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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:NALCN-GRM5 (FusionGDB2 ID:HG259232TG2915)

Fusion Gene Summary for NALCN-GRM5

check button Fusion gene summary
Fusion gene informationFusion gene name: NALCN-GRM5
Fusion gene ID: hg259232tg2915
HgeneTgene
Gene symbol

NALCN

GRM5

Gene ID

259232

2915

Gene namesodium leak channel, non-selectiveglutamate metabotropic receptor 5
SynonymsCLIFAHDD|CanIon|IHPRF|IHPRF1|INNFD|VGCNL1|bA430M15.1GPRC1E|MGLUR5|PPP1R86|mGlu5
Cytomap('NALCN')('GRM5')

13q32.3-q33.1

11q14.2-q14.3

Type of geneprotein-codingprotein-coding
Descriptionsodium leak channel non-selective proteinfour repeat voltage-gated ion channelvoltage gated channel like 1metabotropic glutamate receptor 5glutamate receptor, metabotropic 5protein phosphatase 1, regulatory subunit 86
Modification date2020031320200329
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000251127, ENST00000376196, 
ENST00000376200, ENST00000470333, 
Fusion gene scores* DoF score4 X 4 X 1=167 X 5 X 4=140
# samples 47
** MAII scorelog2(4/16*10)=1.32192809488736
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0		log2(7/140*10)=-1
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: NALCN [Title/Abstract] AND GRM5 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointNALCN(101960103)-GRM5(88279241), # 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
* 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


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Fusion Gene ORF analysis for NALCN-GRM5

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

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 NALCN-GRM5


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)


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Fusion Protein Features for NALCN-GRM5


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/:101960103/:88279241)
- 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 NALCN-GRM5


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 NALCN-GRM5


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 NALCN-GRM5


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 NALCN-GRM5


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneNALCNC3809454HYPOTONIA, INFANTILE, WITH PSYCHOMOTOR RETARDATION AND CHARACTERISTIC FACIES 12CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneNALCNC4225398CONGENITAL CONTRACTURES OF THE LIMBS AND FACE, HYPOTONIA, AND DEVELOPMENTAL DELAY2CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneNALCNC0220662ARTHROGRYPOSIS, DISTAL, TYPE 11ORPHANET
HgeneNALCNC0265224Freeman-Sheldon syndrome1ORPHANET
HgeneNALCNC1834523ARTHROGRYPOSIS, DISTAL, TYPE 2B1ORPHANET
HgeneNALCNC1852085Digitotalar Dysmorphism1ORPHANET
TgeneC0036341Schizophrenia3PSYGENET
TgeneC0041696Unipolar Depression3PSYGENET
TgeneC1269683Major Depressive Disorder3PSYGENET
TgeneC0038220Status Epilepticus2CTD_human
TgeneC0041671Attention Deficit Disorder2CTD_human
TgeneC0270823Petit mal status2CTD_human
TgeneC0311335Grand Mal Status Epilepticus2CTD_human
TgeneC0393734Complex Partial Status Epilepticus2CTD_human
TgeneC0751522Status Epilepticus, Subclinical2CTD_human
TgeneC0751523Non-Convulsive Status Epilepticus2CTD_human
TgeneC0751524Simple Partial Status Epilepticus2CTD_human
TgeneC1263846Attention deficit hyperactivity disorder2CTD_human
TgeneC1321905Minimal Brain Dysfunction2CTD_human
TgeneC0005586Bipolar Disorder1PSYGENET
TgeneC0009171Cocaine Abuse1CTD_human
TgeneC0011882Diabetic Neuropathies1CTD_human
TgeneC0013146Drug abuse1CTD_human
TgeneC0013170Drug habituation1CTD_human
TgeneC0013222Drug Use Disorders1CTD_human
TgeneC0014556Epilepsy, Temporal Lobe1CTD_human
TgeneC0014558Uncinate Epilepsy1CTD_human
TgeneC0027796Neuralgia1CTD_human
TgeneC0029231Organic Mental Disorders, Substance-Induced1CTD_human
TgeneC0038580Substance Dependence1CTD_human
TgeneC0038586Substance Use Disorders1CTD_human
TgeneC0038870Neuralgia, Supraorbital1CTD_human
TgeneC0042656Neuralgia, Vidian1CTD_human
TgeneC0234247Neuralgia, Atypical1CTD_human
TgeneC0234249Neuralgia, Stump1CTD_human
TgeneC0236736Cocaine-Related Disorders1CTD_human
TgeneC0236969Substance-Related Disorders1CTD_human
TgeneC0271673Symmetric Diabetic Proximal Motor Neuropathy1CTD_human
TgeneC0271674Asymmetric Diabetic Proximal Motor Neuropathy1CTD_human
TgeneC0271678Diabetic Mononeuropathy1CTD_human
TgeneC0271680Diabetic Polyneuropathies1CTD_human
TgeneC0271685Diabetic Amyotrophy1CTD_human
TgeneC0271686Diabetic Autonomic Neuropathy1CTD_human
TgeneC0393672Epilepsy, Benign Psychomotor, Childhood1CTD_human
TgeneC0393682Epilepsy, Lateral Temporal1CTD_human
TgeneC0393835Diabetic Asymmetric Polyneuropathy1CTD_human
TgeneC0423711Neuralgia, Perineal1CTD_human
TgeneC0423712Neuralgia, Iliohypogastric Nerve1CTD_human
TgeneC0600427Cocaine Dependence1CTD_human
TgeneC0740858Substance abuse problem1CTD_human
TgeneC0751074Diabetic Neuralgia1CTD_human
TgeneC0751371Neuralgia, Ilioinguinal1CTD_human
TgeneC0751372Nerve Pain1CTD_human
TgeneC0751373Paroxysmal Nerve Pain1CTD_human
TgeneC1510472Drug Dependence1CTD_human
TgeneC4316881Prescription Drug Abuse1CTD_human