eRAM
encyclopedia of Rare Disease Annotation for Precision Medicine
| alkaptonuria | ||||
| Disease ID | 55 |
|---|---|
| Disease | alkaptonuria |
| Definition | An inborn error of amino acid metabolism resulting from a defect in the enzyme HOMOGENTISATE 1,2-DIOXYGENASE, an enzyme involved in the breakdown of PHENYLALANINE and TYROSINE. It is characterized by accumulation of HOMOGENTISIC ACID in the urine, OCHRONOSIS in various tissues, and ARTHRITIS. |
| Synonym | aku alcaptonuria alcaptonuria (disorder) alcaptonurias alkaptonuria (disorder) alkaptonuria (disorder) [ambiguous] alkaptonuria (finding) alkaptonuria [disease/finding] deficiency of homogentisate 1,2-dioxygenase deficiency of homogentisate 1,2-dioxygenase (disorder) deficiency of homogentisate oxygenase deficiency of homogentisicase homogentisate 1,2-dioxygenase deficiency homogentisate 1,2-dioxygenase deficiency (disorder) homogentisate 1,2-dioxygenase deficiency [ambiguous] homogentisic acid oxidase deficiency homogentisic acidura homogentisicaciduria |
| Orphanet | |
| OMIM | |
| DOID | |
| UMLS | C0002066 |
| MeSH | |
| SNOMED-CT | |
| Comorbidity | UMLS | Disease | Sentences' Count(Total Sentences:5) C0022408 | arthropathy | 3 C0042373 | vascular disease | 1 C0025637 | methaemoglobinaemia | 1 C0007222 | cardiovascular disease | 1 C0039730 | thalassemia | 1 |
| Curated Gene | Entrez_id | Symbol | Resource(Total Genes:1) |
| Inferring Gene | (Waiting for update.) |
| Text Mined Gene | Entrez_id | Symbol | Score | Resource(Total Genes:13) 262 | AMD1 | 1.629 | DISEASES 200894 | ARL13B | 2.97 | DISEASES 149466 | C1orf210 | 2.577 | DISEASES 1294 | COL7A1 | 1.619 | DISEASES 1644 | DDC | 1.697 | DISEASES 2108 | ETFA | 2.396 | DISEASES 2271 | FH | 1.666 | DISEASES 8200 | GDF5 | 1.913 | DISEASES 55361 | PI4K2A | 1.366 | DISEASES 10216 | PRG4 | 1.659 | DISEASES 6288 | SAA1 | 2.539 | DISEASES 6452 | SH3BP2 | 2.409 | DISEASES 6708 | SPTA1 | 2.486 | DISEASES |
| Locus | Symbol | Locus(Total Locus:1) HGD | 3q13.33 |
| Disease ID | 55 |
|---|---|
| Disease | alkaptonuria |
| Integrated Phenotype | HPO | Name(Total Integrated Phenotypes:42) HP:0001507 | Abnormal growth HP:0000787 | Nephrolithiasis HP:0000598 | Ear anomaly HP:0001654 | Abnormality of the heart valves HP:0002948 | Fusion of vertebral bodies HP:0000592 | Blue sclerae HP:0001000 | Abnormality of skin pigmentation HP:0001373 | Joint dislocation HP:0000366 | Abnormality of the nose HP:0001724 | Aortic dilatation HP:0002829 | Arthralgia HP:0001939 | Laboratory abnormality HP:0001717 | Coronary artery calcification HP:0002808 | Gibbus deformity HP:0100593 | Calcification of cartilage HP:0000822 | Hypertension HP:0004380 | Aortic valve calcification HP:0008419 | Degeneration of intervertebral disks HP:0000478 | Abnormality of the eye HP:0003418 | Back pain HP:0001658 | Myocardial infarction HP:0007400 | Irregular hyperpigmentation HP:0001386 | Joint swelling HP:0004690 | Thickened Achilles tendon HP:0002621 | Atherosclerosis HP:0003355 | Aminoaciduria HP:0005645 | Intervertebral disk calcification HP:0100550 | Tendon rupture HP:0002758 | Osteoarthritis HP:0100773 | Cartilage destruction HP:0007832 | Pigmentation of the sclera HP:0003040 | Arthropathy HP:0001597 | Abnormality of the nail HP:0000504 | Abnormality of vision HP:0000079 | Urinary tract anomalies HP:0001369 | Arthritis HP:0001387 | Joint stiffness HP:0000364 | Hearing abnormality HP:0000024 | Prostatitis HP:0004349 | Reduced bone mineral density HP:0002829 | Arthralgias HP:0004382 | Mitral valve calcification |
| Text Mined Phenotype | HPO | Name | Sentences' Count(Total Phenotypes:3) |
| Disease ID | 55 |
|---|---|
| Disease | alkaptonuria |
| Manually Symptom | UMLS | Name(Total Manually Symptoms:8) |
| Text Mined Symptom | UMLS | Name | Sentences' Count(Total Symptoms:2) |
Manually Genotype(Total Text Mining Genotypes:0) |
|---|
| (Waiting for update.) |
Text Mining Genotype(Total Genotypes:0) | |
|---|---|
| (Waiting for update.) | |
All Snps(Total Genotypes:29) | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| snpId | pubmedId | geneId | geneSymbol | diseaseId | sourceId | sentence | score | Year | geneSymbol_dbSNP | CHROMOSOME | POS | REF | ALT |
| rs120074170 | NA | 3081 | HGD | umls:C0002066 | CLINVAR | NA | 0.57413484 | NA | HGD | 3 | 120638562 | A | C |
| rs120074170 | 25681086 | 3081 | HGD | umls:C0002066 | UNIPROT | Analysis of HGD Gene Mutations in Patients with Alkaptonuria from the United Kingdom: Identification of Novel Mutations. | 0.57413484 | 2014 | HGD | 3 | 120638562 | A | C |
| rs120074171 | 10594001 | 3081 | HGD | umls:C0002066 | UNIPROT | Mutational analysis of the HGO gene in Finnish alkaptonuria patients. | 0.57413484 | 1999 | HGD | 3 | 120638471 | C | A |
| rs120074171 | NA | 3081 | HGD | umls:C0002066 | CLINVAR | NA | 0.57413484 | NA | HGD | 3 | 120638471 | C | A |
| rs120074172 | NA | 3081 | HGD | umls:C0002066 | CLINVAR | NA | 0.57413484 | NA | HGD | 3 | 120633223 | T | C |
| rs120074173 | NA | 3081 | HGD | umls:C0002066 | CLINVAR | NA | 0.57413484 | NA | HGD | 3 | 120633233 | T | C |
| rs120074173 | 25681086 | 3081 | HGD | umls:C0002066 | UNIPROT | Analysis of HGD Gene Mutations in Patients with Alkaptonuria from the United Kingdom: Identification of Novel Mutations. | 0.57413484 | 2014 | HGD | 3 | 120633233 | T | C |
| rs120074174 | NA | 3081 | HGD | umls:C0002066 | CLINVAR | NA | 0.57413484 | NA | HGD | 3 | 120641660 | C | T |
| rs143370662 | NA | 3081 | HGD | umls:C0002066 | CLINVAR | NA | 0.57413484 | NA | HGD | 3 | 120628382 | A | G |
| rs149165166 | NA | 3081 | HGD | umls:C0002066 | CLINVAR | NA | 0.57413484 | NA | HGD | 3 | 120650848 | A | C,G |
| rs200412910 | 23430897 | 3081 | HGD | umls:C0002066 | UNIPROT | Identification of 11 Novel Homogentisate 1,2 Dioxygenase Variants in Alkaptonuria Patients and Establishment of a Novel LOVD-Based HGD Mutation Database. | 0.57413484 | 2012 | HGD | 3 | 120682104 | T | G |
| rs28941783 | NA | 3081 | HGD | umls:C0002066 | CLINVAR | NA | 0.57413484 | NA | HGD | 3 | 120647041 | C | T |
| rs28941783 | 25681086 | 3081 | HGD | umls:C0002066 | UNIPROT | Analysis of HGD Gene Mutations in Patients with Alkaptonuria from the United Kingdom: Identification of Novel Mutations. | 0.57413484 | 2014 | HGD | 3 | 120647041 | C | T |
| rs28942100 | NA | 3081 | HGD | umls:C0002066 | CLINVAR | NA | 0.57413484 | NA | HGD | 3 | 120644405 | G | A |
| rs28942100 | 25681086 | 3081 | HGD | umls:C0002066 | UNIPROT | Analysis of HGD Gene Mutations in Patients with Alkaptonuria from the United Kingdom: Identification of Novel Mutations. | 0.57413484 | 2014 | HGD | 3 | 120644405 | G | A |
| rs369517993 | NA | 3081 | HGD | umls:C0002066 | CLINVAR | NA | 0.57413484 | NA | HGD | 3 | 120674937 | G | A,T |
| rs397515346 | NA | 3081 | HGD | umls:C0002066 | CLINVAR | NA | 0.57413484 | NA | HGD | 3 | 120647888 | - | C |
| rs397515347 | NA | 3081 | HGD | umls:C0002066 | CLINVAR | NA | 0.57413484 | NA | HGD | 3 | 120675864 | C | T |
| rs397515516 | NA | 3081 | HGD | umls:C0002066 | CLINVAR | NA | 0.57413484 | NA | HGD | 3 | 120633223 | - | G |
| rs397515517 | NA | 3081 | HGD | umls:C0002066 | CLINVAR | NA | 0.57413484 | NA | HGD | 3 | 120674903 | T | - |
| rs397515518 | NA | 3081 | HGD | umls:C0002066 | CLINVAR | NA | 0.57413484 | NA | HGD | 3 | 120652591 | C | T,A |
| rs544956641 | 19862842 | 3081 | HGD | umls:C0002066 | UNIPROT | Mutation spectrum of homogentisic acid oxidase (HGD) in alkaptonuria. | 0.57413484 | 2009 | HGD | 3 | 120650843 | G | A |
| rs544956641 | NA | 3081 | HGD | umls:C0002066 | CLINVAR | NA | 0.57413484 | NA | HGD | 3 | 120650843 | G | A |
| rs562853291 | NA | 3081 | HGD | umls:C0002066 | CLINVAR | NA | 0.57413484 | NA | HGD | 3 | 120644419 | C | G,T |
| rs562853291 | 25681086 | 3081 | HGD | umls:C0002066 | UNIPROT | Analysis of HGD Gene Mutations in Patients with Alkaptonuria from the United Kingdom: Identification of Novel Mutations. | 0.57413484 | 2014 | HGD | 3 | 120644419 | C | G,T |
| rs564979861 | 25681086 | 3081 | HGD | umls:C0002066 | UNIPROT | Analysis of HGD Gene Mutations in Patients with Alkaptonuria from the United Kingdom: Identification of Novel Mutations. | 0.57413484 | 2014 | HGD | 3 | 120650841 | C | T |
| rs569846003 | 23430897 | 3081 | HGD | umls:C0002066 | UNIPROT | Identification of 11 Novel Homogentisate 1,2 Dioxygenase Variants in Alkaptonuria Patients and Establishment of a Novel LOVD-Based HGD Mutation Database. | 0.57413484 | 2012 | HGD | 3 | 120650861 | A | G |
| rs786204422 | NA | 3081 | HGD | umls:C0002066 | CLINVAR | NA | 0.57413484 | NA | HGD | 3 | 120682101 | A | T |
| rs786204662 | NA | 3081 | HGD | umls:C0002066 | CLINVAR | NA | 0.57413484 | NA | HGD | 3 | 120644441 | C | - |
GWASdb Annotation(Total Genotypes:0) | |
|---|---|
| (Waiting for update.) | |
GWASdb Snp Trait(Total Genotypes:0) | |
|---|---|
| (Waiting for update.) | |
Mapped by lexical matching(Total Items:15) | ||||
|---|---|---|---|---|
| HP ID | HP Name | MP ID | MP Name | Annotation |
| HP:0000366 | Abnormality of the nose | MP:0012069 | abnormal horizontal basal cell of olfactory epithelium morphology | any structural anomaly of the flat or angular epithelial cell with condensed nuclei and darkly staining cytoplasm containing numerous intermediate filaments inserted into desmosomes contacting surrounding supporting cells, that lie in contact with the bas |
| HP:0001387 | Joint stiffness | MP:0003098 | decreased tendon stiffness | reduced ability of tendon to maintain tensile strength and load |
| HP:0001654 | Abnormality of the heart valves | MP:0008158 | increased diameter of femur | increased width of the cross-sectional distance that extends from one lateral edge of the femur, through its center and to the opposite lateral edge |
| HP:0000478 | Abnormality of the eye | MP:0012069 | abnormal horizontal basal cell of olfactory epithelium morphology | any structural anomaly of the flat or angular epithelial cell with condensed nuclei and darkly staining cytoplasm containing numerous intermediate filaments inserted into desmosomes contacting surrounding supporting cells, that lie in contact with the bas |
| HP:0001000 | Abnormality of skin pigmentation | MP:0009536 | abnormal interstitial cell of Cajal morphology | any structural anomaly in the type of cell found in the gastrointestinal tract and serving as a pacemaker that triggers gut contraction; ICCs mediate inputs from the enteric nervous system to smooth muscle cells and are thought to be the cells from which |
| HP:0001386 | Joint swelling | MP:0002936 | joint swelling | enlargement of the joints, usually due to an accumulation of fluid |
| HP:0100593 | Calcification of cartilage | MP:0010988 | abnormal bronchial cartilage morphology | any structural anomaly of the hyaline cartilaginous structures that support the bronchi, present as irregular rings in the larger bronchi (and not as regular as in the trachea), and as small plates and islands in the smaller bronchi; as the branching cont |
| HP:0002948 | Vertebral fusion | MP:0004613 | fusion of vertebral arches | improper union of the dorsal part of adjacent vertebra |
| HP:0000504 | Abnormality of vision | MP:0012528 | abnormal zone of polarizing activity morphology | any structural anomaly of the subset of cells found in the posterior mesenchyme region of the vertebrate limb bud; Sonic hedgehog (Shh) produced by ZPA represents the key mediator of the polarizing activity that regulates patterning of the limb along the |
| HP:0004349 | Reduced bone mineral density | MP:0013630 | increased bone trabecular spacing | increase in the amount of space between trabeculae in cancellous bone |
| HP:0000598 | Abnormality of the ear | MP:0010465 | aberrant origin of the right subclavian artery | the right subclavian artery arises from an atypical location on the aortic arch or the proximal descending aorta |
| HP:0000079 | Abnormality of the urinary system | 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:0001597 | Abnormality of the nail | MP:0011205 | excessive folding of visceral yolk sac | the appearance of wrinkles or folds on the surface of the visceral yolk sac |
| HP:0001717 | Coronary artery calcification | MP:0006133 | calcified artery | pathologic deposition of calcium salts in the arteries |
| HP:0001939 | Abnormality of metabolism/homeostasis | 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 |
Mapped by homologous gene(Total Items:41) | ||||
|---|---|---|---|---|
| HP ID | HP Name | MP ID | MP Name | Annotation |
| HP:0002758 | Osteoarthritis | MP:0020254 | decreased collagen level | decreased level of the main structural protein of the various connective tissues in animals |
| HP:0007832 | Pigmentation of the sclera | MP:0003619 | abnormal urine color | any alteration from the usual straw-coloration of the urine |
| HP:0004380 | Aortic valve calcification | MP:0011108 | embryonic lethality during organogenesis, 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 embryo turning and the completion of organogenesis (Mus: E9-9.5 to less than E14) |
| HP:0001654 | Abnormality of the heart valves | MP:0013696 | increased granulocyte monocyte progenitor cell number | increase in the number of a hematopoietic progenitor cell that is committed to the granulocyte and monocyte lineages; these cells are CD123-positive, and do not express Gata1 or Gata2 but do express C/EBPa, and Pu.1 |
| HP:0001369 | Arthritis | MP:0020316 | decreased vascular endothelial cell proliferation | decrease in the expansion rate of any vascular endothelial cell population by cell division |
| HP:0003040 | Arthropathy | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| HP:0000592 | Blue sclerae | MP:0020254 | decreased collagen level | decreased level of the main structural protein of the various connective tissues in animals |
| HP:0000598 | Abnormality of the ear | MP:0014175 | abnormal ciliary epithelium morphology | any structural anomaly of the double layer lining the inner surfaces of the ciliary processes and the pars plana (i.e. the posterior portion of the ciliary body, aka orbicularis ciliari); the outer layer is the pigmented epithelium, which is composed of l |
| HP:0000364 | Hearing abnormality | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| HP:0100550 | Tendon rupture | MP:0011108 | embryonic lethality during organogenesis, 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 embryo turning and the completion of organogenesis (Mus: E9-9.5 to less than E14) |
| HP:0001717 | Coronary artery calcification | 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:0100773 | Cartilage destruction | 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:0003355 | Aminoaciduria | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| HP:0001000 | Abnormality of skin pigmentation | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| HP:0004382 | Mitral valve calcification | MP:0011108 | embryonic lethality during organogenesis, 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 embryo turning and the completion of organogenesis (Mus: E9-9.5 to less than E14) |
| HP:0001373 | Joint dislocation | MP:0020254 | decreased collagen level | decreased level of the main structural protein of the various connective tissues in animals |
| HP:0001724 | Aortic dilatation | MP:0020321 | increased vascular endothelial cell apoptosis | increase in the timing or the number of vascular endothelial cells undergoing programmed cell death |
| HP:0001597 | Abnormality of the nail | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| HP:0002621 | Atherosclerosis | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| HP:0002829 | Arthralgia | MP:0020154 | impaired humoral immune response | impaired response of the immune system that mediates secreted antibodies produced in B cells |
| HP:0002948 | Vertebral fusion | 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:0008419 | Intervertebral disc degeneration | MP:0011405 | tubulointerstitial nephritis | diffuse or local inflammation and edema of the interstitial tissue of the kidney, including the renal tubules; usually secondary to drug sensitization, systemic infection, graft rejection, or autoimmune disease |
| HP:0007400 | Irregular hyperpigmentation | MP:0014171 | increased fatty acid oxidation | increased rate or incidence of the process of removal of one or more electrons from a fatty acid, with or without the concomitant removal of a proton or protons, by reaction with an electron-accepting substance, by addition of oxygen or by removal of hydr |
| HP:0000787 | Nephrolithiasis | MP:0020316 | decreased vascular endothelial cell proliferation | decrease in the expansion rate of any vascular endothelial cell population by cell division |
| HP:0005645 | Intervertebral disk calcification | MP:0003619 | abnormal urine color | any alteration from the usual straw-coloration of the urine |
| HP:0001939 | Abnormality of metabolism/homeostasis | MP:0020254 | decreased collagen level | decreased level of the main structural protein of the various connective tissues in animals |
| HP:0001507 | Growth abnormality | MP:0020254 | decreased collagen level | decreased level of the main structural protein of the various connective tissues in animals |
| HP:0000366 | Abnormality of the nose | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| HP:0001658 | Myocardial infarction | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| HP:0001386 | Joint swelling | MP:0013743 | ciliary body hypoplasia | underdevelopment or reduced size, usually due to a reduced number of cells, of the thickened portion of the vascular tunic which lies between the choroid and the iris |
| HP:0000504 | Abnormality of vision | MP:0013545 | cleft hard palate | cleft in the anterior portion of the palate consisting of bone and mucous membranes; the hard palate is formed from bony processes of the maxilla, premaxilla and palatine bones |
| HP:0001387 | Joint stiffness | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| HP:0000079 | Abnormality of the urinary system | 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:0000478 | Abnormality of the eye | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| HP:0000024 | Prostatitis | MP:0010766 | abnormal NK cell physiology | any functional anomaly of a lymphocyte that can spontaneously kill a variety of target cells without prior antigenic activation via germline encoded activation receptors, and also regulate immune responses via cytokine release and direct contact with othe |
| HP:0004349 | Reduced bone mineral density | MP:0020254 | decreased collagen level | decreased level of the main structural protein of the various connective tissues in animals |
| HP:0002808 | Kyphosis | MP:0020254 | decreased collagen level | decreased level of the main structural protein of the various connective tissues in animals |
| HP:0100593 | Calcification of cartilage | 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:0000822 | Hypertension | MP:0020216 | decreased circulating complement protein level | less than normal levels of the serum proteins that act sequentially to allow for the direct killing of microbes, the disposal of immune complexes, and the regulation of other immune processes |
| HP:0004690 | Thickened Achilles tendon | MP:0003619 | abnormal urine color | any alteration from the usual straw-coloration of the urine |
| HP:0003418 | Back pain | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| Disease ID | 55 |
|---|---|
| Disease | alkaptonuria |
| Case | (Waiting for update.) |