eRAM
encyclopedia of Rare Disease Annotation for Precision Medicine
| spondyloepimetaphyseal dysplasia with joint laxity | ||||
| Disease ID | 1525 |
|---|---|
| Disease | spondyloepimetaphyseal dysplasia with joint laxity |
| Synonym | semdjl semdjl1 spondyloepimetaphyseal dysplasia with joint laxity (disorder) spondyloepimetaphyseal dysplasia with joint laxity, type 1, with or without fractures |
| Orphanet | |
| OMIM | |
| UMLS | C0432243 |
| SNOMED-CT | |
| Comorbidity | UMLS | Disease | Sentences' Count(Total Sentences:1) |
| Curated Gene | Entrez_id | Symbol | Resource(Total Genes:1) |
| Inferring Gene | (Waiting for update.) |
| Text Mined Gene | (Waiting for update.) |
| Locus | Symbol | Locus(Total Locus:1) B3GALT6 | 1p36.33 |
| Disease ID | 1525 |
|---|---|
| Disease | spondyloepimetaphyseal dysplasia with joint laxity |
| Integrated Phenotype | HPO | Name(Total Integrated Phenotypes:32) HP:0001263 | Global developmental delay HP:0000520 | Proptosis HP:0004322 | Short stature HP:0000545 | Myopia HP:0000592 | Blue sclerae HP:0002251 | Aganglionic megacolon HP:0005930 | Abnormality of epiphysis morphology HP:0000218 | High palate HP:0001373 | Joint dislocation HP:0000974 | Hyperextensible skin HP:0002652 | Skeletal dysplasia HP:0003307 | Hyperlordosis HP:0001762 | Talipes equinovarus HP:0005692 | Joint hyperflexibility HP:0000343 | Long philtrum HP:0004279 | Short palm HP:0001773 | Short foot HP:0000175 | Cleft palate HP:0011849 | Abnormal bone ossification HP:0002650 | Scoliosis HP:0003042 | Elbow dislocation HP:0002808 | Kyphosis HP:0000926 | Platyspondyly HP:0001249 | Intellectual disability HP:0100866 | Short iliac bones HP:0001083 | Ectopia lentis HP:0002651 | Spondyloepimetaphyseal dysplasia HP:0100777 | Exostoses HP:0002827 | Hip dislocation HP:0001671 | Abnormality of the cardiac septa HP:0000944 | Abnormality of the metaphyses HP:0002983 | Micromelia |
| Text Mined Phenotype | HPO | Name | Sentences' Count(Total Phenotypes:2) |
| Disease ID | 1525 |
|---|---|
| Disease | spondyloepimetaphyseal dysplasia with joint laxity |
| 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 |
| rs397514717 | 23664117 | 126792 | B3GALT6 | umls:C0432243 | UNIPROT | By exome sequencing, we found that B3GALT6 encoding an enzyme involved in the biosynthesis of the GAG linker region is responsible for a severe skeletal dysplasia, spondyloepimetaphyseal dysplasia with joint laxity type 1 (SEMD-JL1). | 0.360271442 | 2013 | SDF4;B3GALT6 | 1 | 1232972 | C | T |
| rs397514717 | NA | 126792 | B3GALT6 | umls:C0432243 | CLINVAR | NA | 0.360271442 | NA | SDF4;B3GALT6 | 1 | 1232972 | C | T |
| rs397514718 | NA | 126792 | B3GALT6 | umls:C0432243 | CLINVAR | NA | 0.360271442 | NA | SDF4;B3GALT6 | 1 | 1232744 | G | A |
| rs397514719 | NA | 126792 | B3GALT6 | umls:C0432243 | CLINVAR | NA | 0.360271442 | NA | SDF4;B3GALT6 | 1 | 1232471 | A | G |
| rs397514720 | NA | 126792 | B3GALT6 | umls:C0432243 | CLINVAR | NA | 0.360271442 | NA | SDF4;B3GALT6 | 1 | 1232478 | C | T |
| rs786200938 | NA | 126792 | B3GALT6 | umls:C0432243 | CLINVAR | NA | 0.360271442 | NA | SDF4;B3GALT6 | 1 | 1232279 | A | G |
| rs786200939 | NA | 126792 | B3GALT6 | umls:C0432243 | CLINVAR | NA | 0.360271442 | NA | SDF4;B3GALT6 | 1 | 1233177 | G | C |
GWASdb Annotation(Total Genotypes:0) | |
|---|---|
| (Waiting for update.) | |
GWASdb Snp Trait(Total Genotypes:0) | |
|---|---|
| (Waiting for update.) | |
Mapped by lexical matching(Total Items:11) | ||||
|---|---|---|---|---|
| HP ID | HP Name | MP ID | MP Name | Annotation |
| HP:0000175 | Cleft palate | MP:0013550 | abnormal secondary palate morphology | |
| HP:0000974 | Hyperextensible skin | MP:0010678 | abnormal skin adnexa morphology | any structural anomaly of the tissue or structures associated with or embedded in the skin such as hair and hair follicles, sweat glands, sebaceous glands and claws or nails |
| HP:0001671 | Abnormality of the cardiac septa | MP:0012167 | abnormal epigenetic regulation of gene expression | any anomaly in the process that modulates the frequency, rate or extent of gene expression, in which the process is mitotically or meiotically heritable, or is stably self-propagated in the cytoplasm of a resting cell, and does not entail a change in DNA |
| HP:0100866 | Short iliac bones | MP:0004686 | decreased length of long bones | reduced end-to-end length of the several elongated bones of the extremities |
| HP:0001773 | Short foot | MP:0008138 | absent podocyte foot process | absence of the footlike extension of podocytes that interdigitate with one another to form the walls of the glomerular capillaries |
| 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:0000218 | High palate | MP:0011615 | submucous cleft palate | a cleft of the palate with cardinal signs including a bifid uvula, a V-shaped notch at the back of the hard palate, and/or a translucent line in the midline of the soft palate and a short palate |
| HP:0001263 | Global developmental delay | MP:0002084 | abnormal developmental patterning | abnormal systematic arrangement of the developing body along an axis |
| HP:0001083 | Ectopia lentis | MP:0005263 | ectopia lentis | congenital displacement of the lens due to defective zonule formation |
| HP:0000944 | Abnormality of the metaphyses | 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:0002251 | Aganglionic megacolon | MP:0002926 | aganglionic megacolon | extreme dilation of the colon due to defects in innervation from the ganglia, or absence of the ganglia of the myenteric plexus |
Mapped by homologous gene(Total Items:31) | ||||
|---|---|---|---|---|
| HP ID | HP Name | MP ID | MP Name | Annotation |
| HP:0002650 | Scoliosis | MP:0020309 | increased creatine kinase activity | increased ability of to catalyze the reaction: ATP + creatine = N-phosphocreatine + ADP + 2 H(+). |
| HP:0005930 | Abnormality of epiphysis morphology | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| HP:0001773 | Short foot | MP:0020157 | abnormal behavioral response to alcohol | any anomaly in the behavioral response induced by alcohol, such as induced hyperactivity or stereotypic behavior |
| HP:0003307 | Hyperlordosis | MP:0020309 | increased creatine kinase activity | increased ability of to catalyze the reaction: ATP + creatine = N-phosphocreatine + ADP + 2 H(+). |
| HP:0000592 | Blue sclerae | MP:0020254 | decreased collagen level | decreased level of the main structural protein of the various connective tissues in animals |
| HP:0002651 | Spondyloepimetaphyseal dysplasia | MP:0020254 | decreased collagen level | decreased level of the main structural protein of the various connective tissues in animals |
| HP:0004322 | Short stature | MP:3000003 | abnormal Ebner's gland morphology | any structural anomaly of the serous salivary glands which reside adjacent to the moats surrounding the circumvallate and foliate papillae just anterior to the posterior third of the tongue, anterior to the terminal sulcus; these exocrine glands secrete l |
| HP:0002827 | Hip dislocation | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| HP:0003042 | Elbow dislocation | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| HP:0002251 | Aganglionic megacolon | MP:0020220 | decreased tear production | decreased production of the amount of fluid produced in the eye |
| HP:0001373 | Joint dislocation | MP:0020254 | decreased collagen level | decreased level of the main structural protein of the various connective tissues in animals |
| HP:0100866 | Short iliac bones | MP:0013203 | abnormal primary cilium morphology | any structural anomaly of a cilium found on many different cell types that is typically present in a single copy per cell; a primary cilium may have a variable array of axonemal microtubules and may or may not contain molecular motors |
| HP:0001263 | Global developmental delay | MP:3000003 | abnormal Ebner's gland morphology | any structural anomaly of the serous salivary glands which reside adjacent to the moats surrounding the circumvallate and foliate papillae just anterior to the posterior third of the tongue, anterior to the terminal sulcus; these exocrine glands secrete l |
| HP:0000520 | Proptosis | MP:0020321 | increased vascular endothelial cell apoptosis | increase in the timing or the number of vascular endothelial cells undergoing programmed cell death |
| HP:0000175 | Cleft palate | MP:3000003 | abnormal Ebner's gland morphology | any structural anomaly of the serous salivary glands which reside adjacent to the moats surrounding the circumvallate and foliate papillae just anterior to the posterior third of the tongue, anterior to the terminal sulcus; these exocrine glands secrete l |
| HP:0001249 | Intellectual disability | MP:0020316 | decreased vascular endothelial cell proliferation | decrease in the expansion rate of any vascular endothelial cell population by cell division |
| HP:0002983 | Micromelia | MP:0020254 | decreased collagen level | decreased level of the main structural protein of the various connective tissues in animals |
| HP:0004279 | Short palm | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| HP:0000218 | High palate | MP:0020321 | increased vascular endothelial cell apoptosis | increase in the timing or the number of vascular endothelial cells undergoing programmed cell death |
| HP:0001671 | Abnormality of the cardiac septa | MP:0013901 | absent female preputial gland | absence of the paired, lobulated, modified sebaceous glands located on the side of the clitoris in female rodents; in contrast to the preputial glands in male rodents, clitoral glands are a minor source of olfactory stimuli contributing to sexual attracti |
| HP:0002652 | Skeletal dysplasia | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| HP:0000343 | Long philtrum | MP:0020254 | decreased collagen level | decreased level of the main structural protein of the various connective tissues in animals |
| HP:0001762 | Talipes equinovarus | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| HP:0000545 | Myopia | MP:0020254 | decreased collagen level | decreased level of the main structural protein of the various connective tissues in animals |
| HP:0000926 | Platyspondyly | MP:0020254 | decreased collagen level | decreased level of the main structural protein of the various connective tissues in animals |
| HP:0005692 | Joint hyperflexibility | MP:0012125 | decreased bronchoconstrictive response | reduction in the expected bronchoconstrictive response to provocation challenge with lipopolysaccharide, bradykinin, histamine or other antigen/allergen or agent, often measured by plethysmography |
| HP:0100777 | Exostoses | MP:0014178 | increased brain apoptosis | increase in the number of cells of the brain undergoing programmed cell death |
| HP:0002808 | Kyphosis | MP:0020254 | decreased collagen level | decreased level of the main structural protein of the various connective tissues in animals |
| HP:0000974 | Hyperextensible skin | MP:0020254 | decreased collagen level | decreased level of the main structural protein of the various connective tissues in animals |
| HP:0000944 | Abnormality of the metaphyses | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| HP:0001083 | Ectopia lentis | MP:0020254 | decreased collagen level | decreased level of the main structural protein of the various connective tissues in animals |
| Disease ID | 1525 |
|---|---|
| Disease | spondyloepimetaphyseal dysplasia with joint laxity |
| Case | (Waiting for update.) |