eRAM
encyclopedia of Rare Disease Annotation for Precision Medicine
| spondyloepiphyseal dysplasia tarda | ||||
| Disease ID | 745 |
|---|---|
| Disease | spondyloepiphyseal dysplasia tarda |
| Definition | A disorder of bone growth affecting the vertebrae and the ends of the long bones (epiphyses). [HPO:probinson] |
| Synonym | dysplasia, spondyloepiphyseal spondyloepiphyseal dysplasia spondyloepiphyseal dysplasia, nos spondyloepiphyseal dysplasias |
| Orphanet | |
| DOID | |
| ICD10 | |
| UMLS | C0038015 |
| Comorbidity | UMLS | Disease | Sentences' Count(Total Sentences:2) |
| Curated Gene | Entrez_id | Symbol | Resource(Total Genes:5) |
| Inferring Gene | (Waiting for update.) |
| Text Mined Gene | (Waiting for update.) |
| Locus | Symbol | Locus(Total Locus:1) TRAPPC2 | Xp22.2 |
| Disease ID | 745 |
|---|---|
| Disease | spondyloepiphyseal dysplasia tarda |
| Integrated Phenotype | HPO | Name(Total Integrated Phenotypes:17) HP:0002829 | Arthralgia HP:0002938 | Lumbar hyperlordosis HP:0000470 | Short neck HP:0002812 | Coxa vara HP:0001552 | Barrel-shaped chest HP:0002866 | Hypoplastic iliac wing HP:0009824 | Upper limb undergrowth HP:0002942 | Thoracic kyphosis HP:0002650 | Scoliosis HP:0008843 | Hip osteoarthritis HP:0003498 | Disproportionate short stature HP:0002758 | Osteoarthritis HP:0005930 | Abnormality of epiphysis morphology HP:0000926 | Platyspondyly HP:0003311 | Hypoplasia of the odontoid process HP:0010306 | Short thorax HP:0002655 | Spondyloepiphyseal dysplasia |
| Text Mined Phenotype | HPO | Name | Sentences' Count(Total Phenotypes:9) HP:0003040 | Arthropathy | 5 HP:0001510 | Growth deficiency | 2 HP:0000691 | Decreased width of tooth | 1 HP:0006311 | Decreased width of all teeth | 1 HP:0001373 | Joint dislocations | 1 HP:0000668 | Failure of development of between one and six teeth | 1 HP:0002857 | Genu valgum | 1 HP:0000768 | Pectus carinatum | 1 HP:0002758 | Osteoarthritis | 1 |
| Disease ID | 745 |
|---|---|
| Disease | spondyloepiphyseal dysplasia tarda |
| Manually Symptom | (Waiting for update.) |
| Text Mined Symptom | (Waiting for update.) |
Manually Genotype(Total Text Mining Genotypes:0) |
|---|
| (Waiting for update.) |
Text Mining Genotype(Total Genotypes:0) | |
|---|---|
| (Waiting for update.) | |
All Snps(Total Genotypes:7) | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| snpId | pubmedId | geneId | geneSymbol | diseaseId | sourceId | sentence | score | Year | geneSymbol_dbSNP | CHROMOSOME | POS | REF | ALT |
| rs121912870 | NA | 1280 | COL2A1 | umls:C0038015 | CLINVAR | NA | 0.125428837 | NA | COL2A1 | 12 | 47975971 | C | T |
| rs121912874 | NA | 1280 | COL2A1 | umls:C0038015 | CLINVAR | NA | 0.125428837 | NA | COL2A1 | 12 | 47978329 | G | A |
| rs121912880 | NA | 1280 | COL2A1 | umls:C0038015 | CLINVAR | NA | 0.125428837 | NA | COL2A1 | 12 | 47986353 | C | A |
| rs121912883 | NA | 1280 | COL2A1 | umls:C0038015 | CLINVAR | NA | 0.125428837 | NA | COL2A1 | 12 | 47976043 | C | G |
| rs121912886 | NA | 1280 | COL2A1 | umls:C0038015 | CLINVAR | NA | 0.125428837 | NA | COL2A1 | 12 | 47974090 | G | T,A |
| rs794727339 | NA | 1280 | COL2A1 | umls:C0038015 | CLINVAR | NA | 0.125428837 | NA | COL2A1 | 12 | 47987085 | C | G |
| rs794727684 | NA | 1280 | COL2A1 | umls:C0038015 | CLINVAR | NA | 0.125428837 | NA | COL2A1 | 12 | 47977154 | C | T |
GWASdb Annotation(Total Genotypes:0) | |
|---|---|
| (Waiting for update.) | |
GWASdb Snp Trait(Total Genotypes:0) | |
|---|---|
| (Waiting for update.) | |
Mapped by lexical matching(Total Items:8) | ||||
|---|---|---|---|---|
| HP ID | HP Name | MP ID | MP Name | Annotation |
| HP:0002942 | Thoracic kyphosis | MP:0000160 | kyphosis | forward curvature of the spine, characterized by extensive flexion |
| HP:0003311 | Hypoplasia of the odontoid process | MP:0014164 | abnormal ciliary process morphology | any structural anomaly of any of the pigmented processes that radiate from the ciliary muscle and give attachments to ligaments supporting the lens of the eye; these processes increase in thickness as they advance from the orbiculus ciliaris to the exter |
| HP:0001552 | Barrel-shaped chest | MP:0004134 | abnormal chest morphology | any structural anomaly of the part of the body between the neck and the abdomen |
| HP:0009824 | Upper limb undergrowth | MP:0005650 | abnormal limb bud morphology | any structural anomaly of the mesenchymal outgrowth on the lateral trunk of the embryo that develops into the limbs |
| HP:0005930 | Abnormality of epiphysis morphology | MP:0013621 | decreased internal diameter of femur | reduced cross-sectional distance that extends from one lateral edge of the femur long bone marrow cavity, through its center and to the opposite lateral edge of the bone marrow cavity through the mid point of the femur |
| HP:0000470 | Short neck | MP:0012720 | elongated neck | increased length of the neck |
| HP:0003498 | Disproportionate short stature | MP:0009071 | short oviduct | length reduction or truncation of the tube through which the ova pass from the ovary to the uterus |
| HP:0008843 | Hip osteoarthritis | MP:0003560 | osteoarthritis | a type of arthritis that results in the breakdown and eventual loss of the auricular cartilage of one or more joints |
Mapped by homologous gene(Total Items:17) | ||||
|---|---|---|---|---|
| HP ID | HP Name | MP ID | MP Name | Annotation |
| HP:0002942 | Thoracic kyphosis | MP:0014164 | abnormal ciliary process morphology | any structural anomaly of any of the pigmented processes that radiate from the ciliary muscle and give attachments to ligaments supporting the lens of the eye; these processes increase in thickness as they advance from the orbiculus ciliaris to the exter |
| HP:0009824 | Upper limb undergrowth | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| HP:0002650 | Scoliosis | MP:0020309 | increased creatine kinase activity | increased ability of to catalyze the reaction: ATP + creatine = N-phosphocreatine + ADP + 2 H(+). |
| HP:0008843 | Hip osteoarthritis | MP:0014164 | abnormal ciliary process morphology | any structural anomaly of any of the pigmented processes that radiate from the ciliary muscle and give attachments to ligaments supporting the lens of the eye; these processes increase in thickness as they advance from the orbiculus ciliaris to the exter |
| HP:0002758 | Osteoarthritis | MP:0020254 | decreased collagen level | decreased level of the main structural protein of the various connective tissues in animals |
| HP:0002829 | Arthralgia | MP:0020154 | impaired humoral immune response | impaired response of the immune system that mediates secreted antibodies produced in B cells |
| HP:0005930 | Abnormality of epiphysis morphology | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| HP:0000926 | Platyspondyly | MP:0020254 | decreased collagen level | decreased level of the main structural protein of the various connective tissues in animals |
| HP:0010306 | Short thorax | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| HP:0000470 | Short neck | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| HP:0002812 | Coxa vara | MP:0020254 | decreased collagen level | decreased level of the main structural protein of the various connective tissues in animals |
| HP:0001552 | Barrel-shaped chest | MP:0020254 | decreased collagen level | decreased level of the main structural protein of the various connective tissues in animals |
| HP:0003311 | Hypoplasia of the odontoid process | MP:0020254 | decreased collagen level | decreased level of the main structural protein of the various connective tissues in animals |
| HP:0003498 | Disproportionate short stature | MP:0011495 | abnormal head shape | any anomaly in the characteristic surface outline or contour of a head of an organism |
| HP:0002655 | Spondyloepiphyseal dysplasia | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| HP:0002866 | Hypoplastic iliac wing | MP:0020039 | increased bone ossification | increase in the formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone or a bony substance |
| HP:0002938 | Lumbar hyperlordosis | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| Disease ID | 745 |
|---|---|
| Disease | spondyloepiphyseal dysplasia tarda |
| Case | (Waiting for update.) |