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_006218.4(PIK3CA):c.1173A>G (p.Ile391Met)

CA161490

135038 (ClinVar)

Gene: PIK3CA
Condition: overgrowth syndrome and/or cerebral malformations due to abnormalities in MTOR pathway genes
Inheritance Mode: Autosomal dominant inheritance
UUID: b2be4058-24f0-4813-a90c-a8752970cfd2
Approved on: 2022-02-17
Published on: 2022-02-17

HGVS expressions

NM_006218.4:c.1173A>G
NM_006218.4(PIK3CA):c.1173A>G (p.Ile391Met)
NC_000003.12:g.179209622A>G
CM000665.2:g.179209622A>G
NC_000003.11:g.178927410A>G
CM000665.1:g.178927410A>G
NC_000003.10:g.180410104A>G
NG_012113.2:g.66100A>G
ENST00000263967.4:c.1173A>G
ENST00000643187.1:c.1173A>G
ENST00000674534.1:n.927A>G
ENST00000675467.1:n.3980A>G
ENST00000675786.1:c.1173A>G
ENST00000263967.3:c.1173A>G
NM_006218.2:c.1173A>G
NM_006218.3:c.1173A>G
More

Benign

Met criteria codes 4
PM1_Supporting BA1 BS2 PP2

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Brain Malformations VCEP
The c.1173A>G (NM_006218.4) variant in PIK3CA is a missense variant predicted to cause substitution of (p.Ile391Met). 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 highest population minor allele frequency in gnomAD v2.1.1 is 0.2113 in African/African American population, which is higher than the ClinGen BMEP threshold ([>=0.00185]) for BA1, and therefore meets this criterion (BA1). This variant was identified the homozygous state in >3 individuals within control databases (BS2). 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). In summary, this variant meets the criteria to be classified as 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: PM1_P, BA1, BS2, PP2; -10 points (VCEP specifications version 1; Approved: 1/31/2021)
Met criteria codes
PM1_Supporting
kinase domain
BA1
21% AF
BS2
1032 homozygotes
PP2
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.