Schema for GenCC - The Gene Curation Coalition Annotations
  Database: hg38    Primary Table: genCC Data last updated: 2022-05-24
Big Bed File: /gbdb/hg38/bbi/genCC.bb
Item Count: 16,128
Format description: Data from the Gene Curation Coalition
fieldexampledescription
chromchr1Reference sequence chromosome or scaffold
chromStart167430639Start position in chrom
chromEnd167518529End position in chrom
nameCD247 Orphanet:169160Reference SNP identifier
score0Not used
strand-Which DNA strand contains the observed alleles
thickStart167430639Same as chromStart
thickEnd167518529Same as chromEnd
itemRgb99,179,237RGB corresponding to evidence classification
ensTranscriptENST00000362089.10Ensembl transcript ID
ensGeneENSG00000198821.12Ensembl gene ID
refSeqAccessionNM_198053.3NCBI refseq accession ID
uuidGENCC_000110-HGNC_1677-Orphanet_169160-HP_0000007-GENCC_100009uuid: GenCC submission ID
gene_curieHGNC:1677Gene curie
gene_symbolCD247Gene symbol
disease_curieMONDO:0015703Disease curie
disease_titleT-B+ severe combined immunodeficiency due to CD3delta/CD3epsilon/CD3zetaDisease title
disease_original_curieOrphanet:169160Disease original curie
disease_original_titleOrphanet:169160Disease original title
classification_curieGENCC:100009Classification curie
classification_titleSupportiveClassification title
moi_curieHP:0000007MOI curie
moi_titleAutosomal recessiveMOI title
submitter_curieGENCC:000110Submitter curie
submitter_titleOrphanetSubmitter title
sub_hgnc_idHGNC:1677Submitted HGNC ID
sub_hgnc_symbolCD247Submitted HGNC symbol
sub_disease_idOrphanet:169160Submitted Disease ID
sub_disease_nameT-B+ severe combined immunodeficiency due to CD3delta/CD3epsilon/CD3zetaSubmitted Disease name
sub_moi_idHP:0000007Submitted MOI ID
sub_moi_nameAutosomal recessive inheritanceSubmitted MOI name
sub_submitter_idGENCC:000110Submitter ID
sub_submitter_nameOrphanetSubmitter name
sub_classification_idGENCC:100009Submitted class ID
sub_classification_nameSupportiveSubmitted class name
sub_date2021-09-14 00:00:00Submitted date
sub_public_report_urlSubmitted pub report URL
sub_notesSubmitted notes
sub_pmidsNULLSubmitted PMIDs
sub_assertion_criteria_urlhttps://www.orpha.net/orphacom/cahiers/docs/GB/Orphanet_Genes_inventory_R1_Ann_gen_EP_02.pdfSubmitted assertion crit URL
sub_submission_id19028Submission ID
sub_run_date2021-09-14Submitted run date

Sample Rows
 
chromchromStartchromEndnamescorestrandthickStartthickEnditemRgbensTranscriptensGenerefSeqAccessionuuidgene_curiegene_symboldisease_curiedisease_titledisease_original_curiedisease_original_titleclassification_curieclassification_titlemoi_curiemoi_titlesubmitter_curiesubmitter_titlesub_hgnc_idsub_hgnc_symbolsub_disease_idsub_disease_namesub_moi_idsub_moi_namesub_submitter_idsub_submitter_namesub_classification_idsub_classification_namesub_datesub_public_report_urlsub_notessub_pmidssub_assertion_criteria_urlsub_submission_idsub_run_date
chr1167430639167518529CD247 Orphanet:1691600-16743063916751852999,179,237ENST00000362089.10ENSG00000198821.12NM_198053.3GENCC_000110-HGNC_1677-Orphanet_169160-HP_0000007-GENCC_100009HGNC:1677CD247MONDO:0015703T-B+ severe combined immunodeficiency due to CD3delta/CD3epsilon/CD3zetaOrphanet:169160Orphanet:169160GENCC:100009SupportiveHP:0000007Autosomal recessiveGENCC:000110OrphanetHGNC:1677CD247Orphanet:169160T-B+ severe combined immunodeficiency due to CD3delta/CD3epsilon/CD3zetaHP:0000007Autosomal recessive inheritanceGENCC:000110OrphanetGENCC:100009Supportive2021-09-14 00:00:00NULLhttps://www.orpha.net/orphacom/cahiers/docs/GB/Orphanet_Genes_inventory_R1_Ann_gen_EP_02.pdf190282021-09-14
chr1167430639167518529CD247 OMIM:6101630-16743063916751852956,161,105ENST00000362089.10ENSG00000198821.12NM_198053.3GENCC_000106-HGNC_1677-OMIM_610163-HP_0000007-GENCC_100002HGNC:1677CD247MONDO:0012426immunodeficiency 25OMIM:610163?Immunodeficiency 25GENCC:100002StrongHP:0000007Autosomal recessiveGENCC:000106InvitaeHGNC:1677CD247OMIM:610163immunodeficiency 25HP:0000007Autosomal recessiveGENCC:000106INVITAEGENCC:100002STRONG2020-02-09 00:00:0017170122, 27555457, 16672702https://view.publitas.com/invitae/invitaeposter_nsgc2019_curatingthehumangenome/page/121CD2470SCID2021-05-25
chr1167430639167518529CD247 OMIM:6101630-167430639167518529252,129,129ENST00000362089.10ENSG00000198821.12NM_198053.3GENCC_000101-HGNC_1677-OMIM_610163-HP_0000007-GENCC_100004HGNC:1677CD247MONDO:0012426immunodeficiency 25OMIM:610163?Immunodeficiency 25GENCC:100004LimitedHP:0000007Autosomal recessiveGENCC:000101Ambry GeneticsHGNC:1677CD247OMIM:610163Immunodeficiency 25HP:0000007Autosomal recessive inheritanceGENCC:000101Ambry GeneticsGENCC:100004Limited2018-08-31 13:29:41PMID: 281063203832020-12-24
chr1167809385167914134ADCY10 Orphanet:21970-16780938516791413499,179,237ENST00000367851.9ENSG00000143199.18NM_018417.6GENCC_000110-HGNC_21285-Orphanet_2197-HP_0000006-GENCC_100009HGNC:21285ADCY10MONDO:0016352idiopathic inherited hypercalciuriaOrphanet:2197Orphanet:2197GENCC:100009SupportiveHP:0000006Autosomal dominantGENCC:000110OrphanetHGNC:21285ADCY10Orphanet:2197Idiopathic hypercalciuriaHP:0000006Autosomal dominant inheritanceGENCC:000110OrphanetGENCC:100009Supportive2021-09-14 00:00:0011932268[PMID]https://www.orpha.net/orphacom/cahiers/docs/GB/Orphanet_Genes_inventory_R1_Ann_gen_EP_02.pdf177382021-09-14
chr1167809385167914134ADCY10 OMIM:1438700-167809385167914134252,129,129ENST00000367851.9ENSG00000143199.18NM_018417.6GENCC_000101-HGNC_21285-OMIM_143870-HP_0000006-GENCC_100004HGNC:21285ADCY10MONDO:0007748hypercalciuria, absorptive, 2OMIM:143870{Hypercalciuria, absorptive, susceptibility to}GENCC:100004LimitedHP:0000006Autosomal dominantGENCC:000101Ambry GeneticsHGNC:21285ADCY10OMIM:143870Hypercalciuria, absorptive, susceptibility toHP:0000006Autosomal dominant inheritanceGENCC:000101Ambry GeneticsGENCC:100004Limited2018-08-31 13:29:16PMID: 28106320775882020-12-24
chr1167809385167914134ADCY10 OMIM:1438700-16780938516791413456,161,105ENST00000367851.9ENSG00000143199.18NM_018417.6GENCC_000106-HGNC_21285-OMIM_143870-HP_0000006-GENCC_100002HGNC:21285ADCY10MONDO:0007748hypercalciuria, absorptive, 2OMIM:143870{Hypercalciuria, absorptive, susceptibility to}GENCC:100002StrongHP:0000006Autosomal dominantGENCC:000106InvitaeHGNC:21285ADCY10OMIM:143870{Hypercalciuria, absorptive, susceptibility to}HP:0000006GENCC:000106INVITAEGENCC:100002STRONG2019-07-01 20:04:4431119281, 26787776, 25296721, 11932268, 27627854https://view.publitas.com/invitae/invitaeposter_nsgc2019_curatingthehumangenome/page/124ADCY100Hyperca2020-12-04
chr1168079541168136930GPR161 Orphanet:954960-16807954116813693099,179,237ENST00000682931.1ENSG00000143147.15NM_001375883.1GENCC_000110-HGNC_23694-Orphanet_95496-HP_0000006-GENCC_100009HGNC:23694GPR161MONDO:0019828pituitary stalk interruption syndromeOrphanet:95496Orphanet:95496GENCC:100009SupportiveHP:0000006Autosomal dominantGENCC:000110OrphanetHGNC:23694GPR161Orphanet:95496Pituitary stalk interruption syndromeHP:0000006Autosomal dominant inheritanceGENCC:000110OrphanetGENCC:100009Supportive2021-09-14 00:00:0025322266[PMID]https://www.orpha.net/orphacom/cahiers/docs/GB/Orphanet_Genes_inventory_R1_Ann_gen_EP_02.pdf232182021-09-14
chr1168280876168314426TBX19 Orphanet:1992960+16828087616831442699,179,237ENST00000367821.8ENSG00000143178.13NM_005149.3GENCC_000110-HGNC_11596-Orphanet_199296-HP_0000007-GENCC_100009HGNC:11596TBX19MONDO:0008720congenital isolated adrenocorticotropic hormone deficiencyOrphanet:199296Orphanet:199296GENCC:100009SupportiveHP:0000007Autosomal recessiveGENCC:000110OrphanetHGNC:11596TBX19Orphanet:199296Congenital isolated ACTH deficiencyHP:0000007Autosomal recessive inheritanceGENCC:000110OrphanetGENCC:100009Supportive2021-09-14 00:00:0015476446[PMID]_15613420[PMID]https://www.orpha.net/orphacom/cahiers/docs/GB/Orphanet_Genes_inventory_R1_Ann_gen_EP_02.pdf155852021-09-14
chr1168280876168314426TBX19 OMIM:2014000+16828087616831442656,161,105ENST00000367821.8ENSG00000143178.13NM_005149.3GENCC_000106-HGNC_11596-OMIM_201400-HP_0000007-GENCC_100002HGNC:11596TBX19MONDO:0008720congenital isolated adrenocorticotropic hormone deficiencyOMIM:201400Adrenocorticotropic hormone deficiencyGENCC:100002StrongHP:0000007Autosomal recessiveGENCC:000106InvitaeHGNC:11596TBX19OMIM:201400acth deficiency, isolatedHP:0000007Autosomal recessiveGENCC:000106INVITAEGENCC:100002STRONG2020-06-24 00:00:0027535729, 28458651, 29858850https://view.publitas.com/invitae/invitaeposter_nsgc2019_curatingthehumangenome/page/955TBX190IAD2021-05-25
chr1168280876168314426TBX19 OMIM:2014000+16828087616831442639,103,73ENST00000367821.8ENSG00000143178.13NM_005149.3GENCC_000101-HGNC_11596-OMIM_201400-HP_0000007-GENCC_100001HGNC:11596TBX19MONDO:0008720congenital isolated adrenocorticotropic hormone deficiencyOMIM:201400Adrenocorticotropic hormone deficiencyGENCC:100001DefinitiveHP:0000007Autosomal recessiveGENCC:000101Ambry GeneticsHGNC:11596TBX19OMIM:201400Adrenocorticotropic hormone deficiencyHP:0000007Autosomal recessive inheritanceGENCC:000101Ambry GeneticsGENCC:100001Definitive2020-04-27 13:32:11PMID: 2810632032372020-12-24

GenCC (genCC) Track Description
 

Description

This track shows annotations from The Gene Curation Coalition (GenCC). The GenCC provides information pertaining to the validity of gene-disease relationships, with a current focus on Mendelian diseases. Curated gene-disease relationships are submitted by GenCC member organizations that currently provide online resources (e.g. ClinGen, DECIPHER, Orphanet, etc.), as well as diagnostic laboratories that have committed to sharing their internal curated gene-level knowledge (e.g. Ambry Genetics, Illumina, Invitae, etc.).

The GenCC aims to clarify overlap between gene curation efforts and develop consistent terminology for validity, allelic requirement and mechanism of disease. Each item on this track corresponds with a gene, and contains a large number of information such as associated disease, evidence classification, specific submission notes and identifiers from different databases. In cases where multiple annotations exist for the same gene, multiple items are displayed.

Display Conventions and Configuration

Each item displayed represents a submission to the GenCC database. The displayed name is a combination of the gene symbol and the disease's original submission ID. This submission ID is either the OMIM#, MONDO# or Orphanet#. Clicking on any item will display the complete meta data for that item, including linkouts to the GenCC, NCBI, Ensembl, HGNC, GeneCards, Pombase (MONDO), and Human Phenotype Ontology (HPO). Mousing over any item will display the associated disease for that submission.

Items are colored based on the GenCC classification, or validation, of the evidence in the color scheme seen in the table below. For more information on this process, see the GenCC validity terms FAQ. A filter for the track is also available to display a subset of the items based on their classification.

Color Evidence classification
Definitive
Strong
Moderate
Supportive
Limited
Disputed Evidence
Refuted Evidence
No Known Disease Relationship

Limitations: Most entries include both NM_ accessions as well as ENST and ENSG identifiers. From the original file, which contains no coordinates, two genes were not mapped to the hg38 genome, SLCO1B7 and ATXN8. This means that the hg38 track has 2 fewer items than what can be found in the GenCC download file. For hg19, one additional gene was not mapped, KCNJ18. In addition to this, the GenCC data in the Genome Browser does not include OMIM data due to licensing restrictions. For more information, see the Methods section below.

Data Access

The source data can be explored in GenCC database. The source files can also be found on the GenCC downloads page.

The GenCC data on the UCSC Genome Browser can be explored interactively with the Table Browser or the Data Integrator. For automated download and analysis, the genome annotation is stored at UCSC in bigBed files that can be downloaded from our download server. The data may also be explored interactively using our REST API.

The file for this track may also be locally explored using our tools 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 tools can also be used to obtain features confined to a given range, e.g.,

bigBedToBed -chrom=chr1 -start=100000 -end=100500 http://hgdownload.soe.ucsc.edu/gbdb/hg38/bbi/genCC.bb stdout

Methods

The data were downloaded from the GenCC downloads page in tsv format. Manual curation was performed on the file to remove newline characters and tab characters present in the submission notes, in total fewer than 20 manual edits were made.

The track was first built on hg38 by associating the gene symbols with the NCBI MANE 1.0 release transcripts. These coordinates were added to the items as well as the NM_ accession, ENST ID and ENSG ID. For items where there was no gene symbol match in MANE (~130), the gene symbols were queried against GENCODEv40 comprehensive set release. In places where multiple transcript matches were found, the earliest transcription start and latest end site was used from among the transcripts to encompass the entire gene coordinates. Two genes were not able to be mapped for hg38, SLCO1B7 and ATXN8, resulting in two missing submissions in the Genome Browser when compared to the raw file. Lastly, the items were colored according to their evidence classification as seen on the GenCC database.

For hg19, the hg38 NM_ accessions were used to convert the item coordinates according to the latest hg19 refseq release. For items that failed to convert, the gene symbols were queried using the GENCODEv40 hg19 lift comprehensive set. One additional gene symbol failed to map in hg19, KCNJ18, leading to 3 fewer items on this track when compared to the raw file.

For both assemblies, GenCC OMIM data is excluded do to data restrictions. For complete documentation of the processing of these tracks, read the GenCC MakeDoc.

Credits

Thanks to the entire GenCC committee for creating these annotations and making them available.

References

DiStefano MT, Goehringer S, Babb L, Alkuraya FS, Amberger J, Amin M, Austin-Tse C, Balzotti M, Berg JS, Birney E et al. The Gene Curation Coalition: A global effort to harmonize gene-disease evidence resources. Genet Med. 2022 May 4;. PMID: 35507016