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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:MITF-PSMD6 (FusionGDB2 ID:53668)

Fusion Gene Summary for MITF-PSMD6

check button Fusion gene summary
Fusion gene informationFusion gene name: MITF-PSMD6
Fusion gene ID: 53668
HgeneTgene
Gene symbol

MITF

PSMD6

Gene ID

4286

9861

Gene namemelanocyte inducing transcription factorproteasome 26S subunit, non-ATPase 6
SynonymsCMM8|COMMAD|MI|WS2|WS2A|bHLHe32Rpn7|S10|SGA-113M|p42A|p44S10
Cytomap

3p13

3p14.1

Type of geneprotein-codingprotein-coding
Descriptionmicrophthalmia-associated transcription factorclass E basic helix-loop-helix protein 32melanogenesis associated transcription factormicrophtalmia-associated transcription factor26S proteasome non-ATPase regulatory subunit 6breast cancer-associated protein SGA-113Mphosphonoformate immuno-associated protein 4proteasome (prosome, macropain) 26S subunit, non-ATPase, 6proteasome regulatory particle subunit p44S10
Modification date2020032920200313
UniProtAcc

O75030

.
Ensembl transtripts involved in fusion geneENST00000352241, ENST00000448226, 
ENST00000472437, ENST00000328528, 
ENST00000314589, ENST00000394355, 
ENST00000314557, ENST00000394351, 
ENST00000531774, ENST00000394348, 
ENST00000295901, ENST00000492933, 
ENST00000394431, ENST00000482510, 
Fusion gene scores* DoF score11 X 6 X 6=3965 X 4 X 4=80
# samples 95
** MAII scorelog2(9/396*10)=-2.13750352374993
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(5/80*10)=-0.678071905112638
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: MITF [Title/Abstract] AND PSMD6 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointMITF(69788852)-PSMD6(64008199), # samples:2
Anticipated loss of major functional domain due to fusion event.MITF-PSMD6 seems lost the major protein functional domain in Hgene partner, which is a transcription factor due to the frame-shifted ORF.
MITF-PSMD6 seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF.
MITF-PSMD6 seems lost the major protein functional domain in Tgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
MITF-PSMD6 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
HgeneMITF

GO:0010628

positive regulation of gene expression

22234890

HgeneMITF

GO:0045893

positive regulation of transcription, DNA-templated

9647758

HgeneMITF

GO:0045944

positive regulation of transcription by RNA polymerase II

20530484|21209915

HgeneMITF

GO:0065003

protein-containing complex assembly

20530484

HgeneMITF

GO:2000144

positive regulation of DNA-templated transcription, initiation

8995290|12204775

HgeneMITF

GO:2001141

regulation of RNA biosynthetic process

16411896


check buttonFusion gene breakpoints across MITF (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 PSMD6 (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
ChimerDB4SKCMTCGA-D3-A2JG-06AMITFchr3

69788852

+PSMD6chr3

64008199

-
ChimerDB4SKCMTCGA-D3-A2JG-06AMITFchr3

69788852

+PSMD6chr3

64008199

-


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Fusion Gene ORF analysis for MITF-PSMD6

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
Frame-shiftENST00000352241ENST00000295901MITFchr3

69788852

+PSMD6chr3

64008199

-
Frame-shiftENST00000352241ENST00000492933MITFchr3

69788852

+PSMD6chr3

64008199

-
Frame-shiftENST00000352241ENST00000394431MITFchr3

69788852

+PSMD6chr3

64008199

-
Frame-shiftENST00000352241ENST00000482510MITFchr3

69788852

+PSMD6chr3

64008199

-
Frame-shiftENST00000448226ENST00000295901MITFchr3

69788852

+PSMD6chr3

64008199

-
Frame-shiftENST00000448226ENST00000492933MITFchr3

69788852

+PSMD6chr3

64008199

-
Frame-shiftENST00000448226ENST00000394431MITFchr3

69788852

+PSMD6chr3

64008199

-
Frame-shiftENST00000448226ENST00000482510MITFchr3

69788852

+PSMD6chr3

64008199

-
intron-3CDSENST00000472437ENST00000295901MITFchr3

69788852

+PSMD6chr3

64008199

-
intron-3CDSENST00000472437ENST00000492933MITFchr3

69788852

+PSMD6chr3

64008199

-
intron-3CDSENST00000472437ENST00000394431MITFchr3

69788852

+PSMD6chr3

64008199

-
intron-3CDSENST00000472437ENST00000482510MITFchr3

69788852

+PSMD6chr3

64008199

-
intron-3CDSENST00000328528ENST00000295901MITFchr3

69788852

+PSMD6chr3

64008199

-
intron-3CDSENST00000328528ENST00000492933MITFchr3

69788852

+PSMD6chr3

64008199

-
intron-3CDSENST00000328528ENST00000394431MITFchr3

69788852

+PSMD6chr3

64008199

-
intron-3CDSENST00000328528ENST00000482510MITFchr3

69788852

+PSMD6chr3

64008199

-
intron-3CDSENST00000314589ENST00000295901MITFchr3

69788852

+PSMD6chr3

64008199

-
intron-3CDSENST00000314589ENST00000492933MITFchr3

69788852

+PSMD6chr3

64008199

-
intron-3CDSENST00000314589ENST00000394431MITFchr3

69788852

+PSMD6chr3

64008199

-
intron-3CDSENST00000314589ENST00000482510MITFchr3

69788852

+PSMD6chr3

64008199

-
intron-3CDSENST00000394355ENST00000295901MITFchr3

69788852

+PSMD6chr3

64008199

-
intron-3CDSENST00000394355ENST00000492933MITFchr3

69788852

+PSMD6chr3

64008199

-
intron-3CDSENST00000394355ENST00000394431MITFchr3

69788852

+PSMD6chr3

64008199

-
intron-3CDSENST00000394355ENST00000482510MITFchr3

69788852

+PSMD6chr3

64008199

-
intron-3CDSENST00000314557ENST00000295901MITFchr3

69788852

+PSMD6chr3

64008199

-
intron-3CDSENST00000314557ENST00000492933MITFchr3

69788852

+PSMD6chr3

64008199

-
intron-3CDSENST00000314557ENST00000394431MITFchr3

69788852

+PSMD6chr3

64008199

-
intron-3CDSENST00000314557ENST00000482510MITFchr3

69788852

+PSMD6chr3

64008199

-
intron-3CDSENST00000394351ENST00000295901MITFchr3

69788852

+PSMD6chr3

64008199

-
intron-3CDSENST00000394351ENST00000492933MITFchr3

69788852

+PSMD6chr3

64008199

-
intron-3CDSENST00000394351ENST00000394431MITFchr3

69788852

+PSMD6chr3

64008199

-
intron-3CDSENST00000394351ENST00000482510MITFchr3

69788852

+PSMD6chr3

64008199

-
intron-3CDSENST00000531774ENST00000295901MITFchr3

69788852

+PSMD6chr3

64008199

-
intron-3CDSENST00000531774ENST00000492933MITFchr3

69788852

+PSMD6chr3

64008199

-
intron-3CDSENST00000531774ENST00000394431MITFchr3

69788852

+PSMD6chr3

64008199

-
intron-3CDSENST00000531774ENST00000482510MITFchr3

69788852

+PSMD6chr3

64008199

-
intron-3CDSENST00000394348ENST00000295901MITFchr3

69788852

+PSMD6chr3

64008199

-
intron-3CDSENST00000394348ENST00000492933MITFchr3

69788852

+PSMD6chr3

64008199

-
intron-3CDSENST00000394348ENST00000394431MITFchr3

69788852

+PSMD6chr3

64008199

-
intron-3CDSENST00000394348ENST00000482510MITFchr3

69788852

+PSMD6chr3

64008199

-

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 MITF-PSMD6


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 MITF-PSMD6


check button Go to

FGviewer for the breakpoints of :-:

.
- 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
MITF

O75030

.
FUNCTION: Transcription factor that regulates the expression of genes with essential roles in cell differentiation, proliferation and survival. Binds to M-boxes (5'-TCATGTG-3') and symmetrical DNA sequences (E-boxes) (5'-CACGTG-3') found in the promoters of target genes, such as BCL2 and tyrosinase (TYR). Plays an important role in melanocyte development by regulating the expression of tyrosinase (TYR) and tyrosinase-related protein 1 (TYRP1). Plays a critical role in the differentiation of various cell types, such as neural crest-derived melanocytes, mast cells, osteoclasts and optic cup-derived retinal pigment epithelium. {ECO:0000269|PubMed:10587587, ECO:0000269|PubMed:22647378, ECO:0000269|PubMed:27889061, ECO:0000269|PubMed:9647758}.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

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note


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Fusion Gene Sequence for MITF-PSMD6


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 MITF-PSMD6


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 MITF-PSMD6


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 MITF-PSMD6


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneMITFC2700265Waardenburg Syndrome Type 211CLINGEN;CTD_human;ORPHANET
HgeneMITFC1860339WAARDENBURG SYNDROME, TYPE IIA5CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneMITFC3152204MELANOMA, CUTANEOUS MALIGNANT, SUSCEPTIBILITY TO, 84CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneMITFC4310625COLOBOMA, OSTEOPETROSIS, MICROPHTHALMIA, MACROCEPHALY, ALBINISM, AND DEAFNESS3CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneMITFC0391816Tietz syndrome2CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneMITFC1863198ALBINISM, OCULAR, WITH SENSORINEURAL DEAFNESS (disorder)2GENOMICS_ENGLAND;ORPHANET
HgeneMITFC3266898Waardenburg Syndrome2GENOMICS_ENGLAND;ORPHANET
HgeneMITFC0007134Renal Cell Carcinoma1CTD_human
HgeneMITFC0007621Neoplastic Cell Transformation1CTD_human
HgeneMITFC0011052Prelingual Deafness1CTD_human
HgeneMITFC0011053Deafness1CTD_human
HgeneMITFC0022283Incontinentia Pigmenti Achromians1CTD_human
HgeneMITFC0025202melanoma1CGI;CTD_human
HgeneMITFC0036305Schamberg Disease1CTD_human
HgeneMITFC0078918Albinism, Oculocutaneous1CTD_human
HgeneMITFC0078921Albinism, Tyrosinase-Negative1CTD_human
HgeneMITFC0078922Albinism, Tyrosinase-Positive1CTD_human
HgeneMITFC0078923Albinism, Yellow-Mutant1CTD_human
HgeneMITFC0086395Hearing Loss, Extreme1CTD_human
HgeneMITFC0151779Cutaneous Melanoma1CGI;CTD_human
HgeneMITFC0279702Conventional (Clear Cell) Renal Cell Carcinoma1CTD_human
HgeneMITFC0549567Pigmentation Disorders1CTD_human
HgeneMITFC0581883Complete Hearing Loss1CTD_human
HgeneMITFC0751068Deafness, Acquired1CTD_human
HgeneMITFC1266042Chromophobe Renal Cell Carcinoma1CTD_human
HgeneMITFC1266043Sarcomatoid Renal Cell Carcinoma1CTD_human
HgeneMITFC1266044Collecting Duct Carcinoma of the Kidney1CTD_human
HgeneMITFC1306837Papillary Renal Cell Carcinoma1CTD_human;ORPHANET
HgeneMITFC1708353Hereditary Paraganglioma-Pheochromocytoma Syndrome1CLINGEN
HgeneMITFC1848519WAARDENBURG SYNDROME, TYPE 4A1ORPHANET
HgeneMITFC2314896Familial Atypical Mole Melanoma Syndrome1ORPHANET
HgeneMITFC2700405WAARDENBURG SYNDROME, TYPE IIE1CTD_human
HgeneMITFC3665473Bilateral Deafness1CTD_human
HgeneMITFC4082305Deaf Mutism1CTD_human
HgeneMITFC4518333Clear cell papillary renal cell carcinoma1ORPHANET
HgeneMITFC4750999Ocular albinism with congenital sensorineural deafness1GENOMICS_ENGLAND
TgenePSMD6C0011860Diabetes Mellitus, Non-Insulin-Dependent1CTD_human
TgenePSMD6C0019693HIV Infections1CTD_human
TgenePSMD6C4505456HIV Coinfection1CTD_human