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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:AMACR-C1QTNF3 (FusionGDB2 ID:HG23600TG114899)

Fusion Gene Summary for AMACR-C1QTNF3

check button Fusion gene summary
Fusion gene informationFusion gene name: AMACR-C1QTNF3
Fusion gene ID: hg23600tg114899
HgeneTgene
Gene symbol

AMACR

C1QTNF3

Gene ID

23600

114899

Gene namealpha-methylacyl-CoA racemaseC1q and TNF related 3
SynonymsAMACRD|CBAS4|P504S|RACE|RMC1ATNF3|CORCS|CORS|CORS-26|CORS26|CTRP3
Cytomap('AMACR')('C1QTNF3')

5p13.2

5p13.2

Type of geneprotein-codingprotein-coding
Descriptionalpha-methylacyl-CoA racemase2-methylacyl-CoA racemasecomplement C1q tumor necrosis factor-related protein 3C1q and tumor necrosis factor related protein 3cartonectincollagenous repeat-containing sequence 26 kDa proteincollagenous repeat-containing sequence of 26-kDasecretory protein CORS26
Modification date2020031320200322
UniProtAcc

Q9UHK6

.
Ensembl transtripts involved in fusion geneENST00000335606, ENST00000382085, 
ENST00000426255, ENST00000502637, 
ENST00000512079, ENST00000382068, 
ENST00000382072, ENST00000441713, 
ENST00000514195, 
Fusion gene scores* DoF score2 X 3 X 3=187 X 3 X 6=126
# samples 38
** MAII scorelog2(3/18*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0		log2(8/126*10)=-0.655351828612554
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: AMACR [Title/Abstract] AND C1QTNF3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointAMACR(34004679)-C1QTNF3(34020847), # samples:1
AMACR(34004679)-C1QTNF3(34028988), # samples:1
Anticipated loss of major functional domain due to fusion event.AMACR-C1QTNF3 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
AMACR-C1QTNF3 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
AMACR-C1QTNF3 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
AMACR-C1QTNF3 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
AMACR-C1QTNF3 seems lost the major protein functional domain in Hgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
AMACR-C1QTNF3 seems lost the major protein functional domain in Hgene partner, which is a essential gene 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
HgeneAMACR

GO:0008206

bile acid metabolic process

10655068

TgeneC1QTNF3

GO:0035356

cellular triglyceride homeostasis

20739398

TgeneC1QTNF3

GO:0045721

negative regulation of gluconeogenesis

20952387

TgeneC1QTNF3

GO:0050715

positive regulation of cytokine secretion

18421280

TgeneC1QTNF3

GO:0050728

negative regulation of inflammatory response

16213490

TgeneC1QTNF3

GO:0070165

positive regulation of adiponectin secretion

18421280

TgeneC1QTNF3

GO:0071638

negative regulation of monocyte chemotactic protein-1 production

20739398

TgeneC1QTNF3

GO:1900165

negative regulation of interleukin-6 secretion

16213490

TgeneC1QTNF3

GO:1901223

negative regulation of NIK/NF-kappaB signaling

16213490


check buttonFusion gene breakpoints across AMACR (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure
check buttonFusion gene breakpoints across C1QTNF3 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

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
ChimerDB4BLCATCGA-G2-A3VY-01AAMACRchr5

34004679

-C1QTNF3chr5

34020847

-
ChimerDB4LIHCTCGA-BC-A10Y-01AAMACRchr5

34004679

-C1QTNF3chr5

34028988

-


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Fusion Gene ORF analysis for AMACR-C1QTNF3

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-5UTRENST00000335606ENST00000513065AMACRchr5

34004679

-C1QTNF3chr5

34020847

-
5CDS-5UTRENST00000335606ENST00000513065AMACRchr5

34004679

-C1QTNF3chr5

34028988

-
5CDS-5UTRENST00000382085ENST00000513065AMACRchr5

34004679

-C1QTNF3chr5

34020847

-
5CDS-5UTRENST00000382085ENST00000513065AMACRchr5

34004679

-C1QTNF3chr5

34028988

-
5CDS-5UTRENST00000426255ENST00000513065AMACRchr5

34004679

-C1QTNF3chr5

34020847

-
5CDS-5UTRENST00000426255ENST00000513065AMACRchr5

34004679

-C1QTNF3chr5

34028988

-
5CDS-5UTRENST00000502637ENST00000513065AMACRchr5

34004679

-C1QTNF3chr5

34020847

-
5CDS-5UTRENST00000502637ENST00000513065AMACRchr5

34004679

-C1QTNF3chr5

34028988

-
5CDS-5UTRENST00000512079ENST00000513065AMACRchr5

34004679

-C1QTNF3chr5

34020847

-
5CDS-5UTRENST00000512079ENST00000513065AMACRchr5

34004679

-C1QTNF3chr5

34028988

-
Frame-shiftENST00000335606ENST00000231338AMACRchr5

34004679

-C1QTNF3chr5

34020847

-
Frame-shiftENST00000382085ENST00000231338AMACRchr5

34004679

-C1QTNF3chr5

34020847

-
Frame-shiftENST00000426255ENST00000231338AMACRchr5

34004679

-C1QTNF3chr5

34020847

-
Frame-shiftENST00000502637ENST00000231338AMACRchr5

34004679

-C1QTNF3chr5

34020847

-
Frame-shiftENST00000512079ENST00000231338AMACRchr5

34004679

-C1QTNF3chr5

34020847

-
In-frameENST00000335606ENST00000231338AMACRchr5

34004679

-C1QTNF3chr5

34028988

-
In-frameENST00000335606ENST00000382065AMACRchr5

34004679

-C1QTNF3chr5

34020847

-
In-frameENST00000335606ENST00000382065AMACRchr5

34004679

-C1QTNF3chr5

34028988

-
In-frameENST00000382085ENST00000231338AMACRchr5

34004679

-C1QTNF3chr5

34028988

-
In-frameENST00000382085ENST00000382065AMACRchr5

34004679

-C1QTNF3chr5

34020847

-
In-frameENST00000382085ENST00000382065AMACRchr5

34004679

-C1QTNF3chr5

34028988

-
In-frameENST00000426255ENST00000231338AMACRchr5

34004679

-C1QTNF3chr5

34028988

-
In-frameENST00000426255ENST00000382065AMACRchr5

34004679

-C1QTNF3chr5

34020847

-
In-frameENST00000426255ENST00000382065AMACRchr5

34004679

-C1QTNF3chr5

34028988

-
In-frameENST00000502637ENST00000231338AMACRchr5

34004679

-C1QTNF3chr5

34028988

-
In-frameENST00000502637ENST00000382065AMACRchr5

34004679

-C1QTNF3chr5

34020847

-
In-frameENST00000502637ENST00000382065AMACRchr5

34004679

-C1QTNF3chr5

34028988

-
In-frameENST00000512079ENST00000231338AMACRchr5

34004679

-C1QTNF3chr5

34028988

-
In-frameENST00000512079ENST00000382065AMACRchr5

34004679

-C1QTNF3chr5

34020847

-
In-frameENST00000512079ENST00000382065AMACRchr5

34004679

-C1QTNF3chr5

34028988

-
intron-3CDSENST00000382068ENST00000231338AMACRchr5

34004679

-C1QTNF3chr5

34020847

-
intron-3CDSENST00000382068ENST00000231338AMACRchr5

34004679

-C1QTNF3chr5

34028988

-
intron-3CDSENST00000382068ENST00000382065AMACRchr5

34004679

-C1QTNF3chr5

34020847

-
intron-3CDSENST00000382068ENST00000382065AMACRchr5

34004679

-C1QTNF3chr5

34028988

-
intron-3CDSENST00000382072ENST00000231338AMACRchr5

34004679

-C1QTNF3chr5

34020847

-
intron-3CDSENST00000382072ENST00000231338AMACRchr5

34004679

-C1QTNF3chr5

34028988

-
intron-3CDSENST00000382072ENST00000382065AMACRchr5

34004679

-C1QTNF3chr5

34020847

-
intron-3CDSENST00000382072ENST00000382065AMACRchr5

34004679

-C1QTNF3chr5

34028988

-
intron-3CDSENST00000441713ENST00000231338AMACRchr5

34004679

-C1QTNF3chr5

34020847

-
intron-3CDSENST00000441713ENST00000231338AMACRchr5

34004679

-C1QTNF3chr5

34028988

-
intron-3CDSENST00000441713ENST00000382065AMACRchr5

34004679

-C1QTNF3chr5

34020847

-
intron-3CDSENST00000441713ENST00000382065AMACRchr5

34004679

-C1QTNF3chr5

34028988

-
intron-3CDSENST00000514195ENST00000231338AMACRchr5

34004679

-C1QTNF3chr5

34020847

-
intron-3CDSENST00000514195ENST00000231338AMACRchr5

34004679

-C1QTNF3chr5

34028988

-
intron-3CDSENST00000514195ENST00000382065AMACRchr5

34004679

-C1QTNF3chr5

34020847

-
intron-3CDSENST00000514195ENST00000382065AMACRchr5

34004679

-C1QTNF3chr5

34028988

-
intron-5UTRENST00000382068ENST00000513065AMACRchr5

34004679

-C1QTNF3chr5

34020847

-
intron-5UTRENST00000382068ENST00000513065AMACRchr5

34004679

-C1QTNF3chr5

34028988

-
intron-5UTRENST00000382072ENST00000513065AMACRchr5

34004679

-C1QTNF3chr5

34020847

-
intron-5UTRENST00000382072ENST00000513065AMACRchr5

34004679

-C1QTNF3chr5

34028988

-
intron-5UTRENST00000441713ENST00000513065AMACRchr5

34004679

-C1QTNF3chr5

34020847

-
intron-5UTRENST00000441713ENST00000513065AMACRchr5

34004679

-C1QTNF3chr5

34028988

-
intron-5UTRENST00000514195ENST00000513065AMACRchr5

34004679

-C1QTNF3chr5

34020847

-
intron-5UTRENST00000514195ENST00000513065AMACRchr5

34004679

-C1QTNF3chr5

34028988

-

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 AMACR-C1QTNF3


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.
genomic feature

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Fusion Protein Features for AMACR-C1QTNF3


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/chr5:34004679/chr5:34020847)
- 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
AMACR

Q9UHK6

.
FUNCTION: Catalyzes the interconversion of (R)- and (S)-stereoisomers of alpha-methyl-branched-chain fatty acyl-CoA esters (PubMed:7649182, PubMed:10655068, PubMed:11060359). Acts only on coenzyme A thioesters, not on free fatty acids, and accepts as substrates a wide range of alpha-methylacyl-CoAs, including pristanoyl-CoA, trihydroxycoprostanoyl-CoA (an intermediate in bile acid synthesis), and arylpropionic acids like the anti-inflammatory drug ibuprofen (2-(4-isobutylphenyl)propionic acid) but neither 3-methyl-branched nor linear-chain acyl-CoAs (PubMed:7649182, PubMed:10655068, PubMed:11060359). {ECO:0000269|PubMed:10655068, ECO:0000269|PubMed:11060359, ECO:0000269|PubMed:7649182}.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
HgeneAMACRchr5:34004679chr5:34020847ENST00000335606-35121_126184383.0RegionSubstrate binding
HgeneAMACRchr5:34004679chr5:34020847ENST00000335606-3555_58184383.0RegionSubstrate binding
HgeneAMACRchr5:34004679chr5:34020847ENST00000382085-36121_126184395.0RegionSubstrate binding
HgeneAMACRchr5:34004679chr5:34020847ENST00000382085-3655_58184395.0RegionSubstrate binding
HgeneAMACRchr5:34004679chr5:34028988ENST00000335606-35121_126184383.0RegionSubstrate binding
HgeneAMACRchr5:34004679chr5:34028988ENST00000335606-3555_58184383.0RegionSubstrate binding
HgeneAMACRchr5:34004679chr5:34028988ENST00000382085-36121_126184395.0RegionSubstrate binding
HgeneAMACRchr5:34004679chr5:34028988ENST00000382085-3655_58184395.0RegionSubstrate binding

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneAMACRchr5:34004679chr5:34020847ENST00000335606-35380_382184383.0MotifMicrobody targeting signal
HgeneAMACRchr5:34004679chr5:34020847ENST00000382072-14380_3820199.0MotifMicrobody targeting signal
HgeneAMACRchr5:34004679chr5:34020847ENST00000382085-36380_382184395.0MotifMicrobody targeting signal
HgeneAMACRchr5:34004679chr5:34020847ENST00000441713-14380_3820230.0MotifMicrobody targeting signal
HgeneAMACRchr5:34004679chr5:34028988ENST00000335606-35380_382184383.0MotifMicrobody targeting signal
HgeneAMACRchr5:34004679chr5:34028988ENST00000382072-14380_3820199.0MotifMicrobody targeting signal
HgeneAMACRchr5:34004679chr5:34028988ENST00000382085-36380_382184395.0MotifMicrobody targeting signal
HgeneAMACRchr5:34004679chr5:34028988ENST00000441713-14380_3820230.0MotifMicrobody targeting signal
HgeneAMACRchr5:34004679chr5:34020847ENST00000382072-14121_1260199.0RegionSubstrate binding
HgeneAMACRchr5:34004679chr5:34020847ENST00000382072-1455_580199.0RegionSubstrate binding
HgeneAMACRchr5:34004679chr5:34020847ENST00000441713-14121_1260230.0RegionSubstrate binding
HgeneAMACRchr5:34004679chr5:34020847ENST00000441713-1455_580230.0RegionSubstrate binding
HgeneAMACRchr5:34004679chr5:34028988ENST00000382072-14121_1260199.0RegionSubstrate binding
HgeneAMACRchr5:34004679chr5:34028988ENST00000382072-1455_580199.0RegionSubstrate binding
HgeneAMACRchr5:34004679chr5:34028988ENST00000441713-14121_1260230.0RegionSubstrate binding
HgeneAMACRchr5:34004679chr5:34028988ENST00000441713-1455_580230.0RegionSubstrate binding
TgeneC1QTNF3chr5:34004679chr5:34020847ENST0000023133846113_246193247.0DomainC1q
TgeneC1QTNF3chr5:34004679chr5:34020847ENST000002313384651_113193247.0DomainNote=Collagen-like
TgeneC1QTNF3chr5:34004679chr5:34020847ENST0000038206546113_246266320.0DomainC1q
TgeneC1QTNF3chr5:34004679chr5:34020847ENST000003820654651_113266320.0DomainNote=Collagen-like
TgeneC1QTNF3chr5:34004679chr5:34028988ENST0000023133826113_246117247.0DomainC1q
TgeneC1QTNF3chr5:34004679chr5:34028988ENST000002313382651_113117247.0DomainNote=Collagen-like
TgeneC1QTNF3chr5:34004679chr5:34028988ENST0000038206526113_246190320.0DomainC1q
TgeneC1QTNF3chr5:34004679chr5:34028988ENST000003820652651_113190320.0DomainNote=Collagen-like


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Fusion Gene Sequence for AMACR-C1QTNF3


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 AMACR-C1QTNF3


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 AMACR-C1QTNF3


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 AMACR-C1QTNF3


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneAMACRC0033578Prostatic Neoplasms3CTD_human
HgeneAMACRC0376358Malignant neoplasm of prostate3CTD_human
HgeneAMACRC1858328Bile acid synthesis defect, congenital, 43CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneAMACRC3280428Alpha-Methylacyl-CoA Racemase Deficiency3CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneAMACRC0023893Liver Cirrhosis, Experimental2CTD_human
HgeneAMACRC0001430Adenoma1CTD_human
HgeneAMACRC0009402Colorectal Carcinoma1CTD_human
HgeneAMACRC0009404Colorectal Neoplasms1CTD_human
HgeneAMACRC0011195Dejerine-Sottas Disease (disorder)1CTD_human
HgeneAMACRC0019816Hereditary, Type VII, Motor and Sensory Neuropathy1CTD_human
HgeneAMACRC0023895Liver diseases1CTD_human
HgeneAMACRC0027888Hereditary Motor and Sensory Neuropathies1CTD_human
HgeneAMACRC0036341Schizophrenia1PSYGENET
HgeneAMACRC0086565Liver Dysfunction1CTD_human
HgeneAMACRC0205646Adenoma, Basal Cell1CTD_human
HgeneAMACRC0205647Follicular adenoma1CTD_human
HgeneAMACRC0205648Adenoma, Microcystic1CTD_human
HgeneAMACRC0205649Adenoma, Monomorphic1CTD_human
HgeneAMACRC0205650Papillary adenoma1CTD_human
HgeneAMACRC0205651Adenoma, Trabecular1CTD_human