eRAM
encyclopedia of Rare Disease Annotation for Precision Medicine
| lathosterolosis | ||||
| Disease ID | 1795 |
|---|---|
| Disease | lathosterolosis |
| Definition | An extremely rare inborn error of sterol biosynthesis with manifestations of facial dysmorphism, congenital anomalies (including limb and kidney anomalies), failure to thrive, developmental delay and liver disease. Only 4 cases have been reported in the literature to date. Lathosterolosis is due to mutations in the SC5D gene (11q23.3). A mutation in this gene leads to a deficiency in 3-beta-hydroxysteroid-delta-5-desaturase, which is necessary in the conversion of lathosterol into 7-dehydrocholesterol. This prevents the synthesis of cholesterol, which among other functions acts as a structural lipid, a precursor for bile acids and steroid hormones, and is necessary for the maturation of hedgehog morphogens during embryonic development. Inherited in an autosomal recessive manner. |
| Synonym | 3-beta-hydroxysteroid-delta(5)-desaturase deficiency deficiency of 3-beta-hydroxysteroid-delta(5)-desaturase lathosterolosis (disorder) sc5d deficiency sterol c5 desaturase deficiency sterol c5-desaturase deficiency |
| Orphanet | |
| OMIM | |
| UMLS | C1846421 |
| 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) SC5D | 11q23.3-q24.1 |
| Disease ID | 1795 |
|---|---|
| Disease | lathosterolosis |
| Integrated Phenotype | HPO | Name(Total Integrated Phenotypes:45) HP:0001830 | Postaxial foot polydactyly HP:0001263 | Global developmental delay HP:0011875 | Abnormal platelet morphology HP:0001336 | Myoclonus HP:0000518 | Cataract HP:0005487 | Prominent metopic ridge HP:0003196 | Short nose HP:0000365 | Hearing impairment HP:0001770 | Toe syndactyly HP:0000218 | High palate HP:0008278 | Cerebellar cortical atrophy HP:0000508 | Ptosis HP:0008736 | Hypoplasia of penis HP:0000347 | Micrognathia HP:0001873 | Thrombocytopenia HP:0000343 | Long philtrum HP:0001162 | Postaxial hand polydactyly HP:0001511 | Intrauterine growth retardation HP:0002308 | Arnold-Chiari malformation HP:0002435 | Meningocele HP:0002714 | Downturned corners of mouth HP:0000494 | Downslanted palpebral fissures HP:0001250 | Seizures HP:0000286 | Epicanthus HP:0001406 | Intrahepatic cholestasis HP:0001399 | Hepatic failure HP:0004823 | Anisopoikilocytosis HP:0000293 | Full cheeks HP:0000252 | Microcephaly HP:0002514 | Cerebral calcification HP:0001508 | Failure to thrive HP:0002240 | Hepatomegaly HP:0000085 | Horseshoe kidney HP:0001883 | Talipes HP:0000341 | Narrow forehead HP:0000463 | Anteverted nares HP:0004422 | Biparietal narrowing HP:0001328 | Specific learning disability HP:0100711 | Abnormality of the thoracic spine HP:0000212 | Gingival overgrowth HP:0001252 | Muscular hypotonia HP:0000340 | Sloping forehead HP:0000414 | Bulbous nose HP:0007759 | Opacification of the corneal stroma HP:0000482 | Microcornea |
| Text Mined Phenotype | (Waiting for update.) |
| Disease ID | 1795 |
|---|---|
| Disease | lathosterolosis |
| Manually Symptom | (Waiting for update.) |
| Text Mined Symptom | (Waiting for update.) |
Manually Genotype(Total Text Mining Genotypes:0) |
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| (Waiting for update.) |
Text Mining Genotype(Total Genotypes:0) | |
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| (Waiting for update.) | |
All Snps(Total Genotypes:3) | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| snpId | pubmedId | geneId | geneSymbol | diseaseId | sourceId | sentence | score | Year | geneSymbol_dbSNP | CHROMOSOME | POS | REF | ALT |
| rs104894295 | NA | 6309 | SC5D | umls:C1846421 | CLINVAR | NA | 0.560542884 | NA | SC5D | 11 | 121303461 | G | A |
| rs104894296 | NA | 6309 | SC5D | umls:C1846421 | CLINVAR | NA | 0.560542884 | NA | SC5D | 11 | 121307244 | G | A |
| rs104894297 | NA | 6309 | SC5D | umls:C1846421 | CLINVAR | NA | 0.560542884 | NA | SC5D | 11 | 121303512 | A | 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:0002714 | Downturned corners of mouth | MP:0013283 | failure of ventral body wall closure | failure of the lateral body wall folds (a combination of mesoderm and ectoderm arising on each side of the embryo) to progress ventrally and meet in the midline and/or fuse to close the ventral body wall; normally, this closure is aided by growth of the h |
| HP:0001328 | Specific learning disability | MP:0002802 | abnormal discrimination learning | anomaly in the ability to exhibit a differential response to different stimuli that is achieved by the reinforcement of the desired response for each particular stimulus |
| HP:0001162 | Postaxial hand polydactyly | MP:0009743 | preaxial polydactyly | duplication of all or part of the first ray on one or more of the autopods |
| HP:0000085 | Horseshoe kidney | MP:0011441 | decreased kidney cell proliferation | decrease in the expansion rate of any kidney cell population by cell division |
| 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:0007759 | Opacification of the corneal stroma | MP:0012129 | failure of blastocyst formation | inability to form a blastocyst from a solid ball of cells known as a morula |
| 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:0003196 | Short nose | MP:0002233 | abnormal nose morphology | any structural anomaly of the organ that is specialized for smell and is part of the respiratory system |
| HP:0001263 | Global developmental delay | MP:0002084 | abnormal developmental patterning | abnormal systematic arrangement of the developing body along an axis |
| HP:0001508 | Failure to thrive | MP:0013294 | prenatal lethality prior to heart atrial septation | death prior to the completion of heart atrial septation (Mus: E14.5-15.5) |
| HP:0001252 | Muscular hypotonia | MP:0004144 | hypotonia | decreased muscle tension resulting in limpness of the muscles in the resting state, not to be confused with weakness |
| HP:0001830 | Postaxial foot polydactyly | MP:0009744 | postaxial polydactyly | duplication of all or part of any of the rays except the first ray on one or more of the autopods |
| HP:0001399 | Hepatic failure | MP:0006138 | congestive heart failure | cardiac output is insufficient to supply blood throughout the body, resulting in the accumulation of fluid in the lungs and other body tissues; it is related mainly to salt and water retention in the tissues rather than directly to reduced blood flow; blo |
| HP:0001406 | Intrahepatic cholestasis | MP:0005415 | intrahepatic cholestasis | impairment of bile flow due to injury to the hepatocytes, bile canaliculi, or the intrahepatic bile ducts |
| HP:0008736 | Hypoplasia of penis | MP:0013283 | failure of ventral body wall closure | failure of the lateral body wall folds (a combination of mesoderm and ectoderm arising on each side of the embryo) to progress ventrally and meet in the midline and/or fuse to close the ventral body wall; normally, this closure is aided by growth of the h |
| HP:0001770 | Toe syndactyly | MP:0000564 | syndactyly | any degree of webbing or fusion of the digits, may involve only soft tissues or also can include bone |
Mapped by homologous gene(Total Items:43) | ||||
|---|---|---|---|---|
| HP ID | HP Name | MP ID | MP Name | Annotation |
| HP:0001252 | Muscular hypotonia | 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:0001883 | Talipes | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| HP:0000508 | Ptosis | MP:0020321 | increased vascular endothelial cell apoptosis | increase in the timing or the number of vascular endothelial cells undergoing programmed cell death |
| HP:0000085 | Horseshoe kidney | MP:0014044 | absent cardiac outflow tract | absence of or complete failure to form the common arterial trunk that normally forms the aorta and pulmonary artery and the ventricular outflow regions |
| HP:0001250 | Seizures | 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:0001399 | Hepatic failure | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| HP:0000212 | Gingival overgrowth | MP:0014179 | abnormal blood-retinal barrier function | anomaly in the function of the part of the blood-ocular barrier that consists of cells that are joined tightly together to prevent certain substances from entering the tissue of the retina; the BRB consists of non-fenestrated capillaries of the retinal ci |
| HP:0001830 | Postaxial foot polydactyly | 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:0000463 | Anteverted nares | MP:0020309 | increased creatine kinase activity | increased ability of to catalyze the reaction: ATP + creatine = N-phosphocreatine + ADP + 2 H(+). |
| HP:0003196 | Short nose | MP:0020309 | increased creatine kinase activity | increased ability of to catalyze the reaction: ATP + creatine = N-phosphocreatine + ADP + 2 H(+). |
| HP:0001162 | Postaxial hand polydactyly | MP:0014117 | increased pancreatic beta cell apoptosis | increase in the number of pancreatic beta cells undergoing programmed cell death |
| HP:0002240 | Hepatomegaly | MP:0020329 | decreased capillary density | reduction in the number of capillaries in a given cross-sectional area of a tissue |
| HP:0001336 | Myoclonus | MP:0020329 | decreased capillary density | reduction in the number of capillaries in a given cross-sectional area of a tissue |
| 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:0007759 | Opacification of the corneal stroma | MP:0020329 | decreased capillary density | reduction in the number of capillaries in a given cross-sectional area of a tissue |
| HP:0002435 | Meningocele | MP:0013349 | small Rathke's pouch | reduced size of the pouch of ectoderm which grows out from the upper surface of the embryonic stomodeum and gives rise to the anterior and intermediate lobes of the pituitary gland |
| HP:0002308 | Arnold-Chiari malformation | 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:0001770 | Toe syndactyly | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| HP:0000482 | Microcornea | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| HP:0002714 | Downturned corners of mouth | MP:0020157 | abnormal behavioral response to alcohol | any anomaly in the behavioral response induced by alcohol, such as induced hyperactivity or stereotypic behavior |
| HP:0000340 | Sloping forehead | MP:0020040 | decreased bone ossification | decrease 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: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:0001508 | Failure to thrive | 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: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:0001873 | Thrombocytopenia | MP:0020329 | decreased capillary density | reduction in the number of capillaries in a given cross-sectional area of a tissue |
| HP:0004823 | Anisopoikilocytosis | 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:0001328 | Specific learning disability | 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:0001406 | Intrahepatic cholestasis | MP:0020134 | abnormal gallbladder size | an anomaly in the size of the gall bladder compared to average, the organ that serves as a storage reservoir for bile |
| 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:0008278 | Cerebellar cortical atrophy | MP:0002081 | perinatal lethality | death anytime within the perinatal period (Mus: E18.5 through postnatal day 1) |
| HP:0000365 | Hearing impairment | MP:0020254 | decreased collagen level | decreased level of the main structural protein of the various connective tissues in animals |
| 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:0000286 | Epicanthus | MP:0020254 | decreased collagen level | decreased level of the main structural protein of the various connective tissues in animals |
| HP:0002514 | Cerebral calcification | MP:0020329 | decreased capillary density | reduction in the number of capillaries in a given cross-sectional area of a tissue |
| HP:0000494 | Downslanted palpebral fissures | MP:0020321 | increased vascular endothelial cell apoptosis | increase in the timing or the number of vascular endothelial cells undergoing programmed cell death |
| HP:0004422 | Biparietal narrowing | MP:0012431 | increased lymphoma incidence | greater than the expected number of neoplasms characterized by a proliferation of malignant lymphocytes in lymphoid tissue in a specific population in a given time period |
| HP:0000343 | Long philtrum | MP:0020254 | decreased collagen level | decreased level of the main structural protein of the various connective tissues in animals |
| HP:0000414 | Bulbous nose | MP:0020321 | increased vascular endothelial cell apoptosis | increase in the timing or the number of vascular endothelial cells undergoing programmed cell death |
| HP:0008736 | Hypoplasia of penis | 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:0005487 | Prominent metopic ridge | 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:0000341 | Narrow forehead | MP:0020254 | decreased collagen level | decreased level of the main structural protein of the various connective tissues in animals |
| HP:0000293 | Full cheeks | MP:0020321 | increased vascular endothelial cell apoptosis | increase in the timing or the number of vascular endothelial cells undergoing programmed cell death |
| 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 |
| Disease ID | 1795 |
|---|---|
| Disease | lathosterolosis |
| Case | (Waiting for update.) |