ClinVar Miner

Submissions for variant NM_005027.4(PIK3R2):c.59C>T (p.Pro20Leu)

gnomAD frequency: 0.00003  dbSNP: rs929809973
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001313906 SCV001504417 uncertain significance Megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 1 2022-10-31 criteria provided, single submitter clinical testing In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. 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) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on PIK3R2 protein function. ClinVar contains an entry for this variant (Variation ID: 1015086). This variant has not been reported in the literature in individuals affected with PIK3R2-related conditions. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 20 of the PIK3R2 protein (p.Pro20Leu).
Ambry Genetics RCV004651567 SCV005153762 uncertain significance Inborn genetic diseases 2024-04-27 criteria provided, single submitter clinical testing The c.59C>T (p.P20L) alteration is located in exon 2 (coding exon 1) of the PIK3R2 gene. This alteration results from a C to T substitution at nucleotide position 59, causing the proline (P) at amino acid position 20 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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