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Center for Computational Systems Medicine
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FusionGeneSummary

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FusionProtFeature

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FusionGeneSequence

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FusionGenePPI

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RelatedDrugs

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RelatedDiseases

Fusion gene ID: 30288

FusionGeneSummary for RALGPS1_LMX1B

check button Fusion gene summary
Fusion gene informationFusion gene name: RALGPS1_LMX1B
Fusion gene ID: 30288
HgeneTgene
Gene symbol

RALGPS1

LMX1B

Gene ID

9649

4010

Gene nameRal GEF with PH domain and SH3 binding motif 1LIM homeobox transcription factor 1 beta
SynonymsRALGEF2|RALGPS1ALMX1.2|NPS1
Cytomap

9q33.3

9q33.3

Type of geneprotein-codingprotein-coding
Descriptionras-specific guanine nucleotide-releasing factor RalGPS1Ral guanine nucleotide exchange factor RalGPS1ARalGEF 2ral GEF with PH domain and SH3-binding motif 1ral guanine nucleotide exchange factor 2ralA exchange factor RalGPS1LIM homeobox transcription factor 1-betaLIM/homeobox protein 1.2LMX-1.2
Modification date2018051920180519
UniProtAcc

Q5JS13

O60663

Ensembl transtripts involved in fusion geneENST00000424082, ENST00000259351, 
ENST00000394022, ENST00000373436, 
ENST00000373434, ENST00000394011, 
ENST00000480993, 		ENST00000526117, 
ENST00000373474, ENST00000425646, 
ENST00000355497, ENST00000561065, 
Fusion gene scores* DoF score6 X 5 X 5=1504 X 1 X 2=8
# samples 74
** MAII scorelog2(7/150*10)=-1.09953567355091
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(4/8*10)=2.32192809488736
Context

PubMed: RALGPS1 [Title/Abstract] AND LMX1B [Title/Abstract] AND fusion [Title/Abstract]

Functional or gene categories assigned by FusionGDB annotation
* 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
HgeneRALGPS1

GO:0032485

regulation of Ral protein signal transduction

10747847

TgeneLMX1B

GO:0006355

regulation of transcription, DNA-templated

10767331


check button Fusion gene information from three resources
(ChiTars (NAR, 2018), tumorfusions (NAR, 2018), Gao et al. (Cell, 2018))
* 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.
Data typeSourceCancer typeSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
TCGARVLUSCTCGA-L3-A524-01ARALGPS1chr9

129728230

+LMX1Bchr9

129453115

+
* LD: Li Ding group's fusion gene list
  RV: Roel Verhaak group's fusion gene list
  ChiTaRs fusion database

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-shiftENST00000424082ENST00000526117RALGPS1chr9

129728230

+LMX1Bchr9

129453115

+
Frame-shiftENST00000424082ENST00000373474RALGPS1chr9

129728230

+LMX1Bchr9

129453115

+
Frame-shiftENST00000424082ENST00000425646RALGPS1chr9

129728230

+LMX1Bchr9

129453115

+
Frame-shiftENST00000424082ENST00000355497RALGPS1chr9

129728230

+LMX1Bchr9

129453115

+
Frame-shiftENST00000424082ENST00000561065RALGPS1chr9

129728230

+LMX1Bchr9

129453115

+
Frame-shiftENST00000259351ENST00000526117RALGPS1chr9

129728230

+LMX1Bchr9

129453115

+
Frame-shiftENST00000259351ENST00000373474RALGPS1chr9

129728230

+LMX1Bchr9

129453115

+
Frame-shiftENST00000259351ENST00000425646RALGPS1chr9

129728230

+LMX1Bchr9

129453115

+
Frame-shiftENST00000259351ENST00000355497RALGPS1chr9

129728230

+LMX1Bchr9

129453115

+
Frame-shiftENST00000259351ENST00000561065RALGPS1chr9

129728230

+LMX1Bchr9

129453115

+
Frame-shiftENST00000394022ENST00000526117RALGPS1chr9

129728230

+LMX1Bchr9

129453115

+
Frame-shiftENST00000394022ENST00000373474RALGPS1chr9

129728230

+LMX1Bchr9

129453115

+
Frame-shiftENST00000394022ENST00000425646RALGPS1chr9

129728230

+LMX1Bchr9

129453115

+
Frame-shiftENST00000394022ENST00000355497RALGPS1chr9

129728230

+LMX1Bchr9

129453115

+
Frame-shiftENST00000394022ENST00000561065RALGPS1chr9

129728230

+LMX1Bchr9

129453115

+
Frame-shiftENST00000373436ENST00000526117RALGPS1chr9

129728230

+LMX1Bchr9

129453115

+
Frame-shiftENST00000373436ENST00000373474RALGPS1chr9

129728230

+LMX1Bchr9

129453115

+
Frame-shiftENST00000373436ENST00000425646RALGPS1chr9

129728230

+LMX1Bchr9

129453115

+
Frame-shiftENST00000373436ENST00000355497RALGPS1chr9

129728230

+LMX1Bchr9

129453115

+
Frame-shiftENST00000373436ENST00000561065RALGPS1chr9

129728230

+LMX1Bchr9

129453115

+
Frame-shiftENST00000373434ENST00000526117RALGPS1chr9

129728230

+LMX1Bchr9

129453115

+
Frame-shiftENST00000373434ENST00000373474RALGPS1chr9

129728230

+LMX1Bchr9

129453115

+
Frame-shiftENST00000373434ENST00000425646RALGPS1chr9

129728230

+LMX1Bchr9

129453115

+
Frame-shiftENST00000373434ENST00000355497RALGPS1chr9

129728230

+LMX1Bchr9

129453115

+
Frame-shiftENST00000373434ENST00000561065RALGPS1chr9

129728230

+LMX1Bchr9

129453115

+
Frame-shiftENST00000394011ENST00000526117RALGPS1chr9

129728230

+LMX1Bchr9

129453115

+
Frame-shiftENST00000394011ENST00000373474RALGPS1chr9

129728230

+LMX1Bchr9

129453115

+
Frame-shiftENST00000394011ENST00000425646RALGPS1chr9

129728230

+LMX1Bchr9

129453115

+
Frame-shiftENST00000394011ENST00000355497RALGPS1chr9

129728230

+LMX1Bchr9

129453115

+
Frame-shiftENST00000394011ENST00000561065RALGPS1chr9

129728230

+LMX1Bchr9

129453115

+
3UTR-3CDSENST00000480993ENST00000526117RALGPS1chr9

129728230

+LMX1Bchr9

129453115

+
3UTR-3CDSENST00000480993ENST00000373474RALGPS1chr9

129728230

+LMX1Bchr9

129453115

+
3UTR-3CDSENST00000480993ENST00000425646RALGPS1chr9

129728230

+LMX1Bchr9

129453115

+
3UTR-3CDSENST00000480993ENST00000355497RALGPS1chr9

129728230

+LMX1Bchr9

129453115

+
3UTR-3CDSENST00000480993ENST00000561065RALGPS1chr9

129728230

+LMX1Bchr9

129453115

+

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FusionProtFeatures for RALGPS1_LMX1B


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
RALGPS1

Q5JS13

LMX1B

O60663

Essential for the specification of dorsal limb fate atboth the zeugopodal and autopodal levels.

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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FusionGeneSequence for RALGPS1_LMX1B


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences.
(nt: nucleotides, aa: amino acids)

* Fusion amino acid sequences.

* Fusion transcript sequences (only coding sequence (CDS) region).

* Fusion transcript sequences (Full-length transcript).

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FusionGenePPI for RALGPS1_LMX1B


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
RALGPS1RALA, GRB2, NCK1, APP, C2orf88LMX1BSSBP3, APP, LDB1, MAB21L1, POTEF, ACTB, PKNOX2, PARS2, PBX1, PBX2, PBX3, MEIS1, MEIS2, SSBP2, SSBP4, IDI2, RBSN


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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RelatedDrugs for RALGPS1_LMX1B


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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RelatedDiseases for RALGPS1_LMX1B


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneRALGPS1C0005695Bladder Neoplasm1CTD_human
TgeneLMX1BC0027341Nail-Patella Syndrome6CTD_human;ORPHANET;UNIPROT
TgeneLMX1BC0033687Proteinuria2CTD_human;HPO
TgeneLMX1BC0004936Mental disorders1CTD_human
TgeneLMX1BC0009081Congenital clubfoot1CTD_human;HPO
TgeneLMX1BC0018965Hematuria1CTD_human;HPO
TgeneLMX1BC0020473Hyperlipidemia1CTD_human
TgeneLMX1BC0021603Sleep Initiation and Maintenance Disorders1CTD_human
TgeneLMX1BC0036341Schizophrenia1PSYGENET
TgeneLMX1BC1535926Neurodevelopmental Disorders1CTD_human