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PTEN
Final classification
VUS
PTEN c.544T>G · p.Leu182Val
PTEN

NM_000314.8:c.544T>G (p.Leu182Val) is a missense variant in exon 6 of PTEN. It is absent from gnomAD v2.1 and v4.1 (0/1,612,242 alleles), meeting PM2_Supporting per the PTEN VCEP threshold of <0.001%.

Gene
PTEN
Transcript
NM_000314.8
HGVS · transcript:coding
NM_000314.8:c.544T>G
Consequence
N/A
GRCh38
chr10:87952169 T>G
GRCh37
chr10:89711926 T>G
Basis Richards et.al., 2015 - Combining rules v3.2.0 criteria-combination framework was evaluated deterministically with applied criteria: PS3 moderate, PM2 supporting, PP2 supporting; no rule matched the adjudicated criteria.
Richards et.al., 2015 - Combining rules v3.2.0 criteria-combination framework was evaluated deterministically with applied criteria: PS3 moderate, PM2 supporting, PP2 supporting; no rule matched the adjudicated criteria.
Classification rationale
PS3PM2PP2 VUS
PTEN c.544T>G

NM_000314.8:c.544T>G (p.Leu182Val) is a missense variant in exon 6 of PTEN. It is absent from gnomAD v2.1 and v4.1 (0/1,612,242 alleles), meeting PM2_Supporting per the PTEN VCEP threshold of <0.001%.1 In the Mighell et al. 2018 (PMID:29706350) saturation mutagenesis functional assay, L182V has a cumulative fitness score of -1.24 (High_conf=True), meeting the PTEN VCEP PS3_Moderate threshold of Cum_score <= -1.11, indicating a damaging effect on PTEN phosphatase activity.2 PTEN is a gene with a low rate of benign missense variation where missense variants are a common mechanism of disease (PHTS, autosomal dominant). PP2 is applied at Supporting level per the PTEN VCEP specification.3 L182V REVEL score is 0.682, below the PTEN VCEP PP3 threshold of >0.7, and above the BP4 missense threshold of <0.5. Computational evidence is indeterminate and does not contribute to either pathogenic or benign criteria.4 The variant lies outside PTEN catalytic motifs (WPD loop 90-94, P-loop 123-130, TI-loop 166-168). PM1 is not met.5 L182S (c.545T>C) is a pathogenic ClinVar missense at the same residue, but PM5 is not met because the BLOSUM62 score for Leu->Val (+1) is greater than Leu->Ser (-2), failing the VCEP BLOSUM62 requirement.6 No proband, segregation, de novo, or case-control data are available. PS2, PS4, PM6, PP1, BS4, BP2, and BP5 are not met. Criteria not applicable per the PTEN VCEP include PVS1 (missense, not null), PP4, PP5, BP1, BP6, and BP7.7 Overall, met criteria: PS3_Moderate (1 moderate), PM2_Supporting (1 supporting), PP2 (1 supporting). This yields 1 moderate + 2 supporting pathogenic criteria with no benign criteria. Under the PTEN VCEP/ACMG 2015 combination rules, Likely Pathogenic requires at least 3 moderate, or 2 moderate + >=2 supporting, or 1 strong + >=2 supporting, or 1 strong + 1 moderate. With only 1 moderate + 2 supporting, none of the Pathogenic or Likely Pathogenic rules are satisfied. The variant is classified as a Variant of Uncertain Significance (VUS).8

PS3 + PM2 + PP2 VUS
Gene diagram · NM_000314.8 · variants mapped to exon structure
PTEN NM_000314.8
Fetching transcript structure from UCSC…
Applied criteria · 3 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= 0; MAF= 0.00000%, 0/1612242 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 0; MAF= 0.00000%, 0/74972 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
      Absent · 0 / 1,612,242
      0 hom
      Not observed in any ancestry group.
      + 10 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American, European (non-Finnish))
      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 = 0.682. BayesDel score = 0.205836.
      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. PTEN, a lipid and protein phosphatase, is one of the most frequently mutated genes in 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 previously been reported in somatic cancers (COSMIC; COSV64288496, n = 3 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