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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: 24373

FusionGeneSummary for NIPA1_SMPD1

check button Fusion gene summary
Fusion gene informationFusion gene name: NIPA1_SMPD1
Fusion gene ID: 24373
HgeneTgene
Gene symbol

NIPA1

SMPD1

Gene ID

123606

6609

Gene nameNIPA magnesium transporter 1sphingomyelin phosphodiesterase 1
SynonymsFSP3|SLC57A1|SPG6ASM|ASMASE|NPD
Cytomap

15q11.2

11p15.4

Type of geneprotein-codingprotein-coding
Descriptionmagnesium transporter NIPA1non imprinted in Prader-Willi/Angelman syndrome 1non-imprinted in Prader-Willi/Angelman syndrome region protein 1spastic paraplegia 6 proteinsphingomyelin phosphodiesteraseacid sphingomyelinasesphingomyelin phosphodiesterase 1, acid lysosomal
Modification date2018052320180523
UniProtAcc

Q7RTP0

P17405

Ensembl transtripts involved in fusion geneENST00000337435, ENST00000437912, 
ENST00000538684, ENST00000561183, 
ENST00000356761, ENST00000299397, 
ENST00000342245, ENST00000533196, 
ENST00000527275, 
Fusion gene scores* DoF score1 X 1 X 1=14 X 4 X 2=32
# samples 15
** MAII scorelog2(1/1*10)=3.32192809488736log2(5/32*10)=0.643856189774725
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: NIPA1 [Title/Abstract] AND SMPD1 [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
TgeneSMPD1

GO:0006685

sphingomyelin catabolic process

18815062

TgeneSMPD1

GO:0046513

ceramide biosynthetic process

18815062


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
ChiTaRS3.1AK057846NIPA1chr15

23044062

-SMPD1chr11

6416059

+
* 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
intron-3UTRENST00000337435ENST00000356761NIPA1chr15

23044062

-SMPD1chr11

6416059

+
intron-3UTRENST00000337435ENST00000299397NIPA1chr15

23044062

-SMPD1chr11

6416059

+
intron-3UTRENST00000337435ENST00000342245NIPA1chr15

23044062

-SMPD1chr11

6416059

+
intron-intronENST00000337435ENST00000533196NIPA1chr15

23044062

-SMPD1chr11

6416059

+
intron-intronENST00000337435ENST00000527275NIPA1chr15

23044062

-SMPD1chr11

6416059

+
intron-3UTRENST00000437912ENST00000356761NIPA1chr15

23044062

-SMPD1chr11

6416059

+
intron-3UTRENST00000437912ENST00000299397NIPA1chr15

23044062

-SMPD1chr11

6416059

+
intron-3UTRENST00000437912ENST00000342245NIPA1chr15

23044062

-SMPD1chr11

6416059

+
intron-intronENST00000437912ENST00000533196NIPA1chr15

23044062

-SMPD1chr11

6416059

+
intron-intronENST00000437912ENST00000527275NIPA1chr15

23044062

-SMPD1chr11

6416059

+
intron-3UTRENST00000538684ENST00000356761NIPA1chr15

23044062

-SMPD1chr11

6416059

+
intron-3UTRENST00000538684ENST00000299397NIPA1chr15

23044062

-SMPD1chr11

6416059

+
intron-3UTRENST00000538684ENST00000342245NIPA1chr15

23044062

-SMPD1chr11

6416059

+
intron-intronENST00000538684ENST00000533196NIPA1chr15

23044062

-SMPD1chr11

6416059

+
intron-intronENST00000538684ENST00000527275NIPA1chr15

23044062

-SMPD1chr11

6416059

+
intron-3UTRENST00000561183ENST00000356761NIPA1chr15

23044062

-SMPD1chr11

6416059

+
intron-3UTRENST00000561183ENST00000299397NIPA1chr15

23044062

-SMPD1chr11

6416059

+
intron-3UTRENST00000561183ENST00000342245NIPA1chr15

23044062

-SMPD1chr11

6416059

+
intron-intronENST00000561183ENST00000533196NIPA1chr15

23044062

-SMPD1chr11

6416059

+
intron-intronENST00000561183ENST00000527275NIPA1chr15

23044062

-SMPD1chr11

6416059

+

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FusionProtFeatures for NIPA1_SMPD1


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
NIPA1

Q7RTP0

SMPD1

P17405

Acts as a Mg(2+) transporter. Can also transport otherdivalent cations such as Fe(2+), Sr(2+), Ba(2+), Mn(2+) and Co(2+)but to a much less extent than Mg(2+) (By similarity).{ECO:0000250}. Converts sphingomyelin to ceramide (PubMed:1840600,PubMed:18815062, PubMed:27659707, PubMed:25920558). Also hasphospholipase C activities toward 1,2-diacylglycerolphosphocholineand 1,2-diacylglycerolphosphoglycerol.{ECO:0000269|PubMed:1840600, ECO:0000269|PubMed:18815062,ECO:0000269|PubMed:25920558, ECO:0000269|PubMed:27659707,ECO:0000305}. Isoform 2 lacks residues that bind the cofactor Zn(2+)and has no enzyme activity. {ECO:0000269|PubMed:1840600,ECO:0000305}. Isoform 3 lacks residues that bind the cofactor Zn(2+)and has no enzyme activity. {ECO:0000269|PubMed:1840600,ECO:0000305}.

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 NIPA1_SMPD1


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 NIPA1_SMPD1


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


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 NIPA1_SMPD1


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
TgeneSMPD1P17405DB00381AmlodipineSphingomyelin phosphodiesterasesmall moleculeapproved
TgeneSMPD1P17405DB01151DesipramineSphingomyelin phosphodiesterasesmall moleculeapproved|investigational
TgeneSMPD1P17405DB00477ChlorpromazineSphingomyelin phosphodiesterasesmall moleculeapproved|investigational|vet_approved

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RelatedDiseases for NIPA1_SMPD1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneNIPA1C1838192SPASTIC PARAPLEGIA 6, AUTOSOMAL DOMINANT (disorder)2CTD_human;ORPHANET;UNIPROT
TgeneSMPD1C0268243Niemann-Pick Disease, Type B25CTD_human;ORPHANET;UNIPROT
TgeneSMPD1C0268242Niemann-Pick Disease, Type A20CTD_human;ORPHANET;UNIPROT
TgeneSMPD1C0027626Neoplasm Invasiveness1CTD_human
TgeneSMPD1C0028064Niemann-Pick Diseases1CTD_human