ClinVar Genomic variation as it relates to human health

We were able to detect the known pathogenic mutation c.2370T>G in the PLA2G6 gene in the patient in a heterozygous state. The variant was also detected in the mother of the patient in heterozygous state. The PLA2G6 gene codes for phospholipase A2 of group 6 (MIM *603604). Biallelic pathogenic sequence variants in PLA2G6 have been described with three clinical manifestations of autosomal recessively inherited PLA2G6-associated neurodegeneration: 1) infantile neuroaxonal dystrophy (INAD, MIM: 256600), 2) neurodegeneration with iron accumulation in the brain (NBIA, MIM: 610217) and 3) PLA2G6-dependent dystonia parkinsonism (MIM: 612953). Clinical symptoms include psychomotor regression, symmetrical pyramidal trajectory signs, pronounced trunk hypotension, spastic quadriplegia, visual disturbances and dementia. The clinical course may be variable. The above variation leads to the formation of a premature stop codon and thus most likely to the premature termination of protein biosynthesis. The variant has already been reported in numerous patients in homozygous or compound-heterozygous condition (HGMD: CM063050). The sequence variant is listed in gnomAD 25x in heterozygous state and occurs in the European subpopulation with an allele frequency of 0.015%.

Variant summary: PLA2G6 c.2370T>G (p.Tyr790X) located in the last exon results in a premature termination codon, predicted to cause a truncation of the encoded protein, which is a commonly known mechanism for disease. Truncations downstream of this position have been classified as pathogenic by our laboratory. The variant allele was found at a frequency of 8.2e-05 in 243312 control chromosomes. This frequency is not significantly higher than estimated for a pathogenic variant in PLA2G6 (8.2e-05 vs 0.00085), allowing no conclusion about variant significance. c.2370T>G has been reported in the literature as homozygous and compound heterozygous genotypes in multiple individuals affected with features of PLA2G6-associated neurodegeneration (PLAN), predominantly as infantile neuroaxonal dystrophy (INAD) (example, Carrilho_2008, Gregory_2008, Darling_2019). These data indicate that the variant is very likely to be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function. The most pronounced variant effect results in <10% of normal Phospholipase and lysophospholipase catalytic activities in-vitro (example, Engel_2010). Twelve clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.

The PLA2G6 c.2370T>G variant is predicted to result in premature protein termination (p.Tyr790*). This variant has been reported in the homozygous or compound heterozygous state in multiple individuals with infantile neuroaxonal dystrophy or neurodegeneration with brain iron accumulation (see for example, Gitiaux et al. 2018. PubMed ID: 29859652; AlBanji et al. 2020. PubMed ID: 33101984; Table S1, Brunet et al. 2021. PubMed ID: 33619735). An in vitro experimental study suggests this variant decreases enzymatic activity to less that 10% of wildtype activity (Figure 3, Engel et al. 2010. PubMed ID: 20886109). This variant is reported in 0.015% of alleles in individuals of European (Non-Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/22-38508219-A-C). Nonsense variants in PLA2G6 are expected to be pathogenic. This variant is interpreted as pathogenic.

PLA2G6: PVS1, PM2

The PLA2G6 c.2370T>G (p.Tyr790Ter) variant is a stop-gained variant and has been reported in at least eight studies in a total of 11 probands with PLA2G6-associated neurodegeneration, including in at least five in a homozygous state, in five in a compound heterozygous state, and in one in a heterozygous state (Morgan et al. 2006; Carrilho et al. 2008; Gregory et al. 2008; Pinto et al. 2010; Paisan-Ruiz 2012; Illingworth et al. 2014; Blake et al. 2016; Erro et al. 2016). Of note, another variant, c.2370_2371delTG, which also results in p.Tyr790Ter, has been reported in both a homozygous and compound heterozygous state in other probands. Control data are not available for the p.Tyr790Ter variant, which is reported at a frequency of 0.000148 in the Latino from the Genome Aggregation Database. In vitro studies examining the catalytic function of the p.Tyr790Ter variant demonstrated <10% phospholipase activity compared to wildtype in the presence of two different substrates (Engel et al. 2010). Based on the collective evidence, the p.Tyr790Ter variant is classified as pathogenic for PLA2G6-associated neurodegeneration. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.

This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868]. This variant has been previously reported as disease-causing [PMID 16783378, 27378808, 20886109]

This variant has been previously reported as disease-causing and was found twice in our laboratory with another variant in affected individuals: a 2-year-old male with regression, hearing loss, hypotonia, failure to thrive, cerebellar atrophy, vision loss; a 5-year-old female with regression, dystonia, epilepsy, microcephaly, failure to thrive, cerebellar atrophy. Heterozygotes would be expected to be asymptomatic carriers.

The stop gained c.2370T>G (p.Y790*) in PLA2G6 (NM_003560.4) has been observed in the homozygous and compound heterozygous state in individuals affected with PLA2G6-related conditions (Morgan NV et al; Blake RB et al). Experimental studies have shown that this variant disrupts PLA2G6 enzymatic activity in vitro (Engel LA et al). The observed variant has been reported to ClinVar as Conflicting Interpretations Of Pathogenicity. This variant is predicted to cause loss of normal protein function through protein truncation. For these reasons, this variant has been classified as Pathogenic

The p.Tyr790Ter variant in PLA2G6 has been reported in >10 individuals with PLA2G6-associated neurodegeneration (PMID: 33101984, 18359254, 18799783, 27378808, 30293248, 28716262, 16783378, 28600779, 30340910, 32860008, 34602496, 35122944, Miryounesi 2018, 30868093, 34622992, 30537300, 33619735, 29859652, Silva 2014), segregated with disease in 2 affected relatives from 2 families (PMID: 28716262, 31196701), and has been identified in 0.02% (19/125174) of European (non-Finnish) chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP ID: rs121908680). Although this variant has been seen in the general population in a heterozygous state, its frequency is not high enough to rule out a pathogenic role. This variant has also been reported in ClinVar (Variation ID#: 6195) and has been interpreted as pathogenic and likely pathogenic by multiple submitters, as well as a variant of uncertain significance by the Institute for Medical Genetics and Human Genetics (Charité - Universitätsmedizin Berlin). Of the 26 affected individuals, 12 of those were homozygotes, and 5 were compound heterozygotes that carried reported likely pathogenic variants in trans or with unknown phase, which increases the likelihood that the p.Tyr790Ter variant is pathogenic (Variant ID: 159741, 265448; PMID: 33101984, 18359254, 18799783, 27378808, 30293248, 28716262, 16783378, 28600779, 30340910, 32860008, 34602496, 35122944, Miryounesi 2018). In vitro functional studies provide some evidence that the p.Tyr790Ter variant impacts protein function (PMID: 20886109, 35122944). However, these types of assays may not accurately represent biological function. This nonsense variant leads to a premature termination codon at position 790. This alteration occurs within the last exon and is more likely to escape nonsense mediated decay (NMD) and result in a truncated protein. Loss of function of the PLA2G6 gene is an established disease mechanism in autosomal recessive PLA2G6-associated neurodegeneration. In summary, this variant meets criteria to be classified as pathogenic for autosomal recessive PLA2G6-associated neurodegeneration. ACMG/AMP Criteria applied: PVS1_moderate, PM3_very-strong, PP1, PS3_moderate (Richards 2015).

Functional studies demonstrate that this variant significantly impairs catalytic activity of the PLA2G6 protein (Engel et al., 2010); Nonsense variant in the C-terminus predicted to result in protein truncation, as the last 17 amino acids are lost, and other loss-of-function variants have been reported downstream in the Human Gene Mutation Database (Stenson et al., 2014); This variant is associated with the following publications: (PMID: 18359254, 20886109, 16783378, 27378808, 28600779, 24800972, 18443314, 24847269, 18570303, 24745848, 30537300, 30340910, 20619503, 33101984, 31589614)

The stop gained variant c.2370T>G (p.Tyr790Ter) in PLA2G6 gene has been reported in at least eight studies in a total of 11 probands with PLA2G6-associated neurodegeneration (Morgan NV et.al.,2006). Functional studies demonstrate that this variant significantly impairs catalytic activity of the PLA2G6 protein (Engel et al., 2010). This variant has been reported to the ClinVar database as Pathogenic.The variant is novel (not in any individuals) in 1000 Genomes and allele frequency of 0.009102% is reported in gnomAD. The nucleotide change in PLA2G6 is predicted as conserved by PhyloP across 100 vertebrates.For these reasons, this variant has been classified as Pathogenic

This sequence change creates a premature translational stop signal (p.Tyr790*) in the PLA2G6 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 17 amino acid(s) of the PLA2G6 protein. This variant is present in population databases (rs121908680, gnomAD 0.01%). This premature translational stop signal has been observed in individuals with clinical features of PLA2G6-related conditions (PMID: 16783378, 27378808; Invitae). ClinVar contains an entry for this variant (Variation ID: 6195). Algorithms developed to predict the effect of variants on protein structure and function are not available or were not evaluated for this variant. Experimental studies have shown that this premature translational stop signal affects PLA2G6 function (PMID: 20886109). For these reasons, this variant has been classified as Pathogenic.