eRAM
encyclopedia of Rare Disease Annotation for Precision Medicine
| rhizomelic chondrodysplasia punctata | ||||
| Disease ID | 153 |
|---|---|
| Disease | rhizomelic chondrodysplasia punctata |
| Definition | An autosomal recessive form of CHONDRODYSPLASIA PUNCTATA characterized by defective plasmalogen biosynthesis and impaired peroxisomes. Patients have shortened proximal limbs and severely disturbed endochondral bone formation. The metabolic defects associated with the impaired peroxisomes are present only in the rhizomelic form of chondrodysplasia punctata. (From Scriver et al, Metabolic Basis of Inherited Disease, 6th ed, p1497) |
| Synonym | cdpr chondrodysplasia punctata, autosomal recessive type chondrodysplasia punctata, rhizomelic chondrodysplasia punctata, rhizomelic [disease/finding] chondrodysplasia punctata, rhizomelic form chondrodysplasia punctata, rhizomelic type chondrodysplasia punctatas, rhizomelic punctata, rhizomelic chondrodysplasia punctatas, rhizomelic chondrodysplasia rcdp rcdp - rhizomelic chondrodysplasia punctata rhizomelic chondrodysplasia punctata syndrome rhizomelic chondrodysplasia punctata syndrome (disorder) rhizomelic chondrodysplasia punctatas rhizomelic chrondrodysplasia punctata rhizomelic dwarfism |
| Orphanet | |
| OMIM | |
| DOID | |
| ICD10 | |
| UMLS | C0282529 |
| MeSH | |
| SNOMED-CT | |
| Comorbidity | UMLS | Disease | Sentences' Count(Total Sentences:1) |
| Curated Gene | Entrez_id | Symbol | Resource(Total Genes:4) |
| Inferring Gene | (Waiting for update.) |
| Text Mined Gene | Entrez_id | Symbol | Score | Resource(Total Genes:26) 30 | ACAA1 | 3.139 | DISEASES 375790 | AGRN | 1.699 | DISEASES 224 | ALDH3A2 | 2.116 | DISEASES 415 | ARSE | 1.916 | DISEASES 8451 | CUL4A | 2.351 | DISEASES 1718 | DHCR24 | 1.99 | DISEASES 285489 | DOK7 | 2.337 | DISEASES 10682 | EBP | 3.488 | DISEASES 54942 | FAM206A | 3.467 | DISEASES 84188 | FAR1 | 4.996 | DISEASES 10211 | FLOT1 | 2.322 | DISEASES 23732 | FRRS1L | 3.243 | DISEASES 8443 | GNPAT | 6.374 | DISEASES 26061 | HACL1 | 3.219 | DISEASES 3295 | HSD17B4 | 5.284 | DISEASES 3570 | IL6R | 1.523 | DISEASES 5824 | PEX19 | 2.205 | DISEASES 5828 | PEX2 | 2.71 | DISEASES 8504 | PEX3 | 3.121 | DISEASES 5830 | PEX5 | 7.069 | DISEASES 51555 | PEX5L | 3.611 | DISEASES 5251 | PHEX | 4.286 | DISEASES 23543 | RBFOX2 | 2.815 | DISEASES 6342 | SCP2 | 4.386 | DISEASES 10478 | SLC25A17 | 3.198 | DISEASES 7272 | TTK | 2.158 | DISEASES |
| Locus | (Waiting for update.) |
| Disease ID | 153 |
|---|---|
| Disease | rhizomelic chondrodysplasia punctata |
| Integrated Phenotype | HPO | Name(Total Integrated Phenotypes:20) HP:0010864 | Intellectual disability, severe HP:0000286 | Epicanthus HP:0009826 | Limb undergrowth HP:0001596 | Alopecia HP:0000958 | Dry skin HP:0000518 | Cataract HP:0008905 | Rhizomelia HP:0010655 | Epiphyseal stippling HP:0004322 | Short stature HP:0002650 | Scoliosis HP:0000252 | Microcephaly HP:0003298 | Spina bifida occulta HP:0012368 | Flat face HP:0000164 | Abnormality of the teeth HP:0002231 | Sparse body hair HP:0005930 | Abnormality of epiphysis morphology HP:0001376 | Limitation of joint mobility HP:0000944 | Abnormality of the metaphyses HP:0008064 | Ichthyosis HP:0001510 | Growth delay |
| Text Mined Phenotype | HPO | Name | Sentences' Count(Total Phenotypes:1) |
| Disease ID | 153 |
|---|---|
| Disease | rhizomelic chondrodysplasia punctata |
| Manually Symptom | UMLS | Name(Total Manually Symptoms:1) C0740279 | cerebellar atrophy |
| 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:1) | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| snpId | pubmedId | geneId | geneSymbol | diseaseId | sourceId | sentence | score | Year | geneSymbol_dbSNP | CHROMOSOME | POS | REF | ALT |
| rs796051881 | NA | 5830 | PEX5 | umls:C0282529 | CLINVAR | NA | 0.12 | NA | PEX5 | 12 | 7202275 | - | A |
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:0012368 | Flat face | MP:0012175 | flat face | the appearance of a flattened surface outline or contour of a normally rounded face of an organism |
| HP:0001376 | Limitation of joint mobility | MP:0010732 | abnormal node of Ranvier morphology | any structural anomaly of the short unmyelinated segments of an axon between myelinated segments, where voltage gated channels accumulate and regenerate an action potential as it is conducted along the axon |
| 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: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:0002231 | Sparse body hair | MP:0010682 | abnormal hair follicle infundibulum morphology | any structural anomaly of the most proximal part of the hair follicle relative to the epidermis, extending from the sebaceous duct to the epidermal surface |
| HP:0003298 | Spina bifida occulta | MP:0005297 | spina bifida occulta | defective closure of the laminae of the vertebral column in the lumbosacral region without hernial protrusion of the spinal cord or meninges; the mildest, most common and often asymptomatic form of spina bifida, identified externally by a skin depression |
| HP:0000164 | Abnormality of the teeth | MP:0010382 | abnormal dosage compensation, by inactivation of X chromosome | anomaly in the process of compensating for the two-fold variation in X-chromosome:autosome ratios between sexes by a global inactivation of all, or most of, the genes on one of the X-chromosomes in the XX sex |
| HP:0000958 | Dry 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 |
Mapped by homologous gene(Total Items:20) | ||||
|---|---|---|---|---|
| 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:0008905 | Rhizomelia | MP:0020254 | decreased collagen level | decreased level of the main structural protein of the various connective tissues in animals |
| HP:0003298 | Spina bifida occulta | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| HP:0005930 | Abnormality of epiphysis morphology | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| HP:0008064 | Ichthyosis | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| HP:0000518 | Cataract | 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:0000958 | Dry skin | MP:0020254 | decreased collagen level | decreased level of the main structural protein of the various connective tissues in animals |
| HP:0000164 | Abnormality of the teeth | MP:0020254 | decreased collagen level | decreased level of the main structural protein of the various connective tissues in animals |
| HP:0010655 | Epiphyseal stippling | MP:0020254 | decreased collagen level | decreased level of the main structural protein of the various connective tissues in animals |
| HP:0001510 | Growth delay | MP:0020169 | increased thyroid gland weight | higher than average weight of the thyroid gland |
| HP:0012368 | Flat face | MP:0020309 | increased creatine kinase activity | increased ability of to catalyze the reaction: ATP + creatine = N-phosphocreatine + ADP + 2 H(+). |
| HP:0010864 | Intellectual disability, severe | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| HP:0009826 | Limb undergrowth | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| HP:0002231 | Sparse body hair | MP:0014082 | decreased small intestinal villus height | decreased height of the tiny hair-like projections which protrude from the inside of the small intestine and contain blood vessels that capture digested nutrients that are absorbed through the intestinal wall; usually accompanied by crypt elongation or hy |
| HP:0000252 | Microcephaly | 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:0001376 | Limitation of joint mobility | 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:0000286 | Epicanthus | 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:0001596 | Alopecia | MP:0020220 | decreased tear production | decreased production of the amount of fluid produced in the eye |
| Disease ID | 153 |
|---|---|
| Disease | rhizomelic chondrodysplasia punctata |
| Case | (Waiting for update.) |