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Center for Computational Systems Medicine
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Gene summary

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Gene structures and expression levels

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Exon skipping events with PSIs in TCGA

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Exon skipping events with PSIs in GTEx

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Open reading frame (ORF) annotation in the exon skipping event

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Exon skipping events in the canonical protein sequence

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SNVs in the skipped exons with depth of coverage

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Splicing Quantitative Trait Loci (sQTLs) in the skipped exons

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon

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Related drugs with this gene

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Related diseases with this gene

Gene summary for RET

check button Gene summary
Gene informationGene symbol

RET

Gene ID

5979

Gene nameret proto-oncogene
SynonymsCDHF12|CDHR16|HSCR1|MEN2A|MEN2B|MTC1|PTC|RET-ELE1
Cytomap

10q11.21

Type of geneprotein-coding
Descriptionproto-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 date20180527
UniProtAcc

P07949

ContextPubMed: RET [Title/Abstract] AND exon [Title/Abstract] AND skip [Title/Abstract]
- Title (PMID)

check button Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez
GeneGO IDGO termPubMed ID
RET

GO:0030155

regulation of cell adhesion

21357690

RET

GO:0030335

positive regulation of cell migration

20702524

RET

GO:0033619

membrane protein proteolysis

21357690

RET

GO:0033630

positive regulation of cell adhesion mediated by integrin

20702524

RET

GO:0035860

glial cell-derived neurotrophic factor receptor signaling pathway

28953886

RET

GO:0043410

positive regulation of MAPK cascade

28846099


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Exon skipping events across known transcript of Ensembl for RET from UCSC genome browser

check buttonSkipped exons in TCGA and GTEx based on Ensembl gene isoform structure.
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

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Gene isoform structures and expression levels for RET

check button Expression levels of gene isoforms across TCGA.
gencode gene structure

check button Expression levels of gene isoforms across GTEx.
gencode gene structure


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Exon skipping events with PSIs in TCGA for RET

check button Information of exkip skipping event in TCGA.
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_409171043595906:43596170:43597789:43598077:43600399:4360064143597789:43598077ENSG00000165731.13ENST00000340058.5,ENST00000355710.3
exon_skip_409341043597918:43598077:43600399:43600641:43601823:4360193843600399:43600641ENSG00000165731.13ENST00000340058.5,ENST00000355710.3
exon_skip_409441043604478:43604678:43606654:43606913:43607546:4360767243606654:43606913ENSG00000165731.13ENST00000340058.5,ENST00000355710.3
exon_skip_409451043608300:43608411:43609003:43609123:43609927:4361004143609003:43609123ENSG00000165731.13ENST00000340058.5,ENST00000498820.1,ENST00000355710.3
exon_skip_409461043613820:43613928:43614978:43615193:43615528:4361565143614978:43615193ENSG00000165731.13ENST00000340058.5,ENST00000355710.3
exon_skip_409501043619118:43619256:43620330:43620430:43622022:4362217043620330:43620430ENSG00000165731.13ENST00000340058.5,ENST00000355710.3

check button PSI values of skipped exons in TCGA.
psi tcga

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Exon skipping events with PSIs in GTEx for RET

check button Information of exkip skipping event in GTEx
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_409441043604478:43604678:43606654:43606913:43607546:4360767243606654:43606913ENSG00000165731.13ENST00000355710.3,ENST00000340058.5
exon_skip_409461043613820:43613928:43614978:43615193:43615528:4361565143614978:43615193ENSG00000165731.13ENST00000355710.3,ENST00000340058.5
exon_skip_409501043619118:43619256:43620330:43620430:43622022:4362217043620330:43620430ENSG00000165731.13ENST00000355710.3,ENST00000340058.5

check button PSI values of skipped exons in GTEx.
psi gtex

* Skipped exon sequences.

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Open reading frame (ORF) annotation in the exon skipping event for RET

check button Open reading frame (ORF) of individual exon skipping events in TCGA based on the Ensembl gene structure combined from isoforms.
ENSTStart of skipped exonEnd of skipped exonORF
ENST000003557104360039943600641Frame-shift
ENST000003557104360665443606913Frame-shift
ENST000003557104361497843615193Frame-shift
ENST000003557104362033043620430Frame-shift
ENST000003557104359778943598077In-frame
ENST000003557104360900343609123In-frame

check button Open reading frame (ORF) of individual exon skipping events in GTEx based on the Ensembl gene structure combined from isoforms.
ENSTStart of skipped exonEnd of skipped exonORF
ENST000003557104360665443606913Frame-shift
ENST000003557104361497843615193Frame-shift
ENST000003557104362033043620430Frame-shift

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Infer the effects of exon skipping event on protein functional features for RET

check button Exon skipping at the protein sequence level and followed lost functional features.
* Click on the image to enlarge it in a new window.
prot feature distribution

check button Loci of skipped exons in TCGA across genomic, transcript, and protein sequence levels of In-frame cases.
ENSTLength of mRNALength of AA seq.Genomic startGenomic endmRNA startmRNA endAA startAA end
ENST00000355710567611144359778943598077570857112208
ENST0000035571056761114436090034360912319922111586626

check button Loci of skipped exons in GTEx across genomic, transcript, and protein sequence levels of In-frame cases.
ENSTLength of mRNALength of AA seq.Genomic startGenomic endmRNA startmRNA endAA startAA end

check button Lost protein functional features of individual exon skipping events in TCGA.
UniProt acc.Start of exon skipping (AA)End of exon skipping (AA)Protein feature start (AA)Protein feature end (AA)Category of protein featureDescription of feature
P07949112208120126Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:2X2U
P07949112208142152Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:2X2U
P07949112208174178Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:2X2U
P07949112208184187Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:2X2U
P07949112208202208Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:2X2U
P07949112208291114ChainID=PRO_0000024450;Note=Proto-oncogene tyrosine-protein kinase receptor Ret
P0794911220829707ChainID=PRO_0000415292;Note=Extracellular cell-membrane anchored RET cadherin 120 kDa fragment
P07949112208137142Disulfide bondOntology_term=ECO:0000269;evidence=ECO:0000269|PubMed:20473317;Dbxref=PMID:20473317
P07949112208168272DomainNote=Cadherin;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00043
P07949112208151151GlycosylationNote=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:20473317;Dbxref=PMID:20473317
P07949112208199199GlycosylationNote=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
P07949112208157159HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:2X2U
P07949112208162166HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:2X2U
P07949112208191196HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:2X2U
P07949112208114114Natural variantID=VAR_067101;Note=In HSCR1. R->C;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:22174939;Dbxref=dbSNP:rs747483905,PMID:22174939
P07949112208114114Natural variantID=VAR_018154;Note=In CCHS and HSCR1. R->H;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:12086152,ECO:0000269|PubMed:14566559,ECO:0000269|PubMed:22174939;Dbxref=dbSNP:rs76397662,PMID:12086152,PMID:14566559,PMID:22174939
P07949112208142142Natural variantID=VAR_006298;Note=In HSCR1%3B sporadic form. C->S
P07949112208145145Natural variantID=VAR_035711;Note=In HSCR1%3B also in a colorectal cancer sample%3B somatic mutation. V->G;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:16959974,ECO:0000269|PubMed:22174939;Dbxref=PMID:16959974,PMID:22174939
P07949112208155155Natural variantID=VAR_067102;Note=In HSCR1. P->L;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:22174939;Dbxref=PMID:22174939
P07949112208157157Natural variantID=VAR_009461;Note=In HSCR1%3B unknown pathological significance. C->Y;Ontology_term=ECO:0000269;evidence=ECO:0000269|Ref.60
P07949112208163163Natural variantID=VAR_041762;Note=In a colorectal adenocarcinoma sample%3B somatic mutation. R->Q;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:17344846;Dbxref=dbSNP:rs149403911,PMID:17344846
P07949112208174174Natural variantID=VAR_009462;Note=In HSCR1%3B sporadic form. F->S;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:9094028;Dbxref=PMID:9094028
P07949112208175175Natural variantID=VAR_067103;Note=In HSCR1. R->P;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:22174939;Dbxref=PMID:22174939
P07949112208180180Natural variantID=VAR_009463;Note=In HSCR1%3B sporadic form. R->P;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:9090527;Dbxref=PMID:9090527
P07949112208197197Natural variantID=VAR_009464;Note=In HSCR1%3B sporadic form. C->Y;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:9094028;Dbxref=PMID:9094028
P07949112208198198Natural variantID=VAR_044392;Note=In a patient with renal agenesis%3B unknown pathological significance%3B prevents phosphorylation in response to GDNF. P->T;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:18252215;Dbxref=dbSNP:rs76736111,PMID:18252215
P0794911220829635Topological domainNote=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
P07949112208139141TurnOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:2X2U
P07949586626291114ChainID=PRO_0000024450;Note=Proto-oncogene tyrosine-protein kinase receptor Ret
P0794958662629707ChainID=PRO_0000415292;Note=Extracellular cell-membrane anchored RET cadherin 120 kDa fragment
P07949586626593593Natural variantID=VAR_035712;Note=In a colorectal cancer sample%3B somatic mutation. G->E;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:16959974;Dbxref=PMID:16959974
P07949586626595595Natural variantID=VAR_067116;Note=In HSCR1. E->Q;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:22174939;Dbxref=PMID:22174939
P07949586626600600Natural variantID=VAR_008966;Note=R->Q;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:10612852;Dbxref=dbSNP:rs377767393,PMID:10612852
P07949586626609609Natural variantID=VAR_009470;Note=In MEN2A. C->G;Dbxref=dbSNP:rs77558292
P07949586626609609Natural variantID=VAR_009471;Note=In MEN2A. C->R;Dbxref=dbSNP:rs77558292
P07949586626609609Natural variantID=VAR_006307;Note=In HSCR1%3B familial form. C->W;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:7881414;Dbxref=dbSNP:rs377767396,PMID:7881414
P07949586626609609Natural variantID=VAR_006306;Note=In MTC%2C MEN2A and HSCR1%3B familial and sporadic forms. C->Y;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:7633441,ECO:0000269|PubMed:7849720,ECO:0000269|PubMed:9384613,ECO:0000269|Ref.60;Db
P07949586626611611Natural variantID=VAR_009472;Note=In MTC%3B familial form. C->G;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:9677065;Dbxref=dbSNP:rs377767391,PMID:9677065
P07949586626611611Natural variantID=VAR_009473;Note=In MEN2A. C->R;Dbxref=dbSNP:rs377767391
P07949586626611611Natural variantID=VAR_009474;Note=In MEN2A. C->S;Dbxref=dbSNP:rs377767391
P07949586626611611Natural variantID=VAR_006308;Note=In MEN2A and MTC%3B familial form. C->W;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:8103403;Dbxref=dbSNP:rs80069458,PMID:8103403
P07949586626611611Natural variantID=VAR_006309;Note=In MEN2A. C->Y;Dbxref=dbSNP:rs377767397
P07949586626618618Natural variantID=VAR_006312;Note=In MEN2A and MTC%3B familial form. C->F;Dbxref=dbSNP:rs79781594
P07949586626618618Natural variantID=VAR_006310;Note=In MEN2A. C->G;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:8099202;Dbxref=dbSNP:rs76262710,PMID:8099202
P07949586626618618Natural variantID=VAR_006311;Note=In MEN2A%2C MTC and HSCR1. C->R;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:7849720,ECO:0000269|PubMed:7881414,ECO:0000269|PubMed:7915165,ECO:0000269|PubMed:9259198;Dbxref=dbSNP:rs76262710,P
P07949586626618618Natural variantID=VAR_006313;Note=In MEN2A%2C HSCR1 and MTC%3B familial and sporadic forms. C->S;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:7849720,ECO:0000269|PubMed:7860065,ECO:0000269|PubMed:7915165,ECO:00002
P07949586626618618Natural variantID=VAR_006314;Note=In MEN2A and MTC%3B familial form. C->Y;Dbxref=dbSNP:rs79781594
P07949586626620620Natural variantID=VAR_006318;Note=In MEN2A and MTC%3B familial form. C->F;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:7915165;Dbxref=dbSNP:rs77503355,PMID:7915165
P07949586626620620Natural variantID=VAR_006315;Note=In MEN2A and MTC%3B familial and sporadic forms. C->G;Dbxref=dbSNP:rs77316810
P07949586626620620Natural variantID=VAR_006316;Note=In MEN2A%2C MTC and HSCR1%3B familial and sporadic forms. C->R;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:7633441,ECO:0000269|PubMed:7881414,ECO:0000269|
P07949586626620620Natural variantID=VAR_006317;Note=In MEN2A and MTC%3B familial form. C->S;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:7849720,ECO:0000269|PubMed:7860065;Dbxref=dbSNP:rs77503355,PMID:7849720,PMID:7860065
P07949586626620620Natural variantID=VAR_009475;Note=In MEN2A and HSCR1. C->W;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:9384613;Dbxref=dbSNP:rs79890926,PMID:9384613
P07949586626620620Natural variantID=VAR_006319;Note=In MEN2A. C->Y;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:8103403;Dbxref=dbSNP:rs77503355,PMID:8103403
P07949586626626626Natural variantID=VAR_009476;Note=In HSCR1%3B sporadic form. Q->K;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:10090908;Dbxref=PMID:10090908
P07949586626587588SiteNote=Breakpoint for translocation to form the TRIM27/RET oncogene
P0794958662629635Topological domainNote=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255


check button Lost protein functional features of individual exon skipping events in GTEx.
UniProt acc.Start of exon skipping (AA)End of exon skipping (AA)Protein feature start (AA)Protein feature end (AA)Category of protein featureDescription of feature


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SNVs in the skipped exons for RET

check button - Lollipop plot for presenting exon skipping associated SNVs.
* Click on the image to enlarge it in a new window.
lollipop

check button - Differential PSIs between mutated versus non-mutated samples.

check button - Non-synonymous mutations located in the skipped exons in TCGA.
Cancer typeSampleESIDSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange
UCECTCGA-D1-A177-01exon_skip_40917
43597790435980774359780143597801Frame_Shift_DelC-p.P117fs
MESOTCGA-LK-A4NY-01exon_skip_40917
43597790435980774359782943597842Frame_Shift_DelTCCTGTCACCCACA-p.FLSPT126fs
LIHCTCGA-DD-A39Y-01exon_skip_40917
43597790435980774359793643597936Frame_Shift_DelC-p.P162fs
LIHCTCGA-DD-A3A0-01exon_skip_40944
43606655436069134360667443606674Frame_Shift_DelA-p.E428fs
LIHCTCGA-G3-A3CJ-01exon_skip_40946
43614979436151934361516643615166Frame_Shift_DelG-p.Q860fs
SARCTCGA-DX-AB2X-01exon_skip_40946
43614979436151934361516243615162Nonsense_MutationCAp.S859*

check button - Depth of coverage in the three exons composing exon skipping event
Depth of coverage in three exonsMutation description

check button - Non-synonymous mutations located in the skipped exons in CCLE.
SampleSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange
A704_KIDNEY43606655436069134360686043606860Frame_Shift_DelA-p.Q491fs
HCC33_LUNG43597790435980774359790443597904Missense_MutationAGp.N151S
NCIH2869_PLEURA43597790435980774359796943597969Missense_MutationTCp.S173P
T84_LARGE_INTESTINE43597790435980774359801843598018Missense_MutationGAp.R189H
MHHPREB1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE43597790435980774359805543598055Missense_MutationCGp.S201R
KYSE70_OESOPHAGUS43600400436006414360042443600424Missense_MutationCTp.A217V
NCIH522_LUNG43600400436006414360061643600616Missense_MutationCTp.A281V
NCIH1339_LUNG43606655436069134360667343606673Missense_MutationGAp.E428K
CL34_LARGE_INTESTINE43606655436069134360670343606703Missense_MutationGAp.V438I
A704_KIDNEY43606655436069134360686643606866Missense_MutationCAp.T492N
NCIH2228_LUNG43606655436069134360688443606884Missense_MutationCTp.A498V
SNU1076_UPPER_AERODIGESTIVE_TRACT43606655436069134360690843606908Missense_MutationGAp.G506E
NCIH1105_LUNG43614979436151934361506843615068Missense_MutationGCp.G828R
ISTMEL1_SKIN43614979436151934361509643615096Missense_MutationCTp.S837F
SNUC2A_LARGE_INTESTINE43614979436151934361511643615116Missense_MutationCTp.R844W
SNUC2B_LARGE_INTESTINE43614979436151934361511643615116Missense_MutationCTp.R844W
LB2518EBV_MATCHED_NORMAL_TISSUE43614979436151934361511743615117Missense_MutationGTp.R844L
LB2518MEL_SKIN43614979436151934361511743615117Missense_MutationGTp.R844L
NCIH2066_LUNG43614979436151934361514343615143Missense_MutationTAp.S853T
LNCAPCLONEFGC_PROSTATE43614979436151934361515943615159Missense_MutationTCp.I858T
SKCO1_LARGE_INTESTINE43620331436204304362036243620362Missense_MutationGAp.E991K
DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE43620331436204304362039643620396Missense_MutationGAp.S1002N
JEG3_PLACENTA43620331436204304362040143620401Missense_MutationGTp.D1004Y
NCIH1666_LUNG43614979436151934361499943614999Nonsense_MutationGTp.E805*
NCIH2347_LUNG43614979436151934361497943614980Splice_Site-Cp.GP798fs
M00921_SKIN43620331436204304362042943620429Splice_SiteGAp.R1013K

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for RET

check button sQTL information located at the skipped exons.
Exon skip IDChromosomeThree exonsSkippped exonENSTCancer typeSNP idLocationDNA change (ref/var)P-value

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for RET


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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for RET


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RelatedDrugs for RET

check button Approved drugs targeting this gene.
(DrugBank Version 5.1.0 2018-04-02)
GeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
P07949DB05294VandetanibProto-oncogene tyrosine-protein kinase receptor Ret {ECO:0000305}small moleculeapproved
P07949DB08896RegorafenibProto-oncogene tyrosine-protein kinase receptor Ret {ECO:0000305}small moleculeapproved
P07949DB00398SorafenibProto-oncogene tyrosine-protein kinase receptor Ret {ECO:0000305}small moleculeapproved|investigational
P07949DB08875CabozantinibProto-oncogene tyrosine-protein kinase receptor Ret {ECO:0000305}small moleculeapproved|investigational
P07949DB08901PonatinibProto-oncogene tyrosine-protein kinase receptor Ret {ECO:0000305}small moleculeapproved|investigational
P07949DB12010FostamatinibProto-oncogene tyrosine-protein kinase receptor Ret {ECO:0000305}small moleculeapproved|investigational

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RelatedDiseases for RET

check button Diseases associated with this gene.
(DisGeNet 4.0)
GeneDisease IDDisease name# pubmedsSource
RETC3888239HIRSCHSPRUNG DISEASE, SUSCEPTIBILITY TO, 115UNIPROT
RETC0025268Multiple Endocrine Neoplasia Type 2a14CTD_human;ORPHANET;UNIPROT
RETC1833921Familial medullary thyroid carcinoma14CTD_human;ORPHANET;UNIPROT
RETC0025269Multiple Endocrine Neoplasia Type 2b8CTD_human;ORPHANET;UNIPROT
RETC1275808Congenital central hypoventilation4CTD_human;ORPHANET;UNIPROT
RETC0009404Colorectal Neoplasms2CTD_human
RETC0019569Hirschsprung Disease2CTD_human;HPO;ORPHANET
RETC0006413Burkitt Lymphoma1CTD_human
RETC0027662Multiple Endocrine Neoplasia1CTD_human
RETC0031511Pheochromocytoma1CTD_human;HPO;UNIPROT
RETC0038220Status Epilepticus1CTD_human
RETC0040136Thyroid Neoplasm1CTD_human
RETC0206693Medullary carcinoma1CTD_human
RETC0238462Medullary carcinoma of thyroid1CTD_human;HPO
RETC0740340Amyloidosis, Familial1CTD_human
RETC1609433Congenital absence of kidneys syndrome1CTD_human;ORPHANET