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PIK3R1
Final classification
VUS
PM2
PIK3R1
c.1126G>A
p.Gly376Arg
missense · exon 10

PIK3R1 encodes p85α, the regulatory subunit of phosphoinositide 3-kinase (PI3K), an enzyme complex that produces signaling molecules controlling cell growth, proliferation, and survival. The protein normally stabilizes and inhibits the PI3K catalytic subunit and helps the complex respond to signals from cell-surface receptors, including insulin, so alterations in this gene are associated with insulin resistance. PIK3R1 acts as a tumor suppressor: mutations that disrupt its inhibitory function can lead to abnormally active PI3K/AKT signaling and are found in several cancers, most often glioblastoma, as well as endometrial, breast, and colorectal cancers.

This variant

PIK3R1 encodes p85α, which restrains PI3K signaling, and damaging germline changes are linked to immunodeficiency with insulin resistance, while somatic mutations in this gene drive several cancers. This p.(Gly376Arg) change sits in a region where cancer-associated PIK3R1 mutations cluster, yet it is classified VUS: with only PM2 met, current evidence is insufficient to determine whether this germline change disrupts p85α function.

Transcript
NM_181523.2
HGVS · transcript:coding
NM_181523.2:c.1126G>A
GRCh38
chr5:68293310 G>A
GRCh37
chr5:67589138 G>A
Basis VUS: only PM2 (Supporting, +1 point) is met under the ClinGen Antibody Deficiencies PIK3R1 VCEP's point-based Bayesian framework, total +1 mapping to Uncertain Significance (Rule3: 0–5).
VUS: only PM2 (Supporting, +1 point) is met under the ClinGen Antibody Deficiencies PIK3R1 VCEP's point-based Bayesian framework, total +1 mapping to Uncertain Significance (Rule3: 0–5).
Classification rationale
PM2 VUS
PIK3R1 c.1126G>A missense · exon 10

PM2 (Supporting): absent from gnomAD v4.1, total allele frequency below the VCEP's 0.00000132 threshold. Overall classification VUS: point total +1 under the Bayesian framework (Rule3: 0–5 points).

PM2 VUS
Gene diagram · NM_181523.2 · variants mapped to exon structure
PIK3R1 NM_181523.2
Fetching transcript structure from UCSC…
Applied criteria · 1 applied · 16 assessed
MetEvidence satisfies this criterion.
Not metEvaluated against available evidence; threshold not reached.
Not assessedApplies in principle, but no evidence was found to evaluate it.
N/ADoesn't apply to this variant type.
Applied · 1
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
Met (Supporting): absent from gnomAD v4.1, total allele frequency below the VCEP's 0.00000132 threshold.
gnomAD v4.1 reports NM_181523.2:c.1126G>A (p.Gly376Arg) as absent, corresponding to a total observed allele frequency of zero in that dataset.The PIK3R1 Antibody Deficiencies VCEP specifies PM2 at Supporting strength when total allele frequency across all gnomAD v4.1 populations is <0.00000132.
Assessed · not applied · 3 not met · 13 not assessed
Pathogenic
PS1 Not assessed: no alternate-nucleotide variant producing the same p.(Gly376Arg) change with a pathogenic VCEP classification was identified.
PS2 Not assessed: no parental genotypes, parentage confirmation, or family-history information was available to establish a de novo occurrence.
PS3 Not assessed: no data showed this variant tested in the VCEP-approved functional assays (lipid/AKT kinase, protein binding, conformational dynamics).
PS4 Not assessed: no germline immunodeficiency probands with this variant and evaluable phenotype data were available.
PM5 Not assessed: no different-amino-acid change at codon 376 with a pathogenic VCEP classification was available to compare.
PP1 Not assessed: no relatives' genotypes, phenotypes, or meioses were documented, so co-segregation could not be counted.
PP3 Not assessed: REVEL 0.778 clears the 0.644 threshold, but the required CADD score was unavailable, so the PP3 missense condition could not be confirmed.
PP4 Not assessed: no individual with the germline PIK3R1-related phenotype was documented, so phenotype score and PIK3CD exclusion could not be evaluated.
PP5 Not assessed: no ClinVar expert-panel pathogenic or likely-pathogenic classification exists for this exact variant.
Benign
BA1 Not met: absent from gnomAD v4.1, below the VCEP's 0.00316 GrpMax allele-frequency threshold.
BS1 Not met: absent from gnomAD v4.1, below the VCEP's 0.000316 GrpMax allele-frequency threshold.
BS3 Not assessed: no functional assay data specific to this variant were available, so a benign assay result could not be confirmed.
BS4 Not assessed: no affected relatives reported as lacking this variant were documented, so non-segregation could not be assessed.
BP4 Not met: REVEL 0.778 far exceeds the ≤0.290 ceiling, so the BP4 missense condition fails outright.
BP5 Not assessed: no evidence showed this variant in an individual with an independently established alternative molecular cause.
BP6 Not assessed: no ClinVar expert-panel benign or likely-benign classification exists for this exact variant.
N/A · 11 PVS1 · PM1 · PM3 · PM4 · PM6 · PP2 · BS2 · BP1 · BP2 · BP3 · BP7
Research & evidence
Population frequency
gnomAD v4.1 screenshot
gnomAD v4.1
gnomAD v2.1 screenshot
gnomAD v2.1
v4.1
Absent from gnomAD v4.1.
v2.1
Absent from gnomAD v2.1.
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
gnomAD v2.1
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
gnomAD Canada 🇨🇦
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
ClinVar screenshot
ClinVar
This variant has been reported in ClinVar but submission details could not be extracted. (ClinVarID = 376064)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.778. BayesDel score = 0.536814.
Functional / OncoKB screenshot
Functional Likely Oncogenic
OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Loss-of-function; curated oncogenicity label: Likely Oncogenic.
OncoKB ↗
COSMIC screenshot
COSMIC
Cancer hotspots screenshot
Cancer hotspots
Somatic evidence Hotspot
COSMIC
This variant lies in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV57123316, n = 36 times).
Hotspots
This variant lies in a statistically significant hotspot.
Sources & reference links
9Sources
CSpec VCEP
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Cancer hotspots
Triaged references · 5 PMIDs not cited in assessment
20713702 ↗ Cancer-derived mutations in the regulatory subunit p85alpha of phosphoinositide 3-kinase function through the catalytic subunit p110alpha. ONCOKB
22918138 ↗ Opportunities and challenges associated with clinical diagnostic genome sequencing: a report of the Association for Molecular Pathology. CLINVAR
28528867 ↗ A Pan-Cancer Proteogenomic Atlas of PI3K/AKT/mTOR Pathway Alterations. CLINVAR
29533785 ↗ Systematic Functional Annotation of Somatic Mutations in Cancer. CLINVAR
34131312 ↗ Chromosomal microarray analysis, including constitutional and neoplastic disease applications, 2021 revision: a technical standard of the American College of Medical Genetics and Genomics (ACMG). CLINVAR