRMRELERQQKEEQFTAMRDLYMKNGQGFALVYSITAQSTFND
LQDLREQILRVKDTEDVPMILVGNKCDLEDERVVGKEQGQNLARQWCNCAFLESSAKSKINVNEIFYDLVRQINRKTPVEKKKPKKKSCL

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

>50098_50098_3_LRRFIP2-RAP1A_LRRFIP2_chr3_37170553_ENST00000336686_RAP1A_chr1_112245957_ENST00000436150_length(amino acids)=182AA_BP=59
MGTPASGRKRTPVKDRFSAEDEALSNIAREAEARLAAKRAARAEARDIRMRELERQQKEEQFTAMRDLYMKNGQGFALVYSITAQSTFND
LQDLREQILRVKDTEDVPMILVGNKCDLEDERVVGKEQGQNLARQWCNCAFLESSAKSKINVNEIFYDLVRQINRKTPVEKKKPKKKSCL

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

>50098_50098_4_LRRFIP2-RAP1A_LRRFIP2_chr3_37170553_ENST00000336686_RAP1A_chr1_112245957_ENST00000545460_length(amino acids)=182AA_BP=59
MGTPASGRKRTPVKDRFSAEDEALSNIAREAEARLAAKRAARAEARDIRMRELERQQKEEQFTAMRDLYMKNGQGFALVYSITAQSTFND
LQDLREQILRVKDTEDVPMILVGNKCDLEDERVVGKEQGQNLARQWCNCAFLESSAKSKINVNEIFYDLVRQINRKTPVEKKKPKKKSCL

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

>50098_50098_5_LRRFIP2-RAP1A_LRRFIP2_chr3_37170553_ENST00000440230_RAP1A_chr1_112245957_ENST00000356415_length(amino acids)=182AA_BP=59
MGTPASGRKRTPVKDRFSAEDEALSNIAREAEARLAAKRAARAEARDIRMRELERQQKEEQFTAMRDLYMKNGQGFALVYSITAQSTFND
LQDLREQILRVKDTEDVPMILVGNKCDLEDERVVGKEQGQNLARQWCNCAFLESSAKSKINVNEIFYDLVRQINRKTPVEKKKPKKKSCL

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

>50098_50098_6_LRRFIP2-RAP1A_LRRFIP2_chr3_37170553_ENST00000440230_RAP1A_chr1_112245957_ENST00000369709_length(amino acids)=182AA_BP=59
MGTPASGRKRTPVKDRFSAEDEALSNIAREAEARLAAKRAARAEARDIRMRELERQQKEEQFTAMRDLYMKNGQGFALVYSITAQSTFND
LQDLREQILRVKDTEDVPMILVGNKCDLEDERVVGKEQGQNLARQWCNCAFLESSAKSKINVNEIFYDLVRQINRKTPVEKKKPKKKSCL

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

>50098_50098_7_LRRFIP2-RAP1A_LRRFIP2_chr3_37170553_ENST00000440230_RAP1A_chr1_112245957_ENST00000436150_length(amino acids)=182AA_BP=59
MGTPASGRKRTPVKDRFSAEDEALSNIAREAEARLAAKRAARAEARDIRMRELERQQKEEQFTAMRDLYMKNGQGFALVYSITAQSTFND
LQDLREQILRVKDTEDVPMILVGNKCDLEDERVVGKEQGQNLARQWCNCAFLESSAKSKINVNEIFYDLVRQINRKTPVEKKKPKKKSCL

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

>50098_50098_8_LRRFIP2-RAP1A_LRRFIP2_chr3_37170553_ENST00000440230_RAP1A_chr1_112245957_ENST00000545460_length(amino acids)=182AA_BP=59
MGTPASGRKRTPVKDRFSAEDEALSNIAREAEARLAAKRAARAEARDIRMRELERQQKEEQFTAMRDLYMKNGQGFALVYSITAQSTFND
LQDLREQILRVKDTEDVPMILVGNKCDLEDERVVGKEQGQNLARQWCNCAFLESSAKSKINVNEIFYDLVRQINRKTPVEKKKPKKKSCL

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

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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/chr3:37170553/chr1:112245957)
- 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
LRRFIP2

Q9Y608

.
FUNCTION: May function as activator of the canonical Wnt signaling pathway, in association with DVL3, upstream of CTNNB1/beta-catenin. Positively regulates Toll-like receptor (TLR) signaling in response to agonist probably by competing with the negative FLII regulator for MYD88-binding. {ECO:0000269|PubMed:15677333, ECO:0000269|PubMed:19265123}.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.
- Retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneLRRFIP2chr3:37170553chr1:112245957ENST00000336686-32822_4959.0722.0Coiled coilOntology_term=ECO:0000255
HgeneLRRFIP2chr3:37170553chr1:112245957ENST00000354379-41422_4959.0401.0Coiled coilOntology_term=ECO:0000255
HgeneLRRFIP2chr3:37170553chr1:112245957ENST00000421276-41522_4959.0425.0Coiled coilOntology_term=ECO:0000255
HgeneLRRFIP2chr3:37170553chr1:112245957ENST00000421307-42922_4959.0722.0Coiled coilOntology_term=ECO:0000255
HgeneLRRFIP2chr3:37170553chr1:112245957ENST00000440230-41522_4959.0425.0Coiled coilOntology_term=ECO:0000255
TgeneRAP1Achr3:37170553chr1:112245957ENST0000035641538116_11961.0315.3333333333333Nucleotide bindingGTP
TgeneRAP1Achr3:37170553chr1:112245957ENST0000036970938116_11961.01554.6666666666667Nucleotide bindingGTP
TgeneRAP1Achr3:37170553chr1:112245957ENST0000043615049116_11961.0484.0Nucleotide bindingGTP
TgeneRAP1Achr3:37170553chr1:112245957ENST0000054546038116_11961.0137.0Nucleotide bindingGTP

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneLRRFIP2chr3:37170553chr1:112245957ENST00000336686-328349_52459.0722.0Coiled coilOntology_term=ECO:0000255
HgeneLRRFIP2chr3:37170553chr1:112245957ENST00000336686-328566_71459.0722.0Coiled coilOntology_term=ECO:0000255
HgeneLRRFIP2chr3:37170553chr1:112245957ENST00000354379-414349_52459.0401.0Coiled coilOntology_term=ECO:0000255
HgeneLRRFIP2chr3:37170553chr1:112245957ENST00000354379-414566_71459.0401.0Coiled coilOntology_term=ECO:0000255
HgeneLRRFIP2chr3:37170553chr1:112245957ENST00000421276-415349_52459.0425.0Coiled coilOntology_term=ECO:0000255
HgeneLRRFIP2chr3:37170553chr1:112245957ENST00000421276-415566_71459.0425.0Coiled coilOntology_term=ECO:0000255
HgeneLRRFIP2chr3:37170553chr1:112245957ENST00000421307-429349_52459.0722.0Coiled coilOntology_term=ECO:0000255
HgeneLRRFIP2chr3:37170553chr1:112245957ENST00000421307-429566_71459.0722.0Coiled coilOntology_term=ECO:0000255
HgeneLRRFIP2chr3:37170553chr1:112245957ENST00000440230-415349_52459.0425.0Coiled coilOntology_term=ECO:0000255
HgeneLRRFIP2chr3:37170553chr1:112245957ENST00000440230-415566_71459.0425.0Coiled coilOntology_term=ECO:0000255
HgeneLRRFIP2chr3:37170553chr1:112245957ENST00000336686-328118_34259.0722.0Compositional biasNote=Ser-rich
HgeneLRRFIP2chr3:37170553chr1:112245957ENST00000354379-414118_34259.0401.0Compositional biasNote=Ser-rich
HgeneLRRFIP2chr3:37170553chr1:112245957ENST00000421276-415118_34259.0425.0Compositional biasNote=Ser-rich
HgeneLRRFIP2chr3:37170553chr1:112245957ENST00000421307-429118_34259.0722.0Compositional biasNote=Ser-rich
HgeneLRRFIP2chr3:37170553chr1:112245957ENST00000440230-415118_34259.0425.0Compositional biasNote=Ser-rich
HgeneLRRFIP2chr3:37170553chr1:112245957ENST00000336686-3281_37059.0722.0RegionNote=DVL3-binding
HgeneLRRFIP2chr3:37170553chr1:112245957ENST00000354379-4141_37059.0401.0RegionNote=DVL3-binding
HgeneLRRFIP2chr3:37170553chr1:112245957ENST00000421276-4151_37059.0425.0RegionNote=DVL3-binding
HgeneLRRFIP2chr3:37170553chr1:112245957ENST00000421307-4291_37059.0722.0RegionNote=DVL3-binding
HgeneLRRFIP2chr3:37170553chr1:112245957ENST00000440230-4151_37059.0425.0RegionNote=DVL3-binding
TgeneRAP1Achr3:37170553chr1:112245957ENST000003564153832_4061.0315.3333333333333MotifEffector region
TgeneRAP1Achr3:37170553chr1:112245957ENST000003697093832_4061.01554.6666666666667MotifEffector region
TgeneRAP1Achr3:37170553chr1:112245957ENST000004361504932_4061.0484.0MotifEffector region
TgeneRAP1Achr3:37170553chr1:112245957ENST000005454603832_4061.0137.0MotifEffector region
TgeneRAP1Achr3:37170553chr1:112245957ENST000003564153810_1861.0315.3333333333333Nucleotide bindingGTP
TgeneRAP1Achr3:37170553chr1:112245957ENST000003564153829_3561.0315.3333333333333Nucleotide bindingGTP
TgeneRAP1Achr3:37170553chr1:112245957ENST000003697093810_1861.01554.6666666666667Nucleotide bindingGTP
TgeneRAP1Achr3:37170553chr1:112245957ENST000003697093829_3561.01554.6666666666667Nucleotide bindingGTP
TgeneRAP1Achr3:37170553chr1:112245957ENST000004361504910_1861.0484.0Nucleotide bindingGTP
TgeneRAP1Achr3:37170553chr1:112245957ENST000004361504929_3561.0484.0Nucleotide bindingGTP
TgeneRAP1Achr3:37170553chr1:112245957ENST000005454603810_1861.0137.0Nucleotide bindingGTP
TgeneRAP1Achr3:37170553chr1:112245957ENST000005454603829_3561.0137.0Nucleotide bindingGTP


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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
LRRFIP2
RAP1A


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


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Related Drugs to LRRFIP2-RAP1A


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 LRRFIP2-RAP1A


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