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Center for Computational Systems Medicine
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FusionGeneSummary

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FusionProtFeature

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FusionGeneSequence

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FusionGenePPI

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RelatedDrugs

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RelatedDiseases

Fusion gene ID: 26357

FusionGeneSummary for PDCD6_SDHA

check button Fusion gene summary
Fusion gene informationFusion gene name: PDCD6_SDHA
Fusion gene ID: 26357
HgeneTgene
Gene symbol

PDCD6

SDHA

Gene ID

10016

6389

Gene nameprogrammed cell death 6succinate dehydrogenase complex flavoprotein subunit A
SynonymsALG-2|ALG2|PEF1BCMD1GG|FP|PGL5|SDH1|SDH2|SDHF
Cytomap

5p15.33

5p15.33

Type of geneprotein-codingprotein-coding
Descriptionprogrammed cell death protein 6apoptosis-linked gene 2 proteinapoptosis-linked gene 2 protein homologprobable calcium-binding protein ALG-2succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrialflavoprotein subunit of complex IIsuccinate dehydrogenase complex, subunit A, flavoprotein (Fp)
Modification date2018051920180523
UniProtAcc

O75340

P31040

Ensembl transtripts involved in fusion geneENST00000264933, ENST00000505221, 
ENST00000509581, ENST00000507528, 
ENST00000511482, 		ENST00000264932, 
ENST00000504309, ENST00000510361, 
ENST00000507522, 
Fusion gene scores* DoF score5 X 4 X 5=1004 X 5 X 4=80
# samples 65
** MAII scorelog2(6/100*10)=-0.736965594166206
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(5/80*10)=-0.678071905112638
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: PDCD6 [Title/Abstract] AND SDHA [Title/Abstract] AND fusion [Title/Abstract]

Functional or gene categories assigned by FusionGDB annotationTumor suppressor gene involved fusion gene, in-frame but not retained their domain.
Tumor suppressor gene involved fusion gene, retained protein feature but frameshift.
DDR (DNA damage repair) gene involved fusion gene, in-frame but not retained their domain.
* 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
HgenePDCD6

GO:0001938

positive regulation of endothelial cell proliferation

21893193

HgenePDCD6

GO:0006886

intracellular protein transport

21122810

HgenePDCD6

GO:0010595

positive regulation of endothelial cell migration

21893193

HgenePDCD6

GO:0030948

negative regulation of vascular endothelial growth factor receptor signaling pathway

21893193

HgenePDCD6

GO:0032007

negative regulation of TOR signaling

21893193

HgenePDCD6

GO:0034605

cellular response to heat

21122810

HgenePDCD6

GO:0036324

vascular endothelial growth factor receptor-2 signaling pathway

21893193

HgenePDCD6

GO:0043280

positive regulation of cysteine-type endopeptidase activity involved in apoptotic process

16132846

HgenePDCD6

GO:0045766

positive regulation of angiogenesis

21893193

HgenePDCD6

GO:0051898

negative regulation of protein kinase B signaling

21893193

TgeneSDHA

GO:0006105

succinate metabolic process

7550341

TgeneSDHA

GO:0022904

respiratory electron transport chain

7550341

TgeneSDHA

GO:0055114

oxidation-reduction process

7550341


check button Fusion gene information from three resources
(ChiTars (NAR, 2018), tumorfusions (NAR, 2018), Gao et al. (Cell, 2018))
* 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.
Data typeSourceCancer typeSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
TCGARVLUSCTCGA-77-A5GH-01APDCD6chr5

272887

+SDHAchr5

240473

+
* LD: Li Ding group's fusion gene list
  RV: Roel Verhaak group's fusion gene list
  ChiTaRs fusion database

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
In-frameENST00000264933ENST00000264932PDCD6chr5

272887

+SDHAchr5

240473

+
In-frameENST00000264933ENST00000504309PDCD6chr5

272887

+SDHAchr5

240473

+
In-frameENST00000264933ENST00000510361PDCD6chr5

272887

+SDHAchr5

240473

+
5CDS-intronENST00000264933ENST00000507522PDCD6chr5

272887

+SDHAchr5

240473

+
In-frameENST00000505221ENST00000264932PDCD6chr5

272887

+SDHAchr5

240473

+
In-frameENST00000505221ENST00000504309PDCD6chr5

272887

+SDHAchr5

240473

+
In-frameENST00000505221ENST00000510361PDCD6chr5

272887

+SDHAchr5

240473

+
5CDS-intronENST00000505221ENST00000507522PDCD6chr5

272887

+SDHAchr5

240473

+
In-frameENST00000509581ENST00000264932PDCD6chr5

272887

+SDHAchr5

240473

+
In-frameENST00000509581ENST00000504309PDCD6chr5

272887

+SDHAchr5

240473

+
In-frameENST00000509581ENST00000510361PDCD6chr5

272887

+SDHAchr5

240473

+
5CDS-intronENST00000509581ENST00000507522PDCD6chr5

272887

+SDHAchr5

240473

+
In-frameENST00000507528ENST00000264932PDCD6chr5

272887

+SDHAchr5

240473

+
In-frameENST00000507528ENST00000504309PDCD6chr5

272887

+SDHAchr5

240473

+
In-frameENST00000507528ENST00000510361PDCD6chr5

272887

+SDHAchr5

240473

+
5CDS-intronENST00000507528ENST00000507522PDCD6chr5

272887

+SDHAchr5

240473

+
intron-3CDSENST00000511482ENST00000264932PDCD6chr5

272887

+SDHAchr5

240473

+
intron-3CDSENST00000511482ENST00000504309PDCD6chr5

272887

+SDHAchr5

240473

+
intron-3CDSENST00000511482ENST00000510361PDCD6chr5

272887

+SDHAchr5

240473

+
intron-intronENST00000511482ENST00000507522PDCD6chr5

272887

+SDHAchr5

240473

+

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FusionProtFeatures for PDCD6_SDHA


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
PDCD6

O75340

SDHA

P31040

Calcium sensor that plays a key role in processes suchas endoplasmic reticulum (ER)-Golgi vesicular transport, endosomalbiogenesis or membrane repair. Acts as an adapter that bridgesunrelated proteins or stabilizes weak protein-protein complexes inresponse to calcium: calcium-binding triggers exposure of apolarsurface, promoting interaction with different sets of proteinsthanks to 3 different hydrophobic pockets, leading totranslocation to membranes (PubMed:20691033, PubMed:25667979).Involved in ER-Golgi transport by promoting the associationbetween PDCD6IP and TSG101, thereby bridging together the ESCRT-III and ESCRT-I complexes (PubMed:19520058). Together with PEF1,acts as calcium-dependent adapter for the BCR(KLHL12) complex, acomplex involved in ER-Golgi transport by regulating the size ofCOPII coats (PubMed:27716508). In response to cytosolic calciumincrease, the heterodimer formed with PEF1 interacts with, andbridges together the BCR(KLHL12) complex and SEC31 (SEC31A orSEC31B), promoting monoubiquitination of SEC31 and subsequentcollagen export, which is required for neural crest specification(PubMed:27716508). Involved in the regulation of the distributionand function of MCOLN1 in the endosomal pathway (PubMed:19864416).Promotes localization and polymerization of TFG at endoplasmicreticulum exit site (PubMed:27813252). Required for T-cellreceptor-, Fas-, and glucocorticoid-induced apoptosis (Bysimilarity). May mediate Ca(2+)-regulated signals along the deathpathway: interaction with DAPK1 can accelerate apoptotic celldeath by increasing caspase-3 activity (PubMed:16132846). Its rolein apoptosis may however be indirect, as suggested by knockoutexperiments (By similarity). May inhibit KDR/VEGFR2-dependentangiogenesis; the function involves inhibition of VEGF-inducedphosphorylation of the Akt signaling pathway (PubMed:21893193). Incase of infection by HIV-1 virus, indirectly inhibits HIV-1production by affecting viral Gag expression and distribution(PubMed:27784779). {ECO:0000250|UniProtKB:P12815,ECO:0000269|PubMed:16132846, ECO:0000269|PubMed:19520058,ECO:0000269|PubMed:19864416, ECO:0000269|PubMed:20691033,ECO:0000269|PubMed:21893193, ECO:0000269|PubMed:25667979,ECO:0000269|PubMed:27716508, ECO:0000269|PubMed:27784779,ECO:0000269|PubMed:27813252}. Isoform 2: Has a lower Ca(2+) affinity than isoform 1(By similarity). {ECO:0000250|UniProtKB:P12815}. Flavoprotein (FP) subunit of succinate dehydrogenase(SDH) that is involved in complex II of the mitochondrial electrontransport chain and is responsible for transferring electrons fromsuccinate to ubiquinone (coenzyme Q) (PubMed:24781757). Can act asa tumor suppressor (PubMed:20484225).{ECO:0000269|PubMed:20484225, ECO:0000305|PubMed:24781757}.

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
HgenePDCD6chr5:272887chr5:240473ENST00000264933+2636_4754192Calcium binding1
HgenePDCD6chr5:272887chr5:240473ENST00000505221+2436_475470Calcium binding1
HgenePDCD6chr5:272887chr5:240473ENST00000507528+2636_4754190Calcium binding1

- In-frame and not-retained protein feature among the 13 regional features.
>>>>>>>>>>>>>>>>>>>>>
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgenePDCD6chr5:272887chr5:240473ENST00000264933+26103_11454192Calcium binding3
HgenePDCD6chr5:272887chr5:240473ENST00000264933+2673_8454192Calcium binding2
HgenePDCD6chr5:272887chr5:240473ENST00000505221+24103_1145470Calcium binding3
HgenePDCD6chr5:272887chr5:240473ENST00000505221+2473_845470Calcium binding2
HgenePDCD6chr5:272887chr5:240473ENST00000507528+26103_11454190Calcium binding3
HgenePDCD6chr5:272887chr5:240473ENST00000507528+2673_8454190Calcium binding2
HgenePDCD6chr5:272887chr5:240473ENST00000264933+26126_16154192DomainEF-hand 4
HgenePDCD6chr5:272887chr5:240473ENST00000264933+26162_19154192DomainEF-hand 5
HgenePDCD6chr5:272887chr5:240473ENST00000264933+2623_5854192DomainEF-hand 1
HgenePDCD6chr5:272887chr5:240473ENST00000264933+2659_8954192DomainEF-hand 2
HgenePDCD6chr5:272887chr5:240473ENST00000264933+2690_12554192DomainEF-hand 3
HgenePDCD6chr5:272887chr5:240473ENST00000505221+24126_1615470DomainEF-hand 4
HgenePDCD6chr5:272887chr5:240473ENST00000505221+24162_1915470DomainEF-hand 5
HgenePDCD6chr5:272887chr5:240473ENST00000505221+2423_585470DomainEF-hand 1
HgenePDCD6chr5:272887chr5:240473ENST00000505221+2459_895470DomainEF-hand 2
HgenePDCD6chr5:272887chr5:240473ENST00000505221+2490_1255470DomainEF-hand 3
HgenePDCD6chr5:272887chr5:240473ENST00000507528+26126_16154190DomainEF-hand 4
HgenePDCD6chr5:272887chr5:240473ENST00000507528+26162_19154190DomainEF-hand 5
HgenePDCD6chr5:272887chr5:240473ENST00000507528+2623_5854190DomainEF-hand 1
HgenePDCD6chr5:272887chr5:240473ENST00000507528+2659_8954190DomainEF-hand 2
HgenePDCD6chr5:272887chr5:240473ENST00000507528+2690_12554190DomainEF-hand 3
TgeneSDHAchr5:272887chr5:240473ENST00000264932+915456_457477665Nucleotide bindingFAD
TgeneSDHAchr5:272887chr5:240473ENST00000264932+91568_73477665Nucleotide bindingFAD
TgeneSDHAchr5:272887chr5:240473ENST00000264932+91591_106477665Nucleotide bindingFAD


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FusionGeneSequence for PDCD6_SDHA


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences.
(nt: nucleotides, aa: amino acids)

* Fusion amino acid sequences.

* Fusion transcript sequences (only coding sequence (CDS) region).

* Fusion transcript sequences (Full-length transcript).

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FusionGenePPI for PDCD6_SDHA


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
PDCD6HEBP2, MAPK1IP1L, PDCD6, MAP3K5, FAS, PDCD6IP, SH3KBP1, PEF1, ANXA11, H2AFX, CUL5, CUL2, CUL1, CAND1, IGBP1, GCN1L1, ABCB7, IKBIP, FUBP1, ERLIN2, VCP, VCAM1, FN1, ITGA4, CFTR, BAG3, YWHAQ, CDKN2A, DDX1, FLII, MAP4, NMT1, DROSHA, AURKA, HAUS2, TP53, DAPK1, VPS37C, MOV10, NXF1, HNRNPU, HNRNPUL1, HNRNPUL2, IGF2BP3, ITPA, MIF, PCBP1, AKR1A1, ANXA2, ANXA5, ARFIP1, CLIC4, CRKL, CSK, CSTB, HNRNPH1, HNRNPH2, HNRNPH3, HSPA9, IMPA2, LMAN1, MRPL37, NUDT13, PABPC1, PABPC4, QDPR, RAB1B, SEPHS1, TARDBP, TKT, TXN, TYMS, UBQLN1, SAR1B, TSTA3, MED4, MED20, XPO1, CCNA2, CCNB1, MAGEA1, MYC, MYH7, TSNAX, GOLT1B, MYH7B, FERMT3, SAMD1, MCM2, NF2, DUSP21, TRIM25SDHAUBC, ICT1, CSNK2B, ARRB2, SIRT7, CUL3, CUL4A, CUL5, CUL2, CUL1, COPS5, COPS6, DCUN1D1, CAND1, NEDD8, SDHB, SUCLA2, SUCLG1, SUCLG2, UQCRFS1, UQCRB, SYNE2, MTERF3, RAVER1, TIMM50, LRRC8A, MDH1, SAMM50, DHODH, TOMM70A, TAP1, TMEM14B, HIGD1A, NDUFS2, OXCT1, MRPL1, MRPS9, ZC3H4, NDUFS3, CYB5R3, NDUFS6, NDUFS8, NDUFV2, EIF4A1, XRCC6, MARC1, IMPAD1, ACAT1, GCN1L1, PSMD1, PROCR, SLC2A14, SLC27A2, SQSTM1, PDHA1, ATP5F1, NDUFV1, FN1, ITGA4, FBXO6, NXF1, APOA1BP, ATP1B1, CPNE1, CPNE3, CYC1, DLD, DNAJA3, HSPA9, HSPB1, MDH2, MTCH1, NDUFA2, PPIB, RAB14, ACLY, CS, GLOD4, SDHC, UQCRQ, NTRK1, HSPB2, CEP128, RPGRIP1L, TMEM67, SDHAF2, CRY1, CRY2, UBXN10, OTUB1, NFATC2, DUSP4, DUSP9, C6orf57, PDZRN3, PDSS2, PDSS1, PDP1, ACN9, SIRT3, ACAD9, WBP2, SEC22B, YWHAB, PPIA, MYL12A, HSD17B10, BANF1, CKB, ANXA5, SFXN1, LDHA, RPL30, HNRNPH3, EEF2, ATP1A1, HIST1H2AD, CCT2, EIF4A3, CCT8, RPL26, EEF1G, CDK1, SLC25A5, CHCHD2, RPN2, ATP5H, PPIAL4B, RPL12, LDHAL6A, LDHB, PDIA3, SLC25A3, ARL6IP5, PMVK, HMGB3, RAB10, CKAP4, HSP90B1, MAP4K1, SERPINH1, PSMC2, TMED10, PDIA6, RAB21, EEF1B2, CHCHD3, RUVBL2, TMED9, GANAB, UQCRC1, TMEM109, YWHAQ, YWHAZ, TFAM, YWHAG, SHMT2, PGAM1, YWHAE, PRDX3, MCM3, CCT7, TPI1, PPP2R1A, CANX, EMC2, LMNB2, EIF2S1, APEX1, ELAVL1, LMNA, NDFIP2, ATP6V0D1, DNAJB11, HLA-B, HLA-A, IDH3A, HNRNPA1, JUP, MAT2A, PSMC5, SERBP1, PSMC1, UQCRC2, PRPH, NAMPT, DARS, FARSA, ASNS, LMNB1, RPN1, TKT, SSRP1, DSP, MCM5, HSD17B4, DDX1, PCSK1, CPT1A, DGKG, MCM6, HSPA4, KPNB1, PSMD2, AARS2, TPR, SMC3, COPA, FASN, HDLBP, EPRS, HIST1H2AE, HIST1H2AB, HIST1H2BD, HIST1H2BG, HIST1H2BF, HIST1H2BE, HIST1H2BI, HIST1H2BC


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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RelatedDrugs for PDCD6_SDHA


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
HgenePDCD6O75340DB11093Calcium CitrateProgrammed cell death protein 6small moleculeapproved
HgenePDCD6O75340DB11348Calcium PhosphateProgrammed cell death protein 6small moleculeapproved
HgenePDCD6O75340DB01593ZincProgrammed cell death protein 6small moleculeapproved|investigational
HgenePDCD6O75340DB01373CalciumProgrammed cell death protein 6small moleculeapproved|nutraceutical
TgeneSDHAP31040DB09270UbidecarenoneSuccinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrialsmall moleculeapproved|investigational|nutraceutical

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RelatedDiseases for PDCD6_SDHA


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgenePDCD6C0011573Endogenous depression1PSYGENET
TgeneSDHAC0023264Leigh Disease3CTD_human;ORPHANET;UNIPROT
TgeneSDHAC1855008Mitochondrial Complex II Deficiency2CTD_human;ORPHANET;UNIPROT
TgeneSDHAC0029408Degenerative polyarthritis1CTD_human
TgeneSDHAC0036341Schizophrenia1PSYGENET
TgeneSDHAC3279992PARAGANGLIOMAS 51UNIPROT