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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:FAM162A-CSTA (FusionGDB2 ID:28631)

Fusion Gene Summary for FAM162A-CSTA

check button Fusion gene summary
Fusion gene informationFusion gene name: FAM162A-CSTA
Fusion gene ID: 28631
HgeneTgene
Gene symbol

FAM162A

CSTA

Gene ID

26355

1475

Gene namefamily with sequence similarity 162 member Acystatin A
SynonymsC3orf28|E2IG5|HGTD-PAREI|PSS4|STF1|STFA
Cytomap

3q21.1

3q21.1

Type of geneprotein-codingprotein-coding
Descriptionprotein FAM162AE2-induced gene 5 proteinHIF-1 alpha-responsive proapoptotic moleculegrowth and transformation-dependent proteincystatin-Acystatin A (stefin A)cystatin AS
Modification date2020031320200313
UniProtAcc

Q96A26

P01040

Ensembl transtripts involved in fusion geneENST00000469967, ENST00000477892, 
ENST00000232125, 		ENST00000264474, 
ENST00000479204, 
Fusion gene scores* DoF score6 X 5 X 5=1509 X 10 X 4=360
# samples 109
** MAII scorelog2(10/150*10)=-0.584962500721156
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(9/360*10)=-2
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: FAM162A [Title/Abstract] AND CSTA [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointFAM162A(122103146)-CSTA(122044109), # samples:1
FAM162A(122103145)-CSTA(122044107), # samples:1
FAM162A(122103145)-CSTA(122056393), # 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
HgeneFAM162A

GO:0006919

activation of cysteine-type endopeptidase activity involved in apoptotic process

15082785

HgeneFAM162A

GO:0043065

positive regulation of apoptotic process

15082785

HgeneFAM162A

GO:0071456

cellular response to hypoxia

15082785

HgeneFAM162A

GO:0090200

positive regulation of release of cytochrome c from mitochondria

15082785

TgeneCSTA

GO:0010466

negative regulation of peptidase activity

6203523

TgeneCSTA

GO:0018149

peptide cross-linking

10908733

TgeneCSTA

GO:0030216

keratinocyte differentiation

10908733

TgeneCSTA

GO:0045861

negative regulation of proteolysis

3488317


check buttonFusion gene breakpoints across FAM162A (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 CSTA (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
ChimerDB4PRADTCGA-G9-A9S4-01AFAM162Achr3

122103145

+CSTAchr3

122044107

+
ChimerDB4PRADTCGA-G9-A9S4-01AFAM162Achr3

122103145

+CSTAchr3

122056393

+
ChimerDB4PRADTCGA-G9-A9S4-01AFAM162Achr3

122103146

-CSTAchr3

122044109

+


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Fusion Gene ORF analysis for FAM162A-CSTA

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
5CDS-5UTRENST00000469967ENST00000264474FAM162Achr3

122103145

+CSTAchr3

122044107

+
5CDS-5UTRENST00000469967ENST00000264474FAM162Achr3

122103146

-CSTAchr3

122044109

+
5CDS-5UTRENST00000469967ENST00000479204FAM162Achr3

122103145

+CSTAchr3

122044107

+
5CDS-5UTRENST00000469967ENST00000479204FAM162Achr3

122103146

-CSTAchr3

122044109

+
5CDS-5UTRENST00000477892ENST00000264474FAM162Achr3

122103145

+CSTAchr3

122044107

+
5CDS-5UTRENST00000477892ENST00000264474FAM162Achr3

122103146

-CSTAchr3

122044109

+
5CDS-5UTRENST00000477892ENST00000479204FAM162Achr3

122103145

+CSTAchr3

122044107

+
5CDS-5UTRENST00000477892ENST00000479204FAM162Achr3

122103146

-CSTAchr3

122044109

+
5UTR-3CDSENST00000232125ENST00000264474FAM162Achr3

122103145

+CSTAchr3

122056393

+
5UTR-3CDSENST00000232125ENST00000479204FAM162Achr3

122103145

+CSTAchr3

122056393

+
5UTR-5UTRENST00000232125ENST00000264474FAM162Achr3

122103145

+CSTAchr3

122044107

+
5UTR-5UTRENST00000232125ENST00000264474FAM162Achr3

122103146

-CSTAchr3

122044109

+
5UTR-5UTRENST00000232125ENST00000479204FAM162Achr3

122103145

+CSTAchr3

122044107

+
5UTR-5UTRENST00000232125ENST00000479204FAM162Achr3

122103146

-CSTAchr3

122044109

+
Frame-shiftENST00000469967ENST00000264474FAM162Achr3

122103145

+CSTAchr3

122056393

+
Frame-shiftENST00000469967ENST00000479204FAM162Achr3

122103145

+CSTAchr3

122056393

+
Frame-shiftENST00000477892ENST00000264474FAM162Achr3

122103145

+CSTAchr3

122056393

+
Frame-shiftENST00000477892ENST00000479204FAM162Achr3

122103145

+CSTAchr3

122056393

+

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 FAM162A-CSTA


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)
FAM162Achr3122103146+CSTAchr3122044108+1.24E-050.9999876
FAM162Achr3122103146+CSTAchr3122056393+1.92E-060.9999981
FAM162Achr3122103146+CSTAchr3122044108+1.24E-050.9999876
FAM162Achr3122103146+CSTAchr3122056393+1.92E-060.9999981

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.
genomic feature of top 1%

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Fusion Protein Features for FAM162A-CSTA


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/:122103146/:122044109)
- 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
FAM162A

Q96A26

CSTA

P01040

FUNCTION: Proposed to be involved in regulation of apoptosis; the exact mechanism may differ between cell types/tissues (PubMed:15082785). May be involved in hypoxia-induced cell death of transformed cells implicating cytochrome C release and caspase activation (such as CASP9) and inducing mitochondrial permeability transition (PubMed:15082785). May be involved in hypoxia-induced cell death of neuronal cells probably by promoting release of AIFM1 from mitochondria to cytoplasm and its translocation to the nucleus; however, the involvement of caspases has been reported conflictingly (By similarity). {ECO:0000250|UniProtKB:Q9D6U8, ECO:0000269|PubMed:15082785}.FUNCTION: This is an intracellular thiol proteinase inhibitor. Has an important role in desmosome-mediated cell-cell adhesion in the lower levels of the epidermis. {ECO:0000269|PubMed:21944047}.

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 FAM162A-CSTA


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 FAM162A-CSTA


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 FAM162A-CSTA


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 FAM162A-CSTA


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource