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	Fusion Gene Summary
	Fusion Gene Sample Information
	Fusion ORF Analysis
	Fusion Amino Acid Sequences
	Fusion Protein Functional Features
	Fusion Protein-Protein Interaction
	Related drugs with this fusion protein
	Related disease with this fusion protein

Fusion Protein:TMEM241-SNX29

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: TMEM241-SNX29
	FusionPDB ID: 91964
	FusionGDB2.0 ID: 91964
		Hgene	Tgene
	Gene symbol	TMEM241	SNX29
	Gene ID	85019	92017
	Gene name	transmembrane protein 241	sorting nexin 29
	Synonyms	C18orf45\|hVVT	A-388D4.1\|RUNDC2A
	Cytomap	18q11.2	16p13.13-p13.12
	Type of gene	protein-coding	protein-coding
	Description	transmembrane protein 241putative vertebrate vrg4-like nucleotide-sugar transporter truncated variant2putative vertebrate vrg4-like nucleotide-sugar transporter variant1transmembrane protein C18orf45	sorting nexin-29RUN domain containing 2ARUN domain-containing protein 2A
	Modification date	20200313	20200313
	UniProtAcc	Q24JQ0	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000383233, ENST00000399707, ENST00000542162, ENST00000450466, ENST00000475185,	ENST00000568359, ENST00000306030, ENST00000323433, ENST00000566228,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	11 X 10 X 9=990	15 X 15 X 6=1350
	# samples	13	16
	** MAII score	log2(13/990*10)=-2.92891690193852 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(16/1350*10)=-3.07681559705083 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)	PubMed: TMEM241 [Title/Abstract] AND SNX29 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	TMEM241(20979530)-SNX29(12492303), # samples:1
Anticipated loss of major functional domain due to fusion event.	TMEM241-SNX29 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. TMEM241-SNX29 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. TMEM241-SNX29 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. TMEM241-SNX29 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.

* 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

Fusion gene breakpoints across TMEM241 (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 SNX29 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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Fusion Gene Sample Information

Fusion gene information from FusionGDB2.0.

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	LUAD	TCGA-MP-A5C7-01A	TMEM241	chr18	20979530	-	SNX29	chr16	12492303	+

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Fusion ORF Analysis

Fusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.

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)
ENST00000383233	TMEM241	chr18	20979530	-	ENST00000566228	SNX29	chr16	12492303	+	6535	332	53	874	273
ENST00000383233	TMEM241	chr18	20979530	-	ENST00000323433	SNX29	chr16	12492303	+	815	332	53	814	254
ENST00000383233	TMEM241	chr18	20979530	-	ENST00000306030	SNX29	chr16	12492303	+	6534	332	53	874	273
ENST00000542162	TMEM241	chr18	20979530	-	ENST00000566228	SNX29	chr16	12492303	+	6483	280	1	822	273
ENST00000542162	TMEM241	chr18	20979530	-	ENST00000323433	SNX29	chr16	12492303	+	763	280	1	762	254
ENST00000542162	TMEM241	chr18	20979530	-	ENST00000306030	SNX29	chr16	12492303	+	6482	280	1	822	273
ENST00000399707	TMEM241	chr18	20979530	-	ENST00000566228	SNX29	chr16	12492303	+	6513	310	109	852	247
ENST00000399707	TMEM241	chr18	20979530	-	ENST00000323433	SNX29	chr16	12492303	+	793	310	109	792	228
ENST00000399707	TMEM241	chr18	20979530	-	ENST00000306030	SNX29	chr16	12492303	+	6512	310	109	852	247

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
ENST00000383233	ENST00000566228	TMEM241	chr18	20979530	-	SNX29	chr16	12492303	+	0.007532002	0.99246794
ENST00000383233	ENST00000323433	TMEM241	chr18	20979530	-	SNX29	chr16	12492303	+	0.01242299	0.9875771
ENST00000383233	ENST00000306030	TMEM241	chr18	20979530	-	SNX29	chr16	12492303	+	0.007741166	0.99225885
ENST00000542162	ENST00000566228	TMEM241	chr18	20979530	-	SNX29	chr16	12492303	+	0.007419704	0.99258035
ENST00000542162	ENST00000323433	TMEM241	chr18	20979530	-	SNX29	chr16	12492303	+	0.011486298	0.98851365
ENST00000542162	ENST00000306030	TMEM241	chr18	20979530	-	SNX29	chr16	12492303	+	0.007625644	0.99237436
ENST00000399707	ENST00000566228	TMEM241	chr18	20979530	-	SNX29	chr16	12492303	+	0.008210811	0.9917891
ENST00000399707	ENST00000323433	TMEM241	chr18	20979530	-	SNX29	chr16	12492303	+	0.007641523	0.9923585
ENST00000399707	ENST00000306030	TMEM241	chr18	20979530	-	SNX29	chr16	12492303	+	0.00856771	0.9914323

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Fusion Amino Acid Sequences

For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones.

>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

>91964_91964_1_TMEM241-SNX29_TMEM241_chr18_20979530_ENST00000383233_SNX29_chr16_12492303_ENST00000306030_length(amino acids)=273AA_BP=93
MCVRRSLVGLTFCTCYLASYLTNKYVLSVLKFTYPTLFQGWQTLIGGLLLHVSWKLGWVEINSSSRSHVLVWLPASVLFVGIIYAGSRAL
SRLVPGDLSQTSEDQSLSDFEISNRALINVWIPSVFLRGKAANAFHVYQVYIRIKDDEWNIYRRYTEFRSLHHKLQNKYPQVRAYNFPPK
KAIGNKDAKFVEERRKQLQNYLRSVMNKVIQMVPEFAASPKKETLIQLMPFFVDITPPGEPVNSRPKAASRFPKLSRGQPRETRNVEPQS

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

>91964_91964_2_TMEM241-SNX29_TMEM241_chr18_20979530_ENST00000383233_SNX29_chr16_12492303_ENST00000323433_length(amino acids)=254AA_BP=93
MCVRRSLVGLTFCTCYLASYLTNKYVLSVLKFTYPTLFQGWQTLIGGLLLHVSWKLGWVEINSSSRSHVLVWLPASVLFVGIIYAGSRAL
SRLVPGDLSQTSEDQSLSDFEISNRALINVWIPSVFLRGKAANAFHVYQVYIRIKDDEWNIYRRYTEFRSLHHKLQNKYPQVRAYNFPPK

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

>91964_91964_3_TMEM241-SNX29_TMEM241_chr18_20979530_ENST00000383233_SNX29_chr16_12492303_ENST00000566228_length(amino acids)=273AA_BP=93
MCVRRSLVGLTFCTCYLASYLTNKYVLSVLKFTYPTLFQGWQTLIGGLLLHVSWKLGWVEINSSSRSHVLVWLPASVLFVGIIYAGSRAL
SRLVPGDLSQTSEDQSLSDFEISNRALINVWIPSVFLRGKAANAFHVYQVYIRIKDDEWNIYRRYTEFRSLHHKLQNKYPQVRAYNFPPK
KAIGNKDAKFVEERRKQLQNYLRSVMNKVIQMVPEFAASPKKETLIQLMPFFVDITPPGEPVNSRPKAASRFPKLSRGQPRETRNVEPQS

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

>91964_91964_4_TMEM241-SNX29_TMEM241_chr18_20979530_ENST00000399707_SNX29_chr16_12492303_ENST00000306030_length(amino acids)=247AA_BP=67
MCVRRSLVGLTFCTCYLASYLTNKYVLSVLKFTYPTLFQGSHVLVWLPASVLFVGIIYAGSRALSRLVPGDLSQTSEDQSLSDFEISNRA
LINVWIPSVFLRGKAANAFHVYQVYIRIKDDEWNIYRRYTEFRSLHHKLQNKYPQVRAYNFPPKKAIGNKDAKFVEERRKQLQNYLRSVM

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

>91964_91964_5_TMEM241-SNX29_TMEM241_chr18_20979530_ENST00000399707_SNX29_chr16_12492303_ENST00000323433_length(amino acids)=228AA_BP=67
MCVRRSLVGLTFCTCYLASYLTNKYVLSVLKFTYPTLFQGSHVLVWLPASVLFVGIIYAGSRALSRLVPGDLSQTSEDQSLSDFEISNRA
LINVWIPSVFLRGKAANAFHVYQVYIRIKDDEWNIYRRYTEFRSLHHKLQNKYPQVRAYNFPPKKAIGNKDAKFVEERRKQLQNYLRSVM

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

>91964_91964_6_TMEM241-SNX29_TMEM241_chr18_20979530_ENST00000399707_SNX29_chr16_12492303_ENST00000566228_length(amino acids)=247AA_BP=67
MCVRRSLVGLTFCTCYLASYLTNKYVLSVLKFTYPTLFQGSHVLVWLPASVLFVGIIYAGSRALSRLVPGDLSQTSEDQSLSDFEISNRA
LINVWIPSVFLRGKAANAFHVYQVYIRIKDDEWNIYRRYTEFRSLHHKLQNKYPQVRAYNFPPKKAIGNKDAKFVEERRKQLQNYLRSVM

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

>91964_91964_7_TMEM241-SNX29_TMEM241_chr18_20979530_ENST00000542162_SNX29_chr16_12492303_ENST00000306030_length(amino acids)=273AA_BP=93
MCVRRSLVGLTFCTCYLASYLTNKYVLSVLKFTYPTLFQGWQTLIGGLLLHVSWKLGWVEINSSSRSHVLVWLPASVLFVGIIYAGSRAL
SRLVPGDLSQTSEDQSLSDFEISNRALINVWIPSVFLRGKAANAFHVYQVYIRIKDDEWNIYRRYTEFRSLHHKLQNKYPQVRAYNFPPK
KAIGNKDAKFVEERRKQLQNYLRSVMNKVIQMVPEFAASPKKETLIQLMPFFVDITPPGEPVNSRPKAASRFPKLSRGQPRETRNVEPQS

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

>91964_91964_8_TMEM241-SNX29_TMEM241_chr18_20979530_ENST00000542162_SNX29_chr16_12492303_ENST00000323433_length(amino acids)=254AA_BP=93
MCVRRSLVGLTFCTCYLASYLTNKYVLSVLKFTYPTLFQGWQTLIGGLLLHVSWKLGWVEINSSSRSHVLVWLPASVLFVGIIYAGSRAL
SRLVPGDLSQTSEDQSLSDFEISNRALINVWIPSVFLRGKAANAFHVYQVYIRIKDDEWNIYRRYTEFRSLHHKLQNKYPQVRAYNFPPK

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

>91964_91964_9_TMEM241-SNX29_TMEM241_chr18_20979530_ENST00000542162_SNX29_chr16_12492303_ENST00000566228_length(amino acids)=273AA_BP=93
MCVRRSLVGLTFCTCYLASYLTNKYVLSVLKFTYPTLFQGWQTLIGGLLLHVSWKLGWVEINSSSRSHVLVWLPASVLFVGIIYAGSRAL
SRLVPGDLSQTSEDQSLSDFEISNRALINVWIPSVFLRGKAANAFHVYQVYIRIKDDEWNIYRRYTEFRSLHHKLQNKYPQVRAYNFPPK
KAIGNKDAKFVEERRKQLQNYLRSVMNKVIQMVPEFAASPKKETLIQLMPFFVDITPPGEPVNSRPKAASRFPKLSRGQPRETRNVEPQS

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

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Fusion Protein Functional Features

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr18:20979530/chr16:12492303)
- 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.

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

Hgene	Tgene
TMEM241 Q24JQ0	.
	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.

- 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

TMEM241

chr18:20979530

chr16:12492303

ENST00000383233

32_52

93.0

297.0

Transmembrane

Helical

Hgene

TMEM241

chr18:20979530

chr16:12492303

ENST00000383233

67_87

93.0

297.0

Transmembrane

Helical

Hgene

TMEM241

chr18:20979530

chr16:12492303

ENST00000383233

7_29

93.0

297.0

Transmembrane

Helical

Hgene

TMEM241

chr18:20979530

chr16:12492303

ENST00000399707

32_52

67.0

124.0

Transmembrane

Helical

Hgene

TMEM241

chr18:20979530

chr16:12492303

ENST00000399707

7_29

67.0

124.0

Transmembrane

Helical

Tgene

SNX29

chr18:20979530

chr16:12492303

ENST00000566228

656_779

633.0

814.0

Domain

- 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

TMEM241

chr18:20979530

chr16:12492303

ENST00000383233

121_141

93.0

297.0

Transmembrane

Helical

Hgene

TMEM241

chr18:20979530

chr16:12492303

ENST00000383233

146_166

93.0

297.0

Transmembrane

Helical

Hgene

TMEM241

chr18:20979530

chr16:12492303

ENST00000383233

187_207

93.0

297.0

Transmembrane

Helical

Hgene

TMEM241

chr18:20979530

chr16:12492303

ENST00000383233

211_231

93.0

297.0

Transmembrane

Helical

Hgene

TMEM241

chr18:20979530

chr16:12492303

ENST00000383233

250_270

93.0

297.0

Transmembrane

Helical

Hgene

TMEM241

chr18:20979530

chr16:12492303

ENST00000383233

271_291

93.0

297.0

Transmembrane

Helical

Hgene

TMEM241

chr18:20979530

chr16:12492303

ENST00000383233

93_113

93.0

297.0

Transmembrane

Helical

Hgene

TMEM241

chr18:20979530

chr16:12492303

ENST00000399707

121_141

67.0

124.0

Transmembrane

Helical

Hgene

TMEM241

chr18:20979530

chr16:12492303

ENST00000399707

146_166

67.0

124.0

Transmembrane

Helical

Hgene

TMEM241

chr18:20979530

chr16:12492303

ENST00000399707

187_207

67.0

124.0

Transmembrane

Helical

Hgene

TMEM241

chr18:20979530

chr16:12492303

ENST00000399707

211_231

67.0

124.0

Transmembrane

Helical

Hgene

TMEM241

chr18:20979530

chr16:12492303

ENST00000399707

250_270

67.0

124.0

Transmembrane

Helical

Hgene

TMEM241

chr18:20979530

chr16:12492303

ENST00000399707

271_291

67.0

124.0

Transmembrane

Helical

Hgene

TMEM241

chr18:20979530

chr16:12492303

ENST00000399707

67_87

67.0

124.0

Transmembrane

Helical

Hgene

TMEM241

chr18:20979530

chr16:12492303

ENST00000399707

93_113

67.0

124.0

Transmembrane

Helical

Tgene

SNX29

chr18:20979530

chr16:12492303

ENST00000566228

466_545

633.0

814.0

Coiled coil

Ontology_term=ECO:0000255

Tgene

SNX29

chr18:20979530

chr16:12492303

ENST00000566228

36_180

633.0

814.0

Domain

RUN

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Fusion Protein-Protein Interaction

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 from validated records (BIOGRID-3.4.160)

Gene

PPI interactors

Protein-protein interactors based on sequence similarity (STRING)

Gene	STRING network
TMEM241
SNX29

- Retained interactions in fusion protein (protein functional feature from UniProt).

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Still interaction with

- Lost interactions due to fusion (protein functional feature from UniProt).

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Interaction lost with

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Related Drugs to TMEM241-SNX29

Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)

Hgene

Tgene

Drug

Source

PMID

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Related Diseases to TMEM241-SNX29

Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)

Hgene

Tgene

Disease

Source

PMID

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner

Gene

Disease ID

Disease name

# pubmeds

Source