ClinVar Miner

Submissions for variant NM_003560.4(PLA2G6):c.1187-1G>A

gnomAD frequency: 0.00003  dbSNP: rs1477656610
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Baylor Genetics RCV001004414 SCV001163450 pathogenic Infantile neuroaxonal dystrophy criteria provided, single submitter clinical testing
Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard RCV002549242 SCV003761002 likely pathogenic PLA2G6-associated neurodegeneration 2025-05-06 criteria provided, single submitter curation The c.1187-1G>A variant in PLA2G6 has not been previously reported in the literature in individuals with PLA2G6-associated neurodegeneration, but has been identified in 0.00008% (1/1179968) of European (non-Finnish) chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP ID: rs1477656610). Although this variant has been seen in the general population in a heterozygous state, its frequency is low enough to be consistent with a recessive carrier frequency. This variant has also been reported in ClinVar (Variation ID#: 813443) and has been interpreted as pathogenic by Baylor Genetics. This variant is located in the 5' splice region. Computational tools predict a splicing impact, though this information is not predictive enough to determine pathogenicity. Loss of function of the PLA2G6 gene is an established disease mechanism in autosomal recessive PLA2G6-associated neurodegeneration. In summary, although additional studies are required to fully establish its clinical significance, this variant is likely pathogenic for autosomal recessive PLA2G6-associated neurodegeneration. ACMG/AMP Criteria applied: PVS1, PM2_supporting (Richards 2015).

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