The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]

  • See Evidence submitted by expert panel for details.

Variant: NM_006218.3(PIK3CA):c.2740G>A (p.Gly914Arg)

CA130467

39703 (ClinVar)

Gene: PIK3CA
Condition: overgrowth syndrome and/or cerebral malformations due to abnormalities in MTOR pathway genes
Inheritance Mode: Autosomal dominant inheritance (mosaic)
UUID: 857fcdd5-3e4e-4d8c-bc86-6586a8591ded
Approved on: 2022-02-12
Published on: 2022-02-12

HGVS expressions

NM_006218.3:c.2740G>A
NM_006218.3(PIK3CA):c.2740G>A (p.Gly914Arg)
NC_000003.12:g.179230077G>A
CM000665.2:g.179230077G>A
NC_000003.11:g.178947865G>A
CM000665.1:g.178947865G>A
NC_000003.10:g.180430559G>A
NG_012113.2:g.86555G>A
ENST00000263967.4:c.2740G>A
ENST00000462255.2:n.1763G>A
ENST00000643187.1:c.2740G>A
ENST00000674534.1:n.3648G>A
ENST00000674622.1:n.1161G>A
ENST00000675467.1:n.5547G>A
ENST00000675786.1:c.*1307G>A
ENST00000675796.1:n.2635G>A
ENST00000263967.3:c.2740G>A
NM_006218.2:c.2740G>A
NM_006218.4:c.2740G>A
NM_006218.4(PIK3CA):c.2740G>A (p.Gly914Arg)
More

Pathogenic

Met criteria codes 5
PM1_Supporting PS2 PS4 PP2 PM2_Supporting
Not Met criteria codes 21
BS2 BS4 BS3 BS1 BP5 BP7 BP2 BP3 BP4 BP1 PS1 PS3 PP4 PP1 PP3 BA1 PM6 PM3 PM5 PM4 PVS1

Evidence Links 5

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Brain Malformations VCEP
The c.2740G>A (NM_006218.4) variant in PIK3CA is a missense variant predicted to cause substitution of (p.Gly914Arg). This variant is absent from gnomAD v2.1.1 (PM2_Supporting). PIK3CA, in which the variant was identified, is defined by the ClinGen Brain Malformations Expert Panel as a gene that has a low rate of benign missense variation and where pathogenic missense variants are a common mechanism of disease (PP2). This variant resides within the kinase domain of PIK3CA that is defined as a critical functional domain by the ClinGen BMEP (PMIDs: 26637981, 24459181, 27631024) (PM1_Supporting). The prevalence of the variant in affected individuals is significantly increased compared with the prevalence in controls (PS4; identified in 5 individuals with a clinical diagnosis of megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome; (MPPH) or megalencephaly-capillary malformation-polymicrogyria syndrome; (MCAP), and in 4 individuals with segmental overgrowth or vascular malformation of a limb or region of the body, it has been shown to significantly increase phosphorylation levels in patient cell lines (PMID: 22729224), and it was identified in 2 tumor samples in COSMIC (PMID: 22729224, PMID: 28151489, PMID: 28502725, PMID: 30231930). This variant has been confirmed de novo and has been identified with variable allelic fractions consistent with a post-zygotic event (PS2_Strong; 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, PP2, PM1_P, PS4, PS2; 11 points (VCEP specifications version 1; Approved: 1/31/2021)
Met criteria codes
PM1_Supporting
located in a kinase domain
PS2
PS4
also present in 2 tumor samples in COSMIC Upgraded to very strong

PP2
PIK3CA meets the ExAC constraint z-score of >3.09
PM2_Supporting
absent from gnomAD and ExAC
Not Met criteria codes
BS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS3
BS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP5
BP7
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS3
PP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BA1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM6
PM3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PVS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. If you have questions about the information contained on this website, please see a health care professional.
¤ Powered by BCM's Genboree.