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Fusion Protein:FANCD2-MTMR14

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: FANCD2-MTMR14
	FusionPDB ID: 29328
	FusionGDB2.0 ID: 29328
		Hgene	Tgene
	Gene symbol	FANCD2	MTMR14
	Gene ID	2177	64419
	Gene name	FA complementation group D2	myotubularin related protein 14
	Synonyms	FA-D2\|FA4\|FACD\|FAD\|FAD2\|FANCD	C3orf29
	Cytomap	3p25.3	3p25.3
	Type of gene	protein-coding	protein-coding
	Description	Fanconi anemia group D2 proteinFanconi anemia complementation group D2	myotubularin-related protein 14HCV NS5A-transactivated protein 4 splice variant A-binding protein 1NS5ATP4ABP1egg-derived tyrosine phosphatase homologjumpy
	Modification date	20200313	20200313
	UniProtAcc	Q96PS1 Main function of 5'-partner protein:	Q8NCE2 Main function of 5'-partner protein: FUNCTION: Lipid phosphatase which efficiently dephosphorylates phosphatidylinositol 3-phosphate (PtdIns3P) and PtdIns(3,5)P2; inactive toward PtdIns4P, PtdIns(3,4)P2, PtdIns(4,5)P2 and PtdIns(3,4,5)P3. {ECO:0000269\|PubMed:17008356}.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000287647, ENST00000383806, ENST00000383807, ENST00000419585, ENST00000431693, ENST00000438741,	ENST00000296003, ENST00000351233, ENST00000420925, ENST00000353332,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	7 X 8 X 6=336	2 X 5 X 3=30
	# samples	11	5
	** MAII score	log2(11/336*10)=-1.6109577092541 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(5/30*10)=0.736965594166206 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0
Fusion gene context	PubMed: FANCD2 [Title/Abstract] AND MTMR14 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: FANCD2 [Title/Abstract] AND MTMR14 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	FANCD2(10074656)-MTMR14(9719001), # samples:2
Anticipated loss of major functional domain due to fusion event.	FANCD2-MTMR14 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. FANCD2-MTMR14 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. FANCD2-MTMR14 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. FANCD2-MTMR14 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. FANCD2-MTMR14 seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF. FANCD2-MTMR14 seems lost the major protein functional domain in Tgene partner, which is a cell metabolism 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)

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
Hgene	FANCD2	GO:0010332	response to gamma radiation	12874027

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr3:10074656/chr3:9719001)
- 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.

Retention analysis results 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, are available here.

Fusion gene breakpoints across FANCD2 (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 MTMR14 (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 Amino Acid Sequences

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)
ENST00000287647	FANCD2	chr3	10074656	+	ENST00000353332	MTMR14	chr3	9719000	+	1764	298	84	1343	419
ENST00000383807	FANCD2	chr3	10074656	+	ENST00000353332	MTMR14	chr3	9719000	+	1749	283	69	1328	419
ENST00000383806	FANCD2	chr3	10074656	+	ENST00000353332	MTMR14	chr3	9719000	+	1749	283	69	1328	419
ENST00000419585	FANCD2	chr3	10074656	+	ENST00000353332	MTMR14	chr3	9719000	+	1832	366	152	1411	419
ENST00000431693	FANCD2	chr3	10074656	+	ENST00000353332	MTMR14	chr3	9719000	+	1709	243	29	1288	419
ENST00000287647	FANCD2	chr3	10074656	+	ENST00000353332	MTMR14	chr3	9719001	+	1764	298	84	1343	419
ENST00000383807	FANCD2	chr3	10074656	+	ENST00000353332	MTMR14	chr3	9719001	+	1749	283	69	1328	419
ENST00000383806	FANCD2	chr3	10074656	+	ENST00000353332	MTMR14	chr3	9719001	+	1749	283	69	1328	419
ENST00000419585	FANCD2	chr3	10074656	+	ENST00000353332	MTMR14	chr3	9719001	+	1832	366	152	1411	419
ENST00000431693	FANCD2	chr3	10074656	+	ENST00000353332	MTMR14	chr3	9719001	+	1709	243	29	1288	419
ENST00000287647	FANCD2	chr3	10070405	+	ENST00000353332	MTMR14	chr3	9719001	+	1623	157	84	1202	372
ENST00000383807	FANCD2	chr3	10070405	+	ENST00000353332	MTMR14	chr3	9719001	+	1608	142	69	1187	372
ENST00000383806	FANCD2	chr3	10070405	+	ENST00000353332	MTMR14	chr3	9719001	+	1608	142	69	1187	372
ENST00000419585	FANCD2	chr3	10070405	+	ENST00000353332	MTMR14	chr3	9719001	+	1691	225	152	1270	372
ENST00000431693	FANCD2	chr3	10070405	+	ENST00000353332	MTMR14	chr3	9719001	+	1568	102	29	1147	372
ENST00000287647	FANCD2	chr3	10085548	+	ENST00000353332	MTMR14	chr3	9724862	+	2547	1227	84	2126	680
ENST00000287647	FANCD2	chr3	10085548	+	ENST00000420925	MTMR14	chr3	9724862	+	2361	1227	84	1946	620
ENST00000287647	FANCD2	chr3	10085548	+	ENST00000296003	MTMR14	chr3	9724862	+	2702	1227	84	2282	732
ENST00000287647	FANCD2	chr3	10085548	+	ENST00000351233	MTMR14	chr3	9724862	+	2363	1227	84	1946	620
ENST00000383807	FANCD2	chr3	10085548	+	ENST00000353332	MTMR14	chr3	9724862	+	2532	1212	69	2111	680
ENST00000383807	FANCD2	chr3	10085548	+	ENST00000420925	MTMR14	chr3	9724862	+	2346	1212	69	1931	620
ENST00000383807	FANCD2	chr3	10085548	+	ENST00000296003	MTMR14	chr3	9724862	+	2687	1212	69	2267	732
ENST00000383807	FANCD2	chr3	10085548	+	ENST00000351233	MTMR14	chr3	9724862	+	2348	1212	69	1931	620
ENST00000383806	FANCD2	chr3	10085548	+	ENST00000353332	MTMR14	chr3	9724862	+	2532	1212	69	2111	680
ENST00000383806	FANCD2	chr3	10085548	+	ENST00000420925	MTMR14	chr3	9724862	+	2346	1212	69	1931	620
ENST00000383806	FANCD2	chr3	10085548	+	ENST00000296003	MTMR14	chr3	9724862	+	2687	1212	69	2267	732
ENST00000383806	FANCD2	chr3	10085548	+	ENST00000351233	MTMR14	chr3	9724862	+	2348	1212	69	1931	620
ENST00000419585	FANCD2	chr3	10085548	+	ENST00000353332	MTMR14	chr3	9724862	+	2615	1295	152	2194	680
ENST00000419585	FANCD2	chr3	10085548	+	ENST00000420925	MTMR14	chr3	9724862	+	2429	1295	152	2014	620
ENST00000419585	FANCD2	chr3	10085548	+	ENST00000296003	MTMR14	chr3	9724862	+	2770	1295	152	2350	732
ENST00000419585	FANCD2	chr3	10085548	+	ENST00000351233	MTMR14	chr3	9724862	+	2431	1295	152	2014	620

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
ENST00000287647	ENST00000353332	FANCD2	chr3	10074656	+	MTMR14	chr3	9719000	+	0.015236941	0.9847631
ENST00000383807	ENST00000353332	FANCD2	chr3	10074656	+	MTMR14	chr3	9719000	+	0.015051505	0.98494846
ENST00000383806	ENST00000353332	FANCD2	chr3	10074656	+	MTMR14	chr3	9719000	+	0.015051505	0.98494846
ENST00000419585	ENST00000353332	FANCD2	chr3	10074656	+	MTMR14	chr3	9719000	+	0.014412914	0.9855871
ENST00000431693	ENST00000353332	FANCD2	chr3	10074656	+	MTMR14	chr3	9719000	+	0.015892923	0.984107
ENST00000287647	ENST00000353332	FANCD2	chr3	10074656	+	MTMR14	chr3	9719001	+	0.015236941	0.9847631
ENST00000383807	ENST00000353332	FANCD2	chr3	10074656	+	MTMR14	chr3	9719001	+	0.015051505	0.98494846
ENST00000383806	ENST00000353332	FANCD2	chr3	10074656	+	MTMR14	chr3	9719001	+	0.015051505	0.98494846
ENST00000419585	ENST00000353332	FANCD2	chr3	10074656	+	MTMR14	chr3	9719001	+	0.014412914	0.9855871
ENST00000431693	ENST00000353332	FANCD2	chr3	10074656	+	MTMR14	chr3	9719001	+	0.015892923	0.984107
ENST00000287647	ENST00000353332	FANCD2	chr3	10070405	+	MTMR14	chr3	9719001	+	0.032513086	0.9674869
ENST00000383807	ENST00000353332	FANCD2	chr3	10070405	+	MTMR14	chr3	9719001	+	0.03253139	0.9674686
ENST00000383806	ENST00000353332	FANCD2	chr3	10070405	+	MTMR14	chr3	9719001	+	0.03253139	0.9674686
ENST00000419585	ENST00000353332	FANCD2	chr3	10070405	+	MTMR14	chr3	9719001	+	0.029767172	0.97023284
ENST00000431693	ENST00000353332	FANCD2	chr3	10070405	+	MTMR14	chr3	9719001	+	0.0337184	0.96628153
ENST00000287647	ENST00000353332	FANCD2	chr3	10085548	+	MTMR14	chr3	9724862	+	0.006022366	0.99397767
ENST00000287647	ENST00000420925	FANCD2	chr3	10085548	+	MTMR14	chr3	9724862	+	0.004809678	0.9951904
ENST00000287647	ENST00000296003	FANCD2	chr3	10085548	+	MTMR14	chr3	9724862	+	0.006924452	0.9930755
ENST00000287647	ENST00000351233	FANCD2	chr3	10085548	+	MTMR14	chr3	9724862	+	0.004720345	0.99527967
ENST00000383807	ENST00000353332	FANCD2	chr3	10085548	+	MTMR14	chr3	9724862	+	0.006027026	0.99397296
ENST00000383807	ENST00000420925	FANCD2	chr3	10085548	+	MTMR14	chr3	9724862	+	0.00480057	0.99519944
ENST00000383807	ENST00000296003	FANCD2	chr3	10085548	+	MTMR14	chr3	9724862	+	0.006921629	0.9930783
ENST00000383807	ENST00000351233	FANCD2	chr3	10085548	+	MTMR14	chr3	9724862	+	0.004712741	0.9952872
ENST00000383806	ENST00000353332	FANCD2	chr3	10085548	+	MTMR14	chr3	9724862	+	0.006027026	0.99397296
ENST00000383806	ENST00000420925	FANCD2	chr3	10085548	+	MTMR14	chr3	9724862	+	0.00480057	0.99519944
ENST00000383806	ENST00000296003	FANCD2	chr3	10085548	+	MTMR14	chr3	9724862	+	0.006921629	0.9930783
ENST00000383806	ENST00000351233	FANCD2	chr3	10085548	+	MTMR14	chr3	9724862	+	0.004712741	0.9952872
ENST00000419585	ENST00000353332	FANCD2	chr3	10085548	+	MTMR14	chr3	9724862	+	0.005752752	0.9942472
ENST00000419585	ENST00000420925	FANCD2	chr3	10085548	+	MTMR14	chr3	9724862	+	0.004637033	0.995363
ENST00000419585	ENST00000296003	FANCD2	chr3	10085548	+	MTMR14	chr3	9724862	+	0.006438152	0.99356186
ENST00000419585	ENST00000351233	FANCD2	chr3	10085548	+	MTMR14	chr3	9724862	+	0.004554159	0.99544585

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

Get the fusion protein sequences from here.

Fusion protein sequence information is available in the fasta format.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

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Fusion Protein Breakpoint Sequences for FANCD2-MTMR14

+/-13 AA sequence from the breakpoints of the fusion protein sequences.

Hgene	Hchr	Hbp	Tgene	Tchr	Tbp	Length(fusion protein)	BP in fusion protein	Peptide
FANCD2	chr3	10070405	MTMR14	chr3	9719001	102	25	SEDKESLTEDASSCEFFKEYKDRDYM
FANCD2	chr3	10070405	MTMR14	chr3	9719001	142	25	SEDKESLTEDASSCEFFKEYKDRDYM
FANCD2	chr3	10070405	MTMR14	chr3	9719001	157	25	SEDKESLTEDASSCEFFKEYKDRDYM
FANCD2	chr3	10070405	MTMR14	chr3	9719001	225	25	SEDKESLTEDASSCEFFKEYKDRDYM
FANCD2	chr3	10074656	MTMR14	chr3	9719000	243	71	GIILKTGESQNQLGCEFFKEYKDRDY
FANCD2	chr3	10074656	MTMR14	chr3	9719000	283	71	GIILKTGESQNQLGCEFFKEYKDRDY
FANCD2	chr3	10074656	MTMR14	chr3	9719000	298	71	GIILKTGESQNQLGCEFFKEYKDRDY
FANCD2	chr3	10074656	MTMR14	chr3	9719000	366	71	GIILKTGESQNQLGCEFFKEYKDRDY
FANCD2	chr3	10074656	MTMR14	chr3	9719001	243	71	GIILKTGESQNQLGCEFFKEYKDRDY
FANCD2	chr3	10074656	MTMR14	chr3	9719001	283	71	GIILKTGESQNQLGCEFFKEYKDRDY
FANCD2	chr3	10074656	MTMR14	chr3	9719001	298	71	GIILKTGESQNQLGCEFFKEYKDRDY
FANCD2	chr3	10074656	MTMR14	chr3	9719001	366	71	GIILKTGESQNQLGCEFFKEYKDRDY
FANCD2	chr3	10085548	MTMR14	chr3	9724862	1212	381	KAIENTASVSEHKCWDLVQQTQNYLK
FANCD2	chr3	10085548	MTMR14	chr3	9724862	1227	381	KAIENTASVSEHKCWDLVQQTQNYLK
FANCD2	chr3	10085548	MTMR14	chr3	9724862	1295	381	KAIENTASVSEHKCWDLVQQTQNYLK

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Potential FusionNeoAntigen Information of FANCD2-MTMR14 in HLA I

Multiple sequence alignments of the potential FusionNeoAntigens per fusion breakpoints. If the MSA is empty, then it means that there were predicted fusion neoantigens in this fusion breakpoint, but those predicted fusion neoantigens were not across the breakpoint, which is not fusion-specific.

FANCD2-MTMR14_10070405_9719001.msa
FANCD2-MTMR14_10074656_9719000.msa
FANCD2-MTMR14_10085548_9724862.msa

Potential FusionNeoAntigen Information
* We used NetMHCpan v4.1 (%rank<0.5) and deepHLApan v1.1 (immunogenic score>0.5)

Fusion gene	Hchr	Hbp	Tgene	Tchr	Tbp	HLA I	FusionNeoAntigen peptide	Binding score	Immunogenic score	Neoantigen start (at BP 13)	Neoantigen end (at BP 13)
FANCD2-MTMR14	chr3	10070405	chr3	9719001	157	HLA-B15:17	SSCEFFKEY	0.9914	0.9259	11	20
FANCD2-MTMR14	chr3	10070405	chr3	9719001	157	HLA-B44:03	TEDASSCEF	0.9705	0.8574	7	16
FANCD2-MTMR14	chr3	10070405	chr3	9719001	157	HLA-B58:02	SSCEFFKEY	0.9558	0.9192	11	20
FANCD2-MTMR14	chr3	10070405	chr3	9719001	157	HLA-B15:16	SSCEFFKEY	0.9468	0.5132	11	20
FANCD2-MTMR14	chr3	10070405	chr3	9719001	157	HLA-B18:01	TEDASSCEF	0.8536	0.8581	7	16
FANCD2-MTMR14	chr3	10070405	chr3	9719001	157	HLA-C15:04	SSCEFFKEY	0.9014	0.9315	11	20
FANCD2-MTMR14	chr3	10070405	chr3	9719001	157	HLA-B39:08	TEDASSCEF	0.2252	0.842	7	16
FANCD2-MTMR14	chr3	10070405	chr3	9719001	157	HLA-C03:14	SSCEFFKEY	0.1989	0.9854	11	20
FANCD2-MTMR14	chr3	10070405	chr3	9719001	157	HLA-C12:04	SSCEFFKEY	0.1802	0.9944	11	20
FANCD2-MTMR14	chr3	10070405	chr3	9719001	157	HLA-C06:03	SSCEFFKEY	0.1785	0.9955	11	20
FANCD2-MTMR14	chr3	10070405	chr3	9719001	157	HLA-C12:12	SSCEFFKEY	0.0521	0.9431	11	20
FANCD2-MTMR14	chr3	10070405	chr3	9719001	157	HLA-B57:04	SSCEFFKEY	0.9897	0.7151	11	20
FANCD2-MTMR14	chr3	10070405	chr3	9719001	157	HLA-B58:06	SSCEFFKEY	0.9802	0.6958	11	20
FANCD2-MTMR14	chr3	10070405	chr3	9719001	157	HLA-B44:07	TEDASSCEF	0.9705	0.8574	7	16
FANCD2-MTMR14	chr3	10070405	chr3	9719001	157	HLA-B44:26	TEDASSCEF	0.9705	0.8574	7	16
FANCD2-MTMR14	chr3	10070405	chr3	9719001	157	HLA-B44:13	TEDASSCEF	0.9705	0.8574	7	16
FANCD2-MTMR14	chr3	10070405	chr3	9719001	157	HLA-B40:04	TEDASSCEF	0.9551	0.6663	7	16
FANCD2-MTMR14	chr3	10070405	chr3	9719001	157	HLA-B35:28	SSCEFFKEY	0.9542	0.9297	11	20
FANCD2-MTMR14	chr3	10070405	chr3	9719001	157	HLA-C03:02	SSCEFFKEY	0.9274	0.9732	11	20
FANCD2-MTMR14	chr3	10070405	chr3	9719001	157	HLA-C15:09	SSCEFFKEY	0.9014	0.9315	11	20
FANCD2-MTMR14	chr3	10070405	chr3	9719001	157	HLA-B18:06	TEDASSCEF	0.8537	0.8695	7	16
FANCD2-MTMR14	chr3	10070405	chr3	9719001	157	HLA-B18:05	TEDASSCEF	0.8536	0.8581	7	16
FANCD2-MTMR14	chr3	10070405	chr3	9719001	157	HLA-B18:04	TEDASSCEF	0.8213	0.8603	7	16
FANCD2-MTMR14	chr3	10070405	chr3	9719001	157	HLA-B18:08	TEDASSCEF	0.8192	0.8496	7	16
FANCD2-MTMR14	chr3	10070405	chr3	9719001	157	HLA-B18:11	TEDASSCEF	0.8119	0.8408	7	16
FANCD2-MTMR14	chr3	10070405	chr3	9719001	157	HLA-B18:03	TEDASSCEF	0.7412	0.847	7	16
FANCD2-MTMR14	chr3	10070405	chr3	9719001	157	HLA-C16:04	SSCEFFKEY	0.4095	0.9906	11	20
FANCD2-MTMR14	chr3	10070405	chr3	9719001	157	HLA-B35:20	TEDASSCEF	0.3821	0.8359	7	16
FANCD2-MTMR14	chr3	10070405	chr3	9719001	157	HLA-C12:02	SSCEFFKEY	0.3155	0.9733	11	20
FANCD2-MTMR14	chr3	10070405	chr3	9719001	157	HLA-C16:02	SSCEFFKEY	0.2163	0.9899	11	20
FANCD2-MTMR14	chr3	10070405	chr3	9719001	157	HLA-B39:11	TEDASSCEF	0.2062	0.8088	7	16
FANCD2-MTMR14	chr3	10070405	chr3	9719001	157	HLA-C12:03	SSCEFFKEY	0.1297	0.9829	11	20
FANCD2-MTMR14	chr3	10070405	chr3	9719001	157	HLA-C16:01	SSCEFFKEY	0.1178	0.9796	11	20
FANCD2-MTMR14	chr3	10070405	chr3	9719001	157	HLA-C02:10	SSCEFFKEY	0.0031	0.9727	11	20
FANCD2-MTMR14	chr3	10070405	chr3	9719001	157	HLA-C02:02	SSCEFFKEY	0.0031	0.9727	11	20
FANCD2-MTMR14	chr3	10074656	chr3	9719000	298	HLA-B15:01	SQNQLGCEF	0.9985	0.8122	8	17
FANCD2-MTMR14	chr3	10074656	chr3	9719000	298	HLA-B15:25	SQNQLGCEF	0.961	0.8954	8	17
FANCD2-MTMR14	chr3	10074656	chr3	9719000	298	HLA-B15:02	SQNQLGCEF	0.9562	0.9035	8	17
FANCD2-MTMR14	chr3	10074656	chr3	9719000	298	HLA-B15:03	SQNQLGCEF	0.8092	0.7801	8	17
FANCD2-MTMR14	chr3	10074656	chr3	9719000	298	HLA-B15:18	SQNQLGCEF	0.7831	0.7197	8	17
FANCD2-MTMR14	chr3	10074656	chr3	9719000	298	HLA-B47:01	SQNQLGCEF	0.701	0.5909	8	17
FANCD2-MTMR14	chr3	10074656	chr3	9719000	298	HLA-B13:01	SQNQLGCEF	0.5013	0.9432	8	17
FANCD2-MTMR14	chr3	10074656	chr3	9719000	298	HLA-B15:01	SQNQLGCEFF	0.9994	0.8239	8	18
FANCD2-MTMR14	chr3	10074656	chr3	9719000	298	HLA-B13:01	SQNQLGCEFF	0.8672	0.9431	8	18
FANCD2-MTMR14	chr3	10074656	chr3	9719000	298	HLA-B44:03	GESQNQLGCEF	0.9991	0.9325	6	17
FANCD2-MTMR14	chr3	10074656	chr3	9719000	298	HLA-B44:05	GESQNQLGCEF	0.9933	0.5342	6	17
FANCD2-MTMR14	chr3	10074656	chr3	9719000	298	HLA-B15:07	SQNQLGCEF	0.9886	0.648	8	17
FANCD2-MTMR14	chr3	10074656	chr3	9719000	298	HLA-B15:04	SQNQLGCEF	0.9643	0.8484	8	17
FANCD2-MTMR14	chr3	10074656	chr3	9719000	298	HLA-B15:21	SQNQLGCEF	0.9526	0.8875	8	17
FANCD2-MTMR14	chr3	10074656	chr3	9719000	298	HLA-B15:05	SQNQLGCEF	0.8362	0.8379	8	17
FANCD2-MTMR14	chr3	10074656	chr3	9719000	298	HLA-B15:31	SQNQLGCEF	0.7733	0.8457	8	17
FANCD2-MTMR14	chr3	10074656	chr3	9719000	298	HLA-B39:08	SQNQLGCEF	0.4657	0.9536	8	17
FANCD2-MTMR14	chr3	10074656	chr3	9719000	298	HLA-B44:08	SQNQLGCEF	0.4485	0.5076	8	17
FANCD2-MTMR14	chr3	10074656	chr3	9719000	298	HLA-B15:05	SQNQLGCEFF	0.8692	0.8548	8	18
FANCD2-MTMR14	chr3	10074656	chr3	9719000	298	HLA-B44:08	GESQNQLGCEF	0.9991	0.6045	6	17
FANCD2-MTMR14	chr3	10074656	chr3	9719000	298	HLA-B44:09	GESQNQLGCEF	0.999	0.6241	6	17
FANCD2-MTMR14	chr3	10074656	chr3	9719000	298	HLA-B44:10	GESQNQLGCEF	0.9836	0.7076	6	17
FANCD2-MTMR14	chr3	10074656	chr3	9719000	298	HLA-B15:33	SQNQLGCEF	0.9985	0.8122	8	17
FANCD2-MTMR14	chr3	10074656	chr3	9719000	298	HLA-B15:34	SQNQLGCEF	0.9985	0.8122	8	17
FANCD2-MTMR14	chr3	10074656	chr3	9719000	298	HLA-B15:125	SQNQLGCEF	0.9985	0.8122	8	17
FANCD2-MTMR14	chr3	10074656	chr3	9719000	298	HLA-B15:27	SQNQLGCEF	0.9984	0.8477	8	17
FANCD2-MTMR14	chr3	10074656	chr3	9719000	298	HLA-B15:135	SQNQLGCEF	0.9982	0.8221	8	17
FANCD2-MTMR14	chr3	10074656	chr3	9719000	298	HLA-B15:50	SQNQLGCEF	0.9971	0.8723	8	17
FANCD2-MTMR14	chr3	10074656	chr3	9719000	298	HLA-B15:24	SQNQLGCEF	0.9962	0.8735	8	17
FANCD2-MTMR14	chr3	10074656	chr3	9719000	298	HLA-B15:35	SQNQLGCEF	0.9851	0.8089	8	17
FANCD2-MTMR14	chr3	10074656	chr3	9719000	298	HLA-B15:12	SQNQLGCEF	0.9763	0.8262	8	17
FANCD2-MTMR14	chr3	10074656	chr3	9719000	298	HLA-B15:39	SQNQLGCEF	0.9657	0.8148	8	17
FANCD2-MTMR14	chr3	10074656	chr3	9719000	298	HLA-B15:53	SQNQLGCEF	0.9656	0.7947	8	17
FANCD2-MTMR14	chr3	10074656	chr3	9719000	298	HLA-B15:73	SQNQLGCEF	0.8724	0.9612	8	17
FANCD2-MTMR14	chr3	10074656	chr3	9719000	298	HLA-B15:54	SQNQLGCEF	0.8392	0.7736	8	17
FANCD2-MTMR14	chr3	10074656	chr3	9719000	298	HLA-B15:20	SQNQLGCEF	0.8273	0.8798	8	17
FANCD2-MTMR14	chr3	10074656	chr3	9719000	298	HLA-B15:13	SQNQLGCEF	0.8171	0.6698	8	17
FANCD2-MTMR14	chr3	10074656	chr3	9719000	298	HLA-B35:28	SQNQLGCEF	0.7957	0.8822	8	17
FANCD2-MTMR14	chr3	10074656	chr3	9719000	298	HLA-B15:68	SQNQLGCEF	0.7593	0.6182	8	17
FANCD2-MTMR14	chr3	10074656	chr3	9719000	298	HLA-B15:30	SQNQLGCEF	0.7328	0.9307	8	17
FANCD2-MTMR14	chr3	10074656	chr3	9719000	298	HLA-B35:20	SQNQLGCEF	0.7258	0.8887	8	17
FANCD2-MTMR14	chr3	10074656	chr3	9719000	298	HLA-B48:02	SQNQLGCEF	0.6377	0.8731	8	17
FANCD2-MTMR14	chr3	10074656	chr3	9719000	298	HLA-B18:04	SQNQLGCEF	0.4675	0.9168	8	17
FANCD2-MTMR14	chr3	10074656	chr3	9719000	298	HLA-B15:33	SQNQLGCEFF	0.9994	0.8239	8	18
FANCD2-MTMR14	chr3	10074656	chr3	9719000	298	HLA-B15:125	SQNQLGCEFF	0.9994	0.8239	8	18
FANCD2-MTMR14	chr3	10074656	chr3	9719000	298	HLA-B15:135	SQNQLGCEFF	0.9994	0.8335	8	18
FANCD2-MTMR14	chr3	10074656	chr3	9719000	298	HLA-B15:27	SQNQLGCEFF	0.9994	0.8524	8	18
FANCD2-MTMR14	chr3	10074656	chr3	9719000	298	HLA-B15:34	SQNQLGCEFF	0.9994	0.8239	8	18
FANCD2-MTMR14	chr3	10074656	chr3	9719000	298	HLA-B15:24	SQNQLGCEFF	0.9992	0.8759	8	18
FANCD2-MTMR14	chr3	10074656	chr3	9719000	298	HLA-B15:50	SQNQLGCEFF	0.9992	0.8884	8	18
FANCD2-MTMR14	chr3	10074656	chr3	9719000	298	HLA-B15:54	SQNQLGCEFF	0.9959	0.786	8	18
FANCD2-MTMR14	chr3	10074656	chr3	9719000	298	HLA-B15:12	SQNQLGCEFF	0.9958	0.8379	8	18
FANCD2-MTMR14	chr3	10074656	chr3	9719000	298	HLA-B15:53	SQNQLGCEFF	0.9957	0.8094	8	18
FANCD2-MTMR14	chr3	10074656	chr3	9719000	298	HLA-B15:20	SQNQLGCEFF	0.8629	0.894	8	18
FANCD2-MTMR14	chr3	10074656	chr3	9719000	298	HLA-B44:26	GESQNQLGCEF	0.9991	0.9325	6	17
FANCD2-MTMR14	chr3	10074656	chr3	9719000	298	HLA-B44:13	GESQNQLGCEF	0.9991	0.9325	6	17
FANCD2-MTMR14	chr3	10074656	chr3	9719000	298	HLA-B44:07	GESQNQLGCEF	0.9991	0.9325	6	17
FANCD2-MTMR14	chr3	10085548	chr3	9724862	1227	HLA-B57:01	ASVSEHKCW	0.9993	0.98	6	15
FANCD2-MTMR14	chr3	10085548	chr3	9724862	1227	HLA-B58:02	ASVSEHKCW	0.9981	0.9566	6	15
FANCD2-MTMR14	chr3	10085548	chr3	9724862	1227	HLA-B58:01	ASVSEHKCW	0.998	0.9182	6	15
FANCD2-MTMR14	chr3	10085548	chr3	9724862	1227	HLA-B15:17	ASVSEHKCW	0.9931	0.8817	6	15
FANCD2-MTMR14	chr3	10085548	chr3	9724862	1227	HLA-B57:03	ASVSEHKCW	0.9779	0.9886	6	15
FANCD2-MTMR14	chr3	10085548	chr3	9724862	1227	HLA-B15:16	ASVSEHKCW	0.9694	0.7595	6	15
FANCD2-MTMR14	chr3	10085548	chr3	9724862	1227	HLA-B57:01	TASVSEHKCW	0.9997	0.9866	5	15
FANCD2-MTMR14	chr3	10085548	chr3	9724862	1227	HLA-B58:02	TASVSEHKCW	0.9985	0.9733	5	15
FANCD2-MTMR14	chr3	10085548	chr3	9724862	1227	HLA-B58:01	TASVSEHKCW	0.9982	0.9624	5	15
FANCD2-MTMR14	chr3	10085548	chr3	9724862	1227	HLA-B57:03	TASVSEHKCW	0.9854	0.992	5	15
FANCD2-MTMR14	chr3	10085548	chr3	9724862	1227	HLA-B57:01	NTASVSEHKCW	1	0.9418	4	15
FANCD2-MTMR14	chr3	10085548	chr3	9724862	1227	HLA-B58:02	NTASVSEHKCW	0.9996	0.9025	4	15
FANCD2-MTMR14	chr3	10085548	chr3	9724862	1227	HLA-B58:01	NTASVSEHKCW	0.9991	0.8943	4	15
FANCD2-MTMR14	chr3	10085548	chr3	9724862	1227	HLA-B57:03	NTASVSEHKCW	0.9979	0.9394	4	15
FANCD2-MTMR14	chr3	10085548	chr3	9724862	1227	HLA-B57:10	ASVSEHKCW	0.9993	0.98	6	15
FANCD2-MTMR14	chr3	10085548	chr3	9724862	1227	HLA-B57:04	ASVSEHKCW	0.9984	0.8326	6	15
FANCD2-MTMR14	chr3	10085548	chr3	9724862	1227	HLA-B58:06	ASVSEHKCW	0.9964	0.8554	6	15
FANCD2-MTMR14	chr3	10085548	chr3	9724862	1227	HLA-B57:02	ASVSEHKCW	0.9858	0.9654	6	15
FANCD2-MTMR14	chr3	10085548	chr3	9724862	1227	HLA-B57:10	TASVSEHKCW	0.9997	0.9866	5	15
FANCD2-MTMR14	chr3	10085548	chr3	9724862	1227	HLA-B57:04	TASVSEHKCW	0.9989	0.8503	5	15
FANCD2-MTMR14	chr3	10085548	chr3	9724862	1227	HLA-B58:06	TASVSEHKCW	0.9977	0.9123	5	15
FANCD2-MTMR14	chr3	10085548	chr3	9724862	1227	HLA-B57:02	TASVSEHKCW	0.9839	0.9643	5	15
FANCD2-MTMR14	chr3	10085548	chr3	9724862	1227	HLA-B57:10	NTASVSEHKCW	1	0.9418	4	15
FANCD2-MTMR14	chr3	10085548	chr3	9724862	1227	HLA-B57:04	NTASVSEHKCW	0.9998	0.7329	4	15
FANCD2-MTMR14	chr3	10085548	chr3	9724862	1227	HLA-B57:02	NTASVSEHKCW	0.9995	0.9264	4	15

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Potential FusionNeoAntigen Information of FANCD2-MTMR14 in HLA II

Potential FusionNeoAntigen Information
* We used NetMHCIIpan v4.1 (%rank<0.5).

Fusion gene

Hchr

Hbp

Tgene

Tchr

Tbp

HLA II

FusionNeoAntigen peptide

Neoantigen start (at BP 13)

Neoantigen end (at BP 13)

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Fusion breakpoint peptide structures of FANCD2-MTMR14

3D structures of the fusion breakpoint peptide of 14AA sequence that have potential fusion neoantigens
* The minimum length of the amino acid sequence in RoseTTAFold is 14AA. Here, we predicted the 14AA fusion protein breakpoint sequence not the fusion neoantigen peptide, which is shorter than 14 AA.

File name	BPseq	Hgene	Tgene	Hchr	Hbp	Tchr	Tbp	AAlen
636	ASVSEHKCWDLVQQ	FANCD2	MTMR14	chr3	10085548	chr3	9724862	1227

File name	BPseq	Hgene	Tgene	Hchr	Hbp	Tchr	Tbp	AAlen
2763	GESQNQLGCEFFKE	FANCD2	MTMR14	chr3	10074656	chr3	9719000	298

File name	BPseq	Hgene	Tgene	Hchr	Hbp	Tchr	Tbp	AAlen
5687	LTEDASSCEFFKEY	FANCD2	MTMR14	chr3	10070405	chr3	9719001	157

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of FANCD2-MTMR14

Virtual screening between 25 HLAs (from PDB) and FusionNeoAntigens
* We used Glide to predict the interaction between HLAs and neoantigens.

HLA allele	PDB ID	File name	BPseq	Docking score	Glide score
HLA-B14:02	3BVN	636	ASVSEHKCWDLVQQ	-7.81562	-7.82282
HLA-B52:01	3W39	636	ASVSEHKCWDLVQQ	-5.65668	-5.66388
HLA-A24:02	5HGA	636	ASVSEHKCWDLVQQ	-7.47535	-7.48255
HLA-B44:05	3DX8	636	ASVSEHKCWDLVQQ	-3.54501	-3.55221
HLA-A02:01	6TDR	636	ASVSEHKCWDLVQQ	-1.77875	-1.78595
HLA-B14:02	3BVN	2763	GESQNQLGCEFFKE	-7.9962	-8.1096
HLA-B14:02	3BVN	2763	GESQNQLGCEFFKE	-5.70842	-6.74372
HLA-B52:01	3W39	2763	GESQNQLGCEFFKE	-6.83737	-6.95077
HLA-B52:01	3W39	2763	GESQNQLGCEFFKE	-4.4836	-5.5189
HLA-A11:01	4UQ2	2763	GESQNQLGCEFFKE	-10.0067	-10.1201
HLA-A11:01	4UQ2	2763	GESQNQLGCEFFKE	-9.03915	-10.0745
HLA-A24:02	5HGA	2763	GESQNQLGCEFFKE	-6.56204	-6.67544
HLA-A24:02	5HGA	2763	GESQNQLGCEFFKE	-5.42271	-6.45801
HLA-B44:05	3DX8	2763	GESQNQLGCEFFKE	-7.85648	-8.89178
HLA-B44:05	3DX8	2763	GESQNQLGCEFFKE	-5.3978	-5.5112
HLA-A02:01	6TDR	2763	GESQNQLGCEFFKE	-3.37154	-4.40684
HLA-B14:02	3BVN	5687	LTEDASSCEFFKEY	-7.9962	-8.1096
HLA-B14:02	3BVN	5687	LTEDASSCEFFKEY	-5.70842	-6.74372
HLA-B52:01	3W39	5687	LTEDASSCEFFKEY	-6.83737	-6.95077
HLA-B52:01	3W39	5687	LTEDASSCEFFKEY	-4.4836	-5.5189
HLA-A11:01	4UQ2	5687	LTEDASSCEFFKEY	-10.0067	-10.1201
HLA-A11:01	4UQ2	5687	LTEDASSCEFFKEY	-9.03915	-10.0745
HLA-A24:02	5HGA	5687	LTEDASSCEFFKEY	-6.56204	-6.67544
HLA-A24:02	5HGA	5687	LTEDASSCEFFKEY	-5.42271	-6.45801
HLA-B44:05	3DX8	5687	LTEDASSCEFFKEY	-7.85648	-8.89178
HLA-B44:05	3DX8	5687	LTEDASSCEFFKEY	-5.3978	-5.5112
HLA-A02:01	6TDR	5687	LTEDASSCEFFKEY	-3.37154	-4.40684

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Vaccine Design for the FusionNeoAntigens of FANCD2-MTMR14

mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-Is.

Fusion gene	Hchr	Hbp	Tchr	Tbp	Start in +/-13AA	End in +/-13AA	FusionNeoAntigen peptide sequence	FusionNeoAntigen RNA sequence
FANCD2-MTMR14	chr3	10070405	chr3	9719001	11	20	SSCEFFKEY	CCTCCAGCTGTGAATTTTTCAAGGAAT
FANCD2-MTMR14	chr3	10070405	chr3	9719001	7	16	TEDASSCEF	TGACAGAAGATGCCTCCAGCTGTGAAT
FANCD2-MTMR14	chr3	10074656	chr3	9719000	6	17	GESQNQLGCEF	GAGAGAGTCAGAATCAACTAGGCTGTGAATTTT
FANCD2-MTMR14	chr3	10074656	chr3	9719000	8	17	SQNQLGCEF	GTCAGAATCAACTAGGCTGTGAATTTT
FANCD2-MTMR14	chr3	10074656	chr3	9719000	8	18	SQNQLGCEFF	GTCAGAATCAACTAGGCTGTGAATTTTTCA
FANCD2-MTMR14	chr3	10085548	chr3	9724862	4	15	NTASVSEHKCW	AACACTGCCTCAGTATCTGAACACAAGTGTTGG
FANCD2-MTMR14	chr3	10085548	chr3	9724862	5	15	TASVSEHKCW	ACTGCCTCAGTATCTGAACACAAGTGTTGG
FANCD2-MTMR14	chr3	10085548	chr3	9724862	6	15	ASVSEHKCW	GCCTCAGTATCTGAACACAAGTGTTGG

mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.

Fusion gene

Hchr

Hbp

Tchr

Tbp

Start in +/-13AA

End in +/-13AA

FusionNeoAntigen peptide

FusionNEoAntigen RNA sequence

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Information of the samples that have these potential fusion neoantigens of FANCD2-MTMR14

These samples were reported as having these fusion breakpoints. For individual breakpoints, we checked the open reading frames considering multiple gene isoforms and chose the in-frame fusion genes only. Then, we made fusion protein sequences and predicted the fusion neoantigens. These fusion-positive samples may have these potential fusion neoantigens.

Cancer type	Fusion gene	Hchr	Hbp	Henst	Tchr	Tbp	Tenst	Sample
BRCA	FANCD2-MTMR14	chr3	10085548	ENST00000287647	chr3	9724862	ENST00000296003	TCGA-OL-A5D7-01A
BRCA	FANCD2-MTMR14	chr3	10070405	ENST00000287647	chr3	9719001	ENST00000353332	TCGA-D8-A1JM-01A
BRCA	FANCD2-MTMR14	chr3	10074656	ENST00000287647	chr3	9719000	ENST00000353332	TCGA-D8-A1JM

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Potential target of CAR-T therapy development for FANCD2-MTMR14

Predicted 3D structure. We used RoseTTAFold.

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, to provide the retention of the transmembrane domain, we only show the protein feature retention information of those transmembrane features

* Minus value of BPloci means that the break point is located before the CDS.

- In-frame and retained 'Transmembrane'.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

Subcellular localization prediction of the transmembrane domain retained fusion proteins
* We used DeepLoc 1.0. The order of the X-axis of the barplot is as follows: Entry_ID, Localization, Type, Nucleus, Cytoplasm, Extracellular, Mitochondrion, Cell_membrane, Endoplasmic_reticulum, Plastid, Golgi.apparatus, Lysosome.Vacuole, Peroxisome. Y-axis is the output score of DeepLoc. Clicking the image will open a new tab with a large image.

Hgene

Hchr

Hbp

Henst

Tgene

Tchr

Tbp

Tenst

DeepLoc result

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Related Drugs to FANCD2-MTMR14

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 FANCD2-MTMR14

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

	Fusion Gene and Fusion Protein Summary
	Fusion Amino Acid Sequences (multiple BPs and multiple gene isoforms)
	Fusion Protein Breakpoint Sequences - (for the Screening of the FusionNeoAntigens)
	Potential FusionNeoAntigens in HLA I - (netMHCpan v4.1 + deepHLApan v1.1)
	Potential FusionNeoAntigens in HLA II - (netMHCIIpan v4.1)
	Fusion Breakpoint 14 AA Peptide Structure - (RoseTTAFold)
	Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D - (Glide)
	Vaccine Design for the FusionNeoAntigens (RNA/protein sequences)
	Potential target of CAR-T therapy development
	Information on the samples that have these potential fusion neoantigens
	Fusion Protein Targeting Drugs - (Manual Curation)
	Fusion Protein Related diseases - (Manual Curation)