- 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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Solomon BD. Clinical Genomic Database. Proc Natl Acad Sci U S A. 2013 May 21.
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||unique : 1required : 1|
|HGNC_ID||Identification number of the gene given by HUGO Gene Nomenclature Committee (HGNC)||integer||unique : 1required : 1level : Nominal|
|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||unique : 1required : 1level : Nominal|
|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||required : 1|
|Gene||HGNC ID||Entrez Gene ID||Condition||Inheritance||Age Group||Allelic Conditions||Manifestation Categories||Intervention Categories||Comments||Intervention Or Rationale||References|
|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|
|ABCD4||68||5826||Methylmalonic aciduria and homocystinuria, cblJ type||AR||Pediatric||Allergy/Immunology/Infectious; Biochemical; Cardiovascular; Neurologic||Allergy/Immunology/Infectious; Biochemical; Cardiovascular||Administration of hydroxocobalamin/methylcobalamin has been described as beneficial; Due to infectious risks, administration of G-CSF has been described, and early and aggressive treatment of infections may be benefiical; Surveillance for cardiovascular manifestations may allow early management||22922874; 23141461|
|ACD||25070||65057||Dyskeratosis congenita, autosomal dominant 6; Dyskeratosis congenita, autosomal recessive 7||AD/AR||Pediatric||Allergy/Immunology/Infectious; Hematologic; Oncologic; Neurologic||Allergy/Immunology/Infectious; Hematologic; Oncologic||Surveillance (eg, with regularly performed CBC as well as other measures in the presence of concern for hematologic sequelae) for bone marrow failure, as well as surveillance for multiple cancer types (eg, with self-examination and clinical examination), and pulmonary disease may allow early detection and treatment; HSCT may be indicated due to manifestations including leukemia and bone marrow failure; Awareness of infectious risk may allow prompt diagnosis and treatment of infections||25205116; 25233904|
|ACOX1||119||51||Mitchell syndrome||AD||Pediatric||Allelic with Peroxisomal acyl-CoA oxidase deficiency (AR)||Allergy/Immunology/Infectious; Audiologic/Otolaryngologic; Biochemical; Craniofacial; Neurologic; Ophthalmologic||Allergy/Immunology/Infectious||The condition has been described as manifesting with episodic demyelination, sensorimotor polyneuropathy, and hearing loss, and early diagnosis may allow medical management (eg, immunomodulatory and related treatments have been reported to show some clinical benefits in individuals)||2894756; 8040306; 8279468; 11815777; 17458872; 18536048; 32169171|
|ACP5||124||54||Spondyloenchondrodysplasia with immune dysregulation||AR||Pediatric||Allergy/Immunology/Infectious; Endocrine; Musculoskeletal; Neurologic||Allergy/Immunology/Infectious||Clinically recognizable non-immune features may not be recognized early; The condition can affect multiple organ systems for which early knowledge of disease could be beneficial, including infectious and autoimmune sequelae||Individuals may have immune deficiency, and a variety of infections have been reported, including pneunomia, upper respiratory infections, and severe varicella infections, and thus antiinfectious prophylaxis and early and aggressive treatment of infections may be beneficial; Individuals may also have a variety of autoimmune manifestations, including hypothyroidism, and treatment may be beneficial||12786759; 17497723; 17163538; 18924170; 21217755; 21217752; 26854080; 26951490|
|ADA||186||100||Severe combined immunodeficiency due to adenosine deaminase deficiency||AR||Pediatric||Allergy/Immunology/Infectious; Oncologic||Allergy/Immunology/Infectious; Oncologic||Variants may also contribute to Partial ADA deficiency; Gene therapy may be available, though largely on an experimental basis||Enzyme treatment (with PEG-ADA) is beneficial; Antiinfectious prophylaxis and early and aggressive treatment of infections are indicated; BMT has been described in many individuals; Surveillance for certain neoplasms may be beneficial||4117384; 46025; 1089883; 978319; 18618; 980079; 477037; 38963; 7436484; 6863546; 3781559; 3946419; 3007108; 3475710; 3807953; 3260944; 2783588; 2166947; 8227344; 8099155; 8051429; 1974554; 8023852; 8120281; 9108404; 10021471; 12089448; 14499267; 16905365; 19638621; 21725047; 21865538; 22153773; 22348551; 22447032; 22791287; 22805442; 22968453; 23118212; 23895897|
|ADA2||1839||51816||Vasculitis, autoinflammation, immunodeficiency, and hematologic defects syndrome; Sneddon syndrome||AR||Pediatric||Allergy/Immunology/Infectious; Cardiovascular; Dermatologic||Allergy/Immunology/Infectious||Among other manifestations, individuals have been described as presenting with hypogammaglobulinemia, as well as recurrent bacterial and viral infections, and immunosuppressive treatment has been described as beneficial, though other manifestations have been described as recalcitrant to these types of therapies; Medical management (eg, with TNF inhibitor) has been described as beneficial.||12804991; 24552284; 24552285; 25075844; 25075847|
|ADAM17||195||6868||Inflammatory skin and bowel disease, neonatal 1||AR||Pediatric||Allergy/Immunology/Infectious; Cardiovascular; Dermatologic; Gastrointestinal||Allergy/Immunology/Infectious; Cardiovascular||Antiinfectious prophylaxis and early and aggressive treatment of infections may be beneficial; Individuals may also have cardiovascular manifestations, and surveillance may allow beneficial interventions||22010916|
|AGA||318||175||Aspartylglucosaminuria||AR||Allergy/Immunology/Infectious; Biochemical; Cardiovascular; Craniofacial; Dermatologic; Musculoskeletal; Neurologic||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||4173687; 5512217; 6796777; 6883788; 3228136; 1904874; 1722323; 1703489; 1765378; 1756604; 1301945; 8405810; 8064811; 9427148; 9627765; 10353787; 11174635; 11796409; 12022293; 12366426; 15127757; 16218917; 23271757|
|AGMX2||323||179||Agammaglobulinemia, X-linked 2||XL||Pediatric||Allergy/Immunology/Infectious||Allergy/Immunology/Infectious||Individuals have been described with early-onset, severe infections, and awareness may allow preventative measures and early and aggressive treatment of infections may be beneficial||29636373|