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RGD DISEASE ONTOLOGY - ANNOTATIONS

RGD uses the Human Disease Ontology (DO, https://disease-ontology.org/) for disease curation across species. RGD automatically downloads each new release of the ontology on a monthly basis. Some additional terms which are required for RGD's curation purposes but are not currently covered in the official version of DO have been added. As corresponding terms are added to DO, these custom terms are retired and the DO terms substituted in existing annotations and subsequently used for curation.
Term:spondyloepiphyseal dysplasia
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Accession:DOID:0112280 term browser browse the term
Definition:An osteochondrodysplasia characterized by skeletal dysplasia mainly involving the spine and proximal epiphyses resulting in shortening of the trunk and limbs. (DO)
Synonyms:exact_synonym: SED
 xref: GARD:7687;   MONDO:0016761;   ORDO:253


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spondyloepiphyseal dysplasia term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G B3galt6 UDP-Gal:betaGal beta 1,3-galactosyltransferase, polypeptide 6 ISO ClinVar Annotator: match by term: Spondyloepiphyseal dysplasia ClinVar PMID:24033266 NCBI chr 4:156,073,923...156,077,135
Ensembl chr 4:156,073,923...156,077,106 		JBrowse link
G Glb1 galactosidase, beta 1 ISO ClinVar Annotator: match by term: Spondyloepiphyseal dysplasia ClinVar PMID:8922281 PMID:10841810 PMID:19472408 PMID:21497194 PMID:23831247 More... NCBI chr 9:114,230,146...114,303,447
Ensembl chr 9:114,230,144...114,303,966 		JBrowse link
autosomal recessive spondyloepiphyseal dysplasia tarda term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Ccn6 cellular communication network factor 6 ISO ClinVar Annotator: match by term: Autosomal recessive spondyloepiphyseal dysplasia tarda ClinVar PMID:10471507 PMID:22791401 PMID:25741868 PMID:28492532 PMID:29258992 NCBI chr10:39,026,966...39,049,484
Ensembl chr10:39,026,966...39,039,790 		JBrowse link
spondyloepiphyseal dysplasia congenita term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Bnip1 BCL2/adenovirus E1B interacting protein 1 ISO ClinVar Annotator: match by term: Spondyloepiphyseal dysplasia congenita ClinVar PMID:25741868 NCBI chr17:26,999,876...27,011,539
Ensembl chr17:27,000,040...27,011,539 		JBrowse link
G Chst3 carbohydrate sulfotransferase 3 ISO ClinVar Annotator: match by term: Spondyloepiphyseal dysplasia congenita ClinVar PMID:28492532 NCBI chr10:60,017,349...60,057,936
Ensembl chr10:60,017,354...60,055,082 		JBrowse link
G Clasp1 CLIP associating protein 1 ISO ClinVar Annotator: match by term: Spondyloepiphyseal dysplasia congenita ClinVar PMID:25741868 PMID:26522830 PMID:28492532 PMID:28669401 PMID:30368667 More... NCBI chr 1:118,314,976...118,537,192
Ensembl chr 1:118,316,788...118,540,408 		JBrowse link
G Col2a1 collagen, type II, alpha 1 ISO
IAGP		 DNA:missense mutation:cds:p.R1417C (mouse)
DNA:missense mutation:cds:p.P986L (human)
DNA:missense mutations:cds:p.G504S, p.G801S, p.G1176V (human)
OMIM:183900
CTD Direct Evidence: marker/mechanism
ClinVar Annotator: match by term: Spondyloepiphyseal dysplasia congenita | ClinVar Annotator: match by term: Spondyloepiphyseal dysplasia, congenital type		 OMIM
MouseDO
CTD
ClinVar
RGD		 PMID:1905723 PMID:2339128 PMID:2543071 PMID:7695699 PMID:7752132 More... RGD:729929, RGD:8657353, RGD:11667105 NCBI chr15:97,873,483...97,902,525
Ensembl chr15:97,873,483...97,902,576 		JBrowse link
G Hapln1 hyaluronan and proteoglycan link protein 1 IAGP OMIM:183900 MouseDO NCBI chr13:89,688,654...89,759,951
Ensembl chr13:89,687,915...89,759,771 		JBrowse link
G Trappc2 trafficking protein particle complex 2 ISO ClinVar Annotator: match by term: Spondyloepiphyseal dysplasia congenita ClinVar NCBI chr  X:165,223,747...165,236,136
Ensembl chr  X:165,223,570...165,236,136 		JBrowse link
spondyloepiphyseal dysplasia Kimberley type term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Acan aggrecan ISO CTD Direct Evidence: marker/mechanism
ClinVar Annotator: match by term: Spondyloepiphyseal dysplasia, Kimberley type
DNA:frameshift mutation:exon		 OMIM
CTD
ClinVar
RGD		 PMID:16080123 PMID:25741868 PMID:28492532 PMID:16080123 RGD:11570524 NCBI chr 7:78,702,974...78,764,847
Ensembl chr 7:78,703,231...78,764,847 		JBrowse link
spondyloepiphyseal dysplasia Kondo-Fu type term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Mbtps1 membrane-bound transcription factor peptidase, site 1 ISO ClinVar Annotator: match by term: Spondyloepiphyseal dysplasia, kondo-fu type OMIM
ClinVar		 PMID:25741868 PMID:28492532 PMID:30046013 PMID:30099045 PMID:32064983 NCBI chr 8:120,234,890...120,285,603
Ensembl chr 8:120,234,895...120,285,474 		JBrowse link
spondyloepiphyseal dysplasia Maroteaux type term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Trpv4 transient receptor potential cation channel, subfamily V, member 4 ISO ClinVar Annotator: match by term: PSEUDO-MORQUIO SYNDROME, TYPE 2 | ClinVar Annotator: match by term: SED, Maroteaux type | ClinVar Annotator: match by term: Spondyloepiphyseal dysplasia Maroteaux type
CTD Direct Evidence: marker/mechanism		 OMIM
ClinVar
CTD		 PMID:4056805 PMID:6628444 PMID:8179305 PMID:12884428 PMID:14755468 More... NCBI chr 5:114,760,213...114,796,497
Ensembl chr 5:114,760,213...114,796,482 		JBrowse link
spondyloepiphyseal dysplasia Nishimura type term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Mir140 microRNA 140 ISO ClinVar Annotator: match by term: Spondyloepiphyseal dysplasia, nishimura type OMIM
ClinVar		 PMID:30804514 NCBI chr 8:108,277,876...108,277,945
Ensembl chr 8:108,277,876...108,277,945 		JBrowse link
G Wwp2 WW domain containing E3 ubiquitin protein ligase 2 ISO ClinVar Annotator: match by term: Spondyloepiphyseal dysplasia, nishimura type ClinVar PMID:30804514 NCBI chr 8:108,162,966...108,285,922
Ensembl chr 8:108,162,997...108,285,227 		JBrowse link
spondyloepiphyseal dysplasia Stanescu type term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Aldh18a1 aldehyde dehydrogenase 18 family, member A1 ISO ClinVar Annotator: match by term: Spondyloepiphyseal dysplasia, Stanescu type ClinVar PMID:25741868 PMID:28492532 PMID:36067040 NCBI chr19:40,538,701...40,576,907
Ensembl chr19:40,538,701...40,576,907 		JBrowse link
G Col2a1 collagen, type II, alpha 1 ISO ClinVar Annotator: match by term: SED, STANESCU TYPE | ClinVar Annotator: match by term: Spondyloepiphyseal dysplasia, Stanescu type | ClinVar Annotator: match by term: Spondyloepiphyseal dysplasia, stanescu type OMIM
ClinVar		 PMID:7695699 PMID:7977371 PMID:8218237 PMID:8702139 PMID:8893763 More... NCBI chr15:97,873,483...97,902,525
Ensembl chr15:97,873,483...97,902,576 		JBrowse link
spondyloepiphyseal dysplasia tarda term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Ofd1 OFD1, centriole and centriolar satellite protein ISO ClinVar Annotator: match by term: Spondyloepiphyseal dysplasia tarda ClinVar PMID:9536098 PMID:9990351 PMID:10431248 PMID:10999831 PMID:11326333 More... NCBI chr  X:165,171,503...165,223,704
Ensembl chr  X:165,173,029...165,223,700 		JBrowse link
G Trappc2 trafficking protein particle complex 2 ISO ClinVar Annotator: match by term: Spondyloepiphyseal dysplasia tarda ClinVar PMID:9536098 PMID:9990351 PMID:10431248 PMID:10999831 PMID:11326333 More... NCBI chr  X:165,223,747...165,236,136
Ensembl chr  X:165,223,570...165,236,136 		JBrowse link
spondyloepiphyseal dysplasia with congenital joint dislocations term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Chst3 carbohydrate sulfotransferase 3 ISO ClinVar Annotator: match by term: Spondyloepiphyseal dysplasia with congenital joint dislocations
CTD Direct Evidence: marker/mechanism		 OMIM
ClinVar
CTD		 PMID:112567 PMID:9039660 PMID:15098240 PMID:15215498 PMID:15368507 More... NCBI chr10:60,017,349...60,057,936
Ensembl chr10:60,017,354...60,055,082 		JBrowse link
spondyloepiphyseal dysplasia, sensorineural hearing loss, intellectual developmental disorder, and Leber congenital amaurosis term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Nmnat1 nicotinamide nucleotide adenylyltransferase 1 ISO ClinVar Annotator: match by term: SHILCA SYNDROME OMIM
ClinVar		 PMID:22842227 PMID:22842230 PMID:22842231 PMID:25741868 PMID:26018082 More... NCBI chr 4:149,552,026...149,569,667
Ensembl chr 4:149,552,029...149,569,659 		JBrowse link
X-linked spondyloepiphyseal dysplasia tarda term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Ofd1 OFD1, centriole and centriolar satellite protein ISO ClinVar Annotator: match by term: SED TARDA, X-LINKED | ClinVar Annotator: match by term: Spondyloepiphyseal dysplasia tarda, X-linked ClinVar PMID:9536098 PMID:11326333 PMID:11349230 PMID:15221797 PMID:17576681 More... NCBI chr  X:165,171,503...165,223,704
Ensembl chr  X:165,173,029...165,223,700 		JBrowse link
G Trappc2 trafficking protein particle complex 2 ISO ClinVar Annotator: match by term: SED TARDA, X-LINKED | ClinVar Annotator: match by term: Spondyloepiphyseal dysplasia tarda, X-linked OMIM
ClinVar		 PMID:9536098 PMID:11326333 PMID:11349230 PMID:15221797 PMID:17576681 More... NCBI chr  X:165,223,747...165,236,136
Ensembl chr  X:165,223,570...165,236,136 		JBrowse link
Term paths to the root
Path 1
Term Annotations click to browse term
  disease 18301
    Developmental Disease 17912
      bone development disease 2297
        osteochondrodysplasia 864
          spondyloepiphyseal dysplasia 17
            Spondyloepiphyseal Dysplasia with Atlantoaxial Instability 0
            Spondyloepiphyseal Dysplasia, Myopia, and Sensorineural Deafness 0
            spondyloepiphyseal dysplasia Kimberley type 1
            spondyloepiphyseal dysplasia Kondo-Fu type 1
            spondyloepiphyseal dysplasia Maroteaux type 1
            spondyloepiphyseal dysplasia Nishimura type 2
            spondyloepiphyseal dysplasia Stanescu type 2
            spondyloepiphyseal dysplasia congenita 6
            spondyloepiphyseal dysplasia tarda + 3
            spondyloepiphyseal dysplasia with congenital joint dislocations 1
            spondyloepiphyseal dysplasia with coronal craniosynostosis, cataracts, cleft palate, and intellectual disability 0
            spondyloepiphyseal dysplasia with punctate corneal dystrophy 0
            spondyloepiphyseal dysplasia, sensorineural hearing loss, intellectual developmental disorder, and Leber congenital amaurosis 1
            spondyloepiphyseal dysplasia-brachydactyly and distinctive speech 0
Path 2
Term Annotations click to browse term
  disease 18301
    disease of anatomical entity 15631
      Skin and Connective Tissue Diseases 6944
        connective tissue disease 5393
          bone disease 3899
            bone development disease 2297
              osteochondrodysplasia 864
                spondyloepiphyseal dysplasia 17
                  Spondyloepiphyseal Dysplasia with Atlantoaxial Instability 0
                  Spondyloepiphyseal Dysplasia, Myopia, and Sensorineural Deafness 0
                  spondyloepiphyseal dysplasia Kimberley type 1
                  spondyloepiphyseal dysplasia Kondo-Fu type 1
                  spondyloepiphyseal dysplasia Maroteaux type 1
                  spondyloepiphyseal dysplasia Nishimura type 2
                  spondyloepiphyseal dysplasia Stanescu type 2
                  spondyloepiphyseal dysplasia congenita 6
                  spondyloepiphyseal dysplasia tarda + 3
                  spondyloepiphyseal dysplasia with congenital joint dislocations 1
                  spondyloepiphyseal dysplasia with coronal craniosynostosis, cataracts, cleft palate, and intellectual disability 0
                  spondyloepiphyseal dysplasia with punctate corneal dystrophy 0
                  spondyloepiphyseal dysplasia, sensorineural hearing loss, intellectual developmental disorder, and Leber congenital amaurosis 1
                  spondyloepiphyseal dysplasia-brachydactyly and distinctive speech 0
paths to the root