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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:SERPINA1-APOA2 (FusionGDB2 ID:80139)

Fusion Gene Summary for SERPINA1-APOA2

check button Fusion gene summary
Fusion gene informationFusion gene name: SERPINA1-APOA2
Fusion gene ID: 80139
HgeneTgene
Gene symbol

SERPINA1

APOA2

Gene ID

5265

336

Gene nameserpin family A member 1apolipoprotein A2
SynonymsA1A|A1AT|AAT|PI|PI1|PRO2275|alpha1AT|nNIFApo-AII|ApoA-II|apoAII
Cytomap

14q32.13

1q23.3

Type of geneprotein-codingprotein-coding
Descriptionalpha-1-antitrypsinalpha-1 antitrypsinalpha-1 protease inhibitoralpha-1-antiproteinasealpha-1-antitrypsin nullalpha-1-antitrypsin short transcript variant 1C4alpha-1-antitrypsin short transcript variant 1C5epididymis secretory sperm binding proteinapolipoprotein A-II
Modification date2020032720200327
UniProtAcc.

P02652

Ensembl transtripts involved in fusion geneENST00000440909, ENST00000448921, 
ENST00000437397, ENST00000355814, 
ENST00000393087, ENST00000393088, 
ENST00000404814, ENST00000449399, 
ENST00000402629, ENST00000555289, 
ENST00000367990, ENST00000468465, 
ENST00000463812, ENST00000470459, 
ENST00000464492, ENST00000491350, 
Fusion gene scores* DoF score28 X 24 X 6=403213 X 11 X 6=858
# samples 2815
** MAII scorelog2(28/4032*10)=-3.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(15/858*10)=-2.51601514700366
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: SERPINA1 [Title/Abstract] AND APOA2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointSERPINA1(94844877)-APOA2(161192312), # 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
TgeneAPOA2

GO:0002740

negative regulation of cytokine secretion involved in immune response

12458630

TgeneAPOA2

GO:0006656

phosphatidylcholine biosynthetic process

14967812

TgeneAPOA2

GO:0009395

phospholipid catabolic process

14967812

TgeneAPOA2

GO:0009749

response to glucose

14988251

TgeneAPOA2

GO:0010873

positive regulation of cholesterol esterification

14967812

TgeneAPOA2

GO:0010903

negative regulation of very-low-density lipoprotein particle remodeling

14967812

TgeneAPOA2

GO:0018158

protein oxidation

12576517

TgeneAPOA2

GO:0018206

peptidyl-methionine modification

12576517

TgeneAPOA2

GO:0031647

regulation of protein stability

14967812

TgeneAPOA2

GO:0033344

cholesterol efflux

11162594

TgeneAPOA2

GO:0033700

phospholipid efflux

11162594

TgeneAPOA2

GO:0034370

triglyceride-rich lipoprotein particle remodeling

14967812

TgeneAPOA2

GO:0034374

low-density lipoprotein particle remodeling

8106353

TgeneAPOA2

GO:0034375

high-density lipoprotein particle remodeling

8106353|14967812

TgeneAPOA2

GO:0034380

high-density lipoprotein particle assembly

218942

TgeneAPOA2

GO:0034384

high-density lipoprotein particle clearance

10764676

TgeneAPOA2

GO:0042632

cholesterol homeostasis

14967812

TgeneAPOA2

GO:0043691

reverse cholesterol transport

14967812

TgeneAPOA2

GO:0045416

positive regulation of interleukin-8 biosynthetic process

11591715

TgeneAPOA2

GO:0046340

diacylglycerol catabolic process

14967812

TgeneAPOA2

GO:0050766

positive regulation of phagocytosis

20495215

TgeneAPOA2

GO:0050821

protein stabilization

20495215

TgeneAPOA2

GO:0050995

negative regulation of lipid catabolic process

14967812

TgeneAPOA2

GO:0050996

positive regulation of lipid catabolic process

8640403

TgeneAPOA2

GO:0060192

negative regulation of lipase activity

14967812

TgeneAPOA2

GO:0060621

negative regulation of cholesterol import

10764676

TgeneAPOA2

GO:0060695

negative regulation of cholesterol transporter activity

8106353


check buttonFusion gene breakpoints across SERPINA1 (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 APOA2 (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
ChimerDB4LIHCTCGA-DD-AADKSERPINA1chr14

94844877

-APOA2chr1

161192312

-


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Fusion Gene ORF analysis for SERPINA1-APOA2

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
intron-3CDSENST00000440909ENST00000367990SERPINA1chr14

94844877

-APOA2chr1

161192312

-
intron-3CDSENST00000440909ENST00000468465SERPINA1chr14

94844877

-APOA2chr1

161192312

-
intron-3CDSENST00000440909ENST00000463812SERPINA1chr14

94844877

-APOA2chr1

161192312

-
intron-3CDSENST00000440909ENST00000470459SERPINA1chr14

94844877

-APOA2chr1

161192312

-
intron-3CDSENST00000440909ENST00000464492SERPINA1chr14

94844877

-APOA2chr1

161192312

-
intron-3CDSENST00000440909ENST00000491350SERPINA1chr14

94844877

-APOA2chr1

161192312

-
intron-3CDSENST00000448921ENST00000367990SERPINA1chr14

94844877

-APOA2chr1

161192312

-
intron-3CDSENST00000448921ENST00000468465SERPINA1chr14

94844877

-APOA2chr1

161192312

-
intron-3CDSENST00000448921ENST00000463812SERPINA1chr14

94844877

-APOA2chr1

161192312

-
intron-3CDSENST00000448921ENST00000470459SERPINA1chr14

94844877

-APOA2chr1

161192312

-
intron-3CDSENST00000448921ENST00000464492SERPINA1chr14

94844877

-APOA2chr1

161192312

-
intron-3CDSENST00000448921ENST00000491350SERPINA1chr14

94844877

-APOA2chr1

161192312

-
intron-3CDSENST00000437397ENST00000367990SERPINA1chr14

94844877

-APOA2chr1

161192312

-
intron-3CDSENST00000437397ENST00000468465SERPINA1chr14

94844877

-APOA2chr1

161192312

-
intron-3CDSENST00000437397ENST00000463812SERPINA1chr14

94844877

-APOA2chr1

161192312

-
intron-3CDSENST00000437397ENST00000470459SERPINA1chr14

94844877

-APOA2chr1

161192312

-
intron-3CDSENST00000437397ENST00000464492SERPINA1chr14

94844877

-APOA2chr1

161192312

-
intron-3CDSENST00000437397ENST00000491350SERPINA1chr14

94844877

-APOA2chr1

161192312

-
intron-3CDSENST00000355814ENST00000367990SERPINA1chr14

94844877

-APOA2chr1

161192312

-
intron-3CDSENST00000355814ENST00000468465SERPINA1chr14

94844877

-APOA2chr1

161192312

-
intron-3CDSENST00000355814ENST00000463812SERPINA1chr14

94844877

-APOA2chr1

161192312

-
intron-3CDSENST00000355814ENST00000470459SERPINA1chr14

94844877

-APOA2chr1

161192312

-
intron-3CDSENST00000355814ENST00000464492SERPINA1chr14

94844877

-APOA2chr1

161192312

-
intron-3CDSENST00000355814ENST00000491350SERPINA1chr14

94844877

-APOA2chr1

161192312

-
intron-3CDSENST00000393087ENST00000367990SERPINA1chr14

94844877

-APOA2chr1

161192312

-
intron-3CDSENST00000393087ENST00000468465SERPINA1chr14

94844877

-APOA2chr1

161192312

-
intron-3CDSENST00000393087ENST00000463812SERPINA1chr14

94844877

-APOA2chr1

161192312

-
intron-3CDSENST00000393087ENST00000470459SERPINA1chr14

94844877

-APOA2chr1

161192312

-
intron-3CDSENST00000393087ENST00000464492SERPINA1chr14

94844877

-APOA2chr1

161192312

-
intron-3CDSENST00000393087ENST00000491350SERPINA1chr14

94844877

-APOA2chr1

161192312

-
intron-3CDSENST00000393088ENST00000367990SERPINA1chr14

94844877

-APOA2chr1

161192312

-
intron-3CDSENST00000393088ENST00000468465SERPINA1chr14

94844877

-APOA2chr1

161192312

-
intron-3CDSENST00000393088ENST00000463812SERPINA1chr14

94844877

-APOA2chr1

161192312

-
intron-3CDSENST00000393088ENST00000470459SERPINA1chr14

94844877

-APOA2chr1

161192312

-
intron-3CDSENST00000393088ENST00000464492SERPINA1chr14

94844877

-APOA2chr1

161192312

-
intron-3CDSENST00000393088ENST00000491350SERPINA1chr14

94844877

-APOA2chr1

161192312

-
intron-3CDSENST00000404814ENST00000367990SERPINA1chr14

94844877

-APOA2chr1

161192312

-
intron-3CDSENST00000404814ENST00000468465SERPINA1chr14

94844877

-APOA2chr1

161192312

-
intron-3CDSENST00000404814ENST00000463812SERPINA1chr14

94844877

-APOA2chr1

161192312

-
intron-3CDSENST00000404814ENST00000470459SERPINA1chr14

94844877

-APOA2chr1

161192312

-
intron-3CDSENST00000404814ENST00000464492SERPINA1chr14

94844877

-APOA2chr1

161192312

-
intron-3CDSENST00000404814ENST00000491350SERPINA1chr14

94844877

-APOA2chr1

161192312

-
intron-3CDSENST00000449399ENST00000367990SERPINA1chr14

94844877

-APOA2chr1

161192312

-
intron-3CDSENST00000449399ENST00000468465SERPINA1chr14

94844877

-APOA2chr1

161192312

-
intron-3CDSENST00000449399ENST00000463812SERPINA1chr14

94844877

-APOA2chr1

161192312

-
intron-3CDSENST00000449399ENST00000470459SERPINA1chr14

94844877

-APOA2chr1

161192312

-
intron-3CDSENST00000449399ENST00000464492SERPINA1chr14

94844877

-APOA2chr1

161192312

-
intron-3CDSENST00000449399ENST00000491350SERPINA1chr14

94844877

-APOA2chr1

161192312

-
intron-3CDSENST00000402629ENST00000367990SERPINA1chr14

94844877

-APOA2chr1

161192312

-
intron-3CDSENST00000402629ENST00000468465SERPINA1chr14

94844877

-APOA2chr1

161192312

-
intron-3CDSENST00000402629ENST00000463812SERPINA1chr14

94844877

-APOA2chr1

161192312

-
intron-3CDSENST00000402629ENST00000470459SERPINA1chr14

94844877

-APOA2chr1

161192312

-
intron-3CDSENST00000402629ENST00000464492SERPINA1chr14

94844877

-APOA2chr1

161192312

-
intron-3CDSENST00000402629ENST00000491350SERPINA1chr14

94844877

-APOA2chr1

161192312

-
intron-3CDSENST00000555289ENST00000367990SERPINA1chr14

94844877

-APOA2chr1

161192312

-
intron-3CDSENST00000555289ENST00000468465SERPINA1chr14

94844877

-APOA2chr1

161192312

-
intron-3CDSENST00000555289ENST00000463812SERPINA1chr14

94844877

-APOA2chr1

161192312

-
intron-3CDSENST00000555289ENST00000470459SERPINA1chr14

94844877

-APOA2chr1

161192312

-
intron-3CDSENST00000555289ENST00000464492SERPINA1chr14

94844877

-APOA2chr1

161192312

-
intron-3CDSENST00000555289ENST00000491350SERPINA1chr14

94844877

-APOA2chr1

161192312

-

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 SERPINA1-APOA2


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)

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 SERPINA1-APOA2


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
.APOA2

P02652

FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.FUNCTION: May stabilize HDL (high density lipoprotein) structure by its association with lipids, and affect the HDL metabolism.

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 SERPINA1-APOA2


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 SERPINA1-APOA2


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 SERPINA1-APOA2


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
TgeneAPOA2P02652DB01593ZincSmall moleculeApproved|Investigational
TgeneAPOA2P02652DB09130CopperSmall moleculeApproved|Investigational
TgeneAPOA2P02652DB14487Zinc acetateSmall moleculeApproved|Investigational

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Related Diseases for SERPINA1-APOA2


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneSERPINA1C0023895Liver diseases6CTD_human
HgeneSERPINA1C0086565Liver Dysfunction6CTD_human
HgeneSERPINA1C0221757alpha 1-Antitrypsin Deficiency6CTD_human;GENOMICS_ENGLAND
HgeneSERPINA1C0023890Liver Cirrhosis3CTD_human
HgeneSERPINA1C0239946Fibrosis, Liver3CTD_human
HgeneSERPINA1C0005586Bipolar Disorder2CTD_human;PSYGENET
HgeneSERPINA1C0024117Chronic Obstructive Airway Disease2CTD_human
HgeneSERPINA1C0030328Panniculitis, Nodular Nonsuppurative2CTD_human
HgeneSERPINA1C0525045Mood Disorders2PSYGENET
HgeneSERPINA1C1527303Chronic Airflow Obstruction2CTD_human
HgeneSERPINA1C2239176Liver carcinoma2CTD_human
HgeneSERPINA1C0001418Adenocarcinoma1CTD_human
HgeneSERPINA1C0003469Anxiety Disorders1CTD_human
HgeneSERPINA1C0003850Arteriosclerosis1CTD_human
HgeneSERPINA1C0003949Asbestosis1CTD_human
HgeneSERPINA1C0005587Depression, Bipolar1CTD_human
HgeneSERPINA1C0006267Bronchiectasis1CTD_human
HgeneSERPINA1C0008370Cholestasis1CTD_human
HgeneSERPINA1C0013221Drug toxicity1CTD_human
HgeneSERPINA1C0013990Pathological accumulation of air in tissues1CTD_human
HgeneSERPINA1C0019080Hemorrhage1CTD_human
HgeneSERPINA1C0019693HIV Infections1CTD_human
HgeneSERPINA1C0020615Hypoglycemia1CTD_human
HgeneSERPINA1C0022660Kidney Failure, Acute1CTD_human
HgeneSERPINA1C0024115Lung diseases1CTD_human;GENOMICS_ENGLAND
HgeneSERPINA1C0024121Lung Neoplasms1CTD_human
HgeneSERPINA1C0024623Malignant neoplasm of stomach1CTD_human
HgeneSERPINA1C0024713Manic Disorder1CTD_human
HgeneSERPINA1C0027627Neoplasm Metastasis1CTD_human
HgeneSERPINA1C0034067Pulmonary Emphysema1CTD_human
HgeneSERPINA1C0034069Pulmonary Fibrosis1CTD_human
HgeneSERPINA1C0038356Stomach Neoplasms1CTD_human
HgeneSERPINA1C0039841Thiamine Deficiency1CTD_human
HgeneSERPINA1C0041755Adverse reaction to drug1CTD_human
HgeneSERPINA1C0042384Vasculitis1CTD_human
HgeneSERPINA1C0205641Adenocarcinoma, Basal Cell1CTD_human
HgeneSERPINA1C0205642Adenocarcinoma, Oxyphilic1CTD_human
HgeneSERPINA1C0205643Carcinoma, Cribriform1CTD_human
HgeneSERPINA1C0205644Carcinoma, Granular Cell1CTD_human
HgeneSERPINA1C0205645Adenocarcinoma, Tubular1CTD_human
HgeneSERPINA1C0221227Centriacinar Emphysema1CTD_human
HgeneSERPINA1C0242379Malignant neoplasm of lung1CTD_human
HgeneSERPINA1C0264393Panacinar Emphysema1CTD_human
HgeneSERPINA1C0270715Degenerative Diseases, Central Nervous System1CTD_human
HgeneSERPINA1C0271708Fasting Hypoglycemia1CTD_human
HgeneSERPINA1C0271710Reactive hypoglycemia1CTD_human
HgeneSERPINA1C0338831Manic1CTD_human
HgeneSERPINA1C0376280Anxiety States, Neurotic1CTD_human
HgeneSERPINA1C0524851Neurodegenerative Disorders1CTD_human
HgeneSERPINA1C0751733Degenerative Diseases, Spinal Cord1CTD_human
HgeneSERPINA1C1279420Anxiety neurosis (finding)1CTD_human
HgeneSERPINA1C1565662Acute Kidney Insufficiency1CTD_human
HgeneSERPINA1C1708349Hereditary Diffuse Gastric Cancer1CTD_human
HgeneSERPINA1C2350878Focal Emphysema1CTD_human
HgeneSERPINA1C2609414Acute kidney injury1CTD_human
HgeneSERPINA1C2930617Pulmonary Fibrosis - from Asbestos Exposure1CTD_human
HgeneSERPINA1C2930967Gastro-enteropancreatic neuroendocrine tumor1CTD_human
HgeneSERPINA1C4505456HIV Coinfection1CTD_human
HgeneSERPINA1C4721507Alveolitis, Fibrosing1CTD_human
TgeneAPOA2C0020445Hypercholesterolemia, Familial1CTD_human
TgeneAPOA2C0745103Hyperlipoproteinemia Type IIa1CTD_human;GENOMICS_ENGLAND
TgeneAPOA2C1704417Hyperlipoproteinemia Type IIb1CTD_human