ClinVar Miner

Submissions for variant NM_000169.2(GLA):c.1072_1074del (p.Glu358del) (rs730880453)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000157903 SCV000207834 pathogenic not provided 2016-02-16 criteria provided, single submitter clinical testing The c.1072_1074delGAG mutation in the GLA gene has been reported previously in association with Fabry disease, in an affected male who had no residual enzyme activity (Blanch et al., 1996). This mutation causes an in-frame deletion of a single Glutamic Acid residue.
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000157903 SCV000339433 pathogenic not provided 2017-08-25 criteria provided, single submitter clinical testing
Invitae RCV000815405 SCV000955856 pathogenic Fabry disease 2019-08-23 criteria provided, single submitter clinical testing This variant, c.1072_1074delGAG, results in the deletion of 1 amino acid(s) of the GLA protein (p.Glu358del), but otherwise preserves the integrity of the reading frame. This variant is not present in population databases (ExAC no frequency). This variant has been observed in several individuals affected with Fabry disease (PMID: 26297554, 15712228, 15339079, 15713906, 18154965, 8807334). ClinVar contains an entry for this variant (Variation ID: 180844). Experimental studies and prediction algorithms are not available for this variant, and the functional significance of the affected amino acid(s) is currently unknown. This variant disrupts the p.Glu358 amino acid residue in GLA. Other variants that disrupt this residue have been observed in affected individuals (PMID: 21598360, 26415523, 9452068, 26297554, 12428061, 24386359, 25382311, 16595074), suggesting that it is a clinically significant residue. As a result, variants that disrupt this residue are likely to be causative of disease. For these reasons, this variant has been classified as Pathogenic.
Integrated Genetics/Laboratory Corporation of America RCV000815405 SCV001361588 pathogenic Fabry disease 2019-08-06 criteria provided, single submitter clinical testing Variant summary: GLA c.1072_1074delGAG (p.Glu358del) results in an in-frame deletion that is predicted to remove a Glu amino acid in the alpha galactosidase A, C-terminal beta-sandwich domain of the encoded protein. The variant was absent in 183351 control chromosomes (gnomAD). c.1072_1074delGAG has been reported in the literature in multiple individuals affected with Fabry Disease (Topaloglu_1999, Wu_2004, Shin_2008, Monserrat_2007, Schafer_2005, Blanch_1996). Affected individuals were found to have less than 10% normal activity. Two ClinVar submissions (evaluation after 2014) cite the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.

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