eRAM
encyclopedia of Rare Disease Annotation for Precision Medicine
| short syndrome | ||||
| Disease ID | 659 |
|---|---|
| Disease | short syndrome |
| Definition | SHORT syndrome is a condition in which affected individuals have multiple birth defects in different organ systems. The term SHORT is an acronym with each letter representing one of the common findings in affected persons:.(S)= short stature.(H)= hyperextensibility of joints and/or hernia (inguinal).(O)= ocular depression.(R) =Rieger anomaly.(T) =teething delay.Other characteristics common in SHORT syndrome are a triangular face, small chin with a dimple, a loss of fat under the skin (lipodystrophy), abnormal position of the ears, hearing loss and delayed speech. - NORD Reference: NORD |
| Synonym | lipodystrophy, partial, with rieger anomaly and short stature lipodystrophy, partial, with rieger anomaly, and short stature short stature, hyperextensibility, hernia, ocular depression, rieger anomaly, and teething delay syndrome short |
| Orphanet | |
| OMIM | |
| UMLS | C0878684 |
| Comorbidity | UMLS | Disease | Sentences' Count(Total Sentences:3) |
| 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) PIK3R1 | 5q13.1 |
| Disease ID | 659 |
|---|---|
| Disease | short syndrome |
| Integrated Phenotype | HPO | Name(Total Integrated Phenotypes:37) HP:0000689 | Misalignment of upper and lower dental arches HP:0000518 | Cataract HP:0000347 | Hypoplasia of mandible HP:0002715 | Abnormality of the immune system HP:0000490 | Sunken eyes HP:0009466 | Radially deviated phalanges HP:0000430 | Nasal cartilage hypoplasia HP:0003561 | Birth length <3rd percentile HP:0000963 | Thin skin HP:0000506 | Telecanthus HP:0010751 | Gelasin of chin HP:0000684 | Delayed eruption of teeth HP:0030084 | Clinodactyly HP:0002007 | Frontal protruberance HP:0100578 | Lipoatrophy HP:0009125 | Lipodystrophy HP:0000558 | Rieger anomaly HP:0010580 | Large epiphyses HP:0000750 | Late-onset speech development HP:0100678 | Premature skin wrinkling HP:0000833 | Glucose intolerance HP:0000400 | Large ears HP:0000545 | Near sightedness HP:0001518 | Small for gestational age HP:0001388 | Joint laxity HP:0000485 | Enlarged cornea HP:0002750 | Delayed bone maturation HP:0003074 | High blood glucose HP:0000431 | Broad nasal root HP:0000023 | Inguinal hernia HP:0001511 | Prenatal onset growth retardation HP:0000325 | Triangular face HP:0000407 | sensorineural hearing loss HP:0011220 | Prominent forehead HP:0000501 | Glaucoma HP:0000831 | Insulin-resistant diabetes mellitus HP:0000668 | Failure of development of between one and six teeth |
| Text Mined Phenotype | HPO | Name | Sentences' Count(Total Phenotypes:2) |
| Disease ID | 659 |
|---|---|
| Disease | short syndrome |
| Manually Symptom | (Waiting for update.) |
| Text Mined Symptom | (Waiting for update.) |
Manually Genotype(Total Manually Genotypes:1) | |||
|---|---|---|---|
| Gene | Mutation | DOI | Article Title |
| PIK3R1 | c.1135C>T p.R379W | doi:10.1038/gim.2016.88 | Systematic reanalysis of clinical exome data yields additional diagnoses: implications for providers |
Text Mining Genotype(Total Genotypes:0) | |
|---|---|
| (Waiting for update.) | |
All Snps(Total Genotypes:10) | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| snpId | pubmedId | geneId | geneSymbol | diseaseId | sourceId | sentence | score | Year | geneSymbol_dbSNP | CHROMOSOME | POS | REF | ALT |
| rs397514046 | NA | 5295 | PIK3R1 | umls:C0878684 | CLINVAR | NA | 0.361085767 | NA | PIK3R1 | 5 | 68295194 | ATT | - |
| rs397514047 | NA | 5295 | PIK3R1 | umls:C0878684 | CLINVAR | NA | 0.361085767 | NA | PIK3R1 | 5 | 68294575 | G | A |
| rs397515453 | NA | 5295 | PIK3R1 | umls:C0878684 | CLINVAR | NA | 0.361085767 | NA | PIK3R1 | 5 | 68296301 | C | T |
| rs398122384 | NA | 5295 | PIK3R1 | umls:C0878684 | CLINVAR | NA | 0.361085767 | NA | PIK3R1 | 5 | 68296299 | - | T |
| rs398122385 | NA | 5295 | PIK3R1 | umls:C0878684 | CLINVAR | NA | 0.361085767 | NA | PIK3R1 | 5 | 68296262 | - | C |
| rs515726149 | NA | 5295 | PIK3R1 | umls:C0878684 | CLINVAR | NA | 0.361085767 | NA | PIK3R1 | 5 | 68296248 | G | A |
| rs515726150 | NA | 5295 | PIK3R1 | umls:C0878684 | CLINVAR | NA | 0.361085767 | NA | PIK3R1 | 5 | 68296262 | AA | - |
| rs515726151 | NA | 5295 | PIK3R1 | umls:C0878684 | CLINVAR | NA | 0.361085767 | NA | PIK3R1 | 5 | 68296327 | T | G |
| rs587784325 | NA | 5295 | PIK3R1 | umls:C0878684 | CLINVAR | NA | 0.361085767 | NA | PIK3R1 | 5 | 68293187 | C | T |
| rs797045063 | NA | 5295 | PIK3R1 | umls:C0878684 | CLINVAR | NA | 0.361085767 | NA | PIK3R1 | 5 | 68294570 | T | C |
GWASdb Annotation(Total Genotypes:0) | |
|---|---|
| (Waiting for update.) | |
GWASdb Snp Trait(Total Genotypes:0) | |
|---|---|
| (Waiting for update.) | |
Mapped by lexical matching(Total Items:16) | ||||
|---|---|---|---|---|
| HP ID | HP Name | MP ID | MP Name | Annotation |
| HP:0000689 | Dental malocclusion | MP:0000120 | malocclusion | perturbations in the normal patterned arrangement of the teeth or alignment of the jaw, resulting in the incorrect position of biting or chewing surfaces of the upper and lower teeth |
| HP:0002715 | Abnormality of the immune system | MP:0009403 | increased variability of skeletal muscle fiber size | greater range or dispersion within a distribution of skeletal muscle fiber size within a muscle compared to controls |
| HP:0000963 | Thin 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:0009466 | Radial deviation of finger | MP:0011665 | d-loop transposition of the great arteries | complete transposition of the great arteries; the d- refers to the dextroposition of the bulboventricular loop (ie, the position of the right ventricle, which is on the right side); in addition, the aorta also tends to be on the right and anterior, and th |
| HP:0100678 | Premature skin wrinkling | MP:0005421 | loose skin | condition in which the skin hangs in folds |
| HP:0000431 | Wide nasal bridge | MP:0006292 | abnormal nasal placode morphology | any structural anomaly in the paired ectodermal placodes that come to lie in the bottom of the olfactory pits as the pits are deepened by the growth of the surrounding medial and lateral nasal processes; the nasal placode gives rise to the olfactory epith |
| HP:0001511 | Intrauterine growth retardation | MP:0011109 | lethality throughout fetal growth and development, incomplete penetrance | the appearance of lower than Mendelian ratios of organisms of a given genotype due to death of some, but not all of the organisms between the completion of organogenesis and birth (Mus: E14 to approximately E18.5) |
| HP:0000490 | Deeply set eye | MP:0009829 | enlarged eye anterior chamber | increased size of the space in the eye, filled with aqueous humor, and bounded anteriorly by the cornea and a small portion of the sclera and posteriorly by a small portion of the ciliary body, the iris, and part of the crystalline lens |
| HP:0000325 | Triangular face | MP:0012546 | triangular face | a face whose lower half becomes relatively thin, approaching an appearance of a triangle with a tip facing downwards; usually associated with a prominent forehead and micrognathia |
| HP:0000407 | Sensorineural hearing impairment | MP:0006330 | syndromic hearing impairment | hearing impairment that is usually associated with malformations of the external ear and other inherited signs and symptoms |
| HP:0000023 | Inguinal hernia | MP:0010146 | umbilical hernia | an outward bulging (protrusion) of the abdominal lining or part of the abdominal organ(s) through the area around the umbilicus; occurs when the muscle through which blood vessels pass to feed the developing fetus fails to completely close |
| HP:0001518 | Small for gestational age | MP:0011967 | increased or absent threshold for auditory brainstem response | increase in the value at which one or more sound frequencies or broadband clicks first elicits a recordable response generated by electrical activity of neurons in the ascending auditory system, or complete lack of a recordable response at any frequency o |
| HP:0000750 | Delayed speech and language development | MP:0012251 | abnormal diaphragm development | malformation or incomplete differentiation of the thin musculomembranous barrier separating the abdominal and thoracic cavities and functioning in respiration |
| HP:0000430 | Underdeveloped nasal alae | MP:0004471 | short nasal bone | reduced length of either of two rectangular bone plates forming the bridge of the nose |
| HP:0000684 | Delayed eruption of teeth | MP:0020010 | decreased bone mineral density of femur | reduction in the quatitative measurment value of mineral content of bone in the long bone of the thigh |
| HP:0002750 | Delayed skeletal maturation | MP:0003379 | absent sexual maturation | failure to initiate pubertal changes that result in achievement of full sexual capacity |
Mapped by homologous gene(Total Items:37) | ||||
|---|---|---|---|---|
| HP ID | HP Name | MP ID | MP Name | Annotation |
| HP:0000325 | Triangular face | MP:0020254 | decreased collagen level | decreased level of the main structural protein of the various connective tissues in animals |
| HP:0030084 | Clinodactyly | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| HP:0000689 | Dental malocclusion | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| HP:0009125 | Lipodystrophy | MP:0020234 | decreased basal metabolism | decrease in heat production of an organism at the lowest level of cell chemistry in an inactive, awake, and fasting state |
| HP:0010580 | Enlarged epiphyses | 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:0010751 | Chin dimple | MP:0013767 | decreased palatal rugae number | reduced number of transverse folds (ridges) of the mucosa located on the anterior third part of the secondary (hard) palate of most mammalian species |
| HP:0001518 | Small for gestational age | MP:0020254 | decreased collagen level | decreased level of the main structural protein of the various connective tissues in animals |
| HP:0000506 | Telecanthus | 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:0100678 | Premature skin wrinkling | MP:0012080 | chylous ascites | the extravasation of milky triglyceride-rich chyle into the peritoneal cavity; often a secondary symptom of neoplasms |
| HP:0000347 | Micrognathia | MP:0020321 | increased vascular endothelial cell apoptosis | increase in the timing or the number of vascular endothelial cells undergoing programmed cell death |
| HP:0000501 | Glaucoma | 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:0000407 | Sensorineural hearing impairment | 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:0000485 | Megalocornea | 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:0000490 | Deeply set eye | MP:0020157 | abnormal behavioral response to alcohol | any anomaly in the behavioral response induced by alcohol, such as induced hyperactivity or stereotypic behavior |
| HP:0001511 | Intrauterine growth retardation | MP:0020329 | decreased capillary density | reduction in the number of capillaries in a given cross-sectional area of a tissue |
| HP:0000831 | Insulin-resistant diabetes mellitus | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| HP:0009466 | Radial deviation of finger | 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:0000833 | Glucose intolerance | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| HP:0001388 | Joint laxity | MP:0020321 | increased vascular endothelial cell apoptosis | increase in the timing or the number of vascular endothelial cells undergoing programmed cell death |
| HP:0000963 | Thin skin | MP:0020254 | decreased collagen level | decreased level of the main structural protein of the various connective tissues in animals |
| HP:0100578 | Lipoatrophy | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| HP:0011220 | Prominent forehead | MP:0020321 | increased vascular endothelial cell apoptosis | increase in the timing or the number of vascular endothelial cells undergoing programmed cell death |
| HP:0000684 | Delayed eruption of teeth | MP:0020254 | decreased collagen level | decreased level of the main structural protein of the various connective tissues in animals |
| HP:0000430 | Underdeveloped nasal alae | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| HP:0000558 | Rieger anomaly | 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:0000545 | Myopia | MP:0020254 | decreased collagen level | decreased level of the main structural protein of the various connective tissues in animals |
| HP:0000400 | Macrotia | MP:0020309 | increased creatine kinase activity | increased ability of to catalyze the reaction: ATP + creatine = N-phosphocreatine + ADP + 2 H(+). |
| HP:0002750 | Delayed skeletal maturation | MP:0020169 | increased thyroid gland weight | higher than average weight of the thyroid gland |
| HP:0000750 | Delayed speech and language development | MP:0020309 | increased creatine kinase activity | increased ability of to catalyze the reaction: ATP + creatine = N-phosphocreatine + ADP + 2 H(+). |
| HP:0000023 | Inguinal hernia | MP:0020321 | increased vascular endothelial cell apoptosis | increase in the timing or the number of vascular endothelial cells undergoing programmed cell death |
| HP:0002715 | Abnormality of the immune system | MP:0014125 | decreased amylin secretion | reduction in the production or release of the polypeptide hormone that is normally co-secreted with insulin by the beta cells of the pancreatic islets of Langerhans and is known to inhibit glucagon secretion, delay gastric emptying, and act as a satiety a |
| HP:0000668 | Hypodontia | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| HP:0003074 | Hyperglycemia | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| HP:0003561 | Birth length less than 3rd percentile | MP:0013886 | increased CD4-negative, CD25-positive NK T cell number | increase in the number of CD4-negative NK T cells expressing the activation marker CD25 |
| HP:0002007 | Frontal bossing | 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:0000431 | Wide nasal bridge | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| Disease ID | 659 |
|---|---|
| Disease | short syndrome |
| Case | (Waiting for update.) |