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_005027.4(PIK3R2):c.1117G>A (p.Gly373Arg)

CA130573

39808 (ClinVar)

Gene: PIK3R2
Condition: overgrowth syndrome and/or cerebral malformations due to abnormalities in MTOR pathway genes
Inheritance Mode: Autosomal dominant inheritance (mosaic)
UUID: 421e7cec-5414-46bc-82b2-ecde31fd73a0
Approved on: 2022-02-17
Published on: 2022-02-17

HGVS expressions

NM_005027.4:c.1117G>A
NM_005027.4(PIK3R2):c.1117G>A (p.Gly373Arg)
NC_000019.10:g.18162974G>A
CM000681.2:g.18162974G>A
NC_000019.9:g.18273784G>A
CM000681.1:g.18273784G>A
NC_000019.8:g.18134784G>A
NG_033010.1:g.14797G>A
NG_033010.2:g.14797G>A
ENST00000222254.13:c.1117G>A
ENST00000617130.5:c.*96G>A
ENST00000617642.2:c.*96G>A
ENST00000675271.1:n.63G>A
ENST00000222254.12:c.1117G>A
ENST00000426902.5:c.1117G>A
ENST00000593731.1:c.1117G>A
ENST00000617130.4:n.1117G>A
ENST00000617642.1:n.1117G>A
NM_005027.3:c.1117G>A
NR_073517.1:n.1657G>A
NR_073517.2:n.1672G>A
NR_162071.1:n.1455G>A

Pathogenic

The Expert Panel has overridden the computationally generated classification - "Likely Pathogenic"
Met criteria codes 4
PS2_Moderate PM1_Supporting PS4 PM2_Supporting
Not Met criteria codes 22
BS2 BS4 BS3 BS1 BP5 BP7 BP2 BP3 BP4 BP1 PS3 PS1 PP4 PP1 PP3 PP2 BA1 PM6 PM3 PM4 PM5 PVS1

Evidence Links 2

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Brain Malformations VCEP
The c.1117G>A (NM_005027.4) variant in PIK3R2 is a missense variant predicted to cause substitution of (p.Gly373Arg). This variant is absent from gnomAD v2.1.1 (PM2_Supporting). This variant resides within the PIK3R2 SH2, sequence homology 2 domain of PIK3R2 that is defined as a critical functional domain by the ClinGen BMEP (PMID: 26860062) (PM1_Supporting). The prevalence of the variant in affected individuals is significantly increased compared with the prevalence in controls (PS4_VS; identified in 2 individuals with macrocephaly (>=2 SD) and Developmental Delay or Intellectual disability with cortical malformation, 13 individuals with a clinical diagnosis of megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome; (MPPH) or megalencephaly-capillary malformation-polymicrogyria syndrome; (MCAP), it has been shown to significantly increase phosphorylation levels in patient cell lines (PMID: 22729224), and has been identified in over 15 tumor samples in the literature and COSMIC (PMID: 28086757,22729224, 28502725)). This variant has been identified as a de novo occurrence with confirmed parental relationships (PS2_moderate; 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, PM1_P, PS4_VS, PS2_M; 13 points (VCEP specifications version 1; Approved: 1/31/2021)
Met criteria codes
PS2_Moderate
PM1_Supporting
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS4
16 COSMIC, 27 cBioPortal This variant met criteria to meet PS4_VS >16

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
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
PS3
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
PP2
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
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
PVS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
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