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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:KLHDC10-NBPF10 (FusionGDB2 ID:42718)

Fusion Gene Summary for KLHDC10-NBPF10

check button Fusion gene summary
Fusion gene informationFusion gene name: KLHDC10-NBPF10
Fusion gene ID: 42718
HgeneTgene
Gene symbol

KLHDC10

NBPF10

Gene ID

23008

100132406

Gene namekelch domain containing 10NBPF member 10
SynonymsslimAB6|AG1|NBPF9
Cytomap

7q32.2

1q21.1

Type of geneprotein-codingprotein-coding
Descriptionkelch domain-containing protein 10PNAS-119scruin like at the midline homologneuroblastoma breakpoint family member 10
Modification date2020031320200313
UniProtAcc

Q6PID8

Q6P3W6

Ensembl transtripts involved in fusion geneENST00000335420, ENST00000495724, 
ENST00000369339, ENST00000369338, 
ENST00000342960, 
Fusion gene scores* DoF score9 X 4 X 6=2162 X 2 X 2=8
# samples 92
** MAII scorelog2(9/216*10)=-1.26303440583379
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(2/8*10)=1.32192809488736
Context

PubMed: KLHDC10 [Title/Abstract] AND NBPF10 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointKLHDC10(129710649)-NBPF10(145368441), # samples:1
Anticipated loss of major functional domain due to fusion event.KLHDC10-NBPF10 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
KLHDC10-NBPF10 seems lost the major protein functional domain in Tgene partner, which is a essential gene 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

check buttonFusion gene breakpoints across KLHDC10 (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 NBPF10 (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
ChimerDB4STADTCGA-BR-A4PD-01AKLHDC10chr7

129710649

+NBPF10chr1

145368441

+


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Fusion Gene ORF analysis for KLHDC10-NBPF10

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-frameENST00000335420ENST00000369339KLHDC10chr7

129710649

+NBPF10chr1

145368441

+
Frame-shiftENST00000335420ENST00000369338KLHDC10chr7

129710649

+NBPF10chr1

145368441

+
Frame-shiftENST00000335420ENST00000342960KLHDC10chr7

129710649

+NBPF10chr1

145368441

+
intron-3CDSENST00000495724ENST00000369339KLHDC10chr7

129710649

+NBPF10chr1

145368441

+
intron-3CDSENST00000495724ENST00000369338KLHDC10chr7

129710649

+NBPF10chr1

145368441

+
intron-3CDSENST00000495724ENST00000342960KLHDC10chr7

129710649

+NBPF10chr1

145368441

+

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)
ENST00000335420KLHDC10chr7129710649+ENST00000369339NBPF10chr1145368441+2163300274291

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
ENST00000335420ENST00000369339KLHDC10chr7129710649+NBPF10chr1145368441+0.143171560.8568284

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Fusion Genomic Features for KLHDC10-NBPF10


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)
KLHDC10chr7129710649+NBPF10chr1145368440+3.36E-091
KLHDC10chr7129710649+NBPF10chr1145368440+3.36E-091

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 KLHDC10-NBPF10


check button Go to

FGviewer for the breakpoints of chr7:129710649-chr1:145368441

.
- 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
KLHDC10

Q6PID8

NBPF10

Q6P3W6

FUNCTION: Participates in the oxidative stress-induced cell death through MAP3K5 activation. Inhibits PPP5C phosphatase activity on MAP3K5. {ECO:0000269|PubMed:23102700}.

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
HgeneKLHDC10chr7:129710649chr1:145368441ENST00000335420+11014_4055.333333333333336443.0Compositional biasNote=Gly-rich

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneKLHDC10chr7:129710649chr1:145368441ENST00000335420+110103_16455.333333333333336443.0RepeatNote=Kelch 1
HgeneKLHDC10chr7:129710649chr1:145368441ENST00000335420+110166_21755.333333333333336443.0RepeatNote=Kelch 2
HgeneKLHDC10chr7:129710649chr1:145368441ENST00000335420+110218_27055.333333333333336443.0RepeatNote=Kelch 3
HgeneKLHDC10chr7:129710649chr1:145368441ENST00000335420+110271_31955.333333333333336443.0RepeatNote=Kelch 4
HgeneKLHDC10chr7:129710649chr1:145368441ENST00000335420+110327_37355.333333333333336443.0RepeatNote=Kelch 5
HgeneKLHDC10chr7:129710649chr1:145368441ENST00000335420+110376_41955.333333333333336443.0RepeatNote=Kelch 6


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Fusion Gene Sequence for KLHDC10-NBPF10


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.
>In-frame_ENST00000335420_ENST00000369339_TCGA-BR-A4PD-01A_KLHDC10_chr7_129710649_+_NBPF10_chr1_145368441_length(transcript)=2163nt_BP=300nt
TGGTCTCTGGTGGGACCGGGCGCTGCCCCCTTCCCCTGTCTCCTGGGTCTCTGGAGGAGCCCAGGAAGGAGGCTCCGCTGGTTCCGCTGG
GTCAGGCGCTGACGGGACCGGGCTGCGGCAATCGTTAGCGGGTCATGTCGGCCGCCCAGGGCTGGGACAGGAACCGCCGGAGGGGAGGAG
GCGCCGCCGGCGCTGGTGGCGGAGGTAGCGGGGCCGGCGGGGGCAGTGGGGGCAGCGGGGGTCGGGGGACTGGCCAGCTCAACCGCTTCG
TGCAACTCTCCGGGCGGCCGCACCTGCCAGGCTCAACGGCGTGCTGATGGAAGTGGAAGAGCGTGAAGTCTTACAGGACTCACTGGATAG
ATGTTATTCGACTCCGTCAATGTACTTTGAACTACCTGACTCATTCCAGCACTACAGAAGTGTGTTTTACTCATTTGAGGAACAGCACAT
CAGCTTCGCCCTTTACGTGGACAATAGGTTTTTTACTTTGACGGTGACAAGTCTCCACCTGGTGTTCCAGATGGGAGTCATATTCCCACA
ATAAGCAGCCCTTAGTAATCCGAGAGATGTCATTCCTGCAGGCAGGACCTATAGGCAAGTGAAGATTTGAATGAAAGTACAGTTCCATTT
GGAAGCCCAGACATAGGATGGGTCAGTGGGCATGGCTCTATTCCTATTCTCAAACCATGCCAGTGGCAACCTGTGCGCAGTCTGAAGACA
ATGGACCCACATTAGGTGTGACACGTTCACATAACTGTGCAGCACATGCCGGGAGTGATCAGTCAGACATTTTAATTTGAACCACGTATC
TCTGGGTAGCTACAAAATTCCTCAGGGATTTCATTTTGCAGGCATGTCTCTGAGCTTCTATACCTGCTCAAGGTCATTGTCATCTTTGTG
TTTAGCTCATCCAAAGGTGTTACCCTGGTTTCAATGAACCTAACCTCATTCTTTGTGTCTTCAGTGTTGGCTTGTTTTAGCTGATCCATC
TGTAACACAGGAGGGATCCTTGGCTGAGGATTGTATTTCAGAACCACCAACTGCTCTTGACAATTGTTAACCCGCTAGACTCCTTTGGTT
AGAGAAGCCACAGTCCTTCAGCCTCCAATTGGTGTCAGTACTTAGGAAGACCACAGCTAGATGGACAAACAGCATTGGGAGGCCTTAGCC
CTGCTCCTCTCAATTCCATCCTGTAGAGAACAGGAGTCAGGAGCCGCTGGCAGGAGACAGCATGTCACCCAGGACTCTGCCGGTGCAGAA
TATGAACAATGCCATGTTCTTGCAGAAAACGCTTAGCCTGAGTTTCATAGGAGGTAATCACCAGACAACTGCAGAATGTAGAACACTGAG
CAGGACAACTGACCTGTCTCCTTCACATAGTCCATATCACCACAAATCACACAACAAAAAGGAGAAGAGATATTTTGGGTTCAAAAAAAG
TAAAAAGATAATGTAGCTGCATTTCTTTAGTTATTTTGAACCCCAAATATTTCCTCATCTTTTTGTTGTTGTCATGGATGGTGGTGACAT
GGACTTGTTTATAGAAGACAGGTCAGCTGTCTGGCTCAATGATCTACATTCTGAAGTTGTCTGAAAATGTCTTCATGATTAAATTCAGCC
TAAACGTTTTGCCAGGAACACTGCAGAGACAATGCTGTGAGTTTCCAACCTCAGCCCATCTGCGGGCAGAGAAGGTCTAGTTTGTCCATC
ACCATTATGATATCAGGACTGGTTACTTGGTTAAGGAGGGGTCTAGGAGATCTGTCCCTTTTAGAGACACCTTACTTACAATGAAGTACT
TGGGAAAGTGGTTTTCAAGAGTATAAATATCCTGTATTCTAATGATCATCCTCTAAACATTTTATCATTTATTAATCCTCCCTGCCTGTG
TCTATTATTATATTCATATCTCTACACTGCAAATTTGGGGTCTCAATTTTTACTGTGCCTTTGTTTTTACTAGTGTCTGCTGTTGCAAAA
AGAAGACATTCTCTGCCTGAGTTTTAATTTTTGTCCAAAGTTAATTTTAATCTATACAATTAAAACCTTTTGCCTATCACTCTGGACTTT
TGGATTGTTTTTTACATTCAGTGTTATAATATTTGATTATGGTGATTGGTTTTGGTGGGTACTGATGCGAATTAATAAAAACATTTCATT

>In-frame_ENST00000335420_ENST00000369339_TCGA-BR-A4PD-01A_KLHDC10_chr7_129710649_+_NBPF10_chr1_145368441_length(amino acids)=91AA_start in transcript=274_stop in transcript=2
MHEAVELASPPTPAAPTAPAGPATSATSAGGASSPPAVPVPALGGRHDPLTIAAARSRQRLTQRNQRSLLPGLLQRPRRQGKGAAPGPTR

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

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Fusion Gene PPI Analysis for KLHDC10-NBPF10


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
HgeneKLHDC10chr7:129710649chr1:145368441ENST00000335420+110401_44255.333333333333336443.0CUL2


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 KLHDC10-NBPF10


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 KLHDC10-NBPF10


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneKLHDC10C0006142Malignant neoplasm of breast1CTD_human
HgeneKLHDC10C0678222Breast Carcinoma1CTD_human
HgeneKLHDC10C1257931Mammary Neoplasms, Human1CTD_human
HgeneKLHDC10C1458155Mammary Neoplasms1CTD_human
HgeneKLHDC10C4704874Mammary Carcinoma, Human1CTD_human