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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:LRCH1-PIK3R1 (FusionGDB2 ID:49392)

Fusion Gene Summary for LRCH1-PIK3R1

check button Fusion gene summary
Fusion gene informationFusion gene name: LRCH1-PIK3R1
Fusion gene ID: 49392
HgeneTgene
Gene symbol

LRCH1

PIK3R1

Gene ID

23143

5295

Gene nameleucine rich repeats and calponin homology domain containing 1phosphoinositide-3-kinase regulatory subunit 1
SynonymsCHDC1|NP81AGM7|GRB1|IMD36|p85|p85-ALPHA
Cytomap

13q14.13-q14.2

5q13.1

Type of geneprotein-codingprotein-coding
Descriptionleucine-rich repeat and calponin homology domain-containing protein 1leucine-rich repeats and calponin homology (CH) domain containing 1neuronal protein 81phosphatidylinositol 3-kinase regulatory subunit alphaPI3-kinase subunit p85-alphaPI3K regulatory subunit alphaphosphatidylinositol 3-kinase 85 kDa regulatory subunit alphaphosphatidylinositol 3-kinase, regulatory subunit, polypeptide 1 (p85 alpha)ph
Modification date2020031320200327
UniProtAcc

Q9Y2L9

.
Ensembl transtripts involved in fusion geneENST00000311191, ENST00000389798, 
ENST00000389797, 		ENST00000521381, 
ENST00000521657, ENST00000517643, 
ENST00000274335, ENST00000396611, 
ENST00000320694, ENST00000336483, 
ENST00000523872, 
Fusion gene scores* DoF score12 X 7 X 5=4209 X 9 X 4=324
# samples 139
** MAII scorelog2(13/420*10)=-1.69187770463767
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(9/324*10)=-1.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: LRCH1 [Title/Abstract] AND PIK3R1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointLRCH1(47155523)-PIK3R1(67593268), # samples:1
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
HgeneLRCH1

GO:0034260

negative regulation of GTPase activity

28028151

TgenePIK3R1

GO:0014065

phosphatidylinositol 3-kinase signaling

7782332

TgenePIK3R1

GO:0034976

response to endoplasmic reticulum stress

20348923

TgenePIK3R1

GO:0042307

positive regulation of protein import into nucleus

20348923

TgenePIK3R1

GO:0048009

insulin-like growth factor receptor signaling pathway

7782332

TgenePIK3R1

GO:0050821

protein stabilization

20348923

TgenePIK3R1

GO:0060396

growth hormone receptor signaling pathway

7782332


check buttonFusion gene breakpoints across LRCH1 (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 PIK3R1 (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
ChiTaRS5.0N/ABF849250LRCH1chr13

47155523

+PIK3R1chr5

67593268

+


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Fusion Gene ORF analysis for LRCH1-PIK3R1

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
intron-3CDSENST00000311191ENST00000521381LRCH1chr13

47155523

+PIK3R1chr5

67593268

+
intron-3CDSENST00000311191ENST00000521657LRCH1chr13

47155523

+PIK3R1chr5

67593268

+
intron-intronENST00000311191ENST00000517643LRCH1chr13

47155523

+PIK3R1chr5

67593268

+
intron-intronENST00000311191ENST00000274335LRCH1chr13

47155523

+PIK3R1chr5

67593268

+
intron-intronENST00000311191ENST00000396611LRCH1chr13

47155523

+PIK3R1chr5

67593268

+
intron-intronENST00000311191ENST00000320694LRCH1chr13

47155523

+PIK3R1chr5

67593268

+
intron-intronENST00000311191ENST00000336483LRCH1chr13

47155523

+PIK3R1chr5

67593268

+
intron-intronENST00000311191ENST00000523872LRCH1chr13

47155523

+PIK3R1chr5

67593268

+
intron-3CDSENST00000389798ENST00000521381LRCH1chr13

47155523

+PIK3R1chr5

67593268

+
intron-3CDSENST00000389798ENST00000521657LRCH1chr13

47155523

+PIK3R1chr5

67593268

+
intron-intronENST00000389798ENST00000517643LRCH1chr13

47155523

+PIK3R1chr5

67593268

+
intron-intronENST00000389798ENST00000274335LRCH1chr13

47155523

+PIK3R1chr5

67593268

+
intron-intronENST00000389798ENST00000396611LRCH1chr13

47155523

+PIK3R1chr5

67593268

+
intron-intronENST00000389798ENST00000320694LRCH1chr13

47155523

+PIK3R1chr5

67593268

+
intron-intronENST00000389798ENST00000336483LRCH1chr13

47155523

+PIK3R1chr5

67593268

+
intron-intronENST00000389798ENST00000523872LRCH1chr13

47155523

+PIK3R1chr5

67593268

+
intron-3CDSENST00000389797ENST00000521381LRCH1chr13

47155523

+PIK3R1chr5

67593268

+
intron-3CDSENST00000389797ENST00000521657LRCH1chr13

47155523

+PIK3R1chr5

67593268

+
intron-intronENST00000389797ENST00000517643LRCH1chr13

47155523

+PIK3R1chr5

67593268

+
intron-intronENST00000389797ENST00000274335LRCH1chr13

47155523

+PIK3R1chr5

67593268

+
intron-intronENST00000389797ENST00000396611LRCH1chr13

47155523

+PIK3R1chr5

67593268

+
intron-intronENST00000389797ENST00000320694LRCH1chr13

47155523

+PIK3R1chr5

67593268

+
intron-intronENST00000389797ENST00000336483LRCH1chr13

47155523

+PIK3R1chr5

67593268

+
intron-intronENST00000389797ENST00000523872LRCH1chr13

47155523

+PIK3R1chr5

67593268

+

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 LRCH1-PIK3R1


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)

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 LRCH1-PIK3R1


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
LRCH1

Q9Y2L9

.
FUNCTION: Acts as a negative regulator of GTPase CDC42 by sequestering CDC42-guanine exchange factor DOCK8. Probably by preventing CDC42 activation, negatively regulates CD4(+) T-cell migration. {ECO:0000269|PubMed:28028151}.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 LRCH1-PIK3R1


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 LRCH1-PIK3R1


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 LRCH1-PIK3R1


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 LRCH1-PIK3R1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneLRCH1C0038454Cerebrovascular accident1CTD_human
HgeneLRCH1C0751956Acute Cerebrovascular Accidents1CTD_human
TgenePIK3R1C0878684SHORT syndrome7CLINGEN;CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgenePIK3R1C0001973Alcoholic Intoxication, Chronic2PSYGENET
TgenePIK3R1C0033578Prostatic Neoplasms2CTD_human
TgenePIK3R1C0376358Malignant neoplasm of prostate2CTD_human
TgenePIK3R1C3554689AGAMMAGLOBULINEMIA 7, AUTOSOMAL RECESSIVE2CTD_human;GENOMICS_ENGLAND
TgenePIK3R1C4014934IMMUNODEFICIENCY 362CTD_human;GENOMICS_ENGLAND
TgenePIK3R1C0001768Agammaglobulinemia1GENOMICS_ENGLAND
TgenePIK3R1C0006267Bronchiectasis1GENOMICS_ENGLAND
TgenePIK3R1C0006413Burkitt Lymphoma1CTD_human
TgenePIK3R1C0007097Carcinoma1CTD_human
TgenePIK3R1C0021655Insulin Resistance1CTD_human
TgenePIK3R1C0024667Animal Mammary Neoplasms1CTD_human
TgenePIK3R1C0024668Mammary Neoplasms, Experimental1CTD_human
TgenePIK3R1C0042900Vitiligo1CTD_human
TgenePIK3R1C0205696Anaplastic carcinoma1CTD_human
TgenePIK3R1C0205697Carcinoma, Spindle-Cell1CTD_human
TgenePIK3R1C0205698Undifferentiated carcinoma1CTD_human
TgenePIK3R1C0205699Carcinomatosis1CTD_human
TgenePIK3R1C0343640African Burkitt's lymphoma1CTD_human
TgenePIK3R1C0494261Combined immunodeficiency1GENOMICS_ENGLAND
TgenePIK3R1C0920563Insulin Sensitivity1CTD_human
TgenePIK3R1C1257925Mammary Carcinoma, Animal1CTD_human
TgenePIK3R1C1832241Agammaglobulinemia, non-Bruton type1ORPHANET
TgenePIK3R1C3714976ACTIVATED PI3K-DELTA SYNDROME1ORPHANET
TgenePIK3R1C4721444Burkitt Leukemia1CTD_human