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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:ATIC-SCN9A (FusionGDB2 ID:HG471TG6335)

Fusion Gene Summary for ATIC-SCN9A

check button Fusion gene summary
Fusion gene informationFusion gene name: ATIC-SCN9A
Fusion gene ID: hg471tg6335
HgeneTgene
Gene symbol

ATIC

SCN9A

Gene ID

471

6335

Gene name5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolasesodium voltage-gated channel alpha subunit 9
SynonymsAICAR|AICARFT|HEL-S-70p|IMPCHASE|PURHETHA|FEB3B|GEFSP7|HSAN2D|NE-NA|NENA|Nav1.7|PN1|SFNP
Cytomap('ATIC')('SCN9A')

2q35

2q24.3

Type of geneprotein-codingprotein-coding
Descriptionbifunctional purine biosynthesis protein PURH5-aminoimidazole-4-carboxamide-1-beta-D-ribonucleotide transformylase/inosinicaseAICAR formyltransferase/IMP cyclohydrolase bifunctional enzymeAICARFT/IMPCHASEepididymis secretory sperm binding protein Li 7sodium channel protein type 9 subunit alphahNE-Naneuroendocrine sodium channelperipheral sodium channel 1sodium channel protein type IX subunit alphasodium channel, voltage-gated, type IX, alpha polypeptidesodium channel, voltage-gated, type IX, alp
Modification date2020031320200313
UniProtAcc

P31939

.
Ensembl transtripts involved in fusion geneENST00000236959, ENST00000435675, 
ENST00000540518, 
Fusion gene scores* DoF score9 X 9 X 4=3245 X 4 X 4=80
# samples 95
** MAII scorelog2(9/324*10)=-1.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(5/80*10)=-0.678071905112638
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: ATIC [Title/Abstract] AND SCN9A [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointATIC(216214479)-SCN9A(167076420), # 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
TgeneSCN9A

GO:0035725

sodium ion transmembrane transport

17145499



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 ATIC-SCN9A

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 ATIC-SCN9A


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 ATIC-SCN9A


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/:216214479/:167076420)
- 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
ATIC

P31939

.
FUNCTION: Bifunctional enzyme that catalyzes the last two steps of purine biosynthesis (PubMed:11948179, PubMed:14756554). Acts as a transformylase that incorporates a formyl group to the AMP analog AICAR (5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide) to produce the intermediate formyl-AICAR (FAICAR) (PubMed:9378707, PubMed:11948179, PubMed:10985775). Can use both 10-formyldihydrofolate and 10-formyltetrahydrofolate as the formyl donor in this reaction (PubMed:10985775). Also catalyzes the cyclization of FAICAR to IMP (PubMed:11948179, PubMed:14756554). Is able to convert thio-AICAR to 6-mercaptopurine ribonucleotide, an inhibitor of purine biosynthesis used in the treatment of human leukemias (PubMed:10985775). Promotes insulin receptor/INSR autophosphorylation and is involved in INSR internalization (PubMed:25687571). {ECO:0000269|PubMed:10985775, ECO:0000269|PubMed:11948179, ECO:0000269|PubMed:14756554, ECO:0000269|PubMed:25687571, ECO:0000269|PubMed:9378707}.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 ATIC-SCN9A


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 ATIC-SCN9A


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 ATIC-SCN9A


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
HgeneATICP31939DB00563MethotrexateInhibitorSmall moleculeApproved
HgeneATICP31939DB00563MethotrexateInhibitorSmall moleculeApproved
HgeneATICP31939DB00563MethotrexateInhibitorSmall moleculeApproved
HgeneATICP31939DB00642PemetrexedInhibitorSmall moleculeApproved|Investigational
HgeneATICP31939DB00642PemetrexedInhibitorSmall moleculeApproved|Investigational
HgeneATICP31939DB00642PemetrexedInhibitorSmall moleculeApproved|Investigational

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Related Diseases for ATIC-SCN9A


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneATICC0001787Osteoporosis, Age-Related1CTD_human
HgeneATICC0003873Rheumatoid Arthritis1CTD_human
HgeneATICC0013221Drug toxicity1CTD_human
HgeneATICC0029456Osteoporosis1CTD_human
HgeneATICC0029459Osteoporosis, Senile1CTD_human
HgeneATICC0041755Adverse reaction to drug1CTD_human
HgeneATICC0155003Blindness, Transient1CTD_human
HgeneATICC0221473Blindness, Hysterical1CTD_human
HgeneATICC0271215Blindness, Legal1CTD_human
HgeneATICC0339730Blindness, Acquired1CTD_human
HgeneATICC0376288Amaurosis1CTD_human
HgeneATICC0456909Blindness1CTD_human
HgeneATICC0750958Blindness, Monocular1CTD_human
HgeneATICC0751406Post-Traumatic Osteoporosis1CTD_human
HgeneATICC1837530AICAR Transformylase Inosine Monophosphate Cyclohydrolase Deficiency1CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneATICC1879328Blindness both eyes NOS (disorder)1CTD_human
HgeneATICC3714756Intellectual Disability1GENOMICS_ENGLAND
TgeneC0014805Primary Erythermalgia15CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneC0014544Epilepsy6CLINGEN
TgeneC1833661PAROXYSMAL EXTREME PAIN DISORDER5CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneC0751122Infantile Severe Myoclonic Epilepsy4CTD_human;ORPHANET
TgeneC1855739Indifference to Pain, Congenital, Autosomal Recessive4CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneC0014804Erythromelalgia3CTD_human
TgeneC2751778Generalized Epilepsy With Febrile Seizures Plus, 73CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneC0002768Congenital Pain Insensitivity2GENOMICS_ENGLAND;ORPHANET
TgeneC0019372Herpesviridae Infections1CTD_human
TgeneC0020072Hereditary Sensory Autonomic Neuropathy, Type 21ORPHANET
TgeneC0020075Hereditary Sensory Autonomic Neuropathy, Type 51ORPHANET
TgeneC0027796Neuralgia1CTD_human
TgeneC0032768Postherpetic neuralgia1CTD_human
TgeneC0033774Pruritus1CTD_human
TgeneC0037140B Virus Infection1CTD_human
TgeneC0038870Neuralgia, Supraorbital1CTD_human
TgeneC0042656Neuralgia, Vidian1CTD_human
TgeneC0150055Chronic pain1CTD_human
TgeneC0234247Neuralgia, Atypical1CTD_human
TgeneC0234249Neuralgia, Stump1CTD_human
TgeneC0270914Hereditary Motor and Sensory-Neuropathy Type II1ORPHANET
TgeneC0423711Neuralgia, Perineal1CTD_human
TgeneC0423712Neuralgia, Iliohypogastric Nerve1CTD_human
TgeneC0432262Dysosteosclerosis1GENOMICS_ENGLAND
TgeneC0598589Inherited neuropathies1GENOMICS_ENGLAND
TgeneC0699739Sensory Neuropathy, Hereditary1GENOMICS_ENGLAND
TgeneC0751371Neuralgia, Ilioinguinal1CTD_human
TgeneC0751372Nerve Pain1CTD_human
TgeneC0751373Paroxysmal Nerve Pain1CTD_human
TgeneC3178789Widespread Chronic Pain1CTD_human
TgeneC4551549Early Infantile Epileptic Encephalopathy 61GENOMICS_ENGLAND