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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: 9020

FusionGeneSummary for CUX1_RET

check button Fusion gene summary
Fusion gene informationFusion gene name: CUX1_RET
Fusion gene ID: 9020
HgeneTgene
Gene symbol

CUX1

RET

Gene ID

1523

5979

Gene namecut like homeobox 1ret proto-oncogene
SynonymsCASP|CDP|CDP/Cut|CDP1|COY1|CUTL1|CUX|Clox|Cux/CDP|GOLIM6|Nbla10317|p100|p110|p200|p75CDHF12|CDHR16|HSCR1|MEN2A|MEN2B|MTC1|PTC|RET-ELE1
Cytomap

7q22.1

10q11.21

Type of geneprotein-codingprotein-coding
Descriptionprotein CASPCCAAT displacement proteincut homologgolgi integral membrane protein 6homeobox protein cux-1putative protein product of Nbla10317proto-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 date2018052320180527
UniProtAcc

Q13948

P07949

Ensembl transtripts involved in fusion geneENST00000437600, ENST00000292538, 
ENST00000393824, ENST00000547394, 
ENST00000360264, ENST00000425244, 
ENST00000292535, ENST00000549414, 
ENST00000556210, ENST00000550008, 
ENST00000546411, ENST00000560541, 
ENST00000355710, ENST00000340058, 
Fusion gene scores* DoF score20 X 18 X 9=324018 X 10 X 7=1260
# samples 2265
** MAII scorelog2(22/3240*10)=-3.88041838424733
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: CUX1 [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.
Tumor suppressor gene involved fusion gene, in-frame but not 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
ChiTaRS3.1KF421948CUX1chr7

101813831

+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-frameENST00000437600ENST00000355710CUX1chr7

101813831

+RETchr10

43612031

+
In-frameENST00000437600ENST00000340058CUX1chr7

101813831

+RETchr10

43612031

+
In-frameENST00000292538ENST00000355710CUX1chr7

101813831

+RETchr10

43612031

+
In-frameENST00000292538ENST00000340058CUX1chr7

101813831

+RETchr10

43612031

+
In-frameENST00000393824ENST00000355710CUX1chr7

101813831

+RETchr10

43612031

+
In-frameENST00000393824ENST00000340058CUX1chr7

101813831

+RETchr10

43612031

+
In-frameENST00000547394ENST00000355710CUX1chr7

101813831

+RETchr10

43612031

+
In-frameENST00000547394ENST00000340058CUX1chr7

101813831

+RETchr10

43612031

+
In-frameENST00000360264ENST00000355710CUX1chr7

101813831

+RETchr10

43612031

+
In-frameENST00000360264ENST00000340058CUX1chr7

101813831

+RETchr10

43612031

+
In-frameENST00000425244ENST00000355710CUX1chr7

101813831

+RETchr10

43612031

+
In-frameENST00000425244ENST00000340058CUX1chr7

101813831

+RETchr10

43612031

+
In-frameENST00000292535ENST00000355710CUX1chr7

101813831

+RETchr10

43612031

+
In-frameENST00000292535ENST00000340058CUX1chr7

101813831

+RETchr10

43612031

+
In-frameENST00000549414ENST00000355710CUX1chr7

101813831

+RETchr10

43612031

+
In-frameENST00000549414ENST00000340058CUX1chr7

101813831

+RETchr10

43612031

+
In-frameENST00000556210ENST00000355710CUX1chr7

101813831

+RETchr10

43612031

+
In-frameENST00000556210ENST00000340058CUX1chr7

101813831

+RETchr10

43612031

+
In-frameENST00000550008ENST00000355710CUX1chr7

101813831

+RETchr10

43612031

+
In-frameENST00000550008ENST00000340058CUX1chr7

101813831

+RETchr10

43612031

+
In-frameENST00000546411ENST00000355710CUX1chr7

101813831

+RETchr10

43612031

+
In-frameENST00000546411ENST00000340058CUX1chr7

101813831

+RETchr10

43612031

+
3UTR-3CDSENST00000560541ENST00000355710CUX1chr7

101813831

+RETchr10

43612031

+
3UTR-3CDSENST00000560541ENST00000340058CUX1chr7

101813831

+RETchr10

43612031

+

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FusionProtFeatures for CUX1_RET


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
CUX1

Q13948

RET

P07949

May be involved in intra-Golgi retrograde transport.{ECO:0000269|PubMed:15718469}. 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
TgeneRETchr7:101813831chr10:43612031ENST00000340058+1019724_10167121073DomainProtein kinase
TgeneRETchr7:101813831chr10:43612031ENST00000355710+1020724_10167121115DomainProtein kinase
TgeneRETchr7:101813831chr10:43612031ENST00000340058+1019730_7387121073Nucleotide bindingATP
TgeneRETchr7:101813831chr10:43612031ENST00000355710+1020730_7387121115Nucleotide bindingATP
TgeneRETchr7:101813831chr10:43612031ENST00000340058+1019805_8077121073RegionNote=Inhibitors binding
TgeneRETchr7:101813831chr10:43612031ENST00000355710+1020805_8077121115RegionNote=Inhibitors binding

- In-frame and not-retained protein feature among the 13 regional features.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneCUX1chr7:101813831chr10:43612031ENST00000292535+102456_4072761506Coiled coilOntology_term=ECO:0000255
HgeneCUX1chr7:101813831chr10:43612031ENST00000292538+1023502_556287679Coiled coilOntology_term=ECO:0000255
HgeneCUX1chr7:101813831chr10:43612031ENST00000292538+102367_450287679Coiled coilOntology_term=ECO:0000255
HgeneCUX1chr7:101813831chr10:43612031ENST00000360264+102456_4072871517Coiled coilOntology_term=ECO:0000255
HgeneCUX1chr7:101813831chr10:43612031ENST00000393824+922502_556250640Coiled coilOntology_term=ECO:0000255
HgeneCUX1chr7:101813831chr10:43612031ENST00000393824+92267_450250640Coiled coilOntology_term=ECO:0000255
HgeneCUX1chr7:101813831chr10:43612031ENST00000425244+92256_407241633Coiled coilOntology_term=ECO:0000255
HgeneCUX1chr7:101813831chr10:43612031ENST00000437600+1023502_556287677Coiled coilOntology_term=ECO:0000255
HgeneCUX1chr7:101813831chr10:43612031ENST00000437600+102367_450287677Coiled coilOntology_term=ECO:0000255
HgeneCUX1chr7:101813831chr10:43612031ENST00000546411+102456_4072761404Coiled coilOntology_term=ECO:0000255
HgeneCUX1chr7:101813831chr10:43612031ENST00000547394+922502_556271663Coiled coilOntology_term=ECO:0000255
HgeneCUX1chr7:101813831chr10:43612031ENST00000547394+92267_450271663Coiled coilOntology_term=ECO:0000255
HgeneCUX1chr7:101813831chr10:43612031ENST00000549414+102356_4072761484Coiled coilOntology_term=ECO:0000255
HgeneCUX1chr7:101813831chr10:43612031ENST00000550008+102256_4072761450Coiled coilOntology_term=ECO:0000255
HgeneCUX1chr7:101813831chr10:43612031ENST00000556210+102256_4072761348Coiled coilOntology_term=ECO:0000255
HgeneCUX1chr7:101813831chr10:43612031ENST00000292535+10241406_14382761506Compositional biasNote=Ala-rich
HgeneCUX1chr7:101813831chr10:43612031ENST00000360264+10241406_14382871517Compositional biasNote=Ala-rich
HgeneCUX1chr7:101813831chr10:43612031ENST00000425244+9221406_1438241633Compositional biasNote=Ala-rich
HgeneCUX1chr7:101813831chr10:43612031ENST00000546411+10241406_14382761404Compositional biasNote=Ala-rich
HgeneCUX1chr7:101813831chr10:43612031ENST00000549414+10231406_14382761484Compositional biasNote=Ala-rich
HgeneCUX1chr7:101813831chr10:43612031ENST00000550008+10221406_14382761450Compositional biasNote=Ala-rich
HgeneCUX1chr7:101813831chr10:43612031ENST00000556210+10221406_14382761348Compositional biasNote=Ala-rich
HgeneCUX1chr7:101813831chr10:43612031ENST00000292535+10241117_12042761506DNA bindingCUT 3
HgeneCUX1chr7:101813831chr10:43612031ENST00000292535+10241244_13032761506DNA bindingHomeobox
HgeneCUX1chr7:101813831chr10:43612031ENST00000292535+1024542_6292761506DNA bindingCUT 1
HgeneCUX1chr7:101813831chr10:43612031ENST00000292535+1024934_10212761506DNA bindingCUT 2
HgeneCUX1chr7:101813831chr10:43612031ENST00000360264+10241117_12042871517DNA bindingCUT 3
HgeneCUX1chr7:101813831chr10:43612031ENST00000360264+10241244_13032871517DNA bindingHomeobox
HgeneCUX1chr7:101813831chr10:43612031ENST00000360264+1024542_6292871517DNA bindingCUT 1
HgeneCUX1chr7:101813831chr10:43612031ENST00000360264+1024934_10212871517DNA bindingCUT 2
HgeneCUX1chr7:101813831chr10:43612031ENST00000425244+9221117_1204241633DNA bindingCUT 3
HgeneCUX1chr7:101813831chr10:43612031ENST00000425244+9221244_1303241633DNA bindingHomeobox
HgeneCUX1chr7:101813831chr10:43612031ENST00000425244+922542_629241633DNA bindingCUT 1
HgeneCUX1chr7:101813831chr10:43612031ENST00000425244+922934_1021241633DNA bindingCUT 2
HgeneCUX1chr7:101813831chr10:43612031ENST00000546411+10241117_12042761404DNA bindingCUT 3
HgeneCUX1chr7:101813831chr10:43612031ENST00000546411+10241244_13032761404DNA bindingHomeobox
HgeneCUX1chr7:101813831chr10:43612031ENST00000546411+1024542_6292761404DNA bindingCUT 1
HgeneCUX1chr7:101813831chr10:43612031ENST00000546411+1024934_10212761404DNA bindingCUT 2
HgeneCUX1chr7:101813831chr10:43612031ENST00000549414+10231117_12042761484DNA bindingCUT 3
HgeneCUX1chr7:101813831chr10:43612031ENST00000549414+10231244_13032761484DNA bindingHomeobox
HgeneCUX1chr7:101813831chr10:43612031ENST00000549414+1023542_6292761484DNA bindingCUT 1
HgeneCUX1chr7:101813831chr10:43612031ENST00000549414+1023934_10212761484DNA bindingCUT 2
HgeneCUX1chr7:101813831chr10:43612031ENST00000550008+10221117_12042761450DNA bindingCUT 3
HgeneCUX1chr7:101813831chr10:43612031ENST00000550008+10221244_13032761450DNA bindingHomeobox
HgeneCUX1chr7:101813831chr10:43612031ENST00000550008+1022542_6292761450DNA bindingCUT 1
HgeneCUX1chr7:101813831chr10:43612031ENST00000550008+1022934_10212761450DNA bindingCUT 2
HgeneCUX1chr7:101813831chr10:43612031ENST00000556210+10221117_12042761348DNA bindingCUT 3
HgeneCUX1chr7:101813831chr10:43612031ENST00000556210+10221244_13032761348DNA bindingHomeobox
HgeneCUX1chr7:101813831chr10:43612031ENST00000556210+1022542_6292761348DNA bindingCUT 1
HgeneCUX1chr7:101813831chr10:43612031ENST00000556210+1022934_10212761348DNA bindingCUT 2
HgeneCUX1chr7:101813831chr10:43612031ENST00000292538+10231_619287679Topological domainCytoplasmic
HgeneCUX1chr7:101813831chr10:43612031ENST00000292538+1023641_678287679Topological domainLumenal
HgeneCUX1chr7:101813831chr10:43612031ENST00000393824+9221_619250640Topological domainCytoplasmic
HgeneCUX1chr7:101813831chr10:43612031ENST00000393824+922641_678250640Topological domainLumenal
HgeneCUX1chr7:101813831chr10:43612031ENST00000437600+10231_619287677Topological domainCytoplasmic
HgeneCUX1chr7:101813831chr10:43612031ENST00000437600+1023641_678287677Topological domainLumenal
HgeneCUX1chr7:101813831chr10:43612031ENST00000547394+9221_619271663Topological domainCytoplasmic
HgeneCUX1chr7:101813831chr10:43612031ENST00000547394+922641_678271663Topological domainLumenal
HgeneCUX1chr7:101813831chr10:43612031ENST00000292538+1023620_640287679TransmembraneHelical%3B Anchor for type IV membrane protein
HgeneCUX1chr7:101813831chr10:43612031ENST00000393824+922620_640250640TransmembraneHelical%3B Anchor for type IV membrane protein
HgeneCUX1chr7:101813831chr10:43612031ENST00000437600+1023620_640287677TransmembraneHelical%3B Anchor for type IV membrane protein
HgeneCUX1chr7:101813831chr10:43612031ENST00000547394+922620_640271663TransmembraneHelical%3B Anchor for type IV membrane protein
TgeneRETchr7:101813831chr10:43612031ENST00000340058+1019168_2727121073DomainCadherin
TgeneRETchr7:101813831chr10:43612031ENST00000355710+1020168_2727121115DomainCadherin
TgeneRETchr7:101813831chr10:43612031ENST00000340058+101929_6357121073Topological domainExtracellular
TgeneRETchr7:101813831chr10:43612031ENST00000340058+1019658_11147121073Topological domainCytoplasmic
TgeneRETchr7:101813831chr10:43612031ENST00000355710+102029_6357121115Topological domainExtracellular
TgeneRETchr7:101813831chr10:43612031ENST00000355710+1020658_11147121115Topological domainCytoplasmic
TgeneRETchr7:101813831chr10:43612031ENST00000340058+1019636_6577121073TransmembraneHelical
TgeneRETchr7:101813831chr10:43612031ENST00000355710+1020636_6577121115TransmembraneHelical


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FusionGeneSequence for CUX1_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 CUX1_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
CUX1RB1, CREBBP, KAT2B, BIN1, ELAC2, RECQL5, CDK7, CCNA1, CDK1, SATB1, TLE4, MAX, SOX2, KCND3, EHMT2, ECT2, TP53BP1, SUMO2, MAGEA10, HLA-DQA1, STX6, WDR83, PTH1R, GABRE, SLC39A4, NIT1, NTRK1, TACC3, SPATS2L, NFATC1, RBPJ, FOXD3, FOXE1, FOXG1, FOXJ2, GAN, FOXK2, FOXN1, FOXO1, FOXP1, FOXQ1, SLC39A12, EXT2, RAB30, LAMP1, POTEB3, TRIM25RETSTAT3, 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


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


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RelatedDrugs for CUX1_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 CUX1_RET


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCUX1C0041696Unipolar Depression3PSYGENET
HgeneCUX1C1269683Major Depressive Disorder3PSYGENET
HgeneCUX1C0525045Mood Disorders1PSYGENET
HgeneCUX1C0596263Carcinogenesis1CTD_human
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