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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:HAPLN1-GNAS (FusionGDB2 ID:HG1404TG2778)

Fusion Gene Summary for HAPLN1-GNAS

check button Fusion gene summary
Fusion gene informationFusion gene name: HAPLN1-GNAS
Fusion gene ID: hg1404tg2778
HgeneTgene
Gene symbol

HAPLN1

GNAS

Gene ID

1404

2778

Gene namehyaluronan and proteoglycan link protein 1GNAS complex locus
SynonymsCRT1|CRTL1AHO|C20orf45|GNAS1|GPSA|GSA|GSP|NESP|PITA3|POH|SCG6|SgVI
Cytomap('HAPLN1')('GNAS')

5q14.3

20q13.32

Type of geneprotein-codingprotein-coding
Descriptionhyaluronan and proteoglycan link protein 1Cartilage link proteincartilage-link proteincartilage-linking protein 1proteoglycan link proteinprotein 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
Modification date2020031320200329
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000274341, ENST00000514416, 
Fusion gene scores* DoF score6 X 5 X 2=60111 X 41 X 18=81918
# samples 6111
** MAII scorelog2(6/60*10)=0log2(111/81918*10)=-6.20554891117303
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: HAPLN1 [Title/Abstract] AND GNAS [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointHAPLN1(83016606)-GNAS(57470665), # 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


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/ACN403028HAPLN1chr5

83016606

-GNASchr20

57470665

+


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Fusion Gene ORF analysis for HAPLN1-GNAS

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
5UTR-3UTRENST00000274341ENST00000313949HAPLN1chr5

83016606

-GNASchr20

57470665

+
5UTR-3UTRENST00000274341ENST00000371075HAPLN1chr5

83016606

-GNASchr20

57470665

+
5UTR-3UTRENST00000274341ENST00000371098HAPLN1chr5

83016606

-GNASchr20

57470665

+
5UTR-3UTRENST00000274341ENST00000371100HAPLN1chr5

83016606

-GNASchr20

57470665

+
5UTR-3UTRENST00000274341ENST00000464624HAPLN1chr5

83016606

-GNASchr20

57470665

+
5UTR-intronENST00000274341ENST00000265620HAPLN1chr5

83016606

-GNASchr20

57470665

+
5UTR-intronENST00000274341ENST00000306090HAPLN1chr5

83016606

-GNASchr20

57470665

+
5UTR-intronENST00000274341ENST00000306120HAPLN1chr5

83016606

-GNASchr20

57470665

+
5UTR-intronENST00000274341ENST00000354359HAPLN1chr5

83016606

-GNASchr20

57470665

+
5UTR-intronENST00000274341ENST00000371081HAPLN1chr5

83016606

-GNASchr20

57470665

+
5UTR-intronENST00000274341ENST00000371085HAPLN1chr5

83016606

-GNASchr20

57470665

+
5UTR-intronENST00000274341ENST00000371095HAPLN1chr5

83016606

-GNASchr20

57470665

+
5UTR-intronENST00000274341ENST00000371099HAPLN1chr5

83016606

-GNASchr20

57470665

+
5UTR-intronENST00000274341ENST00000371102HAPLN1chr5

83016606

-GNASchr20

57470665

+
intron-3UTRENST00000514416ENST00000313949HAPLN1chr5

83016606

-GNASchr20

57470665

+
intron-3UTRENST00000514416ENST00000371075HAPLN1chr5

83016606

-GNASchr20

57470665

+
intron-3UTRENST00000514416ENST00000371098HAPLN1chr5

83016606

-GNASchr20

57470665

+
intron-3UTRENST00000514416ENST00000371100HAPLN1chr5

83016606

-GNASchr20

57470665

+
intron-3UTRENST00000514416ENST00000464624HAPLN1chr5

83016606

-GNASchr20

57470665

+
intron-intronENST00000514416ENST00000265620HAPLN1chr5

83016606

-GNASchr20

57470665

+
intron-intronENST00000514416ENST00000306090HAPLN1chr5

83016606

-GNASchr20

57470665

+
intron-intronENST00000514416ENST00000306120HAPLN1chr5

83016606

-GNASchr20

57470665

+
intron-intronENST00000514416ENST00000354359HAPLN1chr5

83016606

-GNASchr20

57470665

+
intron-intronENST00000514416ENST00000371081HAPLN1chr5

83016606

-GNASchr20

57470665

+
intron-intronENST00000514416ENST00000371085HAPLN1chr5

83016606

-GNASchr20

57470665

+
intron-intronENST00000514416ENST00000371095HAPLN1chr5

83016606

-GNASchr20

57470665

+
intron-intronENST00000514416ENST00000371099HAPLN1chr5

83016606

-GNASchr20

57470665

+
intron-intronENST00000514416ENST00000371102HAPLN1chr5

83016606

-GNASchr20

57470665

+

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 HAPLN1-GNAS


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)
HAPLN1chr583016607-GNASchr2057470666+9.24E-050.9999075
HAPLN1chr583016607-GNASchr2057470666+9.24E-050.9999075


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.
genomic feature of top 1%

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Fusion Protein Features for HAPLN1-GNAS


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/:83016606/:57470665)
- 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
..
FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.

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 HAPLN1-GNAS


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 HAPLN1-GNAS


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 HAPLN1-GNAS


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 HAPLN1-GNAS


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneHAPLN1C0003873Rheumatoid Arthritis1CTD_human
HgeneHAPLN1C0009402Colorectal Carcinoma1CTD_human;UNIPROT
HgeneHAPLN1C0009404Colorectal Neoplasms1CTD_human
HgeneHAPLN1C0013336Dwarfism1CTD_human
HgeneHAPLN1C0206762Limb Deformities, Congenital1CTD_human
HgeneHAPLN1C0376634Craniofacial Abnormalities1CTD_human
TgeneC3494506Pseudohypoparathyroidism, Type Ia17CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneC0242292McCune-Albright Syndrome7CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneC0016065Polyostotic fibrous dysplasia5CTD_human;ORPHANET
TgeneC1864100PSEUDOHYPOPARATHYROIDISM, TYPE IB5CTD_human;GENOMICS_ENGLAND;ORPHANET
TgeneC2931404Albright's hereditary osteodystrophy4CTD_human;GENOMICS_ENGLAND
TgeneC0033806Pseudohypoparathyroidism3CTD_human
TgeneC0334041Osteoma cutis3CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneC0014130Endocrine System Diseases2CTD_human
TgeneC0016064Fibrous Dysplasia, Monostotic2ORPHANET
TgeneC0034013Precocious Puberty2CTD_human
TgeneC0221263Cafe-au-Lait Spots2CTD_human
TgeneC0271527Cryptogenic sexual precocity2CTD_human
TgeneC0342543Central Precocious Puberty2CTD_human
TgeneC1504412Testotoxicosis2CTD_human
TgeneC1857451Acth-Independent Macronodular Adrenal Hyperplasia2CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneC2932716Pseudohypoparathyroidism Type 1C2GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneC0001206Acromegaly1CTD_human
TgeneC0001624Adrenal Gland Neoplasms1CTD_human
TgeneC0003129Anoxemia1CTD_human
TgeneC0003130Anoxia1CTD_human
TgeneC0008370Cholestasis1GENOMICS_ENGLAND
TgeneC0009438Common Bile Duct Calculi1CTD_human
TgeneC0011573Endogenous depression1PSYGENET
TgeneC0019087Hemorrhagic Disorders1CTD_human
TgeneC0020538Hypertensive disease1CTD_human
TgeneC0020796Profound Mental Retardation1CTD_human
TgeneC0021655Insulin Resistance1CTD_human
TgeneC0023897Liver Diseases, Parasitic1CTD_human
TgeneC0025363Mental Retardation, Psychosocial1CTD_human
TgeneC0027819Neuroblastoma1CTD_human
TgeneC0028754Obesity1CTD_human
TgeneC0029396Heterotopic Ossification1CTD_human
TgeneC0032460Polycystic Ovary Syndrome1CTD_human
TgeneC0033835Pseudopseudohypoparathyroidism1CTD_human;GENOMICS_ENGLAND;ORPHANET
TgeneC0035204Respiration Disorders1CTD_human
TgeneC0036341Schizophrenia1PSYGENET
TgeneC0038587Substance Withdrawal Syndrome1CTD_human
TgeneC0039231Tachycardia1CTD_human
TgeneC0080203Tachyarrhythmia1CTD_human
TgeneC0086189Drug Withdrawal Symptoms1CTD_human
TgeneC0087169Withdrawal Symptoms1CTD_human
TgeneC0206698Cholangiocarcinoma1CTD_human
TgeneC0221357Brachydactyly1CTD_human
TgeneC0242184Hypoxia1CTD_human
TgeneC0242216Biliary calculi1CTD_human
TgeneC0345905Intrahepatic Cholangiocarcinoma1CTD_human
TgeneC0346302Growth Hormone-Secreting Pituitary Adenoma1CTD_human
TgeneC0700292Hypoxemia1CTD_human
TgeneC0750887Adrenal Cancer1CTD_human
TgeneC0917816Mental deficiency1CTD_human
TgeneC0920563Insulin Sensitivity1CTD_human
TgeneC1136382Sclerocystic Ovaries1CTD_human
TgeneC2932715Pseudohypoparathyroidism Type 1B1CTD_human;GENOMICS_ENGLAND;ORPHANET
TgeneC3489630Somatotrophinoma, Familial1CTD_human
TgeneC3697137Fibrous dysplasia of bone with intramuscular myxoma1ORPHANET
TgeneC3714756Intellectual Disability1CTD_human
TgeneC3805278Extrahepatic Cholangiocarcinoma1CTD_human