- Organ Systems Genetic Conditions
- Clinical Genomic Database
- Clinical Conditions With Genetic Causes
- Genetic Correlation
- Genetic Association
- Genetic Diseases
- Gene Syndrome
- Genetic Association
- Organ Systems
- Disease Interventions
- Disease Manifestation
Gene Alteration Clinical Condition And Intervention
The Clinical Genomic Database (CGD) purpose is to correlate genetic data with clinical settings, matching diseases with their genetic cause. The database includes all diseases with a known genetic cause of a single gene alteration. The dataset includes descriptions for the gene and inheritance, as well as for the manifestations and interventions to consider. The dataset does not contain contiguous gene syndromes or somatic alterations unless these result from a same gene germline change.
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“The Clinical Genomic Database (CGD) has been constructed to reflect the multisystemic nature of many genetic conditions in order to allow more comprehensive browsing by clinical categories. In the CGD, genes were first categorized into Manifestation categories, or the organ system(s) primarily affected by mutations in the corresponding gene. For many of these organ systems, recognition of the condition’s effects and related supportive care may be clinically beneficial. Conditions not grouped within a specific organ system under the Manifestation categories were included in the General category.
Next, genes were separately categorized under Intervention categories by the organ system(s) for which specific medical interventions were available. In determining the Intervention categories, the following points were considered: 1) the condition must be clinically significant (i.e., at least some manifestations must result in morbidity and mortality); 2) there must be a currently available, potentially beneficial intervention (this intervention may include preventive measures, surveillance, or medical and/or surgical treatments, though experimental/research-based interventions were not included); 3) there should be advantage to early (“genomic”) diagnosis as opposed to discovery of the condition on purely clinical grounds (i.e., without genetic/genomic testing). Regarding this last point, precise diagnosis is challenging for many conditions, and correct recognition based on genetic/genomic diagnosis may allow interventions related to specific manifestations. The efficacy of these interventions would be diminished or lost with later diagnosis, such as might occur based primarily upon clinical presentation.
For the Intervention categories, all genes not meeting the above criteria were included in the General category. As described, for many such conditions, while a more specific intervention may not be currently available, genetic knowledge may be beneficial related to a number of issues, including the selection of optimal supportive care, prognostic considerations related to medical-decision making, informing reproductive decisions, and avoidance of unnecessary testing as part of the diagnostic process.
A key barrier to translating the power of genomic sequencing to the clinical setting involves the time and resources required for clinically-relevant analysis. To help address this barrier, we constructed the Clinical Genomic Database (CGD), a manually curated database of conditions with known genetic causes, focusing on medically significant genetic data with available interventions.
All conditions with identified genetic causes are included in the CGD. For each entry, the database includes the gene symbol, condition(s), allelic conditions, inheritance, age (pediatric or adult) in which interventions are indicated, clinical categorization, and a general description of interventions/rationale. The contents are not intended to serve as nor substitute for comprehensive clinical guidelines, but are rather intended to briefly describe the types of interventions that might be considered.
The database includes only single gene alterations (it does not include contiguous gene syndromes, although some conditions with, for example, digenic inheritance are included), and does not include genetic associations or susceptibility factors related to more complex diseases, such as identified through association-based studies. Somatic alterations, such as commonly occur in cancerous processes, are not included unless a germline change in the same gene results in disease.”
Description source: National Human Genome Research Institute, N.H.G.R.I. (2016). NIH.gov. Retrieved 12 November, 2016.
About this Dataset
John Snow Labs; National Human Genome Research Institute;
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Genetic Correlation, Genetic Association, Genetic Diseases, Gene Syndrome, Genetic Association, Organ Systems, Genomics, Disease Interventions, Disease Manifestation
Organ Systems Genetic Conditions, Clinical Genomic Database, Clinical Conditions With Genetic Causes
|Gene||Symbol of the gene associated with a clinical condition||string||required : 1unique : 1|
|HGNC_ID||Identification number of the gene given by HUGO Gene Nomenclature Committee (HGNC)||integer||level : Nominalrequired : 1unique : 1|
|Entrez_Gene_ID||A unique integer identifier or ID assigned by Entrez Gene which is the gene-specific database at the National Center for Biotechnology Information (NCBI), a division of the National Library of Medicine (NLM).||integer||level : Nominalrequired : 1unique : 1|
|Condition||Conditions with known genetic causes||string||required : 1|
|Inheritance||Type of genetic transmission of traits from parents to offspring. Types are: AR means autosomal recessive, AD means autosomal dominant, XL means sex linked, Digenic, methylation, BG means Blood group related||string||required : 1|
|Age_Group||Age (pediatric or adult) in which interventions are indicated||string||-|
|Allelic_Conditions||Conditions also resulting from mutations in the same gene, but which would otherwise be categorized in the "general" category for intervention categories||string||-|
|Manifestation_Categories||The organ system(s) primarily affected by mutations in the corresponding gene. For many of these organ systems, recognition of the condition's effects and related supportive care may be clinically beneficial. Conditions not grouped within a specific organ system under the Manifestation categories were included in the General category||string||required : 1|
|Intervention_Categories||The organ system(s) for which specific medical interventions were available. In determining the Intervention categories, the following points were considered: 1) the condition must be clinically significant (i.e., at least some manifestations must result in morbidity and mortality); 2) there must be a currently available, potentially beneficial intervention (this intervention may include preventive measures, surveillance, or medical and/or surgical treatments, though experimental/research-based interventions were not included); 3) there should be advantage to early (“genomic”) diagnosis as opposed to discovery of the condition on purely clinical grounds (i.e., without genetic/genomic testing). For the Intervention categories, all genes not meeting the above criteria were included in the General category.||string||required : 1|
|Comments||Some important information about the condition||string||-|
|Intervention_Or_Rationale||Significance of early intervention based on the genetic information in this particular condition||string||required : 1|
|References||Pubmed ID numbers from the NCBI website for referring the article||string||-|
|Gene||HGNC ID||Entrez Gene ID||Condition||Inheritance||Age Group||Allelic Conditions||Manifestation Categories||Intervention Categories||Comments||Intervention Or Rationale||References|
|A2M||7||2||Alpha-2-macroglobulin deficiency||AD||General||General||Variants have been implicated in pulmonary disease, but the evidence appears mixed||The clinical consequences of variants are unclear||94459; 2475424; 1370808|
|A2ML1||23336||144568||Otitis media, susceptibility to||AD||Pediatric||Allergy/Immunology/Infectious||Allergy/Immunology/Infectious||Individuals may have increased susceptibility to otitis media, and awareness may allow awareness leading to prompt diagnosis and treatment of otitis media||26121085|
|A4GALT||18149||53947||Blood group, P1PK system||BG||Pediatric||Hematologic||Hematologic||Variants associated with a blood group may be important in specific situations (eg, related to transfusion)||10993874|
|AAAS||13666||8086||Achalasia-addisonianism-alacrimia syndrome||AR||Pediatric||Dermatologic; Endocrine; Gastrointestinal; Neurologic; Ophthalmologic||Endocrine||Surveillance and treatment/preventive measures (with substitution therapy) to avoid sequelae of adrenal insufficiency, including adrenal crisis, may be beneficial||78049; 6243664; 3565479; 1537368; 8006362; 7895750; 8757578; 11062474; 11159947; 11914417; 12429595; 12752575; 16264411; 16938764; 8628786; 19172511; 18172684; 20051279; 20200814; 20499090; 20447142; 21565631|
|AAGAB||25662||79719||Keratoderma, palmoplantar, punctate type IA||AD||Dermatologic||General||Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing||23000146; 23064416|
|AARS1||20||16||Charcot-Marie-Tooth disease, axonal, type 2N; Developmental and epileptic encephalopathy 29||AD/AR||Audiologic/Otolaryngologic; Craniofacial; Dermatologic; Neurologic||General||Charcot-Marie-Tooth disease, axonal, type 2N can include hearing loss, which is described as postlingual; For epileptic encephalopathy, as with other conditions involving seizures, optimal seizure control is beneficial, and awareness of genetic causes may help with medication selection||Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing||6492094; 20045102; 22206013; 22009580; 22573628; 25817015; 33909043|
|AARS2||21022||57505||Leukoencephalopathy, progressive, with ovarian failure||AR||Pediatric||Allelic with Combined oxidative phosphorylation deficiency 8 (AR)||Biochemical; Cardiovascular; Endocrine; Musculoskeletal; Neurologic; Obstetric||Obstetric||Females may suffer from premature ovarian failure, and measures to allow reproduction (eg,through egg preservation) may be desired||21549344; 24808023; 25058219|
|AASS||17366||10157||Hyperlysinemia, type I||AR||Biochemical||General||Other than increased serum lysine, the evidence of a common phenotype is unclear, and there does not appear to be evidence that measures such as protein restriction or other metabolic treatments are effective||Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing||14209691; 5796356; 5557172; 934735; 10775527; 23570448|
|ABAT||23||18||GABA-transaminase deficiency||AR||Pediatric||Biochemical; Neurologic||Biochemical||The condition includes neonatal or early-onset neurologic sequelae, and medical management (with continuous flumazenil) has been described as beneficial in a patient with a milder phenotype||6148708; 4020531; 10407778; 27596361; 28411234|
|ABCA1||29||19||Hypoalphalipoproteinemia, primary, 1; Tangier disease||AD/AR||Pediatric||Cardiovascular; Neurologic; Ophthalmologic||Cardiovascular||Early cardiovascular events are common (eg, myocardial infarctions due to atherosclerosis), and while specific medical therapy is not currently available, preventive measures to decrease additional contributory atherosclerotic risk factors, as well as surveillance to allow early diagnosis and treatment of cardiovascular manifestations, may be beneficial||14162531; 5831900; 4165386; 4165172; 198431; 190272; 194920; 195100; 75948; 7406376; 4082916; 3677505; 3799433; 3314502; 8432861; 7627690; 10431237; 10431236; 10525055; 9888879; 10533863; 16343506; 10535983; 10431238; 11086027; 11476965; 12084722; 12111371; 12111381; 12702168; 14742612; 16343506; 18955690; 19723515; 22179783; 22913675; 23430904|