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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: 992

FusionGeneSummary for AFAP1_RET

check button Fusion gene summary
Fusion gene informationFusion gene name: AFAP1_RET
Fusion gene ID: 992
HgeneTgene
Gene symbol

AFAP1

RET

Gene ID

60312

5979

Gene nameactin filament associated protein 1ret proto-oncogene
SynonymsAFAP|AFAP-110|AFAP110CDHF12|CDHR16|HSCR1|MEN2A|MEN2B|MTC1|PTC|RET-ELE1
Cytomap

4p16.1

10q11.21

Type of geneprotein-codingprotein-coding
Descriptionactin filament-associated protein 1110 kDa actin filament-associated proteinactin filament-associated protein, 110 kDaproto-oncogene tyrosine-protein kinase receptor RetRET receptor tyrosine kinasecadherin family member 12cadherin-related family member 16proto-oncogene c-Retrearranged during transfectionret proto-oncogene (multiple endocrine neoplasia and medullary
Modification date2018051920180527
UniProtAcc

Q8N556

P07949

Ensembl transtripts involved in fusion geneENST00000360265, ENST00000358461, 
ENST00000420658, ENST00000382543, 
ENST00000513842, 
ENST00000355710, 
ENST00000340058, 
Fusion gene scores* DoF score8 X 10 X 6=48018 X 10 X 7=1260
# samples 1265
** MAII scorelog2(12/480*10)=-2
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(65/1260*10)=-0.954912110471462
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: AFAP1 [Title/Abstract] AND RET [Title/Abstract] AND fusion [Title/Abstract]

Functional or gene categories assigned by FusionGDB annotationOncogene involved fusion gene, in-frame and retained their domain.
Kinase involved fusion gene, inframe and retained kinase domain.
* 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
TgeneRET

GO:0030155

regulation of cell adhesion

21357690

TgeneRET

GO:0030335

positive regulation of cell migration

20702524

TgeneRET

GO:0033619

membrane protein proteolysis

21357690

TgeneRET

GO:0033630

positive regulation of cell adhesion mediated by integrin

20702524

TgeneRET

GO:0035860

glial cell-derived neurotrophic factor receptor signaling pathway

28953886

TgeneRET

GO:0043410

positive regulation of MAPK cascade

28846099


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
ChiTaRS3.1X56348AFAP1chr4

7870348

-RETchr10

43612031

+
* 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
In-frameENST00000360265ENST00000355710AFAP1chr4

7870348

-RETchr10

43612031

+
In-frameENST00000360265ENST00000340058AFAP1chr4

7870348

-RETchr10

43612031

+
In-frameENST00000358461ENST00000355710AFAP1chr4

7870348

-RETchr10

43612031

+
In-frameENST00000358461ENST00000340058AFAP1chr4

7870348

-RETchr10

43612031

+
In-frameENST00000420658ENST00000355710AFAP1chr4

7870348

-RETchr10

43612031

+
In-frameENST00000420658ENST00000340058AFAP1chr4

7870348

-RETchr10

43612031

+
In-frameENST00000382543ENST00000355710AFAP1chr4

7870348

-RETchr10

43612031

+
In-frameENST00000382543ENST00000340058AFAP1chr4

7870348

-RETchr10

43612031

+
intron-3CDSENST00000513842ENST00000355710AFAP1chr4

7870348

-RETchr10

43612031

+
intron-3CDSENST00000513842ENST00000340058AFAP1chr4

7870348

-RETchr10

43612031

+

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FusionProtFeatures for AFAP1_RET


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
AFAP1

Q8N556

RET

P07949

Can cross-link actin filaments into both network andbundle structures (By similarity). May modulate changes in actinfilament integrity and induce lamellipodia formation. May functionas an adapter molecule that links other proteins, such as SRC andPKC to the actin cytoskeleton. Seems to play a role in thedevelopment and progression of prostate adenocarcinoma byregulating cell-matrix adhesions and migration in the cancercells. {ECO:0000250, ECO:0000269|PubMed:15485829}. Receptor tyrosine-protein kinase involved in numerouscellular mechanisms including cell proliferation, neuronalnavigation, cell migration, and cell differentiation upon bindingwith glial cell derived neurotrophic factor family ligands.Phosphorylates PTK2/FAK1. Regulates both cell death/survivalbalance and positional information. Required for the molecularmechanisms orchestration during intestine organogenesis; involvedin the development of enteric nervous system and renalorganogenesis during embryonic life, and promotes the formation ofPeyer's patch-like structures, a major component of the gut-associated lymphoid tissue. Modulates cell adhesion via itscleavage by caspase in sympathetic neurons and mediates cellmigration in an integrin (e.g. ITGB1 and ITGB3)-dependent manner.Involved in the development of the neural crest. Active in theabsence of ligand, triggering apoptosis through a mechanism thatrequires receptor intracellular caspase cleavage. Acts as adependence receptor; in the presence of the ligand GDNF insomatotrophs (within pituitary), promotes survival and downregulates growth hormone (GH) production, but triggers apoptosisin absence of GDNF. Regulates nociceptor survival and size.Triggers the differentiation of rapidly adapting (RA)mechanoreceptors. Mediator of several diseases such asneuroendocrine cancers; these diseases are characterized byaberrant integrins-regulated cell migration. Mediates, throughinteraction with GDF15-receptor GFRAL, GDF15-induced cell-signaling in the brainstem which induces inhibition of food-intake. Activates MAPK- and AKT-signaling pathways(PubMed:28846097, PubMed:28953886, PubMed:28846099). Isoform 1 incomplex with GFRAL induces higher activation of MAPK-signalingpathway than isoform 2 in complex with GFRAL (PubMed:28846099).{ECO:0000269|PubMed:20064382, ECO:0000269|PubMed:20616503,ECO:0000269|PubMed:20702524, ECO:0000269|PubMed:21357690,ECO:0000269|PubMed:21454698, ECO:0000269|PubMed:28846097,ECO:0000269|PubMed:28846099, ECO:0000269|PubMed:28953886}.

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
HgeneAFAP1chr4:7870348chr10:43612031ENST00000358461-31771_7475731MotifSH3-binding
HgeneAFAP1chr4:7870348chr10:43612031ENST00000360265-21671_7475731MotifSH3-binding
HgeneAFAP1chr4:7870348chr10:43612031ENST00000382543-21771_7475815MotifSH3-binding
HgeneAFAP1chr4:7870348chr10:43612031ENST00000420658-31871_7475815MotifSH3-binding
TgeneRETchr4:7870348chr10:43612031ENST00000340058+1019724_10167121073DomainProtein kinase
TgeneRETchr4:7870348chr10:43612031ENST00000355710+1020724_10167121115DomainProtein kinase
TgeneRETchr4:7870348chr10:43612031ENST00000340058+1019730_7387121073Nucleotide bindingATP
TgeneRETchr4:7870348chr10:43612031ENST00000355710+1020730_7387121115Nucleotide bindingATP
TgeneRETchr4:7870348chr10:43612031ENST00000340058+1019805_8077121073RegionNote=Inhibitors binding
TgeneRETchr4:7870348chr10:43612031ENST00000355710+1020805_8077121115RegionNote=Inhibitors binding

- In-frame and not-retained protein feature among the 13 regional features.
>>>>>>>>>>>>>>>>>>>>>>>>
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneAFAP1chr4:7870348chr10:43612031ENST00000358461-317557_64875731Coiled coilOntology_term=ECO:0000255
HgeneAFAP1chr4:7870348chr10:43612031ENST00000360265-216557_64875731Coiled coilOntology_term=ECO:0000255
HgeneAFAP1chr4:7870348chr10:43612031ENST00000382543-217557_64875815Coiled coilOntology_term=ECO:0000255
HgeneAFAP1chr4:7870348chr10:43612031ENST00000420658-318557_64875815Coiled coilOntology_term=ECO:0000255
HgeneAFAP1chr4:7870348chr10:43612031ENST00000358461-31760_10675731Compositional biasNote=Pro-rich
HgeneAFAP1chr4:7870348chr10:43612031ENST00000360265-21660_10675731Compositional biasNote=Pro-rich
HgeneAFAP1chr4:7870348chr10:43612031ENST00000382543-21760_10675815Compositional biasNote=Pro-rich
HgeneAFAP1chr4:7870348chr10:43612031ENST00000420658-31860_10675815Compositional biasNote=Pro-rich
HgeneAFAP1chr4:7870348chr10:43612031ENST00000358461-317153_24975731DomainPH 1
HgeneAFAP1chr4:7870348chr10:43612031ENST00000358461-317347_44175731DomainPH 2
HgeneAFAP1chr4:7870348chr10:43612031ENST00000360265-216153_24975731DomainPH 1
HgeneAFAP1chr4:7870348chr10:43612031ENST00000360265-216347_44175731DomainPH 2
HgeneAFAP1chr4:7870348chr10:43612031ENST00000382543-217153_24975815DomainPH 1
HgeneAFAP1chr4:7870348chr10:43612031ENST00000382543-217347_44175815DomainPH 2
HgeneAFAP1chr4:7870348chr10:43612031ENST00000420658-318153_24975815DomainPH 1
HgeneAFAP1chr4:7870348chr10:43612031ENST00000420658-318347_44175815DomainPH 2
HgeneAFAP1chr4:7870348chr10:43612031ENST00000358461-317451_45675731MotifSH2-binding 2
HgeneAFAP1chr4:7870348chr10:43612031ENST00000358461-31794_9775731MotifSH2-binding 1
HgeneAFAP1chr4:7870348chr10:43612031ENST00000360265-216451_45675731MotifSH2-binding 2
HgeneAFAP1chr4:7870348chr10:43612031ENST00000360265-21694_9775731MotifSH2-binding 1
HgeneAFAP1chr4:7870348chr10:43612031ENST00000382543-217451_45675815MotifSH2-binding 2
HgeneAFAP1chr4:7870348chr10:43612031ENST00000382543-21794_9775815MotifSH2-binding 1
HgeneAFAP1chr4:7870348chr10:43612031ENST00000420658-318451_45675815MotifSH2-binding 2
HgeneAFAP1chr4:7870348chr10:43612031ENST00000420658-31894_9775815MotifSH2-binding 1
TgeneRETchr4:7870348chr10:43612031ENST00000340058+1019168_2727121073DomainCadherin
TgeneRETchr4:7870348chr10:43612031ENST00000355710+1020168_2727121115DomainCadherin
TgeneRETchr4:7870348chr10:43612031ENST00000340058+101929_6357121073Topological domainExtracellular
TgeneRETchr4:7870348chr10:43612031ENST00000340058+1019658_11147121073Topological domainCytoplasmic
TgeneRETchr4:7870348chr10:43612031ENST00000355710+102029_6357121115Topological domainExtracellular
TgeneRETchr4:7870348chr10:43612031ENST00000355710+1020658_11147121115Topological domainCytoplasmic
TgeneRETchr4:7870348chr10:43612031ENST00000340058+1019636_6577121073TransmembraneHelical
TgeneRETchr4:7870348chr10:43612031ENST00000355710+1020636_6577121115TransmembraneHelical


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FusionGeneSequence for AFAP1_RET


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 AFAP1_RET


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
AFAP1AFAP1, ACTC1, PRKCB, PRKCE, PRKCG, PRKCD, PRKCA, MYC, NXF1, BRCA1, CAPZA2, CDK2, DBN1, FLNA, GAK, MYH9, MYO1C, PPP1CB, IQGAP1, SYNPO, MAPRE1, TPX2, LIMA1, ANLN, MYO5C, MYO19, MYO18A, EXT2, TRIM25, TESRETSTAT3, DOK6, DOK5, SRC, SHC1, PTPRF, DOK2, DOK4, DOK1, GRB2, CRK, PLCG1, PDLIM7, GRB7, FRS2, NRTN, GFRA1, GRB10, IKBKG, MCRS1, CBL, CBLC, RET, HSP90AA1, NOTCH2NL, NOTCH3, AIP, EGFR, NTRK1, ZBTB48, HNRNPD, SORT1, SYNCRIP, SGTB, BAG6, HIST1H3A, KYNU, TXNL4A, ZCCHC8, ICE2, MAPK3, PTK2, MAPK1, PTPRR, DUSP26


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
HgeneAFAP1chr4:7870348chr10:43612031ENST00000358461-317594_63775731F-actin
HgeneAFAP1chr4:7870348chr10:43612031ENST00000360265-216594_63775731F-actin
HgeneAFAP1chr4:7870348chr10:43612031ENST00000382543-217594_63775815F-actin
HgeneAFAP1chr4:7870348chr10:43612031ENST00000420658-318594_63775815F-actin


check button - Retained PPIs, but lost function due to frame-shift fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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RelatedDrugs for AFAP1_RET


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
TgeneRETP07949DB05294VandetanibProto-oncogene tyrosine-protein kinase receptor Ret {ECO:0000305}small moleculeapproved
TgeneRETP07949DB08896RegorafenibProto-oncogene tyrosine-protein kinase receptor Ret {ECO:0000305}small moleculeapproved
TgeneRETP07949DB00398SorafenibProto-oncogene tyrosine-protein kinase receptor Ret {ECO:0000305}small moleculeapproved|investigational
TgeneRETP07949DB08875CabozantinibProto-oncogene tyrosine-protein kinase receptor Ret {ECO:0000305}small moleculeapproved|investigational
TgeneRETP07949DB08901PonatinibProto-oncogene tyrosine-protein kinase receptor Ret {ECO:0000305}small moleculeapproved|investigational

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RelatedDiseases for AFAP1_RET


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneRETC3888239HIRSCHSPRUNG DISEASE, SUSCEPTIBILITY TO, 115UNIPROT
TgeneRETC0025268Multiple Endocrine Neoplasia Type 2a14CTD_human;ORPHANET;UNIPROT
TgeneRETC1833921Familial medullary thyroid carcinoma14CTD_human;ORPHANET;UNIPROT
TgeneRETC0025269Multiple Endocrine Neoplasia Type 2b8CTD_human;ORPHANET;UNIPROT
TgeneRETC1275808Congenital central hypoventilation4CTD_human;ORPHANET;UNIPROT
TgeneRETC0009404Colorectal Neoplasms2CTD_human
TgeneRETC0019569Hirschsprung Disease2CTD_human;HPO;ORPHANET
TgeneRETC0006413Burkitt Lymphoma1CTD_human
TgeneRETC0027662Multiple Endocrine Neoplasia1CTD_human
TgeneRETC0031511Pheochromocytoma1CTD_human;HPO;UNIPROT
TgeneRETC0038220Status Epilepticus1CTD_human
TgeneRETC0040136Thyroid Neoplasm1CTD_human
TgeneRETC0206693Medullary carcinoma1CTD_human
TgeneRETC0238462Medullary carcinoma of thyroid1CTD_human;HPO
TgeneRETC0740340Amyloidosis, Familial1CTD_human
TgeneRETC1609433Congenital absence of kidneys syndrome1CTD_human;ORPHANET