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PIK3R1
Final classification
VUS
PIK3R1 c.1345_1347del · p.Leu449del
PIK3R1

NM_181523.2:c.1345_1347del (p.Leu449del) is an in-frame deletion of a single amino acid in exon 11 of PIK3R1, which encodes the p85-alpha regulatory subunit of PI3K. The variant has not been reported in ClinVar and is absent from gnomAD v2.1, v4.1, and gnomAD-Canada, meeting PM2_Supporting under the Antibody Deficiencies VCEP framework (total AF = 0; threshold <0.00000132).

Gene
PIK3R1
Transcript
NM_181523.2
HGVS · transcript:coding
NM_181523.2:c.1345_1347del
Consequence
N/A
GRCh38
chr5:68293752 AATT>A
GRCh37
chr5:67589580 AATT>A
Basis ClinGen Antibody Deficiencies Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for PIK3R1 Version 1.0.0 v1.0.0 point-based framework: PM2 supporting (+1) = 1 points, which maps to VUS.
ClinGen Antibody Deficiencies Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for PIK3R1 Version 1.0.0 v1.0.0 point-based framework: PM2 supporting (+1) = 1 points, which maps to VUS.
Classification rationale
PM2 VUS
PIK3R1 c.1345_1347del

NM_181523.2:c.1345_1347del (p.Leu449del) is an in-frame deletion of a single amino acid in exon 11 of PIK3R1, which encodes the p85-alpha regulatory subunit of PI3K. The variant has not been reported in ClinVar and is absent from gnomAD v2.1, v4.1, and gnomAD-Canada, meeting PM2_Supporting under the Antibody Deficiencies VCEP framework (total AF = 0; threshold <0.00000132).1 The variant has been observed in somatic cancers (COSMIC COSV57127217, n=5) and is annotated as Likely Oncogenic / Likely Loss-of-function by OncoKB. However, no variant-specific germline functional data are available from VCEP-approved assays (lipid kinase activity, AKT kinase activity, protein binding, conformational dynamics, mouse knock-in, or pS6/pAKT T-cell enrichment assay). PS3 and BS3 are not met.2 PVS1, PS1, PM1, PM5, PM6, PP2, PP5, BS2, BP1, BP2, BP3, BP6, and BP7 are not applicable under the Antibody Deficiencies VCEP specifications. PM4 is not met because the deletion removes only one amino acid (threshold: >=2 amino acids). PP3 and BP4 do not apply to in-frame deletions under current VCEP rules. BA1 and BS1 are not met as the variant is absent from population databases.3 PS2, PS4, PP1, PP4, BS4, and BP5 cannot be assessed due to absence of proband phenotype data, family segregation studies, and alternative molecular diagnoses in the available literature and case materials. Applying the PIK3R1 VCEP Bayesian point-based classification framework (Tavtigian 2020 adaptation): the only met criterion is PM2_Supporting (+1 point). Total = 1 point, which falls in the VUS range (0-5 points). The evidence is insufficient to classify this variant as pathogenic or benign at this time.4

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 · 12 assessed
Applied · 1
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
NM_181523.2:c.1345_1347del is absent from gnomAD v2.1, v4.1, and gnomAD-Canada (total allele frequency = 0). This is below the VCEP PM2_Supporting threshold of <0.00000132, supporting pathogenicity.
Absent from gnomAD v2.1 (0 alleles)gnomAD v4.1 (0 alleles)and gnomAD-Canada (0 alleles). Total AF = 0
Assessed · not applied
Pathogenic
PS2 No de novo occurrence data are available for NM_181523.2:c.1345_1347del in any proband with PIK3R1-related immunodeficiency.
PS3 The variant is not included in any VCEP-approved functional assay dataset.
PS4 No probands with PIK3R1-related immunodeficiency harboring NM_181523.2:c.1345_1347del have been identified in the literature or case materials.
PM4 The VCEP PM4 criterion requires an in-frame deletion resulting in a protein length change of >= 2 amino acids with at least one deleted nucleotide having a PhyloP score >= 2.0.
PP1 No co-segregation data are available for NM_181523.2:c.1345_1347del.
PP3 The VCEP PP3 criterion for missense variants requires REVEL >= 0.644 and CADD >= 26.0.
PP4 No proband with NM_181523.2:c.1345_1347del meets the VCEP PP4 phenotype scoring criteria (>=10 points on PS4 counting rubric with genotyping ruling out PIK3CD alterations).
Benign
BA1 NM_181523.2:c.1345_1347del is absent from gnomAD v4.1 (allele frequency = 0).
BS1 NM_181523.2:c.1345_1347del is absent from gnomAD v4.1 (allele frequency = 0).
BS3 The variant is not included in any VCEP-approved functional assay.
BS4 No family segregation data are available to demonstrate lack of co-segregation with PIK3R1-related immunodeficiency.
BP5 The VCEP BP5 criterion requires at least 2 cases with an alternative molecular basis for disease.
N/A · 14 PVS1 · PS1 · PM1 · PM5 · PM6 · PP2 · PP5 · BS2 · BP1 · BP2 · BP3 · BP4 · BP6 · 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 is absent from ClinVar.
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00).
Functional / OncoKB screenshot
Functional Likely Oncogenic
OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Loss-of-function; curated oncogenicity label: Likely Oncogenic.
OncoKB ↗
COSMIC screenshot
COSMIC
Cancer hotspots screenshot
Cancer hotspots
Somatic evidence Not in COSMIC / hotspots
COSMIC
This variant does not lie in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV57127217, n = 5 times).
Hotspots
This variant does not lie 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 · 2 PMIDs not cited in assessment
28481359 ↗ Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients. ONCOKB
29636360 ↗ A First-in-Human Phase 1 Study of LY3023414, an Oral PI3K/mTOR Dual Inhibitor, in Patients with Advanced Cancer. ONCOKB