eRAM
encyclopedia of Rare Disease Annotation for Precision Medicine
| micro syndrome | ||||
| Disease ID | 990 |
|---|---|
| Disease | micro syndrome |
| Definition | Micro syndrome also known as WARBM, and Warburg–Sjo–Fledelius syndrome, is a rare autosomal recessive genetic disorder characterized by microcephaly, microcornea, congenital cataract, intellectual or developmental disability, optic atrophy, and hypogenitalism.[1] - Wikipedia Reference: https://en.wikipedia.org/wiki/micro syndrome |
| Synonym | warburg micro syndrome warburg micro syndrome 1 warburg sjo fledelius syndrome |
| Orphanet | |
| OMIM | |
| DOID | |
| UMLS | C1838625 |
| Curated Gene | Entrez_id | Symbol | Resource(Total Genes:4) |
| Inferring Gene | (Waiting for update.) |
| Text Mined Gene | Entrez_id | Symbol | Score | Resource(Total Genes:28) 3267 | AGFG1 | 2.205 | DISEASES 5832 | ALDH18A1 | 3.306 | DISEASES 57194 | ATP10A | 3.349 | DISEASES 6792 | CDKL5 | 3.185 | DISEASES 10970 | CKAP4 | 3.524 | DISEASES 1415 | CRYBB2 | 3.015 | DISEASES 2224 | FDPS | 1.997 | DISEASES 2290 | FOXG1 | 2.109 | DISEASES 2558 | GABRA5 | 2.998 | DISEASES 9573 | GDF3 | 1.355 | DISEASES 283685 | GOLGA6L2 | 3.549 | DISEASES 55777 | MBD5 | 2.553 | DISEASES 4204 | MECP2 | 2.11 | DISEASES 4948 | OCA2 | 2.086 | DISEASES 22931 | RAB18 | 7.11 | DISEASES 22931 | RAB18 | 5.741 | DISEASES 22930 | RAB3GAP1 | 7.575 | DISEASES 22930 | RAB3GAP1 | 6.512 | DISEASES 25782 | RAB3GAP2 | 7.093 | DISEASES 25782 | RAB3GAP2 | 6.385 | DISEASES 23637 | RABGAP1 | 4.929 | DISEASES 23637 | RABGAP1 | 4.052 | DISEASES 57142 | RTN4 | 1.415 | DISEASES 10479 | SLC9A6 | 2.886 | DISEASES 84679 | SLC9A7 | 3.139 | DISEASES 128637 | TBC1D20 | 6.952 | DISEASES 128637 | TBC1D20 | 6.534 | DISEASES 7337 | UBE3A | 1.805 | DISEASES |
| Locus | Symbol | Locus(Total Locus:4) |
| Disease ID | 990 |
|---|---|
| Disease | micro syndrome |
| Integrated Phenotype | HPO | Name(Total Integrated Phenotypes:42) HP:0001317 | Abnormality of the cerebellum HP:0000028 | Cryptorchidism HP:0001263 | Global developmental delay HP:0010864 | Intellectual disability, severe HP:0000568 | Microphthalmia HP:0000518 | Cataract HP:0001320 | Cerebellar vermis hypoplasia HP:0003196 | Short nose HP:0004322 | Short stature HP:0000218 | High palate HP:0001339 | Lissencephaly HP:0008736 | Hypoplasia of penis HP:0001257 | Spasticity HP:0000347 | Micrognathia HP:0007370 | Aplasia/Hypoplasia of the corpus callosum HP:0000126 | Hydronephrosis HP:0009830 | Peripheral neuropathy HP:0002120 | Cerebral cortical atrophy HP:0001511 | Intrauterine growth retardation HP:0001302 | Pachygyria HP:0001250 | Seizures HP:0002650 | Scoliosis HP:0000252 | Microcephaly HP:0002808 | Kyphosis HP:0000480 | Retinal coloboma HP:0000648 | Optic atrophy HP:0000823 | Delayed puberty HP:0002230 | Generalized hirsutism HP:0000431 | Wide nasal bridge HP:0007703 | Abnormality of retinal pigmentation HP:0100704 | Cortical visual impairment HP:0000060 | Clitoral hypoplasia HP:0000322 | Short philtrum HP:0000064 | Hypoplastic labia minora HP:0001387 | Joint stiffness HP:0100542 | Abnormal localization of kidney HP:0000463 | Anteverted nares HP:0000400 | Macrotia HP:0000368 | Low-set, posteriorly rotated ears HP:0000649 | Abnormality of visual evoked potentials HP:0001252 | Muscular hypotonia HP:0000482 | Microcornea |
| Text Mined Phenotype | (Waiting for update.) |
| Disease ID | 990 |
|---|---|
| Disease | micro syndrome |
| Manually Symptom | UMLS | Name(Total Manually Symptoms:1) C0235025 | motor neuropathy |
| 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) | |
|---|---|
| (Waiting for update.) | |
All Snps(Total Genotypes:13) | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| snpId | pubmedId | geneId | geneSymbol | diseaseId | sourceId | sentence | score | Year | geneSymbol_dbSNP | CHROMOSOME | POS | REF | ALT |
| rs137853052 | NA | 22930 | RAB3GAP1 | umls:C1838625 | CLINVAR | NA | 0.362442977 | NA | RAB3GAP1 | 2 | 135150456 | C | T |
| rs137853053 | NA | 22930 | RAB3GAP1 | umls:C1838625 | CLINVAR | NA | 0.362442977 | NA | RAB3GAP1 | 2 | 135135743 | G | A |
| rs267606996 | NA | 22930 | RAB3GAP1 | umls:C1838625 | CLINVAR | NA | 0.362442977 | NA | RAB3GAP1 | 2 | 135133944 | C | A |
| rs587776651 | NA | 22930 | RAB3GAP1 | umls:C1838625 | CLINVAR | NA | 0.362442977 | NA | RAB3GAP1 | 2 | 135120919 | G | A |
| rs587777152 | NA | 22930 | RAB3GAP1 | umls:C1838625 | CLINVAR | NA | 0.362442977 | NA | RAB3GAP1 | 2 | 135126250 | G | A |
| rs587777153 | NA | 22930 | RAB3GAP1 | umls:C1838625 | CLINVAR | NA | 0.362442977 | NA | RAB3GAP1 | 2 | 135150500 | - | GCTCTCAGATATGGAGTCT |
| rs587777154 | NA | 22930 | RAB3GAP1 | umls:C1838625 | CLINVAR | NA | 0.362442977 | NA | RAB3GAP1 | 2 | 135052463 | A | C |
| rs587777155 | NA | 22930 | RAB3GAP1 | umls:C1838625 | CLINVAR | NA | 0.362442977 | NA | RAB3GAP1 | 2 | 135052482 | A | T |
| rs730882182 | NA | 22930 | RAB3GAP1 | umls:C1838625 | CLINVAR | NA | 0.362442977 | NA | RAB3GAP1 | 2 | 135168636 | C | - |
| rs730882183 | NA | 22930 | RAB3GAP1 | umls:C1838625 | CLINVAR | NA | 0.362442977 | NA | RAB3GAP1 | 2 | 135120817 | A | G |
| rs730882184 | NA | 22930 | RAB3GAP1 | umls:C1838625 | CLINVAR | NA | 0.362442977 | NA | RAB3GAP1 | 2 | 135091111 | AAAGGAT | TTATTA |
| rs794727324 | NA | 22930 | RAB3GAP1 | umls:C1838625 | CLINVAR | NA | 0.362442977 | NA | RAB3GAP1 | 2 | 135162608 | ACCTT | - |
| rs797045905 | NA | 22930 | RAB3GAP1 | umls:C1838625 | CLINVAR | NA | 0.362442977 | NA | RAB3GAP1 | 2 | 135164629 | T | G |
GWASdb Annotation(Total Genotypes:0) | |
|---|---|
| (Waiting for update.) | |
GWASdb Snp Trait(Total Genotypes:0) | |
|---|---|
| (Waiting for update.) | |
Mapped by lexical matching(Total Items:17) | ||||
|---|---|---|---|---|
| HP ID | HP Name | MP ID | MP Name | Annotation |
| 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:0001387 | Joint stiffness | MP:0003098 | decreased tendon stiffness | reduced ability of tendon to maintain tensile strength and load |
| HP:0100542 | Abnormal localization of kidney | MP:0009657 | failure of chorioallantoic fusion | failure to initiate and/or complete the formation of a highly vascularized extra-embryonic fetal membrane by fusion of the chorion and allantois |
| 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:0000649 | Abnormality of visual evoked potentials | 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: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:0001320 | Cerebellar vermis hypoplasia | MP:0000866 | cerebellum vermis hypoplasia | underdevelopment or reduced size, usually due to a reduced number of cells, in the vermis |
| HP:0001263 | Global developmental delay | MP:0002084 | abnormal developmental patterning | abnormal systematic arrangement of the developing body along an axis |
| HP:0002120 | Cerebral cortical atrophy | MP:0012506 | brain atrophy | acquired diminution of the size of the brain associated with wasting as from death and reabsorbtion of cells, diminished cellular proliferation, decreased cellular volume, pressure, ischemia, malnutrition, reduced function or malfunction, or hormonal chan |
| HP:0000480 | Retinal coloboma | MP:0012533 | uveal coloboma | congenital defect of the uvea in which some part of the structure is absent |
| HP:0000648 | Optic atrophy | MP:0012506 | brain atrophy | acquired diminution of the size of the brain associated with wasting as from death and reabsorbtion of cells, diminished cellular proliferation, decreased cellular volume, pressure, ischemia, malnutrition, reduced function or malfunction, or hormonal chan |
| HP:0007370 | Aplasia/Hypoplasia of the corpus callosum | 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:0000060 | Clitoral hypoplasia | MP:0011772 | genital tubercle hypoplasia | underdevelopment or reduced size of the embryonic anlage of the external genitalia, usually due to a reduced number of cells |
| 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: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:0007703 | Abnormality of retinal pigmentation | 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 |
Mapped by homologous gene(Total Items:42) | ||||
|---|---|---|---|---|
| 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:0002650 | Scoliosis | MP:0020309 | increased creatine kinase activity | increased ability of to catalyze the reaction: ATP + creatine = N-phosphocreatine + ADP + 2 H(+). |
| HP:0000060 | Clitoral hypoplasia | MP:0013956 | decreased colon length | reduced length of the portion of the large intestine between the cecum and the rectum |
| HP:0000322 | Short philtrum | 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:0002120 | Cerebral cortical atrophy | MP:0020329 | decreased capillary density | reduction in the number of capillaries in a given cross-sectional area of a tissue |
| HP:0001320 | Cerebellar vermis hypoplasia | 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:0001302 | Pachygyria | MP:0020157 | abnormal behavioral response to alcohol | any anomaly in the behavioral response induced by alcohol, such as induced hyperactivity or stereotypic behavior |
| 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:0009830 | Peripheral neuropathy | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| 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: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: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:0000482 | Microcornea | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| HP:0001257 | Spasticity | MP:0020316 | decreased vascular endothelial cell proliferation | decrease in the expansion rate of any vascular endothelial cell population by cell division |
| HP:0000126 | Hydronephrosis | MP:0020254 | decreased collagen level | decreased level of the main structural protein of the various connective tissues in animals |
| 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: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:0000028 | Cryptorchidism | 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:0007370 | Aplasia/Hypoplasia of the corpus callosum | 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:0000064 | Hypoplastic labia minora | 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:0000480 | Retinal coloboma | 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:0002230 | Generalized hirsutism | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| HP:0001317 | Abnormality of the cerebellum | MP:0011971 | increased circulating lactate dehydrogenase level | elevated blood level of the tetrameric enzyme that, along with the coenzyme NAD+, catalyzes the interconversion of lactate and pyruvate; measurements of circulating levels are used clinically as a diagnostic indicator of tissue breakdown, some forms of ca |
| 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:0000568 | Microphthalmia | 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:0000823 | Delayed puberty | MP:0020087 | increased susceptibility to non-insulin-dependent diabetes | increased likelihood to develop non-insulin-dependent diabetes |
| HP:0010864 | Intellectual disability, severe | 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:0000649 | Abnormality of visual evoked potentials | MP:0020080 | increased bone mineralization | increase in the rate at which minerals are deposited into bone |
| HP:0001339 | Lissencephaly | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| HP:0100704 | Cortical visual impairment | MP:0020194 | abnormal glycosphingolipid level | any anomaly in the concentrations of glycosphingolipids, a subtype of glycolipids containing the amino alcohol sphingosine, in the body |
| HP:0007703 | Abnormality of retinal pigmentation | MP:0020254 | decreased collagen level | decreased level of the main structural protein of the various connective tissues in animals |
| HP:0000368 | Low-set, posteriorly rotated ears | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| HP:0001387 | Joint stiffness | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| 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:0100542 | Abnormal localization of kidney | 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:0000400 | Macrotia | MP:0020309 | increased creatine kinase activity | increased ability of to catalyze the reaction: ATP + creatine = N-phosphocreatine + ADP + 2 H(+). |
| HP:0002808 | Kyphosis | MP:0020254 | decreased collagen level | decreased level of the main structural protein of the various connective tissues in animals |
| 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:0000431 | Wide nasal bridge | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| HP:0000648 | Optic atrophy | 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 | 990 |
|---|---|
| Disease | micro syndrome |
| Case | (Waiting for update.) |