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	Fusion Gene Summary
	Fusion Gene ORF analysis
	Fusion Genomic Features
	Fusion Protein Features
	Fusion Gene Sequence
	Fusion Gene PPI analysis
	Related Drugs
	Related Diseases

Fusion gene:KLHDC10-SND1 (FusionGDB2 ID:42722)

Fusion Gene Summary for KLHDC10-SND1

Fusion gene summary

Fusion gene information	Fusion gene name: KLHDC10-SND1
	Fusion gene ID: 42722
		Hgene	Tgene
	Gene symbol	KLHDC10	SND1
	Gene ID	23008	27044
	Gene name	kelch domain containing 10	staphylococcal nuclease and tudor domain containing 1
	Synonyms	slim	TDRD11\|Tudor-SN\|p100
	Cytomap	7q32.2	7q32.1
	Type of gene	protein-coding	protein-coding
	Description	kelch domain-containing protein 10PNAS-119scruin like at the midline homolog	staphylococcal nuclease domain-containing protein 1EBNA2 coactivator p100testis tissue sperm-binding protein Li 82Ptudor domain-containing protein 11
	Modification date	20200313	20200313
	UniProtAcc	Q6PID8	Q7KZF4
	Ensembl transtripts involved in fusion gene	ENST00000335420, ENST00000495724,	ENST00000354725, ENST00000467238,
Fusion gene scores	* DoF score	9 X 4 X 6=216	29 X 24 X 11=7656
	# samples	9	33
	** MAII score	log2(9/216*10)=-1.26303440583379 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(33/7656*10)=-4.53605290024021 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context	PubMed: KLHDC10 [Title/Abstract] AND SND1 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint	KLHDC10(129769416)-SND1(127447538), # samples:2
Anticipated loss of major functional domain due to fusion event.

* DoF score (Degree of Frequency) = # partners X # break points X # cancer types
** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)

Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez

Partner	Gene	GO ID	GO term	PubMed ID
Tgene	SND1	GO:0010587	miRNA catabolic process	28546213

Fusion 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.

Fusion gene breakpoints across SND1 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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.

Source	Disease	Sample	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
ChimerDB4	OV	TCGA-24-1417-01A	KLHDC10	chr7	129769416	+	SND1	chr7	127447538	+
ChimerDB4	OV	TCGA-24-1417-01A	KLHDC10	chr7	129769416	+	SND1	chr7	127447538	+

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Fusion Gene ORF analysis for KLHDC10-SND1

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.

ORF	Henst	Tenst	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
In-frame	ENST00000335420	ENST00000354725	KLHDC10	chr7	129769416	+	SND1	chr7	127447538	+
5CDS-intron	ENST00000335420	ENST00000467238	KLHDC10	chr7	129769416	+	SND1	chr7	127447538	+
intron-3CDS	ENST00000495724	ENST00000354725	KLHDC10	chr7	129769416	+	SND1	chr7	127447538	+
intron-intron	ENST00000495724	ENST00000467238	KLHDC10	chr7	129769416	+	SND1	chr7	127447538	+

ORFfinder result based on the fusion transcript sequence of in-frame fusion genes.

Henst

Tenst

Hgene

Hchr

Hbp

Hstrand

Tgene

Tchr

Tbp

Tstrand

Seq length
(transcript)

BP loci
(transcript)

Predicted start
(transcript)

Predicted stop
(transcript)

Seq length
(amino acids)

ENST00000335420

KLHDC10

chr7

129769416

ENST00000354725

SND1

chr7

127447538

3383

1253

134

2833

899

DeepORF 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.

Henst	Tenst	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	No-coding score	Coding score
ENST00000335420	ENST00000354725	KLHDC10	chr7	129769416	+	SND1	chr7	127447538	+	0.000962577	0.9990375

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Fusion Genomic Features for KLHDC10-SND1

FusionAI 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.

Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	1-p	p (fusion gene breakpoint)
KLHDC10	chr7	129769416	+	SND1	chr7	127447537	+	7.90E-05	0.99992096
KLHDC10	chr7	129769416	+	SND1	chr7	127447537	+	7.90E-05	0.99992096

Distribution 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.

Distribution 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-SND1

Go to
FGviewer for the breakpoints of chr7:129769416-chr7:127447538
.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.

Main function of each fusion partner protein. (from UniProt)

Hgene	Tgene
KLHDC10 Q6PID8	SND1 Q7KZF4
FUNCTION: Participates in the oxidative stress-induced cell death through MAP3K5 activation. Inhibits PPP5C phosphatase activity on MAP3K5. {ECO:0000269\|PubMed:23102700}.	FUNCTION: Endonuclease that mediates miRNA decay of both protein-free and AGO2-loaded miRNAs (PubMed:28546213, PubMed:18453631). As part of its function in miRNA decay, regulates mRNAs involved in G1-to-S phase transition (PubMed:28546213). Functions as a bridging factor between STAT6 and the basal transcription factor (PubMed:12234934). Plays a role in PIM1 regulation of MYB activity (PubMed:9809063). Functions as a transcriptional coactivator for STAT5 (By similarity). {ECO:0000250\|UniProtKB:Q78PY7, ECO:0000269\|PubMed:12234934, ECO:0000269\|PubMed:18453631, ECO:0000269\|PubMed:28546213, ECO:0000269\|PubMed:9809063}.; FUNCTION: (Microbial infection) Functions as a transcriptional coactivator for the Epstein-Barr virus nuclear antigen 2 (EBNA2). {ECO:0000269\|PubMed:7651391}.

Retention 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.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

Hgene

KLHDC10

chr7:129769416

chr7:127447538

ENST00000335420

14_40

373.0

443.0

Compositional bias

Note=Gly-rich

Hgene

KLHDC10

chr7:129769416

chr7:127447538

ENST00000335420

103_164

373.0

443.0

Repeat

Note=Kelch 1

Hgene

KLHDC10

chr7:129769416

chr7:127447538

ENST00000335420

166_217

373.0

443.0

Repeat

Note=Kelch 2

Hgene

KLHDC10

chr7:129769416

chr7:127447538

ENST00000335420

218_270

373.0

443.0

Repeat

Note=Kelch 3

Hgene

KLHDC10

chr7:129769416

chr7:127447538

ENST00000335420

271_319

373.0

443.0

Repeat

Note=Kelch 4

Hgene

KLHDC10

chr7:129769416

chr7:127447538

ENST00000335420

327_373

373.0

443.0

Repeat

Note=Kelch 5

Tgene

SND1

chr7:129769416

chr7:127447538

ENST00000354725

525_660

384.0

911.0

Domain

TNase-like 4

Tgene

SND1

chr7:129769416

chr7:127447538

ENST00000354725

729_787

384.0

911.0

Domain

Tudor

Tgene

SND1

chr7:129769416

chr7:127447538

ENST00000354725

388_392

384.0

911.0

Motif

Nuclear localization signal

- In-frame and not-retained protein feature among the 13 regional features.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

Hgene

KLHDC10

chr7:129769416

chr7:127447538

ENST00000335420

376_419

373.0

443.0

Repeat

Note=Kelch 6

Tgene

SND1

chr7:129769416

chr7:127447538

ENST00000354725

18_166

384.0

911.0

Domain

TNase-like 1

Tgene

SND1

chr7:129769416

chr7:127447538

ENST00000354725

193_328

384.0

911.0

Domain

TNase-like 2

Tgene

SND1

chr7:129769416

chr7:127447538

ENST00000354725

341_496

384.0

911.0

Domain

TNase-like 3

Tgene

SND1

chr7:129769416

chr7:127447538

ENST00000354725

321_325

384.0

911.0

Motif

Nuclear localization signal

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Fusion Gene Sequence for KLHDC10-SND1

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_ENST00000354725_TCGA-24-1417-01A_KLHDC10_chr7_129769416_+_SND1_chr7_127447538_length(transcript)=3383nt_BP=1253nt
TGGTCTCTGGTGGGACCGGGCGCTGCCCCCTTCCCCTGTCTCCTGGGTCTCTGGAGGAGCCCAGGAAGGAGGCTCCGCTGGTTCCGCTGG
GTCAGGCGCTGACGGGACCGGGCTGCGGCAATCGTTAGCGGGTCATGTCGGCCGCCCAGGGCTGGGACAGGAACCGCCGGAGGGGAGGAG
GCGCCGCCGGCGCTGGTGGCGGAGGTAGCGGGGCCGGCGGGGGCAGTGGGGGCAGCGGGGGTCGGGGGACTGGCCAGCTCAACCGCTTCG
TGCAACTCTCCGGGCGGCCGCACCTGCCAGGTAAGAAGAAAATACGATGGGACCCAGTTAGGAGGCGCTTCATTCAGTCCTGTCCCATCA
TAAGGATCCCTAACAGGTTTTTGAGAGGCCACAGACCTCCACCAGCACGAAGTGGACATCGTTGTGTGGCAGATAATACCAACCTATATG
TGTTTGGAGGTTATAACCCAGATTATGATGAATCGGGAGGGCCTGATAATGAAGACTATCCTCTCTTCAGGGAACTCTGGAGGTATCATT
TTGCTACAGGAGTATGGCACCAGATGGGCACAGATGGCTACATGCCCCGGGAATTGGCATCTATGTCACTTGTGCTGCATGGAAACAACC
TGTTAGTATTTGGAGGTACGGGCATCCCATTTGGAGAGAGCAACGGCAATGACGTCCATGTGTGTAATGTGAAGTATAAGAGATGGGCTT
TGCTCAGCTGTCGGGGGAAGAAACCCAGTCGTATATATGGACAGGCTATGGCCATCATCAATGGCTCCCTTTATGTCTTTGGAGGTACAA
CCGGCTATATTTACAGCACAGACCTGCACAAGTTAGATCTCAATACCAGAGAGTGGACACAACTGAAACCAAACAACCTATCCTGTGATC
TACCAGAAGAGAGATACCGACATGAAATTGCACATGACGGGCAGAGGATTTACATCTTGGGAGGTGGTACTTCCTGGACAGCATATTCCT
TAAACAAGATCCATGCATACAACCTTGAAACGAATGCCTGGGAGGAAATTGCAACAAAACCCCATGAAAAAATAGGCTTTCCTGCAGCCC
GAAGGTGTCACAGTTGTGTTCAAATAAAAAATGATGTATTTATTTGTGGGGGCTATAATGGAGAGGTGATCCTGGGAGATATCTGGAAGT
TGAATCTGCAGACTTTCCAATGGGTGAAGCTCCCAGCTACCATGCCAGAGCCAGTTTATTTTCACTGTGCAGCTGTTACACCAGATAAGA
ACAAGAAACTGCGTCCCCTGTATGACATTCCTTACATGTTTGAGGCCCGGGAATTTCTTCGAAAAAAGCTTATTGGGAAGAAGGTCAATG
TGACGGTGGACTACATTAGACCAGCCAGCCCAGCCACAGAGACAGTGCCTGCCTTTTCAGAGCGTACCTGTGCCACTGTCACCATTGGAG
GAATAAACATTGCTGAGGCTCTTGTCAGCAAAGGTCTAGCCACAGTGATCAGATACCGGCAGGATGATGACCAGAGATCATCACACTACG
ATGAACTGCTTGCTGCAGAGGCCAGAGCTATTAAGAATGGCAAAGGATTGCATAGCAAGAAGGAAGTGCCTATCCACCGTGTTGCAGATA
TATCTGGGGATACCCAAAAAGCAAAGCAGTTCCTGCCTTTTCTTCAGCGGGCAGGTCGTTCTGAAGCTGTGGTGGAATACGTCTTCAGTG
GTTCTCGTCTCAAACTCTATTTGCCAAAGGAAACTTGCCTTATCACCTTCTTGCTTGCAGGCATTGAATGCCCCAGAGGAGCCCGAAACC
TCCCAGGCTTGGTGCAGGAAGGAGAGCCCTTCAGCGAGGAAGCTACACTTTTCACCAAGGAACTGGTGCTGCAGCGAGAGGTGGAGGTGG
AGGTGGAGAGCATGGACAAGGCCGGCAACTTTATCGGCTGGCTGCACATCGACGGTGCCAACCTGTCCGTCCTGCTGGTGGAGCACGCGC
TCTCCAAGGTCCACTTCACCGCCGAACGCAGCTCCTACTACAAGTCCCTGCTGTCTGCCGAGGAGGCCGCAAAGCAGAAGAAAGAGAAGG
TCTGGGCCCACTATGAGGAGCAGCCCGTGGAGGAGGTGATGCCAGTGCTGGAGGAGAAGGAGCGATCTGCTAGCTACAAGCCCGTGTTTG
TGACTGAGATCACTGATGACCTGCACTTCTACGTGCAGGATGTGGAGACCGGCACCCAGTTGGAGAAGCTGATGGAGAACATGCGCAATG
ACATTGCCAGTCACCCCCCTGTAGAGGGCTCCTATGCCCCCCGCAGGGGAGAGTTCTGCATTGCCAAATTTGTAGATGGAGAATGGTACC
GTGCCCGAGTAGAGAAAGTCGAGTCTCCTGCCAAAATACATGTCTTCTACATTGACTACGGCAACAGAGAGGTCCTGCCATCCACCCGCC
TGGGTACCCTATCACCTGCCTTCAGCACTCGGGTGCTGCCAGCTCAAGCCACGGAGTATGCCTTCGCCTTCATCCAGGTGCCCCAAGATG
ATGATGCCCGCACGGACGCCGTGGACAGCGTAGTTCGGGATATCCAGAACACTCAGTGCCTGCTCAACGTGGAACACCTGAGTGCCGGCT
GCCCCCATGTCACCCTGCAGTTTGCAGATTCCAAGGGCGATGTGGGGCTGGGCTTGGTGAAGGAAGGGCTGGTCATGGTGGAGGTGCGCA
AGGAGAAACAGTTCCAGAAAGTGATCACAGAATACCTGAATGCCCAAGAGTCAGCCAAGAGCGCCAGGCTGAACCTGTGGCGCTATGGAG
ACTTTCGAGCTGATGATGCAGACGAATTTGGCTACAGCCGCTAAGGAGGGGATCGGGTTTGGCCCCCAGCCCCGCTCACGCCAGTCCCTC
TTCCTCTGCCGGGAGGGTGTTTTCAACTCCAAACCCCAGAGAGGGGTTGTAGATTGGGTCCAGCTTTGCTTCAGTGTGTGGAAATGTCTC
GTGGGGTGGCATCGGGGCTGCGGGGTGGGGACCCCAAGGCTTTCTGGGGCAGACCCTTGTCCTCTGGGATGATGGGCACTGCTATCCACA
GTCTCTGCCAGTTGGTTTTATTTGGAGGTTTGTGGGCTTTTTTTAAAAAAAAAAAGTCCTCAAATCAGGAAGAAACATCAAAGACTATGT
CCTAGTGGAGGGAGTAATCCTAACACCCAGGCTGGCCGCCAGCTGGCACCTGCCTCTATCCCAGACTGCCCTCGTCCCAGCTCTCTGTCC
AACTGTTGATTATGTGATTTTTCTGATACGTCCATTCTCAAATGCCAGTGTGTTCACATCTTCGCTCTGGCCAGCCCATTCTGTATTTAA

>In-frame_ENST00000335420_ENST00000354725_TCGA-24-1417-01A_KLHDC10_chr7_129769416_+_SND1_chr7_127447538_length(amino acids)=899AA_start in transcript=134_stop in transcript=2833
MSAAQGWDRNRRRGGGAAGAGGGGSGAGGGSGGSGGRGTGQLNRFVQLSGRPHLPGKKKIRWDPVRRRFIQSCPIIRIPNRFLRGHRPPP
ARSGHRCVADNTNLYVFGGYNPDYDESGGPDNEDYPLFRELWRYHFATGVWHQMGTDGYMPRELASMSLVLHGNNLLVFGGTGIPFGESN
GNDVHVCNVKYKRWALLSCRGKKPSRIYGQAMAIINGSLYVFGGTTGYIYSTDLHKLDLNTREWTQLKPNNLSCDLPEERYRHEIAHDGQ
RIYILGGGTSWTAYSLNKIHAYNLETNAWEEIATKPHEKIGFPAARRCHSCVQIKNDVFICGGYNGEVILGDIWKLNLQTFQWVKLPATM
PEPVYFHCAAVTPDKNKKLRPLYDIPYMFEAREFLRKKLIGKKVNVTVDYIRPASPATETVPAFSERTCATVTIGGINIAEALVSKGLAT
VIRYRQDDDQRSSHYDELLAAEARAIKNGKGLHSKKEVPIHRVADISGDTQKAKQFLPFLQRAGRSEAVVEYVFSGSRLKLYLPKETCLI
TFLLAGIECPRGARNLPGLVQEGEPFSEEATLFTKELVLQREVEVEVESMDKAGNFIGWLHIDGANLSVLLVEHALSKVHFTAERSSYYK
SLLSAEEAAKQKKEKVWAHYEEQPVEEVMPVLEEKERSASYKPVFVTEITDDLHFYVQDVETGTQLEKLMENMRNDIASHPPVEGSYAPR
RGEFCIAKFVDGEWYRARVEKVESPAKIHVFYIDYGNREVLPSTRLGTLSPAFSTRVLPAQATEYAFAFIQVPQDDDARTDAVDSVVRDI

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

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Fusion Gene PPI Analysis for KLHDC10-SND1

Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in
ChiPPI page.

Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160)

Hgene

Hgene's interactors

Tgene

Tgene's interactors

- Retained PPIs in in-frame fusion.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Still interaction with

- Lost PPIs in in-frame fusion.

Partner	Gene	Hbp	Tbp	ENST	Strand	BPexon	TotalExon	Protein feature loci	*BPloci	TotalLen	Interaction lost with
Hgene	KLHDC10	chr7:129769416	chr7:127447538	ENST00000335420	+	9	10	401_442	373.0	443.0	CUL2

- Retained PPIs, but lost function due to frame-shift fusion.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Interaction lost with

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Related Drugs for KLHDC10-SND1

Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)

Partner

Gene

UniProtAcc

DrugBank ID

Drug name

Drug activity

Drug type

Drug status

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Related Diseases for KLHDC10-SND1

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner	Gene	Disease ID	Disease name	# pubmeds	Source
Hgene	KLHDC10	C0006142	Malignant neoplasm of breast	1	CTD_human
Hgene	KLHDC10	C0678222	Breast Carcinoma	1	CTD_human
Hgene	KLHDC10	C1257931	Mammary Neoplasms, Human	1	CTD_human
Hgene	KLHDC10	C1458155	Mammary Neoplasms	1	CTD_human
Hgene	KLHDC10	C4704874	Mammary Carcinoma, Human	1	CTD_human
Tgene	SND1	C0004352	Autistic Disorder	1	CTD_human
Tgene	SND1	C0024121	Lung Neoplasms	1	CTD_human
Tgene	SND1	C0242379	Malignant neoplasm of lung	1	CTD_human