ClinVar Genomic variation as it relates to human health

The c.1117G>A (NM_005027.4) variant in PIK3R2 is a missense variant predicted to cause substitution of (p.Gly373Arg). This variant is absent from gnomAD v2.1.1 (PM2_Supporting). This variant resides within the PIK3R2 SH2, sequence homology 2 domain of PIK3R2 that is defined as a critical functional domain by the ClinGen BMEP (PMID: 26860062) (PM1_Supporting). The prevalence of the variant in affected individuals is significantly increased compared with the prevalence in controls (PS4_VS; identified in 2 individuals with macrocephaly (>=2 SD) and Developmental Delay or Intellectual disability with cortical malformation, 13 individuals with a clinical diagnosis of megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome; (MPPH) or megalencephaly-capillary malformation-polymicrogyria syndrome; (MCAP), it has been shown to significantly increase phosphorylation levels in patient cell lines (PMID: 22729224), and has been identified in over 15 tumor samples in the literature and COSMIC (PMID: 28086757,22729224, 28502725)). This variant has been identified as a de novo occurrence with confirmed parental relationships (PS2_moderate; PMID: 22729224). In summary, this variant meets the criteria to be classified as Pathogenic for mosaic autosomal dominant overgrowth with or without cerebral malformations due to abnormalities in MTOR-pathway genes based on the ACMG/AMP criteria applied, as specified by the ClinGen Brain Malformations Expert Panel: PM2_P, PM1_P, PS4_VS, PS2_M; 13 points (VCEP specifications version 1; Approved: 1/31/2021)

For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. Experimental studies have shown that this missense change affects PIK3R2 function (PMID: 22729224). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt PIK3R2 protein function. ClinVar contains an entry for this variant (Variation ID: 39808). This missense change has been observed in individual(s) with megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome, or clinical features of this syndrome (PMID: 22729224, 24497998, 26520804, 28086757). In at least one individual the variant was observed to be de novo. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces glycine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 373 of the PIK3R2 protein (p.Gly373Arg).

[ACMG/AMP: PS2, PS3, PM1, PM2, PS4_moderate, PP1, PP3]; A de novo mosaic variant [PS2] within the PIK3R2 gene was detected and confirmed by sanger sequencing. This is a well-described pathogenic alteration associated with megalencephaly-polymicrogyria-polydactyly-hydrocephalus (MPPH) syndrome (PMID: 27854409) [PS4_moderate]. This variant has been reported to increase PI3K activity in vitro in a lymphoblastoid cell line derived from a patient with this alteration (PMID: 22729224), is absent from large-scale population databases, including gnomAD, and predicated to have a deleterious effect based on in silico modeling [PS3, PM2, PP3]. Mosaicism is the setting of PIK3R2-associated MPPH has been previously documented (PMID: 26520804; 28502725). Of note, autosomal dominant (vertical) transmission of this variant has been described among affected individuals in one pedigree [PP1], and additionally, gonadal mosaicism has been documented (PMID: 26520804; 27854409).

Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0101 - Gain of function is a known mechanism of disease in this gene and is associated with Megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 1 (MIM#603387). (I) 0107 - This gene is associated with autosomal dominant disease. (I) 0200 - Variant is predicted to result in a missense amino acid change from glycine to arginine. (I) 0254 - This variant is suspected mosaic. (I) 0301 - Variant is absent from gnomAD (both v2 and v3). (SP) 0501 - Missense variant with conflicting in silico predictions and very highly conserved with a major amino acid change. (SP) 0600 - Variant is located in the annotated SH2 domain (PDB, NCBI). (I) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant has been reported in multiple individuals with Megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 1 (ClinVar). Most of these individuals had de novo variants and were either heterozygous or mosaic for the variant (PMID: 22729224, 26520804, 28502725). (SP) 1001 - This variant has strong functional evidence supporting abnormal protein function. Analysis of proband lymphoblastoid cells found the variant resulted in elevated PIP3 levels (PMID: 22729224). (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign

PIK3R2: PS2:Very Strong, PM1, PM2, PS4:Moderate, PS3:Supporting

This variant was classified as: Pathogenic. The following ACMG criteria were applied in classifying this variant: PS1,PS3,PM2,PP3.

Same nucleotide change resulting in same amino acid change has been previously reported as de novoo or mosaic in at least two similarly affected unrelated individuals (PMID:22729224,26520804; 28502725, PS2, PS4_M). The missense variant is located in a mutational hot spot and/or well-established functional domain in which established pathogenic variants have been reported (PM1). It is not observed in the gnomAD v2.1.1 dataset (PM2). The variant was observed as assumed (i.e. paternity and maternity not confirmed) de novoo (3billion dataset, PM6). In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.631, PP3). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline.

DNA sequence analysis of the PIK3R2 gene demonstrated a sequence change, c.1117G>A, in exon 10 that results in an amino acid change, p.Gly373Arg. This sequence change is absent from the large population databases such as ExAC and gnomAD (dbSNP rs587776934). This sequence change has previously been described in several patients in de novo state with megalencephaly-polymicrogyria-polydactyly-hydrocephalus (MPPH) syndrome (PMID: 22729224, 24497998, 26520804, 28086757 and 26860062). Clinical variability and germline mosaicism has also been reported with this variant in some families (PMIDs: 24497998, 22729224). Functional studies have reported that this variant results in an increased PI3K activity and elevated PI3K-mTOR signaling with possible impact on PIK3R2 protein function (PMID: 22729224). The p.Gly373Arg change affects a highly conserved amino acid residue located in a domain of the PIK3R2 protein that is known to be functional. The p.Gly373Arg substitution appears to be deleterious using several in-silico pathogenicity prediction tools (SIFT, PolyPhen2, Align GVGD, REVEL). These collective evidences indicate that this sequence change is pathogenic.

Published functional studies demonstrate that G373R results in increased PI3K activity (Riviere et al., 2012); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 27117832, 23619167, 21984976, 22729224, 24816253, 25056374, 25344691, 24497998, 23592320, 26520804, 26860062, 23745724, 23449172, 30293990, 29051493, 28566443, 28086757, 32371413, 34018286, 33144663, 34170046, 33644862, 33726816, 33604570, 33100332, 27535533)

The PIK3R2 c.1117G>A variant is predicted to result in the amino acid substitution p.Gly373Arg. This is the most frequently documented pathogenic variant in PIK3R2. It has been reported with de novo occurrence (constitutional and mosaic) in more than twenty patients with megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome or related phenotypes (see for example, Rivière et al. 2012. PubMed ID: 22729224; Tapper et al. 2014. PubMed ID: 24497998; Mirzaa et al. 2015. PubMed ID: 26520804; Negishi et al. 2017. PubMed ID: 28086757). This variant has not been reported in a large population database, indicating it is rare. It is interpreted as pathogenic by the ClinGen Brain Malformations Variant Curation Expert Panel (https://www.ncbi.nlm.nih.gov/clinvar/variation/39808/). This variant is interpreted as pathogenic.

The mutation was observed in 2 affected individuals of a macrocephaly. Patient, a 2 year-old boy, showed severe developmental delay, hypotonia, and dysmorphic facial features. He had no meaningful words. His last head circumference was 52.4 cm (+3.4SD). Patient, a 6 year-old boy, showed severe developmental delay, hypotonia, seizure, and dysmorphic facial features. He had no meaningful words. His last head circumference was 55.5 cm (+2.5SD). This mutation was confirmed de novo. The expression level of phosphorylated S6 ribosomal protein in their lymphoblastoid cell lines was elevated.