Schema for Orphanet - Orphadata: Aggregated Data From Orphanet
  Database: hg19    Primary Table: orphadata Data last updated: 2021-11-04
Big Bed File: /gbdb/hg19/bbi/orphanet/orphadata.bb
Item Count: 7,913
Format description: Aggregated Phenotype, Epidemiological, and Rare Disease Gene Relationships from Orphanet
fieldexampledescription
chromchr1Reference sequence chromosome or scaffold
chromStart167399877Start position of feature on chromosome
chromEnd167487847End position of feataure on chromosome
name169160Name of disorder
score0Score
strand-Strand
thickStart167399877Coding region start
thickEnd167487847Coding region end
itemRgb0,146,156Color
disorderT-B+ severe combined immunodeficiency due to CD3delta/CD3epsilon/CD3zetaName of disorder
geneSymbolCD247Gene symbol
geneNameCD247 moleculeGene name
ensemblIDENSG00000198821Ensembl ID
geneTypegene with protein productGene type
geneLocus1q24.2Gene locus
assnStatusAssessedAssociation status
assnTypeDisease-causing germline mutation(s) inAssociation type
pmidPMID(s)
orphaCode169160OrphaCode
omim186780OMIM ID
hgnc1677HGNC ID
inheritanceAutosomal recessiveInheritance(s)
onsetListInfancyOnset list
deathListinfantileDeath list
prevalencesPrevalence(s)
veryFreqPhenVery frequent phenotype(s)
freqPhenLymphopenia, 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 cellsFrequent phenotype(s)
occasPhenOtitis 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, HepatitisOccasional phenotype(s)
rarePhenRare phenotype(s)

Sample Rows
 
chromchromStartchromEndnamescorestrandthickStartthickEnditemRgbdisordergeneSymbolgeneNameensemblIDgeneTypegeneLocusassnStatusassnTypepmidorphaCodeomimhgncinheritanceonsetListdeathListprevalencesveryFreqPhenfreqPhenoccasPhenrarePhen
chr11673998771674878471691600-1673998771674878470,146,156T-B+ severe combined immunodeficiency due to CD3delta/CD3epsilon/CD3zetaCD247CD247 moleculeENSG00000198821gene with protein product1q24.2AssessedDisease-causing germline mutation(s) in1691601867801677Autosomal recessiveInfancyinfantileLymphopenia, ...Otitis media, ...
chr1167399877167487847854080-1673998771674878470,146,156Rheumatoid factor-negative polyarticular juvenile idiopathic arthritisCD247CD247 moleculeENSG00000198821gene with protein product1q24.2AssessedMajor susceptibility factor in22294642854081867801677Multigenic/multifactorialChildhoodnormal life expectancyPoint prevalenceArthritis, ...Uveitis, ...Iridocyclitis, ...
chr1167399877167487847854100-1673998771674878470,146,156Oligoarticular juvenile idiopathic arthritisCD247CD247 moleculeENSG00000198821gene with protein product1q24.2AssessedMajor susceptibility factor in22294642854101867801677Multigenic/multifactorialChildhoodnormal life expectancyPoint prevalenceUveitis, ...Visual loss, ...Glaucoma, ...
chr116777862516788345321970-1677786251678834530,146,156Idiopathic hypercalciuriaADCY10adenylate cyclase 10ENSG00000143199gene with protein product1q24.2AssessedDisease-causing germline mutation(s) in11932268219760520521285Autosomal dominantOsteopenia, ...Osteoporosis
chr1168054516168106821954960-1680545161681068210,146,156Pituitary stalk interruption syndromeGPR161G protein-coupled receptor 161ENSG00000143147gene with protein product1q24.2AssessedDisease-causing germline mutation(s) in253222669549661225023694Autosomal dominant, Autosomal recessive, Not applicableChildhoodearly childhoodPoint prevalenceHypothyroidism, ...Cryptorchidism, ...
chr11682502781682836641992960+1682502781682836640,146,156Congenital isolated ACTH deficiencyTBX19T-box transcription factor 19ENSG00000143178gene with protein product1q24.2AssessedDisease-causing germline mutation(s) in15476446,1561342019929660461411596Autosomal recessiveNeonatalinfantileHypoglycemic seizures, ...Hepatitis
chr11691017691693372051010630-1691017691693372050,146,156Situs inversus totalisNME7NME/NM23 family member 7ENSG00000143156gene with protein product1q24.2AssessedDisease-causing germline mutation(s) in2706049110106361346520461Autosomal dominant, Autosomal recessive, Not applicable
chr1169433147169455241498270-1694331471694552410,146,156Thiamine-responsive megaloblastic anemia syndromeSLC19A2solute carrier family 19 member 2ENSG00000117479gene with protein product1q24.2AssessedDisease-causing germline mutation(s) in4982760394110938Autosomal recessiveChildhoodany ageCases/families, Point prevalenceOptic atrophy, ...Retinal dystrophy, ...
chr11694834041695558261310-1694834041695558260,146,156Budd-Chiari syndromeF5coagulation factor VENSG00000198734gene with protein product1q24.2Not yet assessedCandidate gene tested in24755609,262380131316123093542Multigenic/multifactorialAll agesany agePoint prevalence, Annual incidenceCirrhosis, ...Jaundice, ...
chr11694834041695558263260-1694834041695558260,146,156Congenital factor V deficiencyF5coagulation factor VENSG00000198734gene with protein product1q24.2AssessedDisease-causing germline mutation(s) in3266123093542Autosomal recessiveAll agesnormal life expectancyPoint prevalenceEpistaxis, ...Menorrhagia, ...Hemoptysis, ...

Orphanet (orphadata) Track Description
 

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