UTHEALTH HOME ABOUT SBMI A-Z WEBMAIL INSIDE THE UNIVERSITY

Home

Download

Statistics

Examples

Help

Contact

level1

	Fusion Gene Summary
	Fusion Gene Sample Information
	Fusion ORF Analysis
	Fusion Amino Acid Sequences
	Fusion Protein Functional Features
	Fusion Protein-Protein Interaction
	Related drugs with this fusion protein
	Related disease with this fusion protein

Fusion Protein:KDM6A-YEATS4

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: KDM6A-YEATS4
	FusionPDB ID: 41915
	FusionGDB2.0 ID: 41915
		Hgene	Tgene
	Gene symbol	KDM6A	YEATS4
	Gene ID	7403	8089
	Gene name	lysine demethylase 6A	YEATS domain containing 4
	Synonyms	KABUK2\|UTX\|bA386N14.2	4930573H17Rik\|B230215M10Rik\|GAS41\|NUBI-1\|YAF9
	Cytomap	Xp11.3	12q15
	Type of gene	protein-coding	protein-coding
	Description	lysine-specific demethylase 6AbA386N14.2 (ubiquitously transcribed X chromosome tetratricopeptide repeat protein (UTX))histone demethylase UTXlysine (K)-specific demethylase 6Aubiquitously transcribed tetratricopeptide repeat protein X-linkedubiquito	YEATS domain-containing protein 4NuMA binding protein 1glioma-amplified sequence 41nuBI1
	Modification date	20200313	20200313
	UniProtAcc	O15550	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000377967, ENST00000382899, ENST00000536777, ENST00000543216, ENST00000479423,	ENST00000247843, ENST00000548020,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	19 X 9 X 11=1881	10 X 4 X 4=160
	# samples	20	10
	** MAII score	log2(20/1881*10)=-3.23342794374847 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(10/160*10)=-0.678071905112638 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)	PubMed: KDM6A [Title/Abstract] AND YEATS4 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	KDM6A(44920664)-YEATS4(69783927), # samples:2
Anticipated loss of major functional domain due to fusion event.	KDM6A-YEATS4 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF. KDM6A-YEATS4 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF. KDM6A-YEATS4 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF. KDM6A-YEATS4 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.

* 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	YEATS4	GO:0043967	histone H4 acetylation	14966270
Tgene	YEATS4	GO:0043968	histone H2A acetylation	14966270

Fusion gene breakpoints across KDM6A (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 YEATS4 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

Top

Fusion Gene Sample Information

Fusion gene information from FusionGDB2.0.

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-13-0901-01B	KDM6A	chrX	44920664	+	YEATS4	chr12	69783927	+

Top

Fusion ORF Analysis

Fusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.

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)
ENST00000377967	KDM6A	chrX	44920664	+	ENST00000247843	YEATS4	chr12	69783927	+	2116	1466	41	1483	480
ENST00000377967	KDM6A	chrX	44920664	+	ENST00000548020	YEATS4	chr12	69783927	+	1951	1466	41	1483	480
ENST00000382899	KDM6A	chrX	44920664	+	ENST00000247843	YEATS4	chr12	69783927	+	2113	1463	17	1480	487
ENST00000382899	KDM6A	chrX	44920664	+	ENST00000548020	YEATS4	chr12	69783927	+	1948	1463	17	1480	487
ENST00000536777	KDM6A	chrX	44920664	+	ENST00000247843	YEATS4	chr12	69783927	+	1957	1307	17	1324	435
ENST00000536777	KDM6A	chrX	44920664	+	ENST00000548020	YEATS4	chr12	69783927	+	1792	1307	17	1324	435
ENST00000543216	KDM6A	chrX	44920664	+	ENST00000247843	YEATS4	chr12	69783927	+	1940	1290	0	1307	435
ENST00000543216	KDM6A	chrX	44920664	+	ENST00000548020	YEATS4	chr12	69783927	+	1775	1290	0	1307	435

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
ENST00000377967	ENST00000247843	KDM6A	chrX	44920664	+	YEATS4	chr12	69783927	+	0.000302182	0.9996978
ENST00000377967	ENST00000548020	KDM6A	chrX	44920664	+	YEATS4	chr12	69783927	+	0.000493409	0.9995066
ENST00000382899	ENST00000247843	KDM6A	chrX	44920664	+	YEATS4	chr12	69783927	+	0.000462881	0.9995371
ENST00000382899	ENST00000548020	KDM6A	chrX	44920664	+	YEATS4	chr12	69783927	+	0.000770815	0.9992292
ENST00000536777	ENST00000247843	KDM6A	chrX	44920664	+	YEATS4	chr12	69783927	+	0.000209537	0.9997905
ENST00000536777	ENST00000548020	KDM6A	chrX	44920664	+	YEATS4	chr12	69783927	+	0.000341685	0.99965835
ENST00000543216	ENST00000247843	KDM6A	chrX	44920664	+	YEATS4	chr12	69783927	+	0.000216704	0.99978334
ENST00000543216	ENST00000548020	KDM6A	chrX	44920664	+	YEATS4	chr12	69783927	+	0.000358069	0.9996419

Top

Fusion Amino Acid Sequences

For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones.

>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

>41915_41915_1_KDM6A-YEATS4_KDM6A_chrX_44920664_ENST00000377967_YEATS4_chr12_69783927_ENST00000247843_length(amino acids)=480AA_BP=
MKSCGVSLATAAAAAAAFGDEEKKMAAGKASGESEEASPSLTAEEREALGGLDSRLFGFVRFHEDGARTKALLGKAVRCYESLILKAEGK
VESDFFCQLGHFNLLLEDYPKALSAYQRYYSLQSDYWKNAAFLYGLGLVYFHYNAFQWAIKAFQEVLYVDPSFCRAKEIHLRLGLMFKVN
TDYESSLKHFQLALVDCNPCTLSNAEIQFHIAHLYETQRKYHSAKEAYEQLLQTENLSAQVKATVLQQLGWMHHTVDLLGDKATKESYAI
QYLQKSLEADPNSGQSWYFLGRCYSSIGKVQDAFISYRQSIDKSEASADTWCSIGVLYQQQNQPMDALQAYICAVQLDHGHAAAWMDLGT
LYESCNQPQDAIKCYLNATRSKSCSNTSALAARIKYLQAQLCNLPQGSLQNKTKLLPSIEEAWSLPIPAELTSRQGAMNTAQQNTSDNWS

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

>41915_41915_2_KDM6A-YEATS4_KDM6A_chrX_44920664_ENST00000377967_YEATS4_chr12_69783927_ENST00000548020_length(amino acids)=480AA_BP=
MKSCGVSLATAAAAAAAFGDEEKKMAAGKASGESEEASPSLTAEEREALGGLDSRLFGFVRFHEDGARTKALLGKAVRCYESLILKAEGK
VESDFFCQLGHFNLLLEDYPKALSAYQRYYSLQSDYWKNAAFLYGLGLVYFHYNAFQWAIKAFQEVLYVDPSFCRAKEIHLRLGLMFKVN
TDYESSLKHFQLALVDCNPCTLSNAEIQFHIAHLYETQRKYHSAKEAYEQLLQTENLSAQVKATVLQQLGWMHHTVDLLGDKATKESYAI
QYLQKSLEADPNSGQSWYFLGRCYSSIGKVQDAFISYRQSIDKSEASADTWCSIGVLYQQQNQPMDALQAYICAVQLDHGHAAAWMDLGT
LYESCNQPQDAIKCYLNATRSKSCSNTSALAARIKYLQAQLCNLPQGSLQNKTKLLPSIEEAWSLPIPAELTSRQGAMNTAQQNTSDNWS

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

>41915_41915_3_KDM6A-YEATS4_KDM6A_chrX_44920664_ENST00000382899_YEATS4_chr12_69783927_ENST00000247843_length(amino acids)=487AA_BP=
MKSCGVSLATAAAAAAAFGDEEKKMAAGKASGESEEASPSLTAEEREALGGLDSRLFGFVRFHEDGARTKALLGKAVRCYESLILKAEGK
VESDFFCQLGHFNLLLEDYPKALSAYQRYYSLQSDYWKNAAFLYGLGLVYFHYNAFQWAIKAFQEVLYVDPSFCRAKEIHLRLGLMFKVN
TDYESSLKHFQLALVDCNPCTLSNAEIQFHIAHLYETQRKYHSAKEAYEQLLQTENLSAQVKATVLQQLGWMHHTVDLLGDKATKESYAI
QYLQKSLEADPNSGQSWYFLGRCYSSIGKVQDAFISYRQSIDKSEASADTWCSIGVLYQQQNQPMDALQAYICAVQLDHGHAAAWMDLGT
LYESCNQPQDAIKCYLNATRSKSCSNTSALAARIKYLQACKPHHPNTEPVLGLSQTPISQQSLPLHMIPSSQVDDLSSPAKRKRTSSPTK

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

>41915_41915_4_KDM6A-YEATS4_KDM6A_chrX_44920664_ENST00000382899_YEATS4_chr12_69783927_ENST00000548020_length(amino acids)=487AA_BP=
MKSCGVSLATAAAAAAAFGDEEKKMAAGKASGESEEASPSLTAEEREALGGLDSRLFGFVRFHEDGARTKALLGKAVRCYESLILKAEGK
VESDFFCQLGHFNLLLEDYPKALSAYQRYYSLQSDYWKNAAFLYGLGLVYFHYNAFQWAIKAFQEVLYVDPSFCRAKEIHLRLGLMFKVN
TDYESSLKHFQLALVDCNPCTLSNAEIQFHIAHLYETQRKYHSAKEAYEQLLQTENLSAQVKATVLQQLGWMHHTVDLLGDKATKESYAI
QYLQKSLEADPNSGQSWYFLGRCYSSIGKVQDAFISYRQSIDKSEASADTWCSIGVLYQQQNQPMDALQAYICAVQLDHGHAAAWMDLGT
LYESCNQPQDAIKCYLNATRSKSCSNTSALAARIKYLQACKPHHPNTEPVLGLSQTPISQQSLPLHMIPSSQVDDLSSPAKRKRTSSPTK

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

>41915_41915_5_KDM6A-YEATS4_KDM6A_chrX_44920664_ENST00000536777_YEATS4_chr12_69783927_ENST00000247843_length(amino acids)=435AA_BP=
MKSCGVSLATAAAAAAAFGDEEKKMAAGKASGESEEASPSLTAEEREALGGLDSRLFGFVRFHEDGARTKALLGKAVRCYESLILKAEGK
VESDFFCQLGHFNLLLEDYPKALSAYQRYYSLQSDYWKNAAFLYGLGLVYFHYNAFQWAIKAFQEVLYVDPSFCRAKEIHLRLGLMFKVN
TDYESSLKHFQLALVDCNPCTLSNAEIQFHIAHLYETQRKYHSAKEAYEQLLQTENLSAQVKATVLQQLGWMHHTVDLLGDKATKESYAI
QYLQKSLEADPNSGQSWYFLGRCYSSIGKVQDAFISYRQSIDKSEASADTWCSIGVLYQQQNQPMDALQAYICAVQLDHGHAAAWMDLGT

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

>41915_41915_6_KDM6A-YEATS4_KDM6A_chrX_44920664_ENST00000536777_YEATS4_chr12_69783927_ENST00000548020_length(amino acids)=435AA_BP=
MKSCGVSLATAAAAAAAFGDEEKKMAAGKASGESEEASPSLTAEEREALGGLDSRLFGFVRFHEDGARTKALLGKAVRCYESLILKAEGK
VESDFFCQLGHFNLLLEDYPKALSAYQRYYSLQSDYWKNAAFLYGLGLVYFHYNAFQWAIKAFQEVLYVDPSFCRAKEIHLRLGLMFKVN
TDYESSLKHFQLALVDCNPCTLSNAEIQFHIAHLYETQRKYHSAKEAYEQLLQTENLSAQVKATVLQQLGWMHHTVDLLGDKATKESYAI
QYLQKSLEADPNSGQSWYFLGRCYSSIGKVQDAFISYRQSIDKSEASADTWCSIGVLYQQQNQPMDALQAYICAVQLDHGHAAAWMDLGT

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

>41915_41915_7_KDM6A-YEATS4_KDM6A_chrX_44920664_ENST00000543216_YEATS4_chr12_69783927_ENST00000247843_length(amino acids)=435AA_BP=
MKSCGVSLATAAAAAAAFGDEEKKMAAGKASGESEEASPSLTAEEREALGGLDSRLFGFVRFHEDGARTKALLGKAVRCYESLILKAEGK
VESDFFCQLGHFNLLLEDYPKALSAYQRYYSLQSDYWKNAAFLYGLGLVYFHYNAFQWAIKAFQEVLYVDPSFCRAKEIHLRLGLMFKVN
TDYESSLKHFQLALVDCNPCTLSNAEIQFHIAHLYETQRKYHSAKEAYEQLLQTENLSAQVKATVLQQLGWMHHTVDLLGDKATKESYAI
QYLQKSLEADPNSGQSWYFLGRCYSSIGKVQDAFISYRQSIDKSEASADTWCSIGVLYQQQNQPMDALQAYICAVQLDHGHAAAWMDLGT

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

>41915_41915_8_KDM6A-YEATS4_KDM6A_chrX_44920664_ENST00000543216_YEATS4_chr12_69783927_ENST00000548020_length(amino acids)=435AA_BP=
MKSCGVSLATAAAAAAAFGDEEKKMAAGKASGESEEASPSLTAEEREALGGLDSRLFGFVRFHEDGARTKALLGKAVRCYESLILKAEGK
VESDFFCQLGHFNLLLEDYPKALSAYQRYYSLQSDYWKNAAFLYGLGLVYFHYNAFQWAIKAFQEVLYVDPSFCRAKEIHLRLGLMFKVN
TDYESSLKHFQLALVDCNPCTLSNAEIQFHIAHLYETQRKYHSAKEAYEQLLQTENLSAQVKATVLQQLGWMHHTVDLLGDKATKESYAI
QYLQKSLEADPNSGQSWYFLGRCYSSIGKVQDAFISYRQSIDKSEASADTWCSIGVLYQQQNQPMDALQAYICAVQLDHGHAAAWMDLGT

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

Top

Fusion Protein Functional Features

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chrX:44920664/chr12:69783927)
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
- How to search
1. Put your fusion gene symbol.
2. Press the tab key until there will be shown the breakpoint information filled.
4. Go down and press 'Search' tab twice.
4. Go down to have the hyperlink of the search result.
5. Click the hyperlink.
6. See the FGviewer result for your fusion gene.

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

Hgene	Tgene
KDM6A O15550	.
FUNCTION: Histone demethylase that specifically demethylates 'Lys-27' of histone H3, thereby playing a central role in histone code (PubMed:17851529, PubMed:17713478, PubMed:17761849). Demethylates trimethylated and dimethylated but not monomethylated H3 'Lys-27' (PubMed:17851529, PubMed:17713478, PubMed:17761849). Plays a central role in regulation of posterior development, by regulating HOX gene expression (PubMed:17851529). Demethylation of 'Lys-27' of histone H3 is concomitant with methylation of 'Lys-4' of histone H3, and regulates the recruitment of the PRC1 complex and monoubiquitination of histone H2A (PubMed:17761849). Plays a demethylase-independent role in chromatin remodeling to regulate T-box family member-dependent gene expression (By similarity). {ECO:0000250\|UniProtKB:O70546, ECO:0000269\|PubMed:17713478, ECO:0000269\|PubMed:17761849, ECO:0000269\|PubMed:17851529, ECO:0000269\|PubMed:18003914}.	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.

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.

- 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

KDM6A

chrX:44920664

chr12:69783927

ENST00000377967

9_17

475.0

1402.0

Compositional bias

Note=Poly-Ala

Hgene

KDM6A

chrX:44920664

chr12:69783927

ENST00000377967

130_163

475.0

1402.0

Repeat

Note=TPR 2

Hgene

KDM6A

chrX:44920664

chr12:69783927

ENST00000377967

170_199

475.0

1402.0

Repeat

Note=TPR 3

Hgene

KDM6A

chrX:44920664

chr12:69783927

ENST00000377967

205_238

475.0

1402.0

Repeat

Note=TPR 4

Hgene

KDM6A

chrX:44920664

chr12:69783927

ENST00000377967

250_283

475.0

1402.0

Repeat

Note=TPR 5

Hgene

KDM6A

chrX:44920664

chr12:69783927

ENST00000377967

284_317

475.0

1402.0

Repeat

Note=TPR 6

Hgene

KDM6A

chrX:44920664

chr12:69783927

ENST00000377967

318_351

475.0

1402.0

Repeat

Note=TPR 7

Hgene

KDM6A

chrX:44920664

chr12:69783927

ENST00000377967

352_385

475.0

1402.0

Repeat

Note=TPR 8

Hgene

KDM6A

chrX:44920664

chr12:69783927

ENST00000377967

93_126

475.0

1402.0

Repeat

Note=TPR 1

Tgene

YEATS4

chrX:44920664

chr12:69783927

ENST00000247843

178_226

171.33333333333334

228.0

Coiled coil

Ontology_term=ECO:0000255

- 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

KDM6A

chrX:44920664

chr12:69783927

ENST00000377967

1095_1258

475.0

1402.0

Domain

JmjC

Tgene

YEATS4

chrX:44920664

chr12:69783927

ENST00000247843

15_158

171.33333333333334

228.0

Domain

YEATS

Tgene

YEATS4

chrX:44920664

chr12:69783927

ENST00000247843

93_97

171.33333333333334

228.0

Region

Diacetylated histone H3 binding

Top

Fusion Protein-Protein Interaction

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 from validated records (BIOGRID-3.4.160)

Gene

PPI interactors

Protein-protein interactors based on sequence similarity (STRING)

Gene	STRING network
KDM6A
YEATS4

- Retained interactions in fusion protein (protein functional feature from UniProt).

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Still interaction with

- Lost interactions due to fusion (protein functional feature from UniProt).

Partner	Gene	Hbp	Tbp	ENST	Strand	BPexon	TotalExon	Protein feature loci	*BPloci	TotalLen	Interaction lost with
Hgene	KDM6A	chrX:44920664	chr12:69783927	ENST00000377967	+	14	29	1_1095	475.0	1402.0	SUPT6H
Tgene	YEATS4	chrX:44920664	chr12:69783927	ENST00000247843		5	7	163_227	171.33333333333334	228.0	MLLT10
Tgene	YEATS4	chrX:44920664	chr12:69783927	ENST00000247843		5	7	168_227	171.33333333333334	228.0	TACC1

Top

Related Drugs to KDM6A-YEATS4

Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)

Hgene

Tgene

Drug

Source

PMID

Top

Related Diseases to KDM6A-YEATS4

Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)

Hgene

Tgene

Disease

Source

PMID

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner

Gene

Disease ID

Disease name

# pubmeds

Source