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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:GNAS-LRCH1 (FusionGDB2 ID:33515)

Fusion Gene Summary for GNAS-LRCH1

check button Fusion gene summary
Fusion gene informationFusion gene name: GNAS-LRCH1
Fusion gene ID: 33515
HgeneTgene
Gene symbol

GNAS

LRCH1

Gene ID

2778

23143

Gene nameGNAS complex locusleucine rich repeats and calponin homology domain containing 1
SynonymsAHO|C20orf45|GNAS1|GPSA|GSA|GSP|NESP|PITA3|POH|SCG6|SgVICHDC1|NP81
Cytomap

20q13.32

13q14.13-q14.2

Type of geneprotein-codingprotein-coding
Descriptionprotein ALEXprotein GNASprotein SCG6 (secretogranin VI)G protein subunit alpha Sadenylate cyclase-stimulating G alpha proteinalternative gene product encoded by XL-exonextra large alphas proteinguanine nucleotide binding protein (G protein), alpha leucine-rich repeat and calponin homology domain-containing protein 1leucine-rich repeats and calponin homology (CH) domain containing 1neuronal protein 81
Modification date2020032920200313
UniProtAcc

P63092

Q9Y2L9

Ensembl transtripts involved in fusion geneENST00000313949, ENST00000371098, 
ENST00000371075, ENST00000371100, 
ENST00000371099, ENST00000371102, 
ENST00000464624, ENST00000306120, 
ENST00000371095, ENST00000371085, 
ENST00000354359, ENST00000265620, 
ENST00000306090, ENST00000371081, 
ENST00000311191, ENST00000389798, 
ENST00000389797, 
Fusion gene scores* DoF score44 X 25 X 16=1760010 X 9 X 5=450
# samples 5110
** MAII scorelog2(51/17600*10)=-5.10893437155316
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(10/450*10)=-2.16992500144231
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

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

Most frequent breakpointGNAS(57480535)-LRCH1(47255876), # samples:2
Anticipated loss of major functional domain due to fusion event.GNAS-LRCH1 seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF.
GNAS-LRCH1 seems lost the major protein functional domain in Hgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
GNAS-LRCH1 seems lost the major protein functional domain in Tgene partner, which is a essential gene 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
TgeneLRCH1

GO:0034260

negative regulation of GTPase activity

28028151


check buttonFusion gene breakpoints across GNAS (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 LRCH1 (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
ChimerDB4READTCGA-DC-6156-01AGNASchr20

57480535

+LRCH1chr13

47255876

+
ChimerDB4READTCGA-DC-6156GNASchr20

57480535

+LRCH1chr13

47255876

+


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Fusion Gene ORF analysis for GNAS-LRCH1

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
3UTR-3CDSENST00000313949ENST00000311191GNASchr20

57480535

+LRCH1chr13

47255876

+
3UTR-3CDSENST00000313949ENST00000389798GNASchr20

57480535

+LRCH1chr13

47255876

+
3UTR-3CDSENST00000313949ENST00000389797GNASchr20

57480535

+LRCH1chr13

47255876

+
intron-3CDSENST00000371098ENST00000311191GNASchr20

57480535

+LRCH1chr13

47255876

+
intron-3CDSENST00000371098ENST00000389798GNASchr20

57480535

+LRCH1chr13

47255876

+
intron-3CDSENST00000371098ENST00000389797GNASchr20

57480535

+LRCH1chr13

47255876

+
3UTR-3CDSENST00000371075ENST00000311191GNASchr20

57480535

+LRCH1chr13

47255876

+
3UTR-3CDSENST00000371075ENST00000389798GNASchr20

57480535

+LRCH1chr13

47255876

+
3UTR-3CDSENST00000371075ENST00000389797GNASchr20

57480535

+LRCH1chr13

47255876

+
Frame-shiftENST00000371100ENST00000311191GNASchr20

57480535

+LRCH1chr13

47255876

+
Frame-shiftENST00000371100ENST00000389798GNASchr20

57480535

+LRCH1chr13

47255876

+
Frame-shiftENST00000371100ENST00000389797GNASchr20

57480535

+LRCH1chr13

47255876

+
intron-3CDSENST00000371099ENST00000311191GNASchr20

57480535

+LRCH1chr13

47255876

+
intron-3CDSENST00000371099ENST00000389798GNASchr20

57480535

+LRCH1chr13

47255876

+
intron-3CDSENST00000371099ENST00000389797GNASchr20

57480535

+LRCH1chr13

47255876

+
Frame-shiftENST00000371102ENST00000311191GNASchr20

57480535

+LRCH1chr13

47255876

+
Frame-shiftENST00000371102ENST00000389798GNASchr20

57480535

+LRCH1chr13

47255876

+
Frame-shiftENST00000371102ENST00000389797GNASchr20

57480535

+LRCH1chr13

47255876

+
3UTR-3CDSENST00000464624ENST00000311191GNASchr20

57480535

+LRCH1chr13

47255876

+
3UTR-3CDSENST00000464624ENST00000389798GNASchr20

57480535

+LRCH1chr13

47255876

+
3UTR-3CDSENST00000464624ENST00000389797GNASchr20

57480535

+LRCH1chr13

47255876

+
intron-3CDSENST00000306120ENST00000311191GNASchr20

57480535

+LRCH1chr13

47255876

+
intron-3CDSENST00000306120ENST00000389798GNASchr20

57480535

+LRCH1chr13

47255876

+
intron-3CDSENST00000306120ENST00000389797GNASchr20

57480535

+LRCH1chr13

47255876

+
Frame-shiftENST00000371095ENST00000311191GNASchr20

57480535

+LRCH1chr13

47255876

+
Frame-shiftENST00000371095ENST00000389798GNASchr20

57480535

+LRCH1chr13

47255876

+
Frame-shiftENST00000371095ENST00000389797GNASchr20

57480535

+LRCH1chr13

47255876

+
Frame-shiftENST00000371085ENST00000311191GNASchr20

57480535

+LRCH1chr13

47255876

+
Frame-shiftENST00000371085ENST00000389798GNASchr20

57480535

+LRCH1chr13

47255876

+
Frame-shiftENST00000371085ENST00000389797GNASchr20

57480535

+LRCH1chr13

47255876

+
Frame-shiftENST00000354359ENST00000311191GNASchr20

57480535

+LRCH1chr13

47255876

+
Frame-shiftENST00000354359ENST00000389798GNASchr20

57480535

+LRCH1chr13

47255876

+
Frame-shiftENST00000354359ENST00000389797GNASchr20

57480535

+LRCH1chr13

47255876

+
Frame-shiftENST00000265620ENST00000311191GNASchr20

57480535

+LRCH1chr13

47255876

+
Frame-shiftENST00000265620ENST00000389798GNASchr20

57480535

+LRCH1chr13

47255876

+
Frame-shiftENST00000265620ENST00000389797GNASchr20

57480535

+LRCH1chr13

47255876

+
Frame-shiftENST00000306090ENST00000311191GNASchr20

57480535

+LRCH1chr13

47255876

+
Frame-shiftENST00000306090ENST00000389798GNASchr20

57480535

+LRCH1chr13

47255876

+
Frame-shiftENST00000306090ENST00000389797GNASchr20

57480535

+LRCH1chr13

47255876

+
intron-3CDSENST00000371081ENST00000311191GNASchr20

57480535

+LRCH1chr13

47255876

+
intron-3CDSENST00000371081ENST00000389798GNASchr20

57480535

+LRCH1chr13

47255876

+
intron-3CDSENST00000371081ENST00000389797GNASchr20

57480535

+LRCH1chr13

47255876

+

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 GNAS-LRCH1


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)
GNASchr2057480535+LRCH1chr1347255875+7.59E-050.99992406
GNASchr2057480535+LRCH1chr1347255875+7.59E-050.99992406
GNASchr2057480535+LRCH1chr1347255875+7.59E-050.99992406
GNASchr2057480535+LRCH1chr1347255875+7.59E-050.99992406

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 GNAS-LRCH1


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
GNAS

P63092

LRCH1

Q9Y2L9

FUNCTION: Guanine nucleotide-binding proteins (G proteins) function as transducers in numerous signaling pathways controlled by G protein-coupled receptors (GPCRs) (PubMed:17110384). Signaling involves the activation of adenylyl cyclases, resulting in increased levels of the signaling molecule cAMP (PubMed:26206488, PubMed:8702665). GNAS functions downstream of several GPCRs, including beta-adrenergic receptors (PubMed:21488135). Stimulates the Ras signaling pathway via RAPGEF2 (PubMed:12391161). {ECO:0000269|PubMed:12391161, ECO:0000269|PubMed:17110384, ECO:0000269|PubMed:21488135, ECO:0000269|PubMed:26206488, ECO:0000269|PubMed:8702665}.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}.

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 GNAS-LRCH1


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 GNAS-LRCH1


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 GNAS-LRCH1


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 GNAS-LRCH1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneGNASC3494506Pseudohypoparathyroidism, Type Ia17CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneGNASC0242292McCune-Albright Syndrome7CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneGNASC0016065Polyostotic fibrous dysplasia5CTD_human;ORPHANET
HgeneGNASC1864100PSEUDOHYPOPARATHYROIDISM, TYPE IB5CTD_human;GENOMICS_ENGLAND;ORPHANET
HgeneGNASC2931404Albright's hereditary osteodystrophy4CTD_human;GENOMICS_ENGLAND
HgeneGNASC0033806Pseudohypoparathyroidism3CTD_human
HgeneGNASC0334041Osteoma cutis3CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneGNASC0014130Endocrine System Diseases2CTD_human
HgeneGNASC0016064Fibrous Dysplasia, Monostotic2ORPHANET
HgeneGNASC0034013Precocious Puberty2CTD_human
HgeneGNASC0221263Cafe-au-Lait Spots2CTD_human
HgeneGNASC0271527Cryptogenic sexual precocity2CTD_human
HgeneGNASC0342543Central Precocious Puberty2CTD_human
HgeneGNASC1504412Testotoxicosis2CTD_human
HgeneGNASC1857451Acth-Independent Macronodular Adrenal Hyperplasia2CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneGNASC2932716Pseudohypoparathyroidism Type 1C2GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneGNASC0001206Acromegaly1CTD_human
HgeneGNASC0001624Adrenal Gland Neoplasms1CTD_human
HgeneGNASC0003129Anoxemia1CTD_human
HgeneGNASC0003130Anoxia1CTD_human
HgeneGNASC0008370Cholestasis1GENOMICS_ENGLAND
HgeneGNASC0009438Common Bile Duct Calculi1CTD_human
HgeneGNASC0011573Endogenous depression1PSYGENET
HgeneGNASC0019087Hemorrhagic Disorders1CTD_human
HgeneGNASC0020538Hypertensive disease1CTD_human
HgeneGNASC0020796Profound Mental Retardation1CTD_human
HgeneGNASC0021655Insulin Resistance1CTD_human
HgeneGNASC0023897Liver Diseases, Parasitic1CTD_human
HgeneGNASC0025363Mental Retardation, Psychosocial1CTD_human
HgeneGNASC0027819Neuroblastoma1CTD_human
HgeneGNASC0028754Obesity1CTD_human
HgeneGNASC0029396Heterotopic Ossification1CTD_human
HgeneGNASC0032460Polycystic Ovary Syndrome1CTD_human
HgeneGNASC0033835Pseudopseudohypoparathyroidism1CTD_human;GENOMICS_ENGLAND;ORPHANET
HgeneGNASC0035204Respiration Disorders1CTD_human
HgeneGNASC0036341Schizophrenia1PSYGENET
HgeneGNASC0038587Substance Withdrawal Syndrome1CTD_human
HgeneGNASC0039231Tachycardia1CTD_human
HgeneGNASC0080203Tachyarrhythmia1CTD_human
HgeneGNASC0086189Drug Withdrawal Symptoms1CTD_human
HgeneGNASC0087169Withdrawal Symptoms1CTD_human
HgeneGNASC0206698Cholangiocarcinoma1CTD_human
HgeneGNASC0221357Brachydactyly1CTD_human
HgeneGNASC0242184Hypoxia1CTD_human
HgeneGNASC0242216Biliary calculi1CTD_human
HgeneGNASC0345905Intrahepatic Cholangiocarcinoma1CTD_human
HgeneGNASC0346302Growth Hormone-Secreting Pituitary Adenoma1CTD_human
HgeneGNASC0700292Hypoxemia1CTD_human
HgeneGNASC0750887Adrenal Cancer1CTD_human
HgeneGNASC0917816Mental deficiency1CTD_human
HgeneGNASC0920563Insulin Sensitivity1CTD_human
HgeneGNASC1136382Sclerocystic Ovaries1CTD_human
HgeneGNASC2932715Pseudohypoparathyroidism Type 1B1CTD_human;GENOMICS_ENGLAND;ORPHANET
HgeneGNASC3489630Somatotrophinoma, Familial1CTD_human
HgeneGNASC3697137Fibrous dysplasia of bone with intramuscular myxoma1ORPHANET
HgeneGNASC3714756Intellectual Disability1CTD_human
HgeneGNASC3805278Extrahepatic Cholangiocarcinoma1CTD_human
TgeneLRCH1C0038454Cerebrovascular accident1CTD_human
TgeneLRCH1C0751956Acute Cerebrovascular Accidents1CTD_human