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Medical Genetics Resources

Names of Genes & Variants

Genes: There are species-specific rules about naming genes. As this guide is about human genes, naming rules are determined by the HUGO Gene Nomenclature Committee (HGNC). The approved name and gene symbol can be located using the HGNC site (linked to below). The simplest search involves locating the approved gene symbol and searching with that. For a comprehensive search for a gene, you will need to identify synonyms and identifiers from other systems (e.g. the NCBI accession ID).

If you are publishing or otherwise reporting on a human gene, it is recommended that you use the HGNC approved gene symbol. Some journals include this requirement in their instructions to authors. More information about using and obtaining HGNC approved symbols can be found here.

Variants: The Human Genome Variation Society (HGVS) provides detailed recommendations for the unambiguous naming of sequence variants. HGVS notation includes a reference sequence, type of reference sequence (DNA, RNA, protein...), residue number, and type of variation (substitution, deletion, duplication...). The same variant can be named in various ways depending on the reference sequence selected. For example, allele 17, the "ultra-rapid metabolizer," of the CYP2C19 gene may be named: 

 Additional Resources:

  • NG_008384.2:g.4195C>A
  • NM_000769.2:c.-806C>A
  • NC_000010.11:g.94761900C>A (GRCh38)
  • NC_000010.10:g.96521657C>A (GRCh37)

 You may also see the allele name used, CYP2C19*17, or the rs number from dbSNP, rs12248560.

Aggregators

The following resources are aggregators of information about genes and conditions. They’re secondary sources that often provide a great deal of background information as well as links out to literature and molecular data.

In general these resources are organized by phenotype and genotype. You can look up a phenotype or condition and find a list of genes associated with it. Or, vice versa, you can search for a gene symbol and find a list of conditions or phenotypes. MedGen and ClinVar work together this way. MedGen is more focused on phenotype-centric information with links out to ClinVar for detail about the evidence behind clinical assertions about variants.

Using PubMed to Find Gene Information

For many genes, the gene sensor in PubMed will detect when the gene symbol is searched and provide links to records in the Gene database for humans and other organisms where further information about phenotypes, pathways, and other resources can be found. The gene sensor may also return a link to a curated list of articles on the gene's function and to available genetic tests.

Genetic Testing Resources

The following resources have been developed to help clinicians and genetic counselors locate genetic tests, testing laboratories and genetic clinics. 

Other resources: Drugs & Public Health

Much information about how genetic variation impacts health is available in other resources referenced in this guide. The following are specifically focused on the topic of drug response and public health.

Feedback

If you have any questions about this guide or suggestions for edits or additions, please get in touch at the contact information above or send an email.