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PIK3R1
Final classification
VUS
PIK3R1 c.1011T>G · p.Asp337Glu
PIK3R1

NM_181523.2:c.1011T>G (p.Asp337Glu) is a missense variant in exon 8 of PIK3R1. It is absent from all population databases including gnomAD v2.1, v4.1, and gnomAD-Canada, meeting the VCEP PM2_Supporting threshold for rarity (PM2_Supporting).

Gene
PIK3R1
Transcript
NM_181523.2
HGVS · transcript:coding
NM_181523.2:c.1011T>G
Consequence
N/A
GRCh38
chr5:68292353 T>G
GRCh37
chr5:67588181 T>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.1011T>G

NM_181523.2:c.1011T>G (p.Asp337Glu) is a missense variant in exon 8 of PIK3R1. It is absent from all population databases including gnomAD v2.1, v4.1, and gnomAD-Canada, meeting the VCEP PM2_Supporting threshold for rarity (PM2_Supporting).1 REVEL score is 0.333, which falls between the VCEP thresholds for PP3 (>= 0.644) and BP4 (<= 0.290); neither in silico criterion is met. SpliceAI predicts no splicing impact (max delta 0.02).2 No functional studies have tested this variant in any VCEP-approved assay. The variant is absent from ClinVar with no prior classifications. No publications, case reports, or segregation data exist for this variant.3 Under the Bayesian point-based framework adopted by the Antibody Deficiencies VCEP, the only met criterion is PM2_Supporting (+1 point), yielding a total score of +1, which falls in the Uncertain Significance range (0-5 points).4

PM2 VUS
3 vcep_04_08_26_pik3r1_functional_assays_ps3_bs3clinvar ↗
Gene diagram · NM_181523.2 · variants mapped to exon structure
PIK3R1 NM_181523.2
Fetching transcript structure from UCSC…
Applied criteria · 1 applied · 14 assessed
Applied · 1
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
NM_181523.2:c.1011T>G is absent from gnomAD v2.1, v4.1, and gnomAD-Canada. The total allele frequency of 0.0 is below the VCEP PM2_Supporting threshold of <0.00000132 (derived from the Whiffin/Ware calculator using autosomal dominant parameters: prevalence 1/4000, penetrance 0.95).
Absent from gnomAD v2.1 (0 alleles).Absent from gnomAD v4.1 (0 alleles).Absent from gnomAD-Canada v1.0.
Assessed · not applied
Pathogenic
PVS1 NM_181523.2:c.1011T>G is a missense variant (p.Asp337Glu).
PS1 No other nucleotide change encoding the same amino acid (p.Asp337Glu) has been classified as Pathogenic or Likely Pathogenic by the Antibody Deficiencies VCEP.
PS2 No de novo occurrence data are available for NM_181523.2:c.1011T>G.
PS3 No functional studies have been performed on NM_181523.2:c.1011T>G (p.Asp337Glu).
PS4 No probands harboring NM_181523.2:c.1011T>G have been reported.
PP1 No co-segregation data are available for NM_181523.2:c.1011T>G.
PP3 The VCEP PP3 requires REVEL >= 0.644 AND CADD >= 26.0, OR a SpliceAI delta score >= 0.2.
PP4 No proband clinical data are available for NM_181523.2:c.1011T>G.
Benign
BA1 NM_181523.2:c.1011T>G is absent from gnomAD v4.1.0 (allele frequency 0.0).
BS1 NM_181523.2:c.1011T>G is absent from gnomAD v4.1.0 (allele frequency 0.0).
BS3 No functional studies showing a non-damaging effect have been performed on NM_181523.2:c.1011T>G.
BS4 No segregation data are available for NM_181523.2:c.1011T>G.
BP4 The VCEP BP4 requires REVEL <= 0.290 AND CADD <= 21.5 AND all SpliceAI delta scores < 0.1.
BP5 No cases have been reported in which NM_181523.2:c.1011T>G was found in a patient with an alternative molecular basis for disease.
N/A · 13 PM1 · PM3 · PM4 · PM5 · PM6 · PP2 · PP5 · BS2 · BP1 · BP2 · BP3 · 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 = 0.02). REVEL score = 0.333. BayesDel score = -0.104355.
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