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Center for Computational Systems Medicine
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FusionGeneSummary

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FusionProtFeature

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FusionGeneSequence

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FusionGenePPI

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RelatedDrugs

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RelatedDiseases

Fusion gene ID: 16430

FusionGeneSummary for HMGA1_MLH1

check button Fusion gene summary
Fusion gene informationFusion gene name: HMGA1_MLH1
Fusion gene ID: 16430
HgeneTgene
Gene symbol

HMGA1

MLH1

Gene ID

3159

4292

Gene namehigh mobility group AT-hook 1mutL homolog 1
SynonymsHMG-R|HMGA1A|HMGIYCOCA2|FCC2|HNPCC|HNPCC2|hMLH1
Cytomap

6p21.31

3p22.2

Type of geneprotein-codingprotein-coding
Descriptionhigh mobility group protein HMG-I/HMG-Yhigh mobility group protein A1high mobility group protein Rhigh-mobility group (nonhistone chromosomal) protein isoforms I and Ynonhistone chromosomal high-mobility group protein HMG-I/HMG-YDNA mismatch repair protein Mlh1mutL homolog 1, colon cancer, nonpolyposis type 2
Modification date2018052320180523
UniProtAcc

P17096

P40692

Ensembl transtripts involved in fusion geneENST00000447654, ENST00000401473, 
ENST00000311487, ENST00000347617, 
ENST00000395004, ENST00000478214, 
ENST00000374116, 
ENST00000536378, 
ENST00000231790, ENST00000458205, 
ENST00000539477, ENST00000455445, 
ENST00000435176, ENST00000492474, 
Fusion gene scores* DoF score8 X 8 X 3=1926 X 7 X 3=126
# samples 98
** MAII scorelog2(9/192*10)=-1.09310940439148
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(8/126*10)=-0.655351828612554
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: HMGA1 [Title/Abstract] AND MLH1 [Title/Abstract] AND fusion [Title/Abstract]

Functional or gene categories assigned by FusionGDB annotation
* 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
HgeneHMGA1

GO:0035986

senescence-associated heterochromatin focus assembly

16901784

HgeneHMGA1

GO:0090402

oncogene-induced cell senescence

16901784


check button Fusion gene information from three resources
(ChiTars (NAR, 2018), tumorfusions (NAR, 2018), Gao et al. (Cell, 2018))
* 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.
Data typeSourceCancer typeSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChiTaRS3.1BC005866HMGA1chr6

34213057

+MLH1chr3

37067174

+
ChiTaRS3.1BC005833HMGA1chr6

34213057

+MLH1chr3

37067174

+
* LD: Li Ding group's fusion gene list
  RV: Roel Verhaak group's fusion gene list
  ChiTaRs fusion database

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
3UTR-3CDSENST00000447654ENST00000536378HMGA1chr6

34213057

+MLH1chr3

37067174

+
3UTR-3CDSENST00000447654ENST00000231790HMGA1chr6

34213057

+MLH1chr3

37067174

+
3UTR-3CDSENST00000447654ENST00000458205HMGA1chr6

34213057

+MLH1chr3

37067174

+
3UTR-3CDSENST00000447654ENST00000539477HMGA1chr6

34213057

+MLH1chr3

37067174

+
3UTR-3CDSENST00000447654ENST00000455445HMGA1chr6

34213057

+MLH1chr3

37067174

+
3UTR-3CDSENST00000447654ENST00000435176HMGA1chr6

34213057

+MLH1chr3

37067174

+
3UTR-intronENST00000447654ENST00000492474HMGA1chr6

34213057

+MLH1chr3

37067174

+
3UTR-3CDSENST00000401473ENST00000536378HMGA1chr6

34213057

+MLH1chr3

37067174

+
3UTR-3CDSENST00000401473ENST00000231790HMGA1chr6

34213057

+MLH1chr3

37067174

+
3UTR-3CDSENST00000401473ENST00000458205HMGA1chr6

34213057

+MLH1chr3

37067174

+
3UTR-3CDSENST00000401473ENST00000539477HMGA1chr6

34213057

+MLH1chr3

37067174

+
3UTR-3CDSENST00000401473ENST00000455445HMGA1chr6

34213057

+MLH1chr3

37067174

+
3UTR-3CDSENST00000401473ENST00000435176HMGA1chr6

34213057

+MLH1chr3

37067174

+
3UTR-intronENST00000401473ENST00000492474HMGA1chr6

34213057

+MLH1chr3

37067174

+
3UTR-3CDSENST00000311487ENST00000536378HMGA1chr6

34213057

+MLH1chr3

37067174

+
3UTR-3CDSENST00000311487ENST00000231790HMGA1chr6

34213057

+MLH1chr3

37067174

+
3UTR-3CDSENST00000311487ENST00000458205HMGA1chr6

34213057

+MLH1chr3

37067174

+
3UTR-3CDSENST00000311487ENST00000539477HMGA1chr6

34213057

+MLH1chr3

37067174

+
3UTR-3CDSENST00000311487ENST00000455445HMGA1chr6

34213057

+MLH1chr3

37067174

+
3UTR-3CDSENST00000311487ENST00000435176HMGA1chr6

34213057

+MLH1chr3

37067174

+
3UTR-intronENST00000311487ENST00000492474HMGA1chr6

34213057

+MLH1chr3

37067174

+
3UTR-3CDSENST00000347617ENST00000536378HMGA1chr6

34213057

+MLH1chr3

37067174

+
3UTR-3CDSENST00000347617ENST00000231790HMGA1chr6

34213057

+MLH1chr3

37067174

+
3UTR-3CDSENST00000347617ENST00000458205HMGA1chr6

34213057

+MLH1chr3

37067174

+
3UTR-3CDSENST00000347617ENST00000539477HMGA1chr6

34213057

+MLH1chr3

37067174

+
3UTR-3CDSENST00000347617ENST00000455445HMGA1chr6

34213057

+MLH1chr3

37067174

+
3UTR-3CDSENST00000347617ENST00000435176HMGA1chr6

34213057

+MLH1chr3

37067174

+
3UTR-intronENST00000347617ENST00000492474HMGA1chr6

34213057

+MLH1chr3

37067174

+
Frame-shitENST00000395004ENST00000536378HMGA1chr6

34213057

+MLH1chr3

37067174

+
Frame-shitENST00000395004ENST00000231790HMGA1chr6

34213057

+MLH1chr3

37067174

+
Frame-shitENST00000395004ENST00000458205HMGA1chr6

34213057

+MLH1chr3

37067174

+
Frame-shitENST00000395004ENST00000539477HMGA1chr6

34213057

+MLH1chr3

37067174

+
Frame-shitENST00000395004ENST00000455445HMGA1chr6

34213057

+MLH1chr3

37067174

+
Frame-shitENST00000395004ENST00000435176HMGA1chr6

34213057

+MLH1chr3

37067174

+
5CDS-intronENST00000395004ENST00000492474HMGA1chr6

34213057

+MLH1chr3

37067174

+
intron-3CDSENST00000478214ENST00000536378HMGA1chr6

34213057

+MLH1chr3

37067174

+
intron-3CDSENST00000478214ENST00000231790HMGA1chr6

34213057

+MLH1chr3

37067174

+
intron-3CDSENST00000478214ENST00000458205HMGA1chr6

34213057

+MLH1chr3

37067174

+
intron-3CDSENST00000478214ENST00000539477HMGA1chr6

34213057

+MLH1chr3

37067174

+
intron-3CDSENST00000478214ENST00000455445HMGA1chr6

34213057

+MLH1chr3

37067174

+
intron-3CDSENST00000478214ENST00000435176HMGA1chr6

34213057

+MLH1chr3

37067174

+
intron-intronENST00000478214ENST00000492474HMGA1chr6

34213057

+MLH1chr3

37067174

+
3UTR-3CDSENST00000374116ENST00000536378HMGA1chr6

34213057

+MLH1chr3

37067174

+
3UTR-3CDSENST00000374116ENST00000231790HMGA1chr6

34213057

+MLH1chr3

37067174

+
3UTR-3CDSENST00000374116ENST00000458205HMGA1chr6

34213057

+MLH1chr3

37067174

+
3UTR-3CDSENST00000374116ENST00000539477HMGA1chr6

34213057

+MLH1chr3

37067174

+
3UTR-3CDSENST00000374116ENST00000455445HMGA1chr6

34213057

+MLH1chr3

37067174

+
3UTR-3CDSENST00000374116ENST00000435176HMGA1chr6

34213057

+MLH1chr3

37067174

+
3UTR-intronENST00000374116ENST00000492474HMGA1chr6

34213057

+MLH1chr3

37067174

+

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FusionProtFeatures for HMGA1_MLH1


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
HMGA1

P17096

MLH1

P40692

HMG-I/Y bind preferentially to the minor groove of A+Trich regions in double-stranded DNA. It is suggested that theseproteins could function in nucleosome phasing and in the 3'-endprocessing of mRNA transcripts. They are also involved in thetranscription regulation of genes containing, or in closeproximity to A+T-rich regions. Heterodimerizes with PMS2 to form MutL alpha, acomponent of the post-replicative DNA mismatch repair system(MMR). DNA repair is initiated by MutS alpha (MSH2-MSH6) or MutSbeta (MSH2-MSH3) binding to a dsDNA mismatch, then MutL alpha isrecruited to the heteroduplex. Assembly of the MutL-MutS-heteroduplex ternary complex in presence of RFC and PCNA issufficient to activate endonuclease activity of PMS2. Itintroduces single-strand breaks near the mismatch and thusgenerates new entry points for the exonuclease EXO1 to degrade thestrand containing the mismatch. DNA methylation would preventcleavage and therefore assure that only the newly mutated DNAstrand is going to be corrected. MutL alpha (MLH1-PMS2) interactsphysically with the clamp loader subunits of DNA polymerase III,suggesting that it may play a role to recruit the DNA polymeraseIII to the site of the MMR. Also implicated in DNA damagesignaling, a process which induces cell cycle arrest and can leadto apoptosis in case of major DNA damages. Heterodimerizes withMLH3 to form MutL gamma which plays a role in meiosis.{ECO:0000269|PubMed:16873062, ECO:0000269|PubMed:18206974,ECO:0000269|PubMed:20020535, ECO:0000269|PubMed:21120944,ECO:0000269|PubMed:9311737}.

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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FusionGeneSequence for HMGA1_MLH1


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences.
(nt: nucleotides, aa: amino acids)

* Fusion amino acid sequences.

* Fusion transcript sequences (only coding sequence (CDS) region).

* Fusion transcript sequences (Full-length transcript).

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FusionGenePPI for HMGA1_MLH1


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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RelatedDrugs for HMGA1_MLH1


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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RelatedDiseases for HMGA1_MLH1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneHMGA1C0011860Diabetes Mellitus, Non-Insulin-Dependent1CTD_human
HgeneHMGA1C0020456Hyperglycemia1CTD_human
HgeneHMGA1C0021655Insulin Resistance1CTD_human
HgeneHMGA1C0023269leiomyosarcoma1CTD_human
HgeneHMGA1C0036341Schizophrenia1PSYGENET
HgeneHMGA1C0042138Uterine Neoplasms1CTD_human
HgeneHMGA1C0524620Metabolic Syndrome X1CTD_human
TgeneMLH1C1333991Hereditary Non-Polyposis Colon Cancer Type 252CTD_human;UNIPROT
TgeneMLH1C1527249Colorectal Cancer6UNIPROT
TgeneMLH1C0009405Hereditary Nonpolyposis Colorectal Neoplasms5CTD_human
TgeneMLH1C0009404Colorectal Neoplasms3CTD_human
TgeneMLH1C0265325Turcot syndrome (disorder)2CTD_human;ORPHANET;UNIPROT
TgeneMLH1C0009375Colonic Neoplasms1CTD_human
TgeneMLH1C0024299Lymphoma1CTD_human;HPO
TgeneMLH1C0027627Neoplasm Metastasis1CTD_human
TgeneMLH1C0033578Prostatic Neoplasms1CTD_human
TgeneMLH1C0919267ovarian neoplasm1CTD_human