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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: 34961

FusionGeneSummary for SMPD3_ATP6V0D1

check button Fusion gene summary
Fusion gene informationFusion gene name: SMPD3_ATP6V0D1
Fusion gene ID: 34961
HgeneTgene
Gene symbol

SMPD3

ATP6V0D1

Gene ID

55512

9114

Gene namesphingomyelin phosphodiesterase 3ATPase H+ transporting V0 subunit d1
SynonymsNSMASE2ATP6D|ATP6DV|P39|VATX|VMA6|VPATPD
Cytomap

16q22.1

16q22.1

Type of geneprotein-codingprotein-coding
Descriptionsphingomyelin phosphodiesterase 3nSMase-2neutral sphingomyelinase 2neutral sphingomyelinase IIV-type proton ATPase subunit d 132 kDa accessory proteinATPase, H+ transporting, lysosomal (vacuolar proton pump), member DATPase, H+ transporting, lysosomal 38kDa, V0 subunit d1H(+)-transporting two-sector ATPase, subunit DV-ATPase 40 KDa accessory
Modification date2018052220180523
UniProtAcc

Q9NY59

P61421

Ensembl transtripts involved in fusion geneENST00000219334, ENST00000568373, 
ENST00000563226, ENST00000566009, 
ENST00000290949, ENST00000540149, 
ENST00000602876, ENST00000567694, 
Fusion gene scores* DoF score3 X 3 X 3=274 X 4 X 3=48
# samples 34
** MAII scorelog2(3/27*10)=0.15200309344505
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
log2(4/48*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: SMPD3 [Title/Abstract] AND ATP6V0D1 [Title/Abstract] AND fusion [Title/Abstract]

Functional or gene categories assigned by FusionGDB annotation
* 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 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
TCGALDREADTCGA-AF-A56L-01ASMPD3chr16

68397399

-ATP6V0D1chr16

67473254

-
* 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
Frame-shiftENST00000219334ENST00000290949SMPD3chr16

68397399

-ATP6V0D1chr16

67473254

-
Frame-shiftENST00000219334ENST00000540149SMPD3chr16

68397399

-ATP6V0D1chr16

67473254

-
Frame-shiftENST00000219334ENST00000602876SMPD3chr16

68397399

-ATP6V0D1chr16

67473254

-
5CDS-5UTRENST00000219334ENST00000567694SMPD3chr16

68397399

-ATP6V0D1chr16

67473254

-
Frame-shiftENST00000568373ENST00000290949SMPD3chr16

68397399

-ATP6V0D1chr16

67473254

-
Frame-shiftENST00000568373ENST00000540149SMPD3chr16

68397399

-ATP6V0D1chr16

67473254

-
Frame-shiftENST00000568373ENST00000602876SMPD3chr16

68397399

-ATP6V0D1chr16

67473254

-
5CDS-5UTRENST00000568373ENST00000567694SMPD3chr16

68397399

-ATP6V0D1chr16

67473254

-
Frame-shiftENST00000563226ENST00000290949SMPD3chr16

68397399

-ATP6V0D1chr16

67473254

-
Frame-shiftENST00000563226ENST00000540149SMPD3chr16

68397399

-ATP6V0D1chr16

67473254

-
Frame-shiftENST00000563226ENST00000602876SMPD3chr16

68397399

-ATP6V0D1chr16

67473254

-
5CDS-5UTRENST00000563226ENST00000567694SMPD3chr16

68397399

-ATP6V0D1chr16

67473254

-
intron-3CDSENST00000566009ENST00000290949SMPD3chr16

68397399

-ATP6V0D1chr16

67473254

-
intron-3CDSENST00000566009ENST00000540149SMPD3chr16

68397399

-ATP6V0D1chr16

67473254

-
intron-3CDSENST00000566009ENST00000602876SMPD3chr16

68397399

-ATP6V0D1chr16

67473254

-
intron-5UTRENST00000566009ENST00000567694SMPD3chr16

68397399

-ATP6V0D1chr16

67473254

-

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FusionProtFeatures for SMPD3_ATP6V0D1


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
SMPD3

Q9NY59

ATP6V0D1

P61421

Catalyzes the hydrolysis of sphingomyelin to formceramide and phosphocholine. Ceramide mediates numerous cellularfunctions, such as apoptosis and growth arrest, and is capable ofregulating these 2 cellular events independently. Also hydrolyzessphingosylphosphocholine. Regulates the cell cycle by acting as agrowth suppressor in confluent cells. Probably acts as a regulatorof postnatal development and participates in bone and dentinmineralization. {ECO:0000269|PubMed:10823942,ECO:0000269|PubMed:14741383, ECO:0000269|PubMed:15051724}. Subunit of the integral membrane V0 complex of vacuolarATPase. Vacuolar ATPase is responsible for acidifying a variety ofintracellular compartments in eukaryotic cells, thus providingmost of the energy required for transport processes in thevacuolar system. May play a role in coupling of proton transportand ATP hydrolysis (By similarity). May play a role in ciliumbiogenesis through regulation of the transport and thelocalization of proteins to the cilium (By similarity). In aerobicconditions, involved in intracellular iron homeostasis, thustriggering the activity of Fe(2+) prolyl hydroxylase (PHD)enzymes, and leading to HIF1A hydroxylation and subsequentproteasomal degradation (PubMed:28296633). {ECO:0000250,ECO:0000269|PubMed:28296633}.

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

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note


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FusionGeneSequence for SMPD3_ATP6V0D1


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 SMPD3_ATP6V0D1


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
SMPD3CAV1, ENDOD1, STOM, TMEM135, PPP3R1, ATP6V0A1, SOAT1, PPP3CA, APOB, EED, GNB2L1ATP6V0D1UBC, ATXN1, ATP6V1B1, ERC1, LIG4, RPA3, RPA2, RPA1, STAU1, MCAM, ATP6AP2, SERINC2, ATP1A1, ATP5A1, ATP5C1, ATP5O, ATP6V0A1, ATP1A2, ATP1A3, ATP1B3, ATP5B, ATP5D, ATP5F1, ATP6V1A, ATP6V1B2, ATP6V1D, ATP6V1H, EIF3B, GNB2, MTCH1, MTCH2, NDUFA2, NDUFB7, NDUFS1, NSF, RPL5, RPS16, RPS2, SLC25A4, SLC25A5, SLC25A6, VDAC1, VDAC2, VDAC3, YBX3, EIF3A, NDUFB8, NDUFS4, NDUFV1, PSMD3, RAB2A, RPN1, SSR1, UQCRH, CDK1, CLTC, PTPN1, RAB5C, TMPO, RAB7A, VAPA, GOLT1B, RFWD3, TMEM63B, THOC2, CHMP4B, MVD, ATP6V0A2, ATP6V0D2, LEPR, TUBA3C, TMEM199, SNX25, VMA21, ATP6V0C, SLC22A23, TCIRG1, UBB, SLC27A6, CCDC115, USP4, SNX19, FAM210B, SLC10A7, MID1IP1, DHCR24, PTGES2, INPPL1, B3GNT2, IKBIP, ATP6AP1, SLC27A2, CUL4A, KIAA1919, ATP6V1F, KIAA2013, LETM1, LPHN1, SCCPDH, RDH13, ENPP1, ACSL4, SDHA, LAMTOR2, SLC38A9


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 SMPD3_ATP6V0D1


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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RelatedDiseases for SMPD3_ATP6V0D1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneSMPD3C0023418leukemia1CTD_human
HgeneSMPD3C3463824MYELODYSPLASTIC SYNDROME1CTD_human