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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:MLH3-PCNXL4 (FusionGDB2 ID:53849)

Fusion Gene Summary for MLH3-PCNXL4

check button Fusion gene summary
Fusion gene informationFusion gene name: MLH3-PCNXL4
Fusion gene ID: 53849
HgeneTgene
Gene symbol

MLH3

PCNXL4

Gene ID

27030

64430

Gene namemutL homolog 3pecanex 4
SynonymsHNPCC7C14orf135|FBP2|PCNXL4
Cytomap

14q24.3

14q23.1

Type of geneprotein-codingprotein-coding
DescriptionDNA mismatch repair protein Mlh3pecanex-like protein 4HCV F protein-binding protein 2HCV F-interacting proteinhepatitis C virus F protein-binding protein 2pecanex homolog 4pecanex homolog protein 4pecanex-like 4pecanex-like protein C14orf135
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000380968, ENST00000355774, 
ENST00000238662, ENST00000556257, 
ENST00000556740, ENST00000544985, 
ENST00000555671, 		ENST00000317623, 
ENST00000391611, ENST00000406854, 
ENST00000406949, ENST00000404681, 
ENST00000535349, ENST00000553898, 
Fusion gene scores* DoF score2 X 2 X 2=83 X 3 X 2=18
# samples 23
** MAII scorelog2(2/8*10)=1.32192809488736log2(3/18*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: MLH3 [Title/Abstract] AND PCNXL4 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointMLH3(75498771)-PCNXL4(60582437), # samples:1
Anticipated loss of major functional domain due to fusion event.MLH3-PCNXL4 seems lost the major protein functional domain in Hgene partner, which is a tumor suppressor 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 MLH3 (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 PCNXL4 (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-D7-8574-01AMLH3chr14

75498771

-PCNXL4chr14

60582437

+


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Fusion Gene ORF analysis for MLH3-PCNXL4

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-shiftENST00000380968ENST00000317623MLH3chr14

75498771

-PCNXL4chr14

60582437

+
5CDS-intronENST00000380968ENST00000391611MLH3chr14

75498771

-PCNXL4chr14

60582437

+
5CDS-intronENST00000380968ENST00000406854MLH3chr14

75498771

-PCNXL4chr14

60582437

+
5CDS-intronENST00000380968ENST00000406949MLH3chr14

75498771

-PCNXL4chr14

60582437

+
5CDS-intronENST00000380968ENST00000404681MLH3chr14

75498771

-PCNXL4chr14

60582437

+
5CDS-intronENST00000380968ENST00000535349MLH3chr14

75498771

-PCNXL4chr14

60582437

+
5CDS-intronENST00000380968ENST00000553898MLH3chr14

75498771

-PCNXL4chr14

60582437

+
Frame-shiftENST00000355774ENST00000317623MLH3chr14

75498771

-PCNXL4chr14

60582437

+
5CDS-intronENST00000355774ENST00000391611MLH3chr14

75498771

-PCNXL4chr14

60582437

+
5CDS-intronENST00000355774ENST00000406854MLH3chr14

75498771

-PCNXL4chr14

60582437

+
5CDS-intronENST00000355774ENST00000406949MLH3chr14

75498771

-PCNXL4chr14

60582437

+
5CDS-intronENST00000355774ENST00000404681MLH3chr14

75498771

-PCNXL4chr14

60582437

+
5CDS-intronENST00000355774ENST00000535349MLH3chr14

75498771

-PCNXL4chr14

60582437

+
5CDS-intronENST00000355774ENST00000553898MLH3chr14

75498771

-PCNXL4chr14

60582437

+
Frame-shiftENST00000238662ENST00000317623MLH3chr14

75498771

-PCNXL4chr14

60582437

+
5CDS-intronENST00000238662ENST00000391611MLH3chr14

75498771

-PCNXL4chr14

60582437

+
5CDS-intronENST00000238662ENST00000406854MLH3chr14

75498771

-PCNXL4chr14

60582437

+
5CDS-intronENST00000238662ENST00000406949MLH3chr14

75498771

-PCNXL4chr14

60582437

+
5CDS-intronENST00000238662ENST00000404681MLH3chr14

75498771

-PCNXL4chr14

60582437

+
5CDS-intronENST00000238662ENST00000535349MLH3chr14

75498771

-PCNXL4chr14

60582437

+
5CDS-intronENST00000238662ENST00000553898MLH3chr14

75498771

-PCNXL4chr14

60582437

+
intron-3CDSENST00000556257ENST00000317623MLH3chr14

75498771

-PCNXL4chr14

60582437

+
intron-intronENST00000556257ENST00000391611MLH3chr14

75498771

-PCNXL4chr14

60582437

+
intron-intronENST00000556257ENST00000406854MLH3chr14

75498771

-PCNXL4chr14

60582437

+
intron-intronENST00000556257ENST00000406949MLH3chr14

75498771

-PCNXL4chr14

60582437

+
intron-intronENST00000556257ENST00000404681MLH3chr14

75498771

-PCNXL4chr14

60582437

+
intron-intronENST00000556257ENST00000535349MLH3chr14

75498771

-PCNXL4chr14

60582437

+
intron-intronENST00000556257ENST00000553898MLH3chr14

75498771

-PCNXL4chr14

60582437

+
Frame-shiftENST00000556740ENST00000317623MLH3chr14

75498771

-PCNXL4chr14

60582437

+
5CDS-intronENST00000556740ENST00000391611MLH3chr14

75498771

-PCNXL4chr14

60582437

+
5CDS-intronENST00000556740ENST00000406854MLH3chr14

75498771

-PCNXL4chr14

60582437

+
5CDS-intronENST00000556740ENST00000406949MLH3chr14

75498771

-PCNXL4chr14

60582437

+
5CDS-intronENST00000556740ENST00000404681MLH3chr14

75498771

-PCNXL4chr14

60582437

+
5CDS-intronENST00000556740ENST00000535349MLH3chr14

75498771

-PCNXL4chr14

60582437

+
5CDS-intronENST00000556740ENST00000553898MLH3chr14

75498771

-PCNXL4chr14

60582437

+
3UTR-3CDSENST00000544985ENST00000317623MLH3chr14

75498771

-PCNXL4chr14

60582437

+
3UTR-intronENST00000544985ENST00000391611MLH3chr14

75498771

-PCNXL4chr14

60582437

+
3UTR-intronENST00000544985ENST00000406854MLH3chr14

75498771

-PCNXL4chr14

60582437

+
3UTR-intronENST00000544985ENST00000406949MLH3chr14

75498771

-PCNXL4chr14

60582437

+
3UTR-intronENST00000544985ENST00000404681MLH3chr14

75498771

-PCNXL4chr14

60582437

+
3UTR-intronENST00000544985ENST00000535349MLH3chr14

75498771

-PCNXL4chr14

60582437

+
3UTR-intronENST00000544985ENST00000553898MLH3chr14

75498771

-PCNXL4chr14

60582437

+
intron-3CDSENST00000555671ENST00000317623MLH3chr14

75498771

-PCNXL4chr14

60582437

+
intron-intronENST00000555671ENST00000391611MLH3chr14

75498771

-PCNXL4chr14

60582437

+
intron-intronENST00000555671ENST00000406854MLH3chr14

75498771

-PCNXL4chr14

60582437

+
intron-intronENST00000555671ENST00000406949MLH3chr14

75498771

-PCNXL4chr14

60582437

+
intron-intronENST00000555671ENST00000404681MLH3chr14

75498771

-PCNXL4chr14

60582437

+
intron-intronENST00000555671ENST00000535349MLH3chr14

75498771

-PCNXL4chr14

60582437

+
intron-intronENST00000555671ENST00000553898MLH3chr14

75498771

-PCNXL4chr14

60582437

+

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 MLH3-PCNXL4


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 MLH3-PCNXL4


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
..
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.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 MLH3-PCNXL4


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 MLH3-PCNXL4


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 MLH3-PCNXL4


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 MLH3-PCNXL4


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneMLH3C0009405Hereditary Nonpolyposis Colorectal Neoplasms7CLINGEN;CTD_human
HgeneMLH3C1112155Hereditary non-polyposis colorectal cancer syndrome7CLINGEN;ORPHANET
HgeneMLH3C1333990Hereditary Nonpolyposis Colorectal Cancer7CLINGEN;CTD_human;ORPHANET
HgeneMLH3C1333991Hereditary Non-Polyposis Colon Cancer Type 26CLINGEN
HgeneMLH3C2936783Colorectal cancer, hereditary nonpolyposis, type 16CLINGEN
HgeneMLH3C0009402Colorectal Carcinoma1CTD_human
HgeneMLH3C0009404Colorectal Neoplasms1CTD_human
HgeneMLH3C0014859Esophageal Neoplasms1CTD_human
HgeneMLH3C0546837Malignant neoplasm of esophagus1CTD_human
HgeneMLH3C1858380COLORECTAL CANCER, HEREDITARY NONPOLYPOSIS, TYPE 7 (disorder)1CTD_human;UNIPROT
HgeneMLH3C4552100Lynch Syndrome1CTD_human