Schema for PanelApp - Genomics England PanelApp Diagnostics
  Database: hg38    Primary Table: panelAppGenes Data last updated: 2024-04-16
Big Bed File Download: /gbdb/hg38/panelApp/genes.bb
Item Count: 33,675
The data is stored in the binary BigBed format.

Format description: Panel App Genes with color and attributes
fieldexampledescription
chromchr1Reference sequence chromosome or scaffold
chromStart167430640Start position of feature on chromosome
chromEnd167518610End position of feature on chromosome
nameCD247 (COVID-19 research)Name of gene
score0Score
strand.+ or - for strand
thickStart167430640Coding region start
thickEnd167518610Coding region end
itemRgb0,255,0Color based on confidence level
blockCount1Number of gene entry
blockSizes87970Size of gene
blockStarts0Block begins at first chromStart
geneSymbolCD247Gene Symbol
biotypeProtein CodingBiotype
hgncID1677hgnc ID
geneNameCd247 MoleculeGene Name
omimGene186780Reference to OMIM Gene
ensemblGenesENSG00000198821Ensembl Gene ID
entityTypeGeneEntity Type
entityNameCD247Entity Name
confidenceLevel3Confidence Level
penetrancePenetrance
modeOfPanthogenicityMode of Pathogenicity
publicationsPMID26690594, PMID17170122, PMID16672702, PMID25688246, PMID27555457, https://doi.org/10.14785/lpsn-2014-0012Publications
evidenceExpert Review Green IUIS Classification February 2018 SCID v1.6 GOSH PID v.8.0 GRID V2.0 Victorian Clinical Genetics Services ESID Registry 20171117 IUIS Classification February 2018 Victorian Clinical Genetics Services ESID Registry 20171117 GRID V2.0 GOSH PID v.8.0 SCID v1.6Evidence
phenotypes?Immunodeficiency 25 T-B+ severe combined immunodeficiency due to CD3zeta Immunodeficiency 25, 610163 Nl NK, no g/d T cells Atypical Severe Combined Immunodeficiency (Atypical SCID) Immunodeficiencies affecting cellular and humoral immunity T-B+ SCID Severe combined immunodeficiency (SCID)Phenotypes
modeOfInheritanceBIALLELIC, autosomal or pseudoautosomalMode of Inheritance
tagsTags
panelID111Panel ID
panelNameCOVID-19 researchPanel Name
diseaseGroupViral researchDisease Group
diseaseSubgroupDisease Subgroup
statuspublicStatus
panelVersion1.141Panel Version
versionCreated2024-01-04T14:08:43.065350ZDate of Creation
relevantDisordersViral susceptibilityRelevant Disorders
mouseOverFieldGene: CD247; Panel: COVID-19 research; MOI: BIALLELIC, autosomal or pseudoautosomal; Phenotypes: ?Immunodeficiency 25 T-B+ severe combined immunodeficiency due to CD3zeta Immunodeficiency 25, 610163 Nl NK, no g/d T cells Atypical Severe Combined Immunodeficiency (Atypical SCID) Immunodeficiencies affecting cellular and humoral immunity T-B+ SCID Severe combined immunodeficiency (SCID); Confidence: 3;Mouse over field displaying gene symbol, Inheritance, Phenotypes, Confidence Level

Sample Rows
 
chromchromStartchromEndnamescorestrandthickStartthickEnditemRgbblockCountblockSizesblockStartsgeneSymbolbiotypehgncIDgeneNameomimGeneensemblGenesentityTypeentityNameconfidenceLevelpenetrancemodeOfPanthogenicitypublicationsevidencephenotypesmodeOfInheritancetagspanelIDpanelNamediseaseGroupdiseaseSubgroupstatuspanelVersionversionCreatedrelevantDisordersmouseOverField
chr1167430640167518610CD247 (COVID-19 research)0.1674306401675186100,255,01879700CD247Protein Coding1677Cd247 Molecule186780ENSG00000198821GeneCD2473PMID26690594, PMID17170122, PMID16672702, PMID25688246, PMID27555457, https://doi.org/10.14785/lpsn-2014-0012Expert Review Green IUIS Classification February 2018 SCID v1.6 GOSH PID v.8.0 GRID V2.0 Victorian Clinical Genetics Services ES ...?Immunodeficiency 25 T-B+ severe combined immunodeficiency due to CD3zeta Immunodeficiency 25, 610163 Nl NK, no g/d T cells Atyp ...BIALLELIC, autosomal or pseudoautosomal111COVID-19 researchViral researchpublic1.1412024-01-04T14:08:43.065350ZViral susceptibilityGene: CD247; Panel: COVID-19 research; MOI: BIALLELIC, autosomal or pseudoautosomal; Phenotypes: ?Immunodeficiency 25 T-B+ sever ...
chr1167430640167518610CD247 (Primary immunodeficiency or monogenic inflammatory bowel disease)0.1674306401675186100,255,01879700CD247Protein Coding1677Cd247 Molecule186780ENSG00000198821GeneCD2473PMID26690594, PMID26542031, PMID17170122, PMID27555457, PMID25688246, PMID16672702, https://doi.org/10.14785/lpsn-2014-0012Expert Review Green Other IUIS Classification February 2018 Victorian Clinical Genetics Services ESID Registry 20171117 GRID V2. ...T-B+ severe combined immunodeficiency due to CD3zeta ?Immunodeficiency 25 T-B+ SCID Immunodeficiency 25, 610163 Atypical Severe ...BIALLELIC, autosomal or pseudoautosomal398Primary immunodeficiency or monogenic inflammatory bowel diseasepublic4.1992024-04-16T14:37:43.360609ZPrimary immunodeficiency disorders A- or hypo-gammaglobulinaemia Congenital neutropaenia Agranulocytosis Combined B and T cell d ...Gene: CD247; Panel: Primary immunodeficiency or monogenic inflammatory bowel disease; MOI: BIALLELIC, autosomal or pseudoautosom ...
chr1167430640167518610CD247 (Severe Paediatric Disorders)0.1674306401675186100,255,01879700CD247Protein Coding1677Cd247 Molecule186780ENSG00000198821GeneCD2473PMID30847515Next Generation Children Project Expert Review Green Expert listImmunodeficiency 25, 610163BIALLELIC, autosomal or pseudoautosomal921Severe Paediatric Disorderspublic1.1842024-04-09T15:06:23.215649ZGene: CD247; Panel: Severe Paediatric Disorders; MOI: BIALLELIC, autosomal or pseudoautosomal; Phenotypes: Immunodeficiency 25, ...
chr1167630093167706249RCSD1 (Non-syndromic familial congenital anorectal malformations)0.167630093167706249255,0,01761560RCSD1Protein Coding28310Rcsd Domain Containing 1610579ENSG00000198771GeneRCSD11PMID23936318Literatureanorectal malformation253Non-syndromic familial congenital anorectal malformationsGastroenterological disordersGastrointestinal disorderspublic1.92024-03-26T14:53:37.550551ZGene: RCSD1; Panel: Non-syndromic familial congenital anorectal malformations; MOI: ; Phenotypes: anorectal malformation; Confid ...
chr1167809388167914215ADCY10 (Nephrocalcinosis or nephrolithiasis)0.167809388167914215255,0,011048270ADCY10Protein Coding21285Adenylate Cyclase 10605205ENSG00000143199GeneADCY101CompletePMID: 24907563 (review)Expert Review Red ExpertMONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown149Nephrocalcinosis or nephrolithiasisRenal and urinary tract disordersDisorders of functionpublic4.132024-02-13T16:40:27.008021ZRenal tract calcification (or Nephrolithiasis or nephrocalcinosis) Renal tract calcification (or Nephrolithiasis/nephrocalcinosi ...Gene: ADCY10; Panel: Nephrocalcinosis or nephrolithiasis; MOI: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unkno ...
chr1167916729167937040MPC2 (Fetal anomalies)0.167916729167937040255,191,01203110MPC2Protein Coding24515Mitochondrial Pyruvate Carrier 2614737ENSG00000143158GeneMPC22PMID36417180Expert Review AmberMitochondrial pyruvate carrier deficiencyBIALLELIC, autosomal or pseudoautosomal478Fetal anomaliespublic3.1542024-04-16T14:23:17.772921ZR21 Fetal anomalies with a likely genetic cause Fetal anomalies with a likely genetic cause - non urgent R412Gene: MPC2; Panel: Fetal anomalies; MOI: BIALLELIC, autosomal or pseudoautosomal; Phenotypes: Mitochondrial pyruvate carrier def ...
chr1167916729167937040MPC2 (DDG2P)0.167916729167937040255,0,01203110MPC2Protein Coding24515Mitochondrial Pyruvate Carrier 2614737ENSG00000143158GeneMPC21OtherPMID36417180Expert Review Red DD-Gene2PhenotypeMPC2-related metabolic disorderBIALLELIC, autosomal or pseudoautosomal484DDG2Ppublic3.872024-04-09T15:05:58.092503ZGene: MPC2; Panel: DDG2P; MOI: BIALLELIC, autosomal or pseudoautosomal; Phenotypes: MPC2-related metabolic disorder; Confidence: ...
chr1168079543168137667GPR161 (IUGR and IGF abnormalities)0.168079543168137667255,0,01581240GPR161Protein Coding23694G Protein-Coupled Receptor 161612250ENSG00000143147GeneGPR1611CompletePMID25322266Expert Review Red Literature Expert ReviewShort stature with hypopituitarism, intellectual disability, sparse or absent hair in the frontal area, hypotelorism, broad nasa ...BIALLELIC, autosomal or pseudoautosomal131IUGR and IGF abnormalitiesEndocrine disordersGrowth hormone disorderspublic1.592024-04-09T15:06:23.972112ZGene: GPR161; Panel: IUGR and IGF abnormalities; MOI: BIALLELIC, autosomal or pseudoautosomal; Phenotypes: Short stature with hy ...
chr1168079543168137667GPR161 (Childhood solid tumours)0.1680795431681376670,255,01581240GPR161Protein Coding23694G Protein-Coupled Receptor 161612250ENSG00000143147GeneGPR1613PMID29386106, PMID31609649Expert Review Green Literature{Medulloblastoma predisposition syndrome}, OMIM:155255MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown243Childhood solid tumoursTumour syndromesChildhood Tumourspublic4.182024-04-11T12:52:20.613240ZPaediatric congenital malformation-dysmorphism-tumour syndrome Paediatric congenital malformation-dysmorphism-tumour syndromes P ...Gene: GPR161; Panel: Childhood solid tumours; MOI: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown; Phenotyp ...
chr1168079543168137667GPR161 (Pituitary hormone deficiency)0.168079543168137667255,0,01581240GPR161Protein Coding23694G Protein-Coupled Receptor 161612250ENSG00000143147GeneGPR1611PMID25322266Literaturepituitary stalk interruption syndrome, MONDO:0019828BIALLELIC, autosomal or pseudoautosomal483Pituitary hormone deficiencypublic3.112024-03-20T12:08:48.832600ZR159Gene: GPR161; Panel: Pituitary hormone deficiency; MOI: BIALLELIC, autosomal or pseudoautosomal; Phenotypes: pituitary stalk int ...

PanelApp (panelApp) Track Description
 

Description

The Genomics England PanelApp tracks show gene panels that are related to human disorders. Originally developed to aid interpretation of participant genomes in the 100,000 Genomes Project, PanelApp is now also being used as the platform for achieving consensus on gene panels in the NHS Genomic Medicine Service (GMS). As panels in PanelApp are publicly available, they can also be used by other groups and projects. Panels are maintained and updated by Genomics England curators.

Genes and genomic entities (short tandem repeats/STRs and copy number variants/CNVs) have been reviewed by experts to enable a community consensus to be reached on which genes and genomic entities should appear on a diagnostics grade panel for each disorder. A rating system (confidence level 0 - 3) is used to classify the level of evidence supporting association with phenotypes covered by the gene panel in question.

The available data tracks are:

  • Genomics England PanelApp Genes (PanelApp Genes):
    shows genes with evidence supporting a gene-disease relationship.

    NOTE: Due to a bug in the PanelApp gene API, between 5 and 20% of gene entries are missing as of 11/2/22.


  • Genomics England PanelApp STRs (PanelApp STRs):
    shows short tandem repeats that can be disease-causing when a particular number of repeats is present.

  • Only on hg38: Genomics England PanelApp Regions (PanelApp CNV Regions):
    shows copy-number variants (region-loss and region-gain) with evidence supporting a gene-disease relationship.

Display Conventions

The individual tracks are colored by confidence level:

  • Score 3 (lime green) - High level of evidence for this gene-disease association. Demonstrates confidence that this gene should be used for genome interpretation.
  • Score 2 (amber) - Moderate evidence for this gene-disease association. This gene should not be used for genomic interpretation.
  • Score 0 or 1 (red) - Not enough evidence for this gene-disease association. This gene should not be used for genomic interpretation.

Mouseover on items shows the gene name, panel associated, mode of inheritance (if known), phenotypes related to the gene, and confidence level. Tracks can be filtered according to the confidence level of disease association evidence. For more information on the use of this data, see the PanelApp 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.

For automated download and analysis, the genome annotation is stored in a bigBed file that can be downloaded from our download server. The files for this track are called genes.bb, tandRep.bb and cnv.bb. Individual regions or the whole genome annotation can be obtained using our tool bigBedToBed which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tool can also be used to obtain only features within a given range, e.g. bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg38/panelApp/genes.bb -chrom=chr21 -start=0 -end=100000000 stdout

Please refer to our mailing list archives for questions, or our Data Access FAQ for more information.

Data is also freely available on the PanelApp API.

Updates and archiving of old releases

This track is updated automatically every week. If you need to access older releases of the data, you can download them from our archive directory on the download server. To load them into the browser, select a week on the archive directory, copy the link to a file, go to My Data > Custom Tracks, click "Add custom track", paste the link into the box and click "Submit".

Methods

PanelApp files were reformatted at UCSC to the bigBed format. The script that updates the track is called updatePanelApp and can be found in our Github repository.

Credits

Thank you to Genomics England PanelApp, especially Catherine Snow for technical coordination and consultation. Thank you to Beagan Nguy, Christopher Lee, Daniel Schmelter, Ana Benet-Pagès and Maximilian Haeussler of the Genome Browser team for the creation of the tracks.

Reference

Martin AR, Williams E, Foulger RE, Leigh S, Daugherty LC, Niblock O, Leong IUS, Smith KR, Gerasimenko O, Haraldsdottir E et al. PanelApp crowdsources expert knowledge to establish consensus diagnostic gene panels. Nat Genet. 2019 Nov;51(11):1560-1565. PMID: 31676867