ClinVar Miner

Submissions for variant NM_005027.4(PIK3R2):c.1629G>A (p.Glu543=)

gnomAD frequency: 0.00006  dbSNP: rs774532039
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ClinGen Brain Malformations Variant Curation Expert Panel RCV001725205 SCV001960884 likely benign Overgrowth syndrome and/or cerebral malformations due to abnormalities in MTOR pathway genes 2022-02-11 reviewed by expert panel curation This NM_005027.4(PIK3R2): c.1629G>A (p.Glu543=) variant is a synonymous (silent) variant that occurs at a nucleotide that is not conserved according to a PhyloP <0.1 (BP7). The results from in silico splicing predictors MaxEntScan, spliceAI and varSEAK support that this variant does not affect splicing (BP4). In summary, this variant meets the criteria to be classified as Likely benign 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: BP4, BP7; -2 points (VCEP specifications version 1; Approved: 1/31/2021)
Labcorp Genetics (formerly Invitae), Labcorp RCV000960765 SCV001107779 likely benign Megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 1 2021-10-31 criteria provided, single submitter clinical testing

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