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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:SHMT2-NDUFA4L2 (FusionGDB2 ID:81726)

Fusion Gene Summary for SHMT2-NDUFA4L2

check button Fusion gene summary
Fusion gene informationFusion gene name: SHMT2-NDUFA4L2
Fusion gene ID: 81726
HgeneTgene
Gene symbol

SHMT2

NDUFA4L2

Gene ID

6472

56901

Gene nameserine hydroxymethyltransferase 2NDUFA4 mitochondrial complex associated like 2
SynonymsGLYA|HEL-S-51e|SHMTCOXFA4L2|NUOMS
Cytomap

12q13.3

12q13.3

Type of geneprotein-codingprotein-coding
Descriptionserine hydroxymethyltransferase, mitochondrialGLY A+epididymis secretory sperm binding protein Li 51eglycine auxotroph A, human complement for hamsterglycine hydroxymethyltransferaseserine aldolaseserine hydroxymethylaseserine hydroxymethyltransferNADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 4-like 2NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 4-like 2NADH:ubiquinone oxidoreductase MLRQ subunit homologcytochrome c oxidase subunit FA4 like 2
Modification date2020032720200329
UniProtAcc.

Q9NRX3

Ensembl transtripts involved in fusion geneENST00000554600, ENST00000328923, 
ENST00000414700, ENST00000449049, 
ENST00000553474, ENST00000557487, 
ENST00000393827, 		ENST00000393825, 
ENST00000554503, ENST00000556732, 
ENST00000557276, 
Fusion gene scores* DoF score7 X 6 X 4=1682 X 3 X 2=12
# samples 83
** MAII scorelog2(8/168*10)=-1.0703893278914
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(3/12*10)=1.32192809488736
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: SHMT2 [Title/Abstract] AND NDUFA4L2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointSHMT2(57624783)-NDUFA4L2(57629592), # samples:1
SHMT2(57628729)-NDUFA4L2(57628731), # samples:1
Anticipated loss of major functional domain due to fusion event.SHMT2-NDUFA4L2 seems lost the major protein functional domain in Hgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
SHMT2-NDUFA4L2 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
HgeneSHMT2

GO:0006544

glycine metabolic process

25619277|29180469

HgeneSHMT2

GO:0006563

L-serine metabolic process

25619277|29180469

HgeneSHMT2

GO:0006730

one-carbon metabolic process

11516159|29180469|29364879|29452640

HgeneSHMT2

GO:0034340

response to type I interferon

24075985

HgeneSHMT2

GO:0046653

tetrahydrofolate metabolic process

24075985|25619277

HgeneSHMT2

GO:0051262

protein tetramerization

25619277

HgeneSHMT2

GO:0051289

protein homotetramerization

29180469


check buttonFusion gene breakpoints across SHMT2 (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 NDUFA4L2 (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
ChimerDB4KIRCTCGA-CZ-5465-01ASHMT2chr12

57624783

+NDUFA4L2chr12

57629592

-
ChiTaRS5.0N/ABG236790SHMT2chr12

57628729

+NDUFA4L2chr12

57628731

+


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Fusion Gene ORF analysis for SHMT2-NDUFA4L2

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
3UTR-3CDSENST00000554600ENST00000393825SHMT2chr12

57624783

+NDUFA4L2chr12

57629592

-
3UTR-3CDSENST00000554600ENST00000554503SHMT2chr12

57624783

+NDUFA4L2chr12

57629592

-
3UTR-3CDSENST00000554600ENST00000556732SHMT2chr12

57624783

+NDUFA4L2chr12

57629592

-
3UTR-intronENST00000554600ENST00000557276SHMT2chr12

57624783

+NDUFA4L2chr12

57629592

-
5CDS-intronENST00000328923ENST00000557276SHMT2chr12

57624783

+NDUFA4L2chr12

57629592

-
5CDS-intronENST00000414700ENST00000557276SHMT2chr12

57624783

+NDUFA4L2chr12

57629592

-
5CDS-intronENST00000449049ENST00000557276SHMT2chr12

57624783

+NDUFA4L2chr12

57629592

-
5CDS-intronENST00000553474ENST00000557276SHMT2chr12

57624783

+NDUFA4L2chr12

57629592

-
5CDS-intronENST00000557487ENST00000557276SHMT2chr12

57624783

+NDUFA4L2chr12

57629592

-
5UTR-3CDSENST00000393827ENST00000393825SHMT2chr12

57624783

+NDUFA4L2chr12

57629592

-
5UTR-3CDSENST00000393827ENST00000554503SHMT2chr12

57624783

+NDUFA4L2chr12

57629592

-
5UTR-3CDSENST00000393827ENST00000556732SHMT2chr12

57624783

+NDUFA4L2chr12

57629592

-
5UTR-intronENST00000393827ENST00000557276SHMT2chr12

57624783

+NDUFA4L2chr12

57629592

-
Frame-shiftENST00000328923ENST00000393825SHMT2chr12

57624783

+NDUFA4L2chr12

57629592

-
Frame-shiftENST00000328923ENST00000554503SHMT2chr12

57624783

+NDUFA4L2chr12

57629592

-
Frame-shiftENST00000414700ENST00000393825SHMT2chr12

57624783

+NDUFA4L2chr12

57629592

-
Frame-shiftENST00000414700ENST00000554503SHMT2chr12

57624783

+NDUFA4L2chr12

57629592

-
Frame-shiftENST00000449049ENST00000393825SHMT2chr12

57624783

+NDUFA4L2chr12

57629592

-
Frame-shiftENST00000449049ENST00000554503SHMT2chr12

57624783

+NDUFA4L2chr12

57629592

-
Frame-shiftENST00000553474ENST00000393825SHMT2chr12

57624783

+NDUFA4L2chr12

57629592

-
Frame-shiftENST00000553474ENST00000554503SHMT2chr12

57624783

+NDUFA4L2chr12

57629592

-
Frame-shiftENST00000557487ENST00000393825SHMT2chr12

57624783

+NDUFA4L2chr12

57629592

-
Frame-shiftENST00000557487ENST00000554503SHMT2chr12

57624783

+NDUFA4L2chr12

57629592

-
In-frameENST00000328923ENST00000556732SHMT2chr12

57624783

+NDUFA4L2chr12

57629592

-
In-frameENST00000414700ENST00000556732SHMT2chr12

57624783

+NDUFA4L2chr12

57629592

-
In-frameENST00000449049ENST00000556732SHMT2chr12

57624783

+NDUFA4L2chr12

57629592

-
In-frameENST00000553474ENST00000556732SHMT2chr12

57624783

+NDUFA4L2chr12

57629592

-
In-frameENST00000557487ENST00000556732SHMT2chr12

57624783

+NDUFA4L2chr12

57629592

-
intron-3UTRENST00000328923ENST00000393825SHMT2chr12

57628729

+NDUFA4L2chr12

57628731

+
intron-3UTRENST00000328923ENST00000554503SHMT2chr12

57628729

+NDUFA4L2chr12

57628731

+
intron-3UTRENST00000393827ENST00000393825SHMT2chr12

57628729

+NDUFA4L2chr12

57628731

+
intron-3UTRENST00000393827ENST00000554503SHMT2chr12

57628729

+NDUFA4L2chr12

57628731

+
intron-3UTRENST00000414700ENST00000393825SHMT2chr12

57628729

+NDUFA4L2chr12

57628731

+
intron-3UTRENST00000414700ENST00000554503SHMT2chr12

57628729

+NDUFA4L2chr12

57628731

+
intron-3UTRENST00000449049ENST00000393825SHMT2chr12

57628729

+NDUFA4L2chr12

57628731

+
intron-3UTRENST00000449049ENST00000554503SHMT2chr12

57628729

+NDUFA4L2chr12

57628731

+
intron-3UTRENST00000553474ENST00000393825SHMT2chr12

57628729

+NDUFA4L2chr12

57628731

+
intron-3UTRENST00000553474ENST00000554503SHMT2chr12

57628729

+NDUFA4L2chr12

57628731

+
intron-3UTRENST00000554600ENST00000393825SHMT2chr12

57628729

+NDUFA4L2chr12

57628731

+
intron-3UTRENST00000554600ENST00000554503SHMT2chr12

57628729

+NDUFA4L2chr12

57628731

+
intron-3UTRENST00000557487ENST00000393825SHMT2chr12

57628729

+NDUFA4L2chr12

57628731

+
intron-3UTRENST00000557487ENST00000554503SHMT2chr12

57628729

+NDUFA4L2chr12

57628731

+
intron-intronENST00000328923ENST00000556732SHMT2chr12

57628729

+NDUFA4L2chr12

57628731

+
intron-intronENST00000328923ENST00000557276SHMT2chr12

57628729

+NDUFA4L2chr12

57628731

+
intron-intronENST00000393827ENST00000556732SHMT2chr12

57628729

+NDUFA4L2chr12

57628731

+
intron-intronENST00000393827ENST00000557276SHMT2chr12

57628729

+NDUFA4L2chr12

57628731

+
intron-intronENST00000414700ENST00000556732SHMT2chr12

57628729

+NDUFA4L2chr12

57628731

+
intron-intronENST00000414700ENST00000557276SHMT2chr12

57628729

+NDUFA4L2chr12

57628731

+
intron-intronENST00000449049ENST00000556732SHMT2chr12

57628729

+NDUFA4L2chr12

57628731

+
intron-intronENST00000449049ENST00000557276SHMT2chr12

57628729

+NDUFA4L2chr12

57628731

+
intron-intronENST00000553474ENST00000556732SHMT2chr12

57628729

+NDUFA4L2chr12

57628731

+
intron-intronENST00000553474ENST00000557276SHMT2chr12

57628729

+NDUFA4L2chr12

57628731

+
intron-intronENST00000554600ENST00000556732SHMT2chr12

57628729

+NDUFA4L2chr12

57628731

+
intron-intronENST00000554600ENST00000557276SHMT2chr12

57628729

+NDUFA4L2chr12

57628731

+
intron-intronENST00000557487ENST00000556732SHMT2chr12

57628729

+NDUFA4L2chr12

57628731

+
intron-intronENST00000557487ENST00000557276SHMT2chr12

57628729

+NDUFA4L2chr12

57628731

+

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 SHMT2-NDUFA4L2


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

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 SHMT2-NDUFA4L2


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/chr12:57624783/chr12:57629592)
- 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
.NDUFA4L2

Q9NRX3

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 SHMT2-NDUFA4L2


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 SHMT2-NDUFA4L2


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 SHMT2-NDUFA4L2


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 SHMT2-NDUFA4L2


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