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PIK3R1
Final classification
VUS
PIK3R1 c.310A>G · p.Thr104Ala
PIK3R1

NM_181523.2:c.310A>G (p.Thr104Ala) in PIK3R1 is a novel missense variant absent from all population databases including gnomAD v4.1, meeting PM2_Supporting per the VCEP allele frequency threshold (<0.00000132).

Gene
PIK3R1
Transcript
NM_181523.2
HGVS · transcript:coding
NM_181523.2:c.310A>G
Consequence
N/A
GRCh38
chr5:68226985 A>G
GRCh37
chr5:67522813 A>G
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.310A>G

NM_181523.2:c.310A>G (p.Thr104Ala) in PIK3R1 is a novel missense variant absent from all population databases including gnomAD v4.1, meeting PM2_Supporting per the VCEP allele frequency threshold (<0.00000132).1 Computational evidence is benign-leaning: REVEL score is 0.125, BayesDel is -0.618838, and SpliceAI predicts no splice impact (max delta 0.00). PP3 thresholds (REVEL ≥0.644, SpliceAI ≥0.2) are not met.2 No functional studies, clinical cases, co-segregation data, or literature reports were identified for this specific variant. PVS1, PS1-PS5, PP1, PP3-PP5, BA1, BS1, BS3-BS4, and BP5 are not met. Multiple criteria (PM1, PM5, PM6, BP1, BP2, BP6, BP7, PP2, PP5, BS2) are designated as not applicable by the PIK3R1 VCEP. BP4 could not be fully assessed due to absence of CADD score.3 Using the Bayesian point-based framework adopted by the Antibody Deficiencies VCEP (Tavtigian 2020, PMID:32720330), the sole met criterion PM2_Supporting contributes +1 point (supporting). The total score of 1 falls in the 0–5 range, corresponding to a classification of Uncertain Significance.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 · 13 assessed
Applied · 1
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
The variant is absent from gnomAD v4.1.0 (total allele frequency = 0), which is below the VCEP PM2_Supporting threshold of <0.00000132. This supports pathogenicity at the supporting level.
Absent from gnomAD v4.1 (AF=0)v2.1 (AF=0)and gnomAD-Canada v1.0 (AF=0). Total AF 0 < VCEP threshold 0.00000132.
Assessed · not applied
Pathogenic
PS1 No other missense variant at codon 104 of PIK3R1 has been classified as Pathogenic or Likely Pathogenic by the Antibody Deficiencies VCEP.
PS2 No de novo observation has been reported for this variant.
PS3 No variant-specific functional study has been identified for NM_181523.2:c.310A>G (p.Thr104Ala).
PS4 No affected probands harboring this variant have been identified in ClinVar or the literature.
PP1 No co-segregation data are available.
PP3 PP3 is not met per PIK3R1 VCEP rules.
PP4 No proband with a phenotype specific to PIK3R1-related immunodeficiency has been reported for this variant.
Benign
BA1 The variant is absent from gnomAD v4.1.0 (GrpMax filtering AF = 0), which is below the VCEP BA1 Stand Alone threshold of ≥0.00316.
BS1 The variant is absent from gnomAD v4.1.0 (GrpMax filtering AF = 0), which is below the VCEP BS1 Strong threshold of ≥0.000316.
BS3 No variant-specific functional study demonstrating a non-damaging effect has been identified for NM_181523.2:c.310A>G (p.Thr104Ala).
BS4 No family segregation data are available.
BP4 The VCEP BP4 rule requires both REVEL ≤0.290 AND CADD ≤21.5, plus SpliceAI Δ scores <0.1.
BP5 No cases have been identified in which this variant is found alongside an alternative molecular basis for disease.
N/A · 11 PVS1 · PM1 · PM5 · PM6 · PP2 · PP5 · BS2 · BP1 · BP2 · 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). REVEL score = 0.125. BayesDel score = -0.618838.
Functional / OncoKB screenshot
Functional Unknown Oncogenic Effect
OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. PIK3R1, the regulatory subunit of PI3-kinase, is mutated in various cancers, most frequently in glioma, endometrial and colorectal cancers.
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 not previously been reported in somatic cancers (COSMIC).
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