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Center for Computational Systems Medicine
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Fusion Gene Summary

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Fusion Gene ORF analysis

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Fusion Genomic Features

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Fusion Protein Features

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Fusion Gene Sequence

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Fusion Gene PPI analysis

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Related Drugs

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Related Diseases

Fusion gene:NPC1-ANKRD29 (FusionGDB2 ID:59491)

Fusion Gene Summary for NPC1-ANKRD29

check button Fusion gene summary
Fusion gene informationFusion gene name: NPC1-ANKRD29
Fusion gene ID: 59491
HgeneTgene
Gene symbol

NPC1

ANKRD29

Gene ID

4864

147463

Gene nameNPC intracellular cholesterol transporter 1ankyrin repeat domain 29
SynonymsNPC|POGZ|SLC65A1-
Cytomap

18q11.2

18q11.2

Type of geneprotein-codingprotein-coding
DescriptionNPC intracellular cholesterol transporter 1Niemann-Pick C1 proteintruncated Niemann-Pick C1ankyrin repeat domain-containing protein 29
Modification date2020031520200313
UniProtAcc.

Q8N6D5

Ensembl transtripts involved in fusion geneENST00000269228, ENST00000412552, 
ENST00000540608, 		ENST00000592179, 
ENST00000322980, ENST00000585908, 
ENST00000284207, ENST00000586511, 
Fusion gene scores* DoF score7 X 10 X 8=5608 X 6 X 8=384
# samples 1211
** MAII scorelog2(12/560*10)=-2.22239242133645
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(11/384*10)=-1.8036027871965
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: NPC1 [Title/Abstract] AND ANKRD29 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointANKRD29(21209817)-NPC1(21102870), # samples:1
NPC1(21124308)-ANKRD29(21214113), # samples:1
NPC1(21113319)-ANKRD29(21229157), # samples:1
NPC1(21131591)-ANKRD29(21214113), # samples:1
Anticipated loss of major functional domain due to fusion event.NPC1-ANKRD29 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target 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)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
HgeneNPC1

GO:0006486

protein glycosylation

10821832

HgeneNPC1

GO:0030301

cholesterol transport

18772377

HgeneNPC1

GO:0033344

cholesterol efflux

16141411

HgeneNPC1

GO:0042632

cholesterol homeostasis

12719428

HgeneNPC1

GO:0090150

establishment of protein localization to membrane

23360953


check buttonFusion gene breakpoints across NPC1 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check buttonFusion gene breakpoints across ANKRD29 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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-A09A-01ANPC1chr18

21124308

-ANKRD29chr18

21214113

-
ChimerDB4HNSCTCGA-CR-7369NPC1chr18

21113319

-ANKRD29chr18

21229157

-
ChimerDB4UCECTCGA-AX-A3G4-01ANPC1chr18

21131591

-ANKRD29chr18

21214113

-


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Fusion Gene ORF analysis for NPC1-ANKRD29

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-frameENST00000269228ENST00000592179NPC1chr18

21124308

-ANKRD29chr18

21214113

-
In-frameENST00000269228ENST00000322980NPC1chr18

21124308

-ANKRD29chr18

21214113

-
5CDS-intronENST00000269228ENST00000585908NPC1chr18

21124308

-ANKRD29chr18

21214113

-
5CDS-intronENST00000269228ENST00000284207NPC1chr18

21124308

-ANKRD29chr18

21214113

-
5CDS-intronENST00000269228ENST00000586511NPC1chr18

21124308

-ANKRD29chr18

21214113

-
In-frameENST00000412552ENST00000592179NPC1chr18

21124308

-ANKRD29chr18

21214113

-
In-frameENST00000412552ENST00000322980NPC1chr18

21124308

-ANKRD29chr18

21214113

-
5CDS-intronENST00000412552ENST00000585908NPC1chr18

21124308

-ANKRD29chr18

21214113

-
5CDS-intronENST00000412552ENST00000284207NPC1chr18

21124308

-ANKRD29chr18

21214113

-
5CDS-intronENST00000412552ENST00000586511NPC1chr18

21124308

-ANKRD29chr18

21214113

-
5UTR-3CDSENST00000540608ENST00000592179NPC1chr18

21124308

-ANKRD29chr18

21214113

-
5UTR-3CDSENST00000540608ENST00000322980NPC1chr18

21124308

-ANKRD29chr18

21214113

-
5UTR-intronENST00000540608ENST00000585908NPC1chr18

21124308

-ANKRD29chr18

21214113

-
5UTR-intronENST00000540608ENST00000284207NPC1chr18

21124308

-ANKRD29chr18

21214113

-
5UTR-intronENST00000540608ENST00000586511NPC1chr18

21124308

-ANKRD29chr18

21214113

-
Frame-shiftENST00000269228ENST00000592179NPC1chr18

21113319

-ANKRD29chr18

21229157

-
Frame-shiftENST00000269228ENST00000322980NPC1chr18

21113319

-ANKRD29chr18

21229157

-
Frame-shiftENST00000269228ENST00000585908NPC1chr18

21113319

-ANKRD29chr18

21229157

-
Frame-shiftENST00000269228ENST00000284207NPC1chr18

21113319

-ANKRD29chr18

21229157

-
5CDS-intronENST00000269228ENST00000586511NPC1chr18

21113319

-ANKRD29chr18

21229157

-
Frame-shiftENST00000412552ENST00000592179NPC1chr18

21113319

-ANKRD29chr18

21229157

-
Frame-shiftENST00000412552ENST00000322980NPC1chr18

21113319

-ANKRD29chr18

21229157

-
Frame-shiftENST00000412552ENST00000585908NPC1chr18

21113319

-ANKRD29chr18

21229157

-
Frame-shiftENST00000412552ENST00000284207NPC1chr18

21113319

-ANKRD29chr18

21229157

-
5CDS-intronENST00000412552ENST00000586511NPC1chr18

21113319

-ANKRD29chr18

21229157

-
intron-3CDSENST00000540608ENST00000592179NPC1chr18

21113319

-ANKRD29chr18

21229157

-
intron-3CDSENST00000540608ENST00000322980NPC1chr18

21113319

-ANKRD29chr18

21229157

-
intron-3CDSENST00000540608ENST00000585908NPC1chr18

21113319

-ANKRD29chr18

21229157

-
intron-3CDSENST00000540608ENST00000284207NPC1chr18

21113319

-ANKRD29chr18

21229157

-
intron-intronENST00000540608ENST00000586511NPC1chr18

21113319

-ANKRD29chr18

21229157

-
Frame-shiftENST00000269228ENST00000592179NPC1chr18

21131591

-ANKRD29chr18

21214113

-
Frame-shiftENST00000269228ENST00000322980NPC1chr18

21131591

-ANKRD29chr18

21214113

-
5CDS-intronENST00000269228ENST00000585908NPC1chr18

21131591

-ANKRD29chr18

21214113

-
5CDS-intronENST00000269228ENST00000284207NPC1chr18

21131591

-ANKRD29chr18

21214113

-
5CDS-intronENST00000269228ENST00000586511NPC1chr18

21131591

-ANKRD29chr18

21214113

-
intron-3CDSENST00000412552ENST00000592179NPC1chr18

21131591

-ANKRD29chr18

21214113

-
intron-3CDSENST00000412552ENST00000322980NPC1chr18

21131591

-ANKRD29chr18

21214113

-
intron-intronENST00000412552ENST00000585908NPC1chr18

21131591

-ANKRD29chr18

21214113

-
intron-intronENST00000412552ENST00000284207NPC1chr18

21131591

-ANKRD29chr18

21214113

-
intron-intronENST00000412552ENST00000586511NPC1chr18

21131591

-ANKRD29chr18

21214113

-
5UTR-3CDSENST00000540608ENST00000592179NPC1chr18

21131591

-ANKRD29chr18

21214113

-
5UTR-3CDSENST00000540608ENST00000322980NPC1chr18

21131591

-ANKRD29chr18

21214113

-
5UTR-intronENST00000540608ENST00000585908NPC1chr18

21131591

-ANKRD29chr18

21214113

-
5UTR-intronENST00000540608ENST00000284207NPC1chr18

21131591

-ANKRD29chr18

21214113

-
5UTR-intronENST00000540608ENST00000586511NPC1chr18

21131591

-ANKRD29chr18

21214113

-

check buttonORFfinder result based on the fusion transcript sequence of in-frame fusion genes.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)

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

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Fusion Genomic Features for NPC1-ANKRD29


check buttonFusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints.
HgeneHchrHbpHstrandTgeneTchrTbpTstrand1-pp (fusion gene breakpoint)

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page.

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page.

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Fusion Protein Features for NPC1-ANKRD29


check button Go to

FGviewer for the breakpoints of chr18:21124308-chr18:21214113

.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
.ANKRD29

Q8N6D5

FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.

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
HgeneNPC1chr18:21124308chr18:21214113ENST00000269228-1325249_259710.01279.0Compositional biasNote=Poly-Pro
HgeneNPC1chr18:21124308chr18:21214113ENST00000269228-1325175_205710.01279.0RegionNote=Important for cholesterol binding and cholesterol transfer from NPC1 to liposomes
HgeneNPC1chr18:21124308chr18:21214113ENST00000269228-132523_261710.01279.0Topological domainLumenal
HgeneNPC1chr18:21124308chr18:21214113ENST00000269228-1325283_350710.01279.0Topological domainCytoplasmic
HgeneNPC1chr18:21124308chr18:21214113ENST00000269228-1325372_620710.01279.0Topological domainLumenal
HgeneNPC1chr18:21124308chr18:21214113ENST00000269228-1325642_653710.01279.0Topological domainCytoplasmic
HgeneNPC1chr18:21124308chr18:21214113ENST00000269228-1325676_685710.01279.0Topological domainLumenal
HgeneNPC1chr18:21124308chr18:21214113ENST00000269228-1325262_282710.01279.0TransmembraneHelical
HgeneNPC1chr18:21124308chr18:21214113ENST00000269228-1325351_371710.01279.0TransmembraneHelical
HgeneNPC1chr18:21124308chr18:21214113ENST00000269228-1325621_641710.01279.0TransmembraneHelical
HgeneNPC1chr18:21124308chr18:21214113ENST00000269228-1325654_675710.01279.0TransmembraneHelical
HgeneNPC1chr18:21124308chr18:21214113ENST00000269228-1325686_706710.01279.0TransmembraneHelical
TgeneANKRD29chr18:21124308chr18:21214113ENST0000032298039111_140110.0269.0RepeatNote=ANK 4
TgeneANKRD29chr18:21124308chr18:21214113ENST0000032298039144_173110.0269.0RepeatNote=ANK 5
TgeneANKRD29chr18:21124308chr18:21214113ENST0000032298039177_206110.0269.0RepeatNote=ANK 6
TgeneANKRD29chr18:21124308chr18:21214113ENST0000032298039210_239110.0269.0RepeatNote=ANK 7
TgeneANKRD29chr18:21124308chr18:21214113ENST0000032298039242_271110.0269.0RepeatNote=ANK 8
TgeneANKRD29chr18:21124308chr18:21214113ENST00000592179310111_140110.0302.0RepeatNote=ANK 4
TgeneANKRD29chr18:21124308chr18:21214113ENST00000592179310144_173110.0302.0RepeatNote=ANK 5
TgeneANKRD29chr18:21124308chr18:21214113ENST00000592179310177_206110.0302.0RepeatNote=ANK 6
TgeneANKRD29chr18:21124308chr18:21214113ENST00000592179310210_239110.0302.0RepeatNote=ANK 7
TgeneANKRD29chr18:21124308chr18:21214113ENST00000592179310242_271110.0302.0RepeatNote=ANK 8

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneNPC1chr18:21124308chr18:21214113ENST00000269228-1325620_785710.01279.0DomainSSD
HgeneNPC1chr18:21124308chr18:21214113ENST00000269228-13251119_1124710.01279.0Topological domainCytoplasmic
HgeneNPC1chr18:21124308chr18:21214113ENST00000269228-13251146_1150710.01279.0Topological domainLumenal
HgeneNPC1chr18:21124308chr18:21214113ENST00000269228-13251172_1194710.01279.0Topological domainCytoplasmic
HgeneNPC1chr18:21124308chr18:21214113ENST00000269228-13251216_1223710.01279.0Topological domainLumenal
HgeneNPC1chr18:21124308chr18:21214113ENST00000269228-13251245_1278710.01279.0Topological domainCytoplasmic
HgeneNPC1chr18:21124308chr18:21214113ENST00000269228-1325707_730710.01279.0Topological domainCytoplasmic
HgeneNPC1chr18:21124308chr18:21214113ENST00000269228-1325752_759710.01279.0Topological domainLumenal
HgeneNPC1chr18:21124308chr18:21214113ENST00000269228-1325784_832710.01279.0Topological domainCytoplasmic
HgeneNPC1chr18:21124308chr18:21214113ENST00000269228-1325854_1097710.01279.0Topological domainLumenal
HgeneNPC1chr18:21124308chr18:21214113ENST00000269228-13251098_1118710.01279.0TransmembraneHelical
HgeneNPC1chr18:21124308chr18:21214113ENST00000269228-13251125_1145710.01279.0TransmembraneHelical
HgeneNPC1chr18:21124308chr18:21214113ENST00000269228-13251151_1171710.01279.0TransmembraneHelical
HgeneNPC1chr18:21124308chr18:21214113ENST00000269228-13251195_1215710.01279.0TransmembraneHelical
HgeneNPC1chr18:21124308chr18:21214113ENST00000269228-13251224_1244710.01279.0TransmembraneHelical
HgeneNPC1chr18:21124308chr18:21214113ENST00000269228-1325731_751710.01279.0TransmembraneHelical
HgeneNPC1chr18:21124308chr18:21214113ENST00000269228-1325760_783710.01279.0TransmembraneHelical
HgeneNPC1chr18:21124308chr18:21214113ENST00000269228-1325833_853710.01279.0TransmembraneHelical
TgeneANKRD29chr18:21124308chr18:21214113ENST000003229803911_41110.0269.0RepeatNote=ANK 1
TgeneANKRD29chr18:21124308chr18:21214113ENST000003229803945_74110.0269.0RepeatNote=ANK 2
TgeneANKRD29chr18:21124308chr18:21214113ENST000003229803978_107110.0269.0RepeatNote=ANK 3
TgeneANKRD29chr18:21124308chr18:21214113ENST0000059217931011_41110.0302.0RepeatNote=ANK 1
TgeneANKRD29chr18:21124308chr18:21214113ENST0000059217931045_74110.0302.0RepeatNote=ANK 2
TgeneANKRD29chr18:21124308chr18:21214113ENST0000059217931078_107110.0302.0RepeatNote=ANK 3


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Fusion Gene Sequence for NPC1-ANKRD29


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones.

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Fusion Gene PPI Analysis for NPC1-ANKRD29


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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Related Drugs for NPC1-ANKRD29


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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Related Diseases for NPC1-ANKRD29


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneNPC1C3179455Niemann-Pick Disease, Type C126CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneNPC1C0220756Niemann-Pick Disease, Type C3CTD_human;GENOMICS_ENGLAND
HgeneNPC1C0268247Niemann-Pick Disease, Type D2CTD_human;GENOMICS_ENGLAND
HgeneNPC1C0004134Ataxia1CTD_human
HgeneNPC1C0004153Atherosclerosis1CTD_human
HgeneNPC1C0006309Brucellosis1CTD_human
HgeneNPC1C0013362Dysarthria1CTD_human
HgeneNPC1C0023890Liver Cirrhosis1CTD_human
HgeneNPC1C0023895Liver diseases1CTD_human
HgeneNPC1C0028754Obesity1CTD_human
HgeneNPC1C0029089Ophthalmoplegia1CTD_human
HgeneNPC1C0086565Liver Dysfunction1CTD_human
HgeneNPC1C0162292External Ophthalmoplegia1CTD_human
HgeneNPC1C0238198Gastrointestinal Stromal Tumors1CTD_human
HgeneNPC1C0239946Fibrosis, Liver1CTD_human
HgeneNPC1C0240952Dysarthria, Scanning1CTD_human
HgeneNPC1C0240991Ataxia, Sensory1CTD_human
HgeneNPC1C0278161Ataxia, Motor1CTD_human
HgeneNPC1C0339693Internal Ophthalmoplegia1CTD_human
HgeneNPC1C0427190Ataxia, Truncal1CTD_human
HgeneNPC1C0454596Dysarthria, Spastic1CTD_human
HgeneNPC1C0454597Dysarthria, Flaccid1CTD_human
HgeneNPC1C0454598Dysarthria, Mixed1CTD_human
HgeneNPC1C0520966Abnormal coordination1CTD_human
HgeneNPC1C0750937Ataxia, Appendicular1CTD_human
HgeneNPC1C0750940Tremor, Rubral1CTD_human
HgeneNPC1C0751401Ophthalmoparesis1CTD_human
HgeneNPC1C1563666Dysarthria, Guttural1CTD_human
HgeneNPC1C1563937Atherogenesis1CTD_human
HgeneNPC1C2231324Brucellosis, Pulmonary1CTD_human
HgeneNPC1C3179349Gastrointestinal Stromal Sarcoma1CTD_human