eRAM
encyclopedia of Rare Disease Annotation for Precision Medicine
| usher syndrome type 3 | ||||
| Disease ID | 652 |
|---|---|
| Disease | usher syndrome type 3 |
| Definition | A syndrome characterized by postlingual progressive hearing loss, abnormalities in the vestibular system, and onset of retinitis pigmentosa symptoms usually by the second decade of life. |
| Synonym | ush3 ush3a usher syndrome, type 3 usher syndrome, type iii usher syndrome, type iiia |
| Orphanet | |
| OMIM | |
| UMLS | C1568248 |
| Comorbidity | UMLS | Disease | Sentences' Count(Total Sentences:1) |
| Curated Gene | Entrez_id | Symbol | Resource(Total Genes:2) |
| Inferring Gene | (Waiting for update.) |
| Text Mined Gene | Entrez_id | Symbol | Score | Resource(Total Genes:15) 26090 | ABHD12 | 3.125 | DISEASES 64072 | CDH23 | 5.154 | DISEASES 7401 | CLRN1 | 7.389 | DISEASES 7555 | CNBP | 1.689 | DISEASES 2932 | GSK3B | 2.899 | DISEASES 4067 | LYN | 1.355 | DISEASES 116931 | MED12L | 4.072 | DISEASES 4647 | MYO7A | 5.968 | DISEASES 65217 | PCDH15 | 5.077 | DISEASES 79955 | PDZD7 | 3.466 | DISEASES 6477 | SIAH1 | 2.4 | DISEASES 6478 | SIAH2 | 3.723 | DISEASES 9498 | SLC4A8 | 3.169 | DISEASES 6622 | SNCA | 2.231 | DISEASES 10103 | TSPAN1 | 2.906 | DISEASES |
| Locus | Symbol | Locus(Total Locus:3) |
| Disease ID | 652 |
|---|---|
| Disease | usher syndrome type 3 |
| Integrated Phenotype | HPO | Name(Total Integrated Phenotypes:23) HP:0000518 | Cataract HP:0007663 | Central visual loss HP:0000572 | Visual loss HP:0000512 | Abnormal electroretinogram HP:0001251 | Ataxia HP:0008499 | High-grade hypermetropia HP:0007730 | Iris hypopigmentation HP:0000407 | Sensorineural hearing impairment HP:0000739 | Anxiety HP:0000662 | Poor night vision HP:0000483 | Astigmatism HP:0000375 | Abnormality of cochlea HP:0001751 | Vestibular dysfunction HP:0012377 | Hemianopsia HP:0001756 | Vestibular hypofunction HP:0000575 | Scotoma HP:0100753 | Schizophrenia HP:0000510 | Retinitis pigmentosa HP:0000738 | Hallucinations HP:0000716 | Depression HP:0000407 | sensorineural hearing loss HP:0000662 | Nyctalopia HP:0001123 | Partial loss of field of vision |
| Text Mined Phenotype | HPO | Name | Sentences' Count(Total Phenotypes:2) |
| Disease ID | 652 |
|---|---|
| Disease | usher syndrome type 3 |
| Manually Symptom | (Waiting for update.) |
| Text Mined Symptom | (Waiting for update.) |
Manually Genotype(Total Manually Genotypes:1) | |||
|---|---|---|---|
| Gene | Mutation | DOI | Article Title |
| CLRN1 | p.N48K | doi:10.1038/gim.2016.30 | Carrier screening in the era of expanding genetic technology |
Text Mining Genotype(Total Genotypes:0) | |
|---|---|
| (Waiting for update.) | |
All Snps(Total Genotypes:12) | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| snpId | pubmedId | geneId | geneSymbol | diseaseId | sourceId | sentence | score | Year | geneSymbol_dbSNP | CHROMOSOME | POS | REF | ALT |
| rs111033258 | NA | 7401 | CLRN1 | umls:C1568248 | CLINVAR | NA | 0.563800186 | NA | CLRN1;CLRN1-AS1 | 3 | 150972565 | A | C |
| rs111033258 | 26180195 | 7401 | CLRN1 | umls:C1568248 | BeFree | The missense mutation CLRN1(N48K), which affects a conserved N-glycosylation site in hCLRN1, is a common causative USH3 mutation among Ashkenazi Jews. | 0.563800186 | 2015 | CLRN1;CLRN1-AS1 | 3 | 150972565 | A | C |
| rs111033267 | NA | 7401 | CLRN1 | umls:C1568248 | CLINVAR | NA | 0.563800186 | NA | CLRN1;CLRN1-AS1 | 3 | 150972520 | G | T,A |
| rs111033434 | NA | 7401 | CLRN1 | umls:C1568248 | CLINVAR | NA | 0.563800186 | NA | CLRN1;CLRN1-AS1 | 3 | 150972582 | C | T |
| rs121908140 | NA | 7401 | CLRN1 | umls:C1568248 | CLINVAR | NA | 0.563800186 | NA | CLRN1 | 3 | 150928107 | A | G,C |
| rs121908141 | NA | 7401 | CLRN1 | umls:C1568248 | CLINVAR | NA | 0.563800186 | NA | CLRN1 | 3 | 150941656 | A | T,G |
| rs121908142 | NA | 7401 | CLRN1 | umls:C1568248 | CLINVAR | NA | 0.563800186 | NA | CLRN1 | 3 | 150928186 | A | G |
| rs121908143 | NA | 7401 | CLRN1 | umls:C1568248 | CLINVAR | NA | 0.563800186 | NA | CLRN1;CLRN1-AS1 | 3 | 150972591 | A | C |
| rs374963432 | NA | 7401 | CLRN1 | umls:C1568248 | CLINVAR | NA | 0.563800186 | NA | CLRN1 | 3 | 150941647 | G | T |
| rs397517932 | NA | 7401 | CLRN1 | umls:C1568248 | CLINVAR | NA | 0.563800186 | NA | CLRN1 | 3 | 150941710 | ATGAC | - |
| rs746523071 | NA | 7401 | CLRN1 | umls:C1568248 | CLINVAR | NA | 0.563800186 | NA | CLRN1 | 3 | 150928132 | - | T |
| rs786204428 | NA | 7401 | CLRN1 | umls:C1568248 | CLINVAR | NA | 0.563800186 | NA | CLRN1;CLRN1-AS1 | 3 | 150972557 | CCTG | ATTGGACA |
GWASdb Annotation(Total Genotypes:0) | |
|---|---|
| (Waiting for update.) | |
GWASdb Snp Trait(Total Genotypes:0) | |
|---|---|
| (Waiting for update.) | |
Mapped by lexical matching(Total Items:6) | ||||
|---|---|---|---|---|
| HP ID | HP Name | MP ID | MP Name | Annotation |
| HP:0000510 | Rod-cone dystrophy | MP:0003225 | axonal dystrophy | axon degeneration that may result from genetic abnormalities or inadequate or faulty metabolism |
| 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:0007730 | Iris hypopigmentation | MP:0005408 | hypopigmentation | dilution of pigment in any or all tissues or a part of a tissue |
| HP:0001123 | Visual field defect | MP:0010402 | ventricular septal defect | abnormal communications between the two lower chambers of the heart, including such defects in the perimembranous, inlet, outlet (infundibular), central muscular, marginal muscular, or apical muscular regions |
| HP:0007663 | Reduced visual acuity | MP:0006149 | decreased visual acuity | loss of visual acuity or ability to distinguish small details |
| HP:0000572 | Visual loss | MP:0011352 | proximal convoluted tubule brush border loss | attenuation or degeneration of the microvillus brush border normally present on the luminal surface of epithelial cells of the proximal convoluted tubule; may be associated with renal tubular injury and/or cystic changes |
Mapped by homologous gene(Total Items:20) | ||||
|---|---|---|---|---|
| HP ID | HP Name | MP ID | MP Name | Annotation |
| HP:0000483 | Astigmatism | MP:0020157 | abnormal behavioral response to alcohol | any anomaly in the behavioral response induced by alcohol, such as induced hyperactivity or stereotypic behavior |
| HP:0001123 | Visual field defect | 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: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:0000739 | Anxiety | MP:0020329 | decreased capillary density | reduction in the number of capillaries in a given cross-sectional area of a tissue |
| HP:0007663 | Reduced visual acuity | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| HP:0000572 | Visual loss | 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:0000575 | Scotoma | MP:0014059 | abnormal photoreceptor connecting cilium morphology | any structural anomaly of the nonmotile primary cilium that has a 9+0 microtubule array and forms the portion of the axoneme traversing the boundary between the retinal photoreceptor inner and outer segments |
| HP:0001756 | Vestibular hypofunction | 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: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:0000512 | Abnormal electroretinogram | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| HP:0000738 | Hallucinations | MP:0020329 | decreased capillary density | reduction in the number of capillaries in a given cross-sectional area of a tissue |
| HP:0000716 | Depression | MP:0020329 | decreased capillary density | reduction in the number of capillaries in a given cross-sectional area of a tissue |
| HP:0000662 | Nyctalopia | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| HP:0001751 | Vestibular dysfunction | MP:0014185 | cerebellum atrophy | acquired diminution of the size of the cerebellum associated with wasting as from death and reabsorption of cells, diminished cellular proliferation, decreased cellular volume, pressure, ischemia, malnutrition, reduced function or malfunction, or hormonal |
| HP:0000510 | Rod-cone dystrophy | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| HP:0001251 | Ataxia | MP:0020301 | short tongue | decreased length of the mobile mass of muscular tissue and surrounding epithelial tissue occupying the cavity of the mouth and forming part of the floor |
| HP:0007730 | Iris hypopigmentation | 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:0012377 | Hemianopia | MP:0013405 | increased circulating lactate level | greater amount of lactate in the blood which is produced from pyruvate by lactate dehydrogenase |
| HP:0008499 | High-grade hypermetropia | 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:0100753 | Schizophrenia | MP:0013787 | photophobia | abnormal aversion or avoidance behavior in response to light; photophobia is symptom of abnormal intolerance to visual perception of light; as a medical symptom, photophobia is not a morbid fear or phobia, but an experience of discomfort or pain to the e |
| Disease ID | 652 |
|---|---|
| Disease | usher syndrome type 3 |
| Case | (Waiting for update.) |