Analysis in progress
Initialising…
0%
complete
This report is still being assembled — sections appear as each stage finishes. It isn't final yet.
PPARG
Final classification
VUS
PPARG c.338C>T · p.Pro113Leu
PPARG

NM_015869.4:c.338C>T (p.Pro113Leu) in PPARG is a missense variant absent from ClinVar and present at an extremely low allele frequency of 1.24×10⁻⁶ (2/1,613,144 alleles, 0 homozygotes) in gnomAD v4.1, meeting PM2 at supporting strength (well below 0.1% threshold).

Gene
PPARG
Transcript
NM_015869.4
HGVS · transcript:coding
NM_015869.4:c.338C>T
Consequence
N/A
GRCh38
chr3:12381349 C>T
GRCh37
chr3:12422848 C>T
Basis gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM2 supporting, PP3 supporting; combination = 2 supporting, which maps to VUS.
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM2 supporting, PP3 supporting; combination = 2 supporting, which maps to VUS.
Classification rationale
PM2PP3 VUS
PPARG c.338C>T

NM_015869.4:c.338C>T (p.Pro113Leu) in PPARG is a missense variant absent from ClinVar and present at an extremely low allele frequency of 1.24×10⁻⁶ (2/1,613,144 alleles, 0 homozygotes) in gnomAD v4.1, meeting PM2 at supporting strength (well below 0.1% threshold).1 REVEL in silico prediction yields a score of 0.74, exceeding the 0.5 threshold for a deleterious call, meeting PP3 at supporting strength. SpliceAI predicts no splicing impact (max delta score 0.00) and BayesDel (0.293) is borderline.2 No functional studies, de novo reports, segregation data, or disease-specific cohort data were identified for this variant. PVS1 is not applicable as this is a missense variant (ClinGen SVI PVS1 framework, PMC6185798). All remaining assessed pathogenic and benign criteria were not met.3 With only PM2 (supporting) and PP3 (supporting) met, the evidence is insufficient to reach a Likely Pathogenic or Likely Benign classification under generic ACMG/AMP 2015 combination rules (PMID:25741868). This variant is classified as a Variant of Uncertain Significance (VUS).4

PM2 + PP3 VUS
2 revelbayesdelspliceai ↗
3 pvs1_generic_framework ↗pvs1_variant_assessmentoncokb ↗
4 generic_acmg_combination_rules
Gene diagram · NM_015869.4 · variants mapped to exon structure
PPARG NM_015869.4
Fetching transcript structure from UCSC…
Applied criteria · 2 met · select any tile
Met
Not met
Not assessed
N/A
Strength very strong supporting
Pathogenic evidence
PVS
PS
PM
PP
Benign evidence
BA
BS
BP
Rationale
Select a criterion.
Sources
Evidence used
    Gaps remaining
      Rule
      Research & evidence
      Population frequency
      gnomAD v4.1 screenshot
      gnomAD v4.1
      gnomAD v2.1 screenshot
      gnomAD v2.1
      v4.1
      This variant is present in gnomAD v4.1 (AF= 1.23981e-06; MAF= 0.00012%, 2/1613144 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 1.33579e-05; MAF= 0.00134%, 1/74862 alleles, homozygotes = 0).
      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
      0.00012% · 2 / 1,613,144
      0 hom
      African/African American
      1 / 74,862
      0.0013%
      European (non-Finnish)
      1 / 1,179,658
      8.5e-05%
      + 8 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish)
      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 = 0.74. BayesDel score = 0.293355.
      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. PPARG, a nuclear receptor, is known to behave as an oncoprotein when fused with with PAX8 in thyroid cancer.
      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
      8Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      gnomAD-Canada
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots