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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:ARPC1A-TH (FusionGDB2 ID:HG10552TG7054)

Fusion Gene Summary for ARPC1A-TH

check button Fusion gene summary
Fusion gene informationFusion gene name: ARPC1A-TH
Fusion gene ID: hg10552tg7054
HgeneTgene
Gene symbol

ARPC1A

TH

Gene ID

10552

7054

Gene nameactin related protein 2/3 complex subunit 1Atyrosine hydroxylase
SynonymsArc40|HEL-68|HEL-S-307|SOP2Hs|SOP2LDYT14|DYT5b|TYH
Cytomap('ARPC1A')('TH')

7q22.1

11p15.5

Type of geneprotein-codingprotein-coding
Descriptionactin-related protein 2/3 complex subunit 1ASOP2-like proteinactin binding protein (Schizosaccharomyces pombe sop2-like)actin related protein 2/3 complex, subunit 1A, 41kDaepididymis luminal protein 68epididymis secretory protein Li 307epididymis setyrosine 3-monooxygenasedystonia 14tyrosine 3-hydroxylase
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000262942, ENST00000432884, 
ENST00000471960, 
Fusion gene scores* DoF score8 X 6 X 6=2882 X 1 X 2=4
# samples 82
** MAII scorelog2(8/288*10)=-1.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(2/4*10)=2.32192809488736
Context

PubMed: ARPC1A [Title/Abstract] AND TH [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointARPC1A(98942138)-TH(2191101), # samples:2
Anticipated loss of major functional domain due to fusion event.ARPC1A-TH seems lost the major protein functional domain in Tgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
ARPC1A-TH seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target 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
TgeneTH

GO:0001666

response to hypoxia

17520326

TgeneTH

GO:0042416

dopamine biosynthetic process

12457228

TgeneTH

GO:0042418

epinephrine biosynthetic process

12457228

TgeneTH

GO:0042421

norepinephrine biosynthetic process

12457228

TgeneTH

GO:0045471

response to ethanol

18343820



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
ChimerDB4BLCATCGA-UY-A78K-01AARPC1Achr7

98942138

+THchr11

2191101

-


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Fusion Gene ORF analysis for ARPC1A-TH

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-shiftENST00000262942ENST00000333684ARPC1Achr7

98942138

+THchr11

2191101

-
Frame-shiftENST00000262942ENST00000352909ARPC1Achr7

98942138

+THchr11

2191101

-
Frame-shiftENST00000262942ENST00000381175ARPC1Achr7

98942138

+THchr11

2191101

-
Frame-shiftENST00000262942ENST00000381178ARPC1Achr7

98942138

+THchr11

2191101

-
Frame-shiftENST00000432884ENST00000333684ARPC1Achr7

98942138

+THchr11

2191101

-
Frame-shiftENST00000432884ENST00000352909ARPC1Achr7

98942138

+THchr11

2191101

-
Frame-shiftENST00000432884ENST00000381175ARPC1Achr7

98942138

+THchr11

2191101

-
Frame-shiftENST00000432884ENST00000381178ARPC1Achr7

98942138

+THchr11

2191101

-
intron-3CDSENST00000471960ENST00000333684ARPC1Achr7

98942138

+THchr11

2191101

-
intron-3CDSENST00000471960ENST00000352909ARPC1Achr7

98942138

+THchr11

2191101

-
intron-3CDSENST00000471960ENST00000381175ARPC1Achr7

98942138

+THchr11

2191101

-
intron-3CDSENST00000471960ENST00000381178ARPC1Achr7

98942138

+THchr11

2191101

-

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 ARPC1A-TH


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 ARPC1A-TH


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/:98942138/:2191101)
- 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 ARPC1A-TH


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 ARPC1A-TH


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 ARPC1A-TH


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 ARPC1A-TH


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneC2673535DYSTONIA, DOPA-RESPONSIVE, WITH OR WITHOUT HYPERPHENYLALANINEMIA, AUTOSOMAL RECESSIVE (disorder)35CLINGEN;CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneC0001973Alcoholic Intoxication, Chronic5PSYGENET
TgeneC0005586Bipolar Disorder5PSYGENET
TgeneC0011570Mental Depression5PSYGENET
TgeneC0011581Depressive disorder5PSYGENET
TgeneC0525045Mood Disorders5PSYGENET
TgeneC0041696Unipolar Depression4PSYGENET
TgeneC1269683Major Depressive Disorder4PSYGENET
TgeneC3714756Intellectual Disability3CTD_human;GENOMICS_ENGLAND
TgeneC0007370Catalepsy2CTD_human
TgeneC0011206Delirium2PSYGENET
TgeneC0023186Learning Disorders2CTD_human
TgeneC0233612Waxy flexibility2CTD_human
TgeneC0242422Parkinsonian Disorders2CTD_human
TgeneC0242423Ramsay Hunt Paralysis Syndrome2CTD_human
TgeneC0751262Adult Learning Disorders2CTD_human
TgeneC0751263Learning Disturbance2CTD_human
TgeneC0751265Learning Disabilities2CTD_human
TgeneC0752097Autosomal Dominant Juvenile Parkinson Disease2CTD_human
TgeneC0752098Autosomal Dominant Parkinsonism2CTD_human
TgeneC0752100Autosomal Recessive Parkinsonism2CTD_human
TgeneC0752101Parkinsonism, Experimental2CTD_human
TgeneC0752104Familial Juvenile Parkinsonism2CTD_human
TgeneC0752105Parkinsonism, Juvenile2CTD_human
TgeneC1330966Developmental Academic Disorder2CTD_human
TgeneC1851920Dopa-Responsive Dystonia2GENOMICS_ENGLAND
TgeneC1868675PARKINSON DISEASE 2, AUTOSOMAL RECESSIVE JUVENILE2CTD_human
TgeneC0006111Brain Diseases1CTD_human
TgeneC0013386Dyskinesia, Drug-Induced1CTD_human
TgeneC0013421Dystonia1CTD_human
TgeneC0018799Heart Diseases1CTD_human
TgeneC0020538Hypertensive disease1CTD_human
TgeneC0020796Profound Mental Retardation1CTD_human
TgeneC0025363Mental Retardation, Psychosocial1CTD_human
TgeneC0027746Nerve Degeneration1CTD_human
TgeneC0027819Neuroblastoma1CTD_human
TgeneC0030567Parkinson Disease1CTD_human
TgeneC0031511Pheochromocytoma1CTD_human
TgeneC0085584Encephalopathies1CTD_human
TgeneC0221480Recurrent depression1PSYGENET
TgeneC0393588Dystonia, Paroxysmal1CTD_human
TgeneC0393610Dystonia, Diurnal1CTD_human
TgeneC0751088Dyskinesia, Medication-Induced1CTD_human
TgeneC0751093Dystonia, Limb1CTD_human
TgeneC0751217Hyperkinesia, Generalized1CTD_human
TgeneC0752347Lewy Body Disease1CTD_human
TgeneC0917816Mental deficiency1CTD_human
TgeneC1257877Pheochromocytoma, Extra-Adrenal1CTD_human
TgeneC2239176Liver carcinoma1CTD_human
TgeneC3887506Hyperkinesia1CTD_human
TgeneC4524082Segawa syndrome1GENOMICS_ENGLAND