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Center for Computational Systems Medicine level1
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Fusion Gene Summary

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Fusion Gene Sample Information

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Fusion ORF Analysis

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Fusion Amino Acid Sequences

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Fusion Protein Functional Features

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Fusion Protein-Protein Interaction

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Related drugs with this fusion protein

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Related disease with this fusion protein

Fusion Protein:FNDC3A-ZMYM2

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: FNDC3A-ZMYM2
FusionPDB ID: 30906
FusionGDB2.0 ID: 30906
HgeneTgene
Gene symbol

FNDC3A

ZMYM2

Gene ID

22862

7750

Gene namefibronectin type III domain containing 3Azinc finger MYM-type containing 2
SynonymsFNDC3|HUGO|bA203I16.1|bA203I16.5FIM|MYM|RAMP|SCLL|ZNF198
Cytomap

13q14.2

13q12.11

Type of geneprotein-codingprotein-coding
Descriptionfibronectin type-III domain-containing protein 3Ahuman gene expressed in odontoblastszinc finger MYM-type protein 2fused in myeloproliferative disorders proteinrearranged in an atypical myeloproliferative disorderzinc finger protein 198zinc finger, MYM-type 2
Modification date2020031320200313
UniProtAcc

Q9Y2H6

Q9UBW7

Ensembl transtripts involved in fusion geneENST idsENST00000492622, ENST00000541916, 
ENST00000398316, 		ENST00000382871, 
ENST00000382874, ENST00000382881, 
ENST00000382883, ENST00000494061, 
ENST00000382869, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score15 X 12 X 7=12605 X 5 X 4=100
# samples 165
** MAII scorelog2(16/1260*10)=-2.97727992349992
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(5/100*10)=-1
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: FNDC3A [Title/Abstract] AND ZMYM2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)FNDC3A(49580425)-ZMYM2(20625573), # samples:1
Anticipated loss of major functional domain due to fusion event.FNDC3A-ZMYM2 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.
FNDC3A-ZMYM2 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.
FNDC3A-ZMYM2 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.
FNDC3A-ZMYM2 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)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID

check buttonFusion gene breakpoints across FNDC3A (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 ZMYM2 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


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Fusion Gene Sample Information

check buttonFusion gene information from FusionGDB2.0.
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
ChimerDB4BRCATCGA-A8-A096-01AFNDC3Achr13

49580425

+ZMYM2chr13

20625573

+


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Fusion ORF Analysis


check buttonFusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)
ENST00000492622FNDC3Achr1349580425+ENST00000382869ZMYM2chr1320625573+80604042992245648
ENST00000541916FNDC3Achr1349580425+ENST00000382869ZMYM2chr1320625573+7828172672013648

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
ENST00000492622ENST00000382869FNDC3Achr1349580425+ZMYM2chr1320625573+6.64E-050.9999336
ENST00000541916ENST00000382869FNDC3Achr1349580425+ZMYM2chr1320625573+5.61E-050.99994385

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Fusion Amino Acid Sequences


check button 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

>30906_30906_1_FNDC3A-ZMYM2_FNDC3A_chr13_49580425_ENST00000492622_ZMYM2_chr13_20625573_ENST00000382869_length(amino acids)=648AA_BP=35
MIMAEHPPLLDTTQILSSDISLLSAPIVSADGTQQAARCDCCKSQGTLKERVQWRGEMKHFCDQHCLLRFYCQQNEPNMTTQKGPENLHY
DQGCQTSRTKMTGSAPPPSPTPNKEMKNKAVLCKPLTMTKATYCKPHMQTKSCQTDDTWRTEYVPVPIPVPVYIPVPMHMYSQNIPVPTT
VPVPVPVPVFLPAPLDSSEKIPAAIEELKSKVSSDALDTELLTMTDMMSEDEGKTETTNINSVIIETDIIGSDLLKNSDPETQSSMPDVP
YEPDLDIEIDFPRAAEELDMENEFLLPPVFGEEYEEQPRPRSKKKGAKRKAVSGYQSHDDSSDNSECSFPFKYTYGVNAWKHWVKTRQLD
EDLLVLDELKSSKSVKLKEDLLSHTTAELNYGLAHFVNEIRRPNGENYAPDSIYYLCLGIQEYLCGSNRKDNIFIDPGYQTFEQELNKIL
RSWQPSILPDGSIFSRVEEDYLWRIKQLGSHSPVALLNTLFYFNTKYFGLKTVEQHLRLSFGTVFRHWKKNPLTMENKACLRYQVSSLCG
TDNEDKITTGKRKHEDDEPVFEQIENTANPSRCPVKMFECYLSKSPQNLNQRMDVFYLQPECSSSTDSPVWYTSTSLDRNTLENMLVRVL

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

>30906_30906_2_FNDC3A-ZMYM2_FNDC3A_chr13_49580425_ENST00000541916_ZMYM2_chr13_20625573_ENST00000382869_length(amino acids)=648AA_BP=35
MIMAEHPPLLDTTQILSSDISLLSAPIVSADGTQQAARCDCCKSQGTLKERVQWRGEMKHFCDQHCLLRFYCQQNEPNMTTQKGPENLHY
DQGCQTSRTKMTGSAPPPSPTPNKEMKNKAVLCKPLTMTKATYCKPHMQTKSCQTDDTWRTEYVPVPIPVPVYIPVPMHMYSQNIPVPTT
VPVPVPVPVFLPAPLDSSEKIPAAIEELKSKVSSDALDTELLTMTDMMSEDEGKTETTNINSVIIETDIIGSDLLKNSDPETQSSMPDVP
YEPDLDIEIDFPRAAEELDMENEFLLPPVFGEEYEEQPRPRSKKKGAKRKAVSGYQSHDDSSDNSECSFPFKYTYGVNAWKHWVKTRQLD
EDLLVLDELKSSKSVKLKEDLLSHTTAELNYGLAHFVNEIRRPNGENYAPDSIYYLCLGIQEYLCGSNRKDNIFIDPGYQTFEQELNKIL
RSWQPSILPDGSIFSRVEEDYLWRIKQLGSHSPVALLNTLFYFNTKYFGLKTVEQHLRLSFGTVFRHWKKNPLTMENKACLRYQVSSLCG
TDNEDKITTGKRKHEDDEPVFEQIENTANPSRCPVKMFECYLSKSPQNLNQRMDVFYLQPECSSSTDSPVWYTSTSLDRNTLENMLVRVL

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Fusion Protein Functional Features


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/chr13:49580425/chr13:20625573)
- 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
FNDC3A

Q9Y2H6

ZMYM2

Q9UBW7

FUNCTION: Mediates spermatid-Sertoli adhesion during spermatogenesis. {ECO:0000250}.FUNCTION: May function as a transcription factor.

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.
- Retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
TgeneZMYM2chr13:49580425chr13:20625573ENST0000038288108352_3860463.0Zinc fingerNote=MYM-type 1
TgeneZMYM2chr13:49580425chr13:20625573ENST0000038288108398_4360463.0Zinc fingerNote=MYM-type 2
TgeneZMYM2chr13:49580425chr13:20625573ENST0000038288108445_4800463.0Zinc fingerNote=MYM-type 3
TgeneZMYM2chr13:49580425chr13:20625573ENST0000038288108491_5490463.0Zinc fingerNote=MYM-type 4
TgeneZMYM2chr13:49580425chr13:20625573ENST0000038288108559_5970463.0Zinc fingerNote=MYM-type 5
TgeneZMYM2chr13:49580425chr13:20625573ENST0000038288108605_6520463.0Zinc fingerNote=MYM-type 6
TgeneZMYM2chr13:49580425chr13:20625573ENST0000038288108660_6940463.0Zinc fingerNote=MYM-type 7
TgeneZMYM2chr13:49580425chr13:20625573ENST0000038288108701_7400463.0Zinc fingerNote=MYM-type 8
TgeneZMYM2chr13:49580425chr13:20625573ENST0000038288108747_7810463.0Zinc fingerNote=MYM-type 9

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneFNDC3Achr13:49580425chr13:20625573ENST00000398316+12468_13301143.0Compositional biasNote=Pro-rich
HgeneFNDC3Achr13:49580425chr13:20625573ENST00000492622+22668_13333.01199.0Compositional biasNote=Pro-rich
HgeneFNDC3Achr13:49580425chr13:20625573ENST00000541916+22668_13333.01199.0Compositional biasNote=Pro-rich
HgeneFNDC3Achr13:49580425chr13:20625573ENST00000398316+1241046_115101143.0DomainFibronectin type-III 9
HgeneFNDC3Achr13:49580425chr13:20625573ENST00000398316+124268_36901143.0DomainFibronectin type-III 1
HgeneFNDC3Achr13:49580425chr13:20625573ENST00000398316+124373_46501143.0DomainFibronectin type-III 2
HgeneFNDC3Achr13:49580425chr13:20625573ENST00000398316+124469_56201143.0DomainFibronectin type-III 3
HgeneFNDC3Achr13:49580425chr13:20625573ENST00000398316+124566_66001143.0DomainFibronectin type-III 4
HgeneFNDC3Achr13:49580425chr13:20625573ENST00000398316+124664_75701143.0DomainFibronectin type-III 5
HgeneFNDC3Achr13:49580425chr13:20625573ENST00000398316+124761_85101143.0DomainFibronectin type-III 6
HgeneFNDC3Achr13:49580425chr13:20625573ENST00000398316+124861_95001143.0DomainFibronectin type-III 7
HgeneFNDC3Achr13:49580425chr13:20625573ENST00000398316+124951_104501143.0DomainFibronectin type-III 8
HgeneFNDC3Achr13:49580425chr13:20625573ENST00000492622+2261046_115133.01199.0DomainFibronectin type-III 9
HgeneFNDC3Achr13:49580425chr13:20625573ENST00000492622+226268_36933.01199.0DomainFibronectin type-III 1
HgeneFNDC3Achr13:49580425chr13:20625573ENST00000492622+226373_46533.01199.0DomainFibronectin type-III 2
HgeneFNDC3Achr13:49580425chr13:20625573ENST00000492622+226469_56233.01199.0DomainFibronectin type-III 3
HgeneFNDC3Achr13:49580425chr13:20625573ENST00000492622+226566_66033.01199.0DomainFibronectin type-III 4
HgeneFNDC3Achr13:49580425chr13:20625573ENST00000492622+226664_75733.01199.0DomainFibronectin type-III 5
HgeneFNDC3Achr13:49580425chr13:20625573ENST00000492622+226761_85133.01199.0DomainFibronectin type-III 6
HgeneFNDC3Achr13:49580425chr13:20625573ENST00000492622+226861_95033.01199.0DomainFibronectin type-III 7
HgeneFNDC3Achr13:49580425chr13:20625573ENST00000492622+226951_104533.01199.0DomainFibronectin type-III 8
HgeneFNDC3Achr13:49580425chr13:20625573ENST00000541916+2261046_115133.01199.0DomainFibronectin type-III 9
HgeneFNDC3Achr13:49580425chr13:20625573ENST00000541916+226268_36933.01199.0DomainFibronectin type-III 1
HgeneFNDC3Achr13:49580425chr13:20625573ENST00000541916+226373_46533.01199.0DomainFibronectin type-III 2
HgeneFNDC3Achr13:49580425chr13:20625573ENST00000541916+226469_56233.01199.0DomainFibronectin type-III 3
HgeneFNDC3Achr13:49580425chr13:20625573ENST00000541916+226566_66033.01199.0DomainFibronectin type-III 4
HgeneFNDC3Achr13:49580425chr13:20625573ENST00000541916+226664_75733.01199.0DomainFibronectin type-III 5
HgeneFNDC3Achr13:49580425chr13:20625573ENST00000541916+226761_85133.01199.0DomainFibronectin type-III 6
HgeneFNDC3Achr13:49580425chr13:20625573ENST00000541916+226861_95033.01199.0DomainFibronectin type-III 7
HgeneFNDC3Achr13:49580425chr13:20625573ENST00000541916+226951_104533.01199.0DomainFibronectin type-III 8
HgeneFNDC3Achr13:49580425chr13:20625573ENST00000398316+1241177_119701143.0TransmembraneHelical
HgeneFNDC3Achr13:49580425chr13:20625573ENST00000492622+2261177_119733.01199.0TransmembraneHelical
HgeneFNDC3Achr13:49580425chr13:20625573ENST00000541916+2261177_119733.01199.0TransmembraneHelical
TgeneZMYM2chr13:49580425chr13:20625573ENST000003828691125352_386764.01378.0Zinc fingerNote=MYM-type 1
TgeneZMYM2chr13:49580425chr13:20625573ENST000003828691125398_436764.01378.0Zinc fingerNote=MYM-type 2
TgeneZMYM2chr13:49580425chr13:20625573ENST000003828691125445_480764.01378.0Zinc fingerNote=MYM-type 3
TgeneZMYM2chr13:49580425chr13:20625573ENST000003828691125491_549764.01378.0Zinc fingerNote=MYM-type 4
TgeneZMYM2chr13:49580425chr13:20625573ENST000003828691125559_597764.01378.0Zinc fingerNote=MYM-type 5
TgeneZMYM2chr13:49580425chr13:20625573ENST000003828691125605_652764.01378.0Zinc fingerNote=MYM-type 6
TgeneZMYM2chr13:49580425chr13:20625573ENST000003828691125660_694764.01378.0Zinc fingerNote=MYM-type 7
TgeneZMYM2chr13:49580425chr13:20625573ENST000003828691125701_740764.01378.0Zinc fingerNote=MYM-type 8
TgeneZMYM2chr13:49580425chr13:20625573ENST000003828691125747_781764.01378.0Zinc fingerNote=MYM-type 9
TgeneZMYM2chr13:49580425chr13:20625573ENST000003828711226352_386764.01378.0Zinc fingerNote=MYM-type 1
TgeneZMYM2chr13:49580425chr13:20625573ENST000003828711226398_436764.01378.0Zinc fingerNote=MYM-type 2
TgeneZMYM2chr13:49580425chr13:20625573ENST000003828711226445_480764.01378.0Zinc fingerNote=MYM-type 3
TgeneZMYM2chr13:49580425chr13:20625573ENST000003828711226491_549764.01378.0Zinc fingerNote=MYM-type 4
TgeneZMYM2chr13:49580425chr13:20625573ENST000003828711226559_597764.01378.0Zinc fingerNote=MYM-type 5
TgeneZMYM2chr13:49580425chr13:20625573ENST000003828711226605_652764.01378.0Zinc fingerNote=MYM-type 6
TgeneZMYM2chr13:49580425chr13:20625573ENST000003828711226660_694764.01378.0Zinc fingerNote=MYM-type 7
TgeneZMYM2chr13:49580425chr13:20625573ENST000003828711226701_740764.01378.0Zinc fingerNote=MYM-type 8
TgeneZMYM2chr13:49580425chr13:20625573ENST000003828711226747_781764.01378.0Zinc fingerNote=MYM-type 9
TgeneZMYM2chr13:49580425chr13:20625573ENST000003828741226352_386764.01378.0Zinc fingerNote=MYM-type 1
TgeneZMYM2chr13:49580425chr13:20625573ENST000003828741226398_436764.01378.0Zinc fingerNote=MYM-type 2
TgeneZMYM2chr13:49580425chr13:20625573ENST000003828741226445_480764.01378.0Zinc fingerNote=MYM-type 3
TgeneZMYM2chr13:49580425chr13:20625573ENST000003828741226491_549764.01378.0Zinc fingerNote=MYM-type 4
TgeneZMYM2chr13:49580425chr13:20625573ENST000003828741226559_597764.01378.0Zinc fingerNote=MYM-type 5
TgeneZMYM2chr13:49580425chr13:20625573ENST000003828741226605_652764.01378.0Zinc fingerNote=MYM-type 6
TgeneZMYM2chr13:49580425chr13:20625573ENST000003828741226660_694764.01378.0Zinc fingerNote=MYM-type 7
TgeneZMYM2chr13:49580425chr13:20625573ENST000003828741226701_740764.01378.0Zinc fingerNote=MYM-type 8
TgeneZMYM2chr13:49580425chr13:20625573ENST000003828741226747_781764.01378.0Zinc fingerNote=MYM-type 9


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Fusion Protein-Protein Interaction


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 from validated records (BIOGRID-3.4.160)
GenePPI interactors
ZMYM2HDAC2, KDM1A, FUS, SFPQ, HNRNPH3, HNRNPA2B1, UBTF, ZMYM4, HSPA4, RCOR1, HDAC1, TUBA1B, TUBB1, SUMO2, UBE2I, CREB1, SREBF2, ZBTB3, NR2E1, Dynll1, ELAVL1, CEBPE, PML, UBE2A, UBE2B, RAD18, USP15, CTCF, SKIL, SMAD4, ZNF512B, SOX2, HDAC11, SUMO1, EED, MAGEA1, SFXN3, SDF4, ST8SIA1, ALDH3B2, TRIM10, ARRDC1, NUP133, DYNLL1, ZSCAN5A, ZNF644, Cbx1, Kctd5, Gtf3c2, FOXG1, FOXJ2, FOXQ1, NFATC2, TSC22D2, ZNF263, ZNF202, PCK2, TSPYL6, MATN4, RPE65, PDDC1, TRIM35, PSG8, TRIM25, GTF2IRD1, GTF2I, FGFR1, ZMYM2, RNF4, ESR2, HIST1H4A, HIST1H2BB, HIST1H3A, KIAA1429, CREBBP, H2AFX, H2AFZ, H2AFY, ZMYM3, MYC, CSK, PSMD14, GMCL1, PAICS, IKZF3, PLEKHA4, FBXL17, ESR1, PYHIN1, PLEKHG3, CIC, NR3C1, DZIP3, CBX3, HIST1H2BG, TERF2IP, NAA40, CHD4, ZNF174, CHSY1, SFMBT1, PDGFRL, DYNLL2, RCOR2, ZNF460, PCK1, ZKSCAN8, ZBTB9, C1QTNF1, CRYAA, C8A, TUBB4B, NOL4, RCOR3, ACOT13, ADNP, CAPN10, GTF2IRD2B, HDAC3, PTH2R, CRBN, ETV6, HNF4A, KLF12, KLF3, KLF8, PAX6, YY1,


check button Protein-protein interactors based on sequence similarity (STRING)
GeneSTRING network
FNDC3A
ZMYM2all structure


check button - Retained interactions in fusion protein (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost interactions due to fusion (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs to FNDC3A-ZMYM2


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

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Related Diseases to FNDC3A-ZMYM2


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

check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneZMYM2C0020796Profound Mental Retardation1CTD_human
TgeneZMYM2C0025363Mental Retardation, Psychosocial1CTD_human
TgeneZMYM2C0027022Myeloproliferative disease1CTD_human
TgeneZMYM2C0917816Mental deficiency1CTD_human
TgeneZMYM2C3714756Intellectual Disability1CTD_human