Schema for Orphanet - Orphadata: Aggregated Data From Orphanet |
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Database: hg38 Primary Table: orphadata Data last updated: 2021-11-04
Big Bed File Download: /gbdb/hg38/bbi/orphanet/orphadata.bb
Item Count: 7,973
The data is stored in the binary BigBed format.
Format description: Aggregated Phenotype, Epidemiological, and Rare Disease Gene Relationships from Orphanet
| field | example | description |
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| chrom | chr1 | Reference sequence chromosome or scaffold | | chromStart | 167430640 | Start position of feature on chromosome | | chromEnd | 167518610 | End position of feataure on chromosome | | name | 169160 | Name of disorder | | score | 0 | Score | | strand | - | Strand | | thickStart | 167430640 | Coding region start | | thickEnd | 167518610 | Coding region end | | itemRgb | 0,146,156 | Color | | disorder | T-B+ severe combined immunodeficiency due to CD3delta/CD3epsilon/CD3zeta | Name of disorder | | geneSymbol | CD247 | Gene symbol | | geneName | CD247 molecule | Gene name | | ensemblID | ENSG00000198821 | Ensembl ID | | geneType | gene with protein product | Gene type | | geneLocus | 1q24.2 | Gene locus | | assnStatus | Assessed | Association status | | assnType | Disease-causing germline mutation(s) in | Association type | | pmid | | PMID(s) | | orphaCode | 169160 | OrphaCode | | omim | 186780 | OMIM ID | | hgnc | 1677 | HGNC ID | | inheritance | Autosomal recessive | Inheritance(s) | | onsetList | Infancy | Onset list | | deathList | infantile | Death list | | prevalences | | Prevalence(s) | | veryFreqPhen | | Very frequent phenotype(s) | | freqPhen | Lymphopenia, Fever, Decreased circulating total IgA, Decreased circulating IgG level, Failure to thrive secondary to recurrent infections, Decreased lymphocyte proliferation in response to mitogen, Decreased proportion of CD3-positive T cells | Frequent phenotype(s) | | occasPhen | Otitis media, Erythroderma, Hepatosplenomegaly, Eosinophilia, Diarrhea, Anorexia, Pneumonia, Recurrent abscess formation, Protracted diarrhea, Recurrent herpes, Recurrent candida infections, Recurrent pneumonia, Chronic oral candidiasis, Increased antibody level in blood, Hepatitis | Occasional phenotype(s) | | rarePhen | | Rare phenotype(s) |
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Sample Rows
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| chrom | chromStart | chromEnd | name | score | strand | thickStart | thickEnd | itemRgb | disorder | geneSymbol | geneName | ensemblID | geneType | geneLocus | assnStatus | assnType | pmid | orphaCode | omim | hgnc | inheritance | onsetList | deathList | prevalences | veryFreqPhen | freqPhen | occasPhen | rarePhen |
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| chr1 | 167430640 | 167518610 | 169160 | 0 | - | 167430640 | 167518610 | 0,146,156 | T-B+ severe combined immunodeficiency due to CD3delta/CD3epsilon/CD3zeta | CD247 | CD247 molecule | ENSG00000198821 | gene with protein product | 1q24.2 | Assessed | Disease-causing germline mutation(s) in | | 169160 | 186780 | 1677 | Autosomal recessive | Infancy | infantile | | | Lymphopenia, ... | Otitis media, ... | |
| chr1 | 167430640 | 167518610 | 85408 | 0 | - | 167430640 | 167518610 | 0,146,156 | Rheumatoid factor-negative polyarticular juvenile idiopathic arthritis | CD247 | CD247 molecule | ENSG00000198821 | gene with protein product | 1q24.2 | Assessed | Major susceptibility factor in | 22294642 | 85408 | 186780 | 1677 | Multigenic/multifactorial | Childhood | normal life expectancy | Point prevalence | | Arthritis, ... | Uveitis, ... | Iridocyclitis, ... |
| chr1 | 167430640 | 167518610 | 85410 | 0 | - | 167430640 | 167518610 | 0,146,156 | Oligoarticular juvenile idiopathic arthritis | CD247 | CD247 molecule | ENSG00000198821 | gene with protein product | 1q24.2 | Assessed | Major susceptibility factor in | 22294642 | 85410 | 186780 | 1677 | Multigenic/multifactorial | Childhood | normal life expectancy | Point prevalence | | Uveitis, ... | Visual loss, ... | Glaucoma, ... |
| chr1 | 167809388 | 167914215 | 2197 | 0 | - | 167809388 | 167914215 | 0,146,156 | Idiopathic hypercalciuria | ADCY10 | adenylate cyclase 10 | ENSG00000143199 | gene with protein product | 1q24.2 | Assessed | Disease-causing germline mutation(s) in | 11932268 | 2197 | 605205 | 21285 | Autosomal dominant | | | | | Osteopenia, ... | Osteoporosis | |
| chr1 | 168079543 | 168137667 | 95496 | 0 | - | 168079543 | 168137667 | 0,146,156 | Pituitary stalk interruption syndrome | GPR161 | G protein-coupled receptor 161 | ENSG00000143147 | gene with protein product | 1q24.2 | Assessed | Disease-causing germline mutation(s) in | 25322266 | 95496 | 612250 | 23694 | Autosomal dominant, Autosomal recessive, Not applicable | Childhood | early childhood | Point prevalence | | Hypothyroidism, ... | Cryptorchidism, ... | |
| chr1 | 168281040 | 168314426 | 199296 | 0 | + | 168281040 | 168314426 | 0,146,156 | Congenital isolated ACTH deficiency | TBX19 | T-box transcription factor 19 | ENSG00000143178 | gene with protein product | 1q24.2 | Assessed | Disease-causing germline mutation(s) in | 15476446,15613420 | 199296 | 604614 | 11596 | Autosomal recessive | Neonatal | infantile | | | Hypoglycemic seizures, ... | Hepatitis | |
| chr1 | 169132531 | 169367967 | 101063 | 0 | - | 169132531 | 169367967 | 0,146,156 | Situs inversus totalis | NME7 | NME/NM23 family member 7 | ENSG00000143156 | gene with protein product | 1q24.2 | Assessed | Disease-causing germline mutation(s) in | 27060491 | 101063 | 613465 | 20461 | Autosomal dominant, Autosomal recessive, Not applicable | | | | | | | |
| chr1 | 169463909 | 169486003 | 49827 | 0 | - | 169463909 | 169486003 | 0,146,156 | Thiamine-responsive megaloblastic anemia syndrome | SLC19A2 | solute carrier family 19 member 2 | ENSG00000117479 | gene with protein product | 1q24.2 | Assessed | Disease-causing germline mutation(s) in | | 49827 | 603941 | 10938 | Autosomal recessive | Childhood | any age | Cases/families, Point prevalence | | Optic atrophy, ... | Retinal dystrophy, ... | |
| chr1 | 169514166 | 169586588 | 131 | 0 | - | 169514166 | 169586588 | 0,146,156 | Budd-Chiari syndrome | F5 | coagulation factor V | ENSG00000198734 | gene with protein product | 1q24.2 | Not yet assessed | Candidate gene tested in | 24755609,26238013 | 131 | 612309 | 3542 | Multigenic/multifactorial | All ages | any age | Point prevalence, Annual incidence | | Cirrhosis, ... | Jaundice, ... | |
| chr1 | 169514166 | 169586588 | 326 | 0 | - | 169514166 | 169586588 | 0,146,156 | Congenital factor V deficiency | F5 | coagulation factor V | ENSG00000198734 | gene with protein product | 1q24.2 | Assessed | Disease-causing germline mutation(s) in | | 326 | 612309 | 3542 | Autosomal recessive | All ages | normal life expectancy | Point prevalence | | Epistaxis, ... | Menorrhagia, ... | Hemoptysis, ... |
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Orphanet (orphadata) Track Description
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Description
NOTE:
These data are for research purposes only. While the Orphadata data is open to the public,
users seeking information about a personal medical or genetic condition are urged to consult with
a qualified physician for diagnosis and for answers to personal medical questions.
UCSC presents these data for use by qualified professionals, and even such professionals
should use caution in interpreting the significance of information found here. No single data point
should be taken at face value and such data should always be used in conjunction with as much
corroborating data as possible. No treatment protocols should be developed or patient advice given
on the basis of these data without careful consideration of all possible sources of information.
No attempt to identify individual patients should be undertaken. No one is authorized to
attempt to identify patients by any means.
The Orphadata: Aggregated data from Orphanet (Orphanet) track shows genomic positions
of genes and their association to human disorders, related epidemiological data, and phenotypic
annotations. As a consortium of 40 countries throughout the world,
Orphanet
gathers and improves knowledge regarding rare diseases and maintains the Orphanet rare disease
nomenclature (ORPHAcode), essential in improving the visibility of rare diseases in health and
research information systems. The data is updated monthly by Orphanet and updated monthly
on the UCSC Genome Browser.
Display Conventions
Mouseover on items shows the gene name, disorder name, modes of inheritance(s) (if available),
and age(s) of onset (if available). Tracks can be filtered according to gene-disorder association
types, modes of inheritance, and ages of onset. Clicking an item from the browser will return
the complete entry, including gene linkouts to Ensembl, OMIM, and HGNC, as well as phenotype information
using HPO (human phenotype ontology) terms.
For more information on the use of this data, see
the Orphadata FAQs.
Data Access
The raw data can be explored interactively with the Table Browser,
or the Data Integrator.
For automated analysis, the data may be queried from our REST API.
Please refer to our mailing list archives
for questions, or our Data Access FAQ
for more information.
Data is also freely available through
Orphadata datasets.
Methods
Orphadata files were reformatted at UCSC to the
bigBed format.
Credits
Thank you to the Orphanet and Orphadata team and to Tiana Pereira, Christopher Lee,
Daniel Schmelter, and Anna Benet-Pages of the Genome Browser team.
References
Pavan S, Rommel K, Mateo Marquina ME, Höhn S, Lanneau V, Rath A.
Clinical Practice Guidelines for Rare Diseases: The Orphanet Database.
PLoS One. 2017;12(1):e0170365.
PMID: 28099516; PMC: PMC5242437
Nguengang Wakap S, Lambert DM, Olry A, Rodwell C, Gueydan C, Lanneau V, Murphy D, Le Cam Y, Rath A.
Estimating cumulative point prevalence of rare diseases: analysis of the Orphanet database.
Eur J Hum Genet. 2020 Feb;28(2):165-173.
PMID: 31527858; PMC: PMC6974615
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