HGMD

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This annotation reports diseases associated with genetic variants curated from the professional version of HGMD:

  • HGMD_MutationCategory The classification of the association:
    • Disease-associated polymorphism (DP) - A polymorphism reported to be in significant association with a disease/phenotype (p<0.05) that is assumed to be functional (e.g. as a consequence of location, evolutionary conservation, replication studies etc), although there may as yet be no direct evidence (e.g. from an expression study) of a functional effect.
    • Disease-associated polymorphism with additional supporting functional evidence (DFP) - A polymorphism reported to be in significant association with disease (p<0.05) that has evidence of being of direct functional importance (e.g. as a consequence of altered expression, mRNA studies etc).
    • In vitro/laboratory or in vivo functional polymorphism (FP) - A polymorphism reported to affect the structure, function or expression of the gene (or gene product), but with no disease association reported as yet.
    • Frameshift or truncating variant (FTV) - A polymorphic or rare variant reported in the literature (e.g. detected in the process of whole genome/exome screening) that is predicted to truncate or otherwise alter the gene product (i.e. a nonsense or frameshift variant) but with no disease association reported as yet. Please note that any variant affecting the obligate donor/acceptor splice site of a gene will not be included in this category unless there is evidence for an effect on the splicing phenotype. Variants occurring in pseudogenes will also be excluded unless evidence for a functional effect is present for both the pseudogene itself and the variant in question.
    • Disease causing mutation ? (DM?) - Likely pathological mutation reported to be disease causing in the corresponding report, but where the author has indicated that there may be some degree of doubt, or subsequent evidence has come to light in the literature, calling the deleterious nature of the variant into question. De novo mutations identified as part of a large-scale mutation screen for such variants in patients with disorders such as autism, schizophrenia and intellectual disability will be entered under the DM? category unless there is cogent evidence to support their inclusion as DMs. All likely disruptive sequence changes identified in cases (not controls, or unaffected siblings in parent-offspring groups) will be entered. Such variants will include single base substitutions causing missense, nonsense or canonical splice site changes as well as both small and large exonic frameshift deletions/insertions or other complex exonic rearrangements. Other variant types (e.g. synonymous substitutions) may be considered for inclusion if additional evidence supportive of pathogenicity is presented.
    • Disease causing mutation (DM) - Pathological mutation reported to be disease causing in the corresponding report (i.e. all other HGMD data).
  • HGMD_MutantAllele Whether the ALT or REF allele is associated with the phenotype
  • HGMD_ProteinAnnotation The variant's protein alteration
  • HGMD_PrimaryPhenotype The phenotype associated with the variant

Warning.png WARNING: In the opinion of the HGMD curators, the polymorphism data present in HGMD should always be viewed with caution, due to (i) the possibility that the observed disease association may be simply due to a linkage disequilibrium effect, rather than a bona fide underlying functional mechanism and (ii) in vitro studies are not invariably accurate indicators of the in vivo situation.


HGMD.png

Note, this annotation resource requires an additional license to the professional version of HGMD


The current classifier version (for specifying in Land.cfg) is HGMD_20170501* which was built from the 2017.1 release

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