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  • See Evidence submitted by expert panel for details.

Variant: NM_006218.3(PIK3CA):c.2198A>G (p.Lys733Arg)

CA2710903

456537 (ClinVar)

Gene: PIK3CA
Condition: overgrowth syndrome and/or cerebral malformations due to abnormalities in MTOR pathway genes
Inheritance Mode: Autosomal dominant inheritance (mosaic)
UUID: 5b3b96cd-ec1e-4db0-9843-d360ef02fbd0
Approved on: 2022-02-12
Published on: 2022-02-12

HGVS expressions

NM_006218.3:c.2198A>G
NM_006218.3(PIK3CA):c.2198A>G (p.Lys733Arg)
NC_000003.12:g.179224091A>G
CM000665.2:g.179224091A>G
NC_000003.11:g.178941879A>G
CM000665.1:g.178941879A>G
NC_000003.10:g.180424573A>G
NG_012113.2:g.80569A>G
ENST00000263967.4:c.2198A>G
ENST00000462255.2:n.660A>G
ENST00000643187.1:c.2198A>G
ENST00000674534.1:n.3106A>G
ENST00000674622.1:n.619A>G
ENST00000675467.1:n.5005A>G
ENST00000675786.1:c.*765A>G
ENST00000263967.3:c.2198A>G
ENST00000462255.1:n.472A>G
NM_006218.2:c.2198A>G
NM_006218.4:c.2198A>G
NM_006218.4(PIK3CA):c.2198A>G (p.Lys733Arg)
More

Benign

Met criteria codes 2
PP2 BA1
Not Met criteria codes 24
BS2 BS4 BS3 BS1 BP5 BP7 BP2 BP3 BP4 BP1 PS2 PS4 PS3 PS1 PP4 PP1 PP3 PM3 PM1 PM4 PM5 PM6 PM2 PVS1

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Brain Malformations VCEP
The c.2198A>G (NM_006218.4) variant in PIK3CA is a missense variant predicted to cause substitution of (p.Lys733Arg). The highest population minor allele frequency in gnomAD v2.1.1 is 0.005643 in the East Asian population, which is higher than the ClinGen BMEP threshold ([>=0.00185]) for BA1, and therefore meets this criterion (BA1). 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: BA1, PP2; -7 points (VCEP specifications version 1; Approved: 1/31/2021)
Met criteria codes
PP2
PIK3CA meets the ExAC constraint z-score of >3.09
BA1
0.59% ExAC East Asian; 0.56% gnomAD East Asian
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
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
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
PS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS4
2 tumor samples present in COSMIC with unknown somatic sample, but likely germline. Not applied since the variant is not absent from controls.
PS3
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
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
PM3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM1
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
PM5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM6
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM2
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
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