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	Fusion Gene Summary
	Fusion Gene ORF analysis
	Fusion Genomic Features
	Fusion Protein Features
	Fusion Gene Sequence
	Fusion Gene PPI analysis
	Related Drugs
	Related Diseases

Fusion gene:SNX27-THEM4 (FusionGDB2 ID:84364)

Fusion Gene Summary for SNX27-THEM4

Fusion gene summary

Fusion gene information	Fusion gene name: SNX27-THEM4
	Fusion gene ID: 84364
		Hgene	Tgene
	Gene symbol	SNX27	THEM4
	Gene ID	81609	117145
	Gene name	sorting nexin 27	thioesterase superfamily member 4
	Synonyms	MRT1\|MY014	CTMP
	Cytomap	1q21.3	1q21.3
	Type of gene	protein-coding	protein-coding
	Description	sorting nexin-27methamphetamine-responsive transcript 1sorting nexin family member 27	acyl-coenzyme A thioesterase THEM4C-terminal modulator proteinacyl-CoA thioesterase THEM4carboxyl-terminal modulator protein
	Modification date	20200313	20200313
	UniProtAcc	.	.
	Ensembl transtripts involved in fusion gene	ENST00000458013, ENST00000368843, ENST00000368838, ENST00000482791,	ENST00000368814, ENST00000477437, ENST00000489410,
Fusion gene scores	* DoF score	15 X 9 X 10=1350	6 X 5 X 5=150
	# samples	16	7
	** MAII score	log2(16/1350*10)=-3.07681559705083 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(7/150*10)=-1.09953567355091 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context	PubMed: SNX27 [Title/Abstract] AND THEM4 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint	SNX27(151584988)-THEM4(151849601), # samples:3
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)

Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez

Partner	Gene	GO ID	GO term	PubMed ID
Tgene	THEM4	GO:0006631	fatty acid metabolic process	22871024

Fusion gene breakpoints across SNX27 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

Fusion gene breakpoints across THEM4 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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.

Source	Disease	Sample	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
ChimerDB4	BLCA	TCGA-ZF-AA4R-01A	SNX27	chr1	151584988	+	THEM4	chr1	151849601	-
ChimerDB4	BLCA	TCGA-ZF-AA4R	SNX27	chr1	151584988	+	THEM4	chr1	151849601	-
ChimerDB4	BLCA	TCGA-ZF-AA4R-01A	SNX27	chr1	151584988	+	THEM4	chr1	151849601	-

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Fusion Gene ORF analysis for SNX27-THEM4

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.

ORF	Henst	Tenst	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
In-frame	ENST00000458013	ENST00000368814	SNX27	chr1	151584988	+	THEM4	chr1	151849601	-
5CDS-5UTR	ENST00000458013	ENST00000477437	SNX27	chr1	151584988	+	THEM4	chr1	151849601	-
5CDS-intron	ENST00000458013	ENST00000489410	SNX27	chr1	151584988	+	THEM4	chr1	151849601	-
In-frame	ENST00000368843	ENST00000368814	SNX27	chr1	151584988	+	THEM4	chr1	151849601	-
5CDS-5UTR	ENST00000368843	ENST00000477437	SNX27	chr1	151584988	+	THEM4	chr1	151849601	-
5CDS-intron	ENST00000368843	ENST00000489410	SNX27	chr1	151584988	+	THEM4	chr1	151849601	-
intron-3CDS	ENST00000368838	ENST00000368814	SNX27	chr1	151584988	+	THEM4	chr1	151849601	-
intron-5UTR	ENST00000368838	ENST00000477437	SNX27	chr1	151584988	+	THEM4	chr1	151849601	-
intron-intron	ENST00000368838	ENST00000489410	SNX27	chr1	151584988	+	THEM4	chr1	151849601	-
intron-3CDS	ENST00000482791	ENST00000368814	SNX27	chr1	151584988	+	THEM4	chr1	151849601	-
intron-5UTR	ENST00000482791	ENST00000477437	SNX27	chr1	151584988	+	THEM4	chr1	151849601	-
intron-intron	ENST00000482791	ENST00000489410	SNX27	chr1	151584988	+	THEM4	chr1	151849601	-

ORFfinder result based on the fusion transcript sequence of in-frame fusion genes.

Henst

Tenst

Hgene

Hchr

Hbp

Hstrand

Tgene

Tchr

Tbp

Tstrand

Seq length
(transcript)

BP loci
(transcript)

Predicted start
(transcript)

Predicted stop
(transcript)

Seq length
(amino acids)

ENST00000458013

SNX27

chr1

151584988

ENST00000368814

THEM4

chr1

151849601

1901

431

120

596

158

ENST00000368843

SNX27

chr1

151584988

ENST00000368814

THEM4

chr1

151849601

1901

431

120

596

158

DeepORF 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.

Henst	Tenst	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	No-coding score	Coding score
ENST00000458013	ENST00000368814	SNX27	chr1	151584988	+	THEM4	chr1	151849601	-	0.007444006	0.99255604
ENST00000368843	ENST00000368814	SNX27	chr1	151584988	+	THEM4	chr1	151849601	-	0.007444006	0.99255604

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Fusion Genomic Features for SNX27-THEM4

FusionAI 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.

Hgene

Hchr

Hbp

Hstrand

Tgene

Tchr

Tbp

Tstrand

1-p

p (fusion gene breakpoint)

Distribution 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.

Distribution 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 SNX27-THEM4

Go to
FGviewer for the breakpoints of chr1:151584988-chr1:151849601
.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.

Main function of each fusion partner protein. (from UniProt)

Hgene	Tgene
.	.
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: 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.

Retention 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.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

Tgene

THEM4

chr1:151584988

chr1:151849601

ENST00000368814

206_207

185.66666666666666

241.0

Region

Note=Substrate binding

- In-frame and not-retained protein feature among the 13 regional features.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

Hgene

SNX27

chr1:151584988

chr1:151849601

ENST00000368838

161_269

0.0

436.0

Domain

Hgene

SNX27

chr1:151584988

chr1:151849601

ENST00000368838

43_136

0.0

436.0

Domain

PDZ

Hgene

SNX27

chr1:151584988

chr1:151849601

ENST00000368843

161_269

103.66666666666667

529.0

Domain

Hgene

SNX27

chr1:151584988

chr1:151849601

ENST00000368843

43_136

103.66666666666667

529.0

Domain

PDZ

Hgene

SNX27

chr1:151584988

chr1:151849601

ENST00000458013

161_269

103.66666666666667

542.0

Domain

Hgene

SNX27

chr1:151584988

chr1:151849601

ENST00000458013

43_136

103.66666666666667

542.0

Domain

PDZ

Hgene

SNX27

chr1:151584988

chr1:151849601

ENST00000368838

273_362

0.0

436.0

Region

Note=FERM-like region F1

Hgene

SNX27

chr1:151584988

chr1:151849601

ENST00000368838

373_421

0.0

436.0

Region

Note=FERM-like region F2

Hgene

SNX27

chr1:151584988

chr1:151849601

ENST00000368838

425_525

0.0

436.0

Region

Note=FERM-like region F3

Hgene

SNX27

chr1:151584988

chr1:151849601

ENST00000368843

273_362

103.66666666666667

529.0

Region

Note=FERM-like region F1

Hgene

SNX27

chr1:151584988

chr1:151849601

ENST00000368843

373_421

103.66666666666667

529.0

Region

Note=FERM-like region F2

Hgene

SNX27

chr1:151584988

chr1:151849601

ENST00000368843

425_525

103.66666666666667

529.0

Region

Note=FERM-like region F3

Hgene

SNX27

chr1:151584988

chr1:151849601

ENST00000458013

273_362

103.66666666666667

542.0

Region

Note=FERM-like region F1

Hgene

SNX27

chr1:151584988

chr1:151849601

ENST00000458013

373_421

103.66666666666667

542.0

Region

Note=FERM-like region F2

Hgene

SNX27

chr1:151584988

chr1:151849601

ENST00000458013

425_525

103.66666666666667

542.0

Region

Note=FERM-like region F3

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Fusion Gene Sequence for SNX27-THEM4

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.

>In-frame_ENST00000458013_ENST00000368814_TCGA-ZF-AA4R-01A_SNX27_chr1_151584988_+_THEM4_chr1_151849601_length(transcript)=1901nt_BP=431nt
TCCCGCGGCCGGCGGATCGGGCGCGCGCGTCGGGGGTCGTCCGGCTGCCAGGCAGGGCGAGCACGCGCCGGGAGGCCTTGGAGGCGTAGG
GGGCGGGGGTACGGCTCGCCTGCTCGCAAGATGGCGGACGAGGACGGGGAAGGGATTCATCCCTCAGCCCCTCACAGGAACGGAGGTGGC
GGCGGCGGCGGGGGGTCTGGGCTCCACTGCGCCGGGAACGGCGGCGGGGGAGGCGGCGGCCCGCGGGTCGTGCGCATCGTCAAGTCCGAG
TCCGGCTACGGCTTCAACGTGCGGGGCCAAGTGAGCGAGGGCGGGCAACTGCGGAGCATCAACGGGGAGCTGTACGCGCCGCTGCAGCAT
GTGAGCGCCGTGCTGCCCGGGGGGGCGGCCGATCGGGCCGGGGTGCGCAAGGGGGACCGCATCCTGGAGGTACCTATCCCTCTTTGTTCT
GTTGTTATGATAAATAGCCAACTTGATAAAGTTGAAGGAAGGAAATTTTTTGTTTCCTGTAATGTTCAGAGTGTTGATGAGAAGACCCTA
TACTCAGAGGCGACAAGCTTATTTATAAAGCTGAATCCTGCTAAAAGTCTGACATAAAGAGCTGCTGGTGAACTCCATCTCATTCTCGCC
CCTCCAGAAGAAGCAGTTGTCCCCCAAATACTCTGCTCCCTCACTGCTGAATCCCTGTAGGGAGAAGCCTGCCAACAGTGACCTTCCGAA
ACAGCCTTCTGAATACAAAGAGGATTCAGTTTCCATCTTCTCAACTTTTTAACACAGAAATACTTCCTGCGAGCATATCGACAACTCTCG
GGCCAGGCGCTGTGGCTCACACCTATAATCCCAGCACTTTAGGAGGCCGAGGCAGGCGGATTGCCTGAGCTCAGGAGTTCAAGATCAGTC
TGGGCAACACGATGAAACTCCGTCTCTACTAAAATACAAAAAATTATCCAGGCATGGTGGCGTACGCCTGTAGTCCCAGCTACTCAGGAG
GCTGAGGCAGGAGAATTGCTTGAACCCAGGAGGAAGAGGTTGCAGTGAGCCAAGATCATGCCACATCACTCCAACCTGGGCAACAGAACA
AGAACCCATCTCAAACAAACAAACAAACAAAAAAAAAAAACTCTTGTCTCCTTAGGATATGTTACCTGCTCCACTGCAGACTAGAGAAAT
AAATGTGTATTGAACCTTTTACTGCAAACTTGAAAATGCTAGAAAACCAAGCATGAAGAATAAATACATGGTGGGAAACACACAGGCATG
TGCATATGCATATACATTGTAAGTTAGTAAGTTAGAAAGCTAGCTTTGTTGTATCTGAACACATGAATCTTTTTTGGTCAGTGTAGGAAG
CACAGCCAGATCCTATAGGAATGAATACCTCAAATCTGTTGTCTGAGATTCTAGAGATTAAACCACTGTGCCATTTTTAACCCAGGCTGT
ACTGTTGTTTCTTACCAACAGCATAGGTTTTCATCACTGGAAGGAGCCTGTGTTCATTTCCTAGGGCTGCTGTAGCAAAGTAGTACAAAC
TGGATTGTTTAAACCAACAAAAACTCATTGTCTCTCAGTTCTGGAGGCCAGAAGTTCAAAATCAAGGTGTTGACCAAGGCCATTCTCCTG
AAAGTGCTAGGGAAGGAGCTGTCCACGCCTCCCTCCTGGCTTCTGGGAGCCTCAGGTGTTCCTTGGCTTCTAGATGCATCATTCCAGTCC
TCCATCTTCACATGGCATTCCCTCTGTGTGTCTCCACAGTGTCTTCCCTCTGTGCAGATCTATCTCTGTGTCCAAGTCTCCTCTTTTTAT
AAGGAAACCAGTCATAATGGACCCACCTGAATGACCTCATTTTAACTTGATTACCTCTGTAAAAAATGTATTTCCAAATAAAGTGACCTT

>In-frame_ENST00000458013_ENST00000368814_TCGA-ZF-AA4R-01A_SNX27_chr1_151584988_+_THEM4_chr1_151849601_length(amino acids)=158AA_start in transcript=120_stop in transcript=596
MADEDGEGIHPSAPHRNGGGGGGGGSGLHCAGNGGGGGGGPRVVRIVKSESGYGFNVRGQVSEGGQLRSINGELYAPLQHVSAVLPGGAA

--------------------------------------------------------------
>In-frame_ENST00000368843_ENST00000368814_TCGA-ZF-AA4R-01A_SNX27_chr1_151584988_+_THEM4_chr1_151849601_length(transcript)=1901nt_BP=431nt
TCCCGCGGCCGGCGGATCGGGCGCGCGCGTCGGGGGTCGTCCGGCTGCCAGGCAGGGCGAGCACGCGCCGGGAGGCCTTGGAGGCGTAGG
GGGCGGGGGTACGGCTCGCCTGCTCGCAAGATGGCGGACGAGGACGGGGAAGGGATTCATCCCTCAGCCCCTCACAGGAACGGAGGTGGC
GGCGGCGGCGGGGGGTCTGGGCTCCACTGCGCCGGGAACGGCGGCGGGGGAGGCGGCGGCCCGCGGGTCGTGCGCATCGTCAAGTCCGAG
TCCGGCTACGGCTTCAACGTGCGGGGCCAAGTGAGCGAGGGCGGGCAACTGCGGAGCATCAACGGGGAGCTGTACGCGCCGCTGCAGCAT
GTGAGCGCCGTGCTGCCCGGGGGGGCGGCCGATCGGGCCGGGGTGCGCAAGGGGGACCGCATCCTGGAGGTACCTATCCCTCTTTGTTCT
GTTGTTATGATAAATAGCCAACTTGATAAAGTTGAAGGAAGGAAATTTTTTGTTTCCTGTAATGTTCAGAGTGTTGATGAGAAGACCCTA
TACTCAGAGGCGACAAGCTTATTTATAAAGCTGAATCCTGCTAAAAGTCTGACATAAAGAGCTGCTGGTGAACTCCATCTCATTCTCGCC
CCTCCAGAAGAAGCAGTTGTCCCCCAAATACTCTGCTCCCTCACTGCTGAATCCCTGTAGGGAGAAGCCTGCCAACAGTGACCTTCCGAA
ACAGCCTTCTGAATACAAAGAGGATTCAGTTTCCATCTTCTCAACTTTTTAACACAGAAATACTTCCTGCGAGCATATCGACAACTCTCG
GGCCAGGCGCTGTGGCTCACACCTATAATCCCAGCACTTTAGGAGGCCGAGGCAGGCGGATTGCCTGAGCTCAGGAGTTCAAGATCAGTC
TGGGCAACACGATGAAACTCCGTCTCTACTAAAATACAAAAAATTATCCAGGCATGGTGGCGTACGCCTGTAGTCCCAGCTACTCAGGAG
GCTGAGGCAGGAGAATTGCTTGAACCCAGGAGGAAGAGGTTGCAGTGAGCCAAGATCATGCCACATCACTCCAACCTGGGCAACAGAACA
AGAACCCATCTCAAACAAACAAACAAACAAAAAAAAAAAACTCTTGTCTCCTTAGGATATGTTACCTGCTCCACTGCAGACTAGAGAAAT
AAATGTGTATTGAACCTTTTACTGCAAACTTGAAAATGCTAGAAAACCAAGCATGAAGAATAAATACATGGTGGGAAACACACAGGCATG
TGCATATGCATATACATTGTAAGTTAGTAAGTTAGAAAGCTAGCTTTGTTGTATCTGAACACATGAATCTTTTTTGGTCAGTGTAGGAAG
CACAGCCAGATCCTATAGGAATGAATACCTCAAATCTGTTGTCTGAGATTCTAGAGATTAAACCACTGTGCCATTTTTAACCCAGGCTGT
ACTGTTGTTTCTTACCAACAGCATAGGTTTTCATCACTGGAAGGAGCCTGTGTTCATTTCCTAGGGCTGCTGTAGCAAAGTAGTACAAAC
TGGATTGTTTAAACCAACAAAAACTCATTGTCTCTCAGTTCTGGAGGCCAGAAGTTCAAAATCAAGGTGTTGACCAAGGCCATTCTCCTG
AAAGTGCTAGGGAAGGAGCTGTCCACGCCTCCCTCCTGGCTTCTGGGAGCCTCAGGTGTTCCTTGGCTTCTAGATGCATCATTCCAGTCC
TCCATCTTCACATGGCATTCCCTCTGTGTGTCTCCACAGTGTCTTCCCTCTGTGCAGATCTATCTCTGTGTCCAAGTCTCCTCTTTTTAT
AAGGAAACCAGTCATAATGGACCCACCTGAATGACCTCATTTTAACTTGATTACCTCTGTAAAAAATGTATTTCCAAATAAAGTGACCTT

>In-frame_ENST00000368843_ENST00000368814_TCGA-ZF-AA4R-01A_SNX27_chr1_151584988_+_THEM4_chr1_151849601_length(amino acids)=158AA_start in transcript=120_stop in transcript=596
MADEDGEGIHPSAPHRNGGGGGGGGSGLHCAGNGGGGGGGPRVVRIVKSESGYGFNVRGQVSEGGQLRSINGELYAPLQHVSAVLPGGAA

--------------------------------------------------------------

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Fusion Gene PPI Analysis for SNX27-THEM4

Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in
ChiPPI page.

Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160)

Hgene

Hgene's interactors

Tgene

Tgene's interactors

- Retained PPIs in in-frame fusion.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Still interaction with

- Lost PPIs in in-frame fusion.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Interaction lost with

- Retained PPIs, but lost function due to frame-shift fusion.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Interaction lost with

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Related Drugs for SNX27-THEM4

Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)

Partner

Gene

UniProtAcc

DrugBank ID

Drug name

Drug activity

Drug type

Drug status

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Related Diseases for SNX27-THEM4

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner	Gene	Disease ID	Disease name	# pubmeds	Source
Hgene	SNX27	C0036572	Seizures	1	GENOMICS_ENGLAND
Hgene	SNX27	C0557874	Global developmental delay	1	GENOMICS_ENGLAND
Hgene	SNX27	C1858120	Generalized hypotonia	1	GENOMICS_ENGLAND
Hgene	SNX27	C3714756	Intellectual Disability	1	GENOMICS_ENGLAND
Tgene	THEM4	C2239176	Liver carcinoma	1	CTD_human