Starting
Initialising…
0%
PTEN
Final classification
VUS
PTEN c.638C>G · p.Pro213Arg
PTEN

NM_000314.8:c.638C>G (p.Pro213Arg) is absent from all queried population databases (gnomAD v2.1, v4.1, Canada), meeting PM2_Supporting per PTEN VCEP v3.2.0.

Gene
PTEN
Transcript
NM_000314.8
HGVS · transcript:coding
NM_000314.8:c.638C>G
Consequence
N/A
GRCh38
chr10:87957856 C>G
GRCh37
chr10:89717613 C>G
Basis Richards et.al., 2015 - Combining rules v3.2.0 criteria-combination framework was evaluated deterministically with applied criteria: PM2 supporting, PP2 supporting, PP3 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: PM2 supporting, PP2 supporting, PP3 supporting; no rule matched the adjudicated criteria.
Classification rationale
PM2PP2PP3 VUS
PTEN c.638C>G

NM_000314.8:c.638C>G (p.Pro213Arg) is absent from all queried population databases (gnomAD v2.1, v4.1, Canada), meeting PM2_Supporting per PTEN VCEP v3.2.0.1 PP2_Supporting is applied: this is a missense variant in PTEN, a gene with a low rate of benign missense variation where missense variants are a common disease mechanism per PTEN VCEP.2 PP3_Supporting is applied: REVEL score 0.868 exceeds the PTEN VCEP threshold of >0.7 for missense variants, supporting a deleterious computational prediction.3 PS3 was not met: the variant was not directly measured in the Mighell et al. 2018 phosphatase activity assay (Cum_score=NA), and the imputed score (−0.629) does not meet the PS3_Moderate threshold of ≤−1.11. No other variant-specific functional studies were identified.4 PM1 was not met: codon 213 lies outside the VCEP-defined catalytic motifs (residues 90-94, 123-130, 166-168). No statistically significant hotspot was identified at this residue.5 PVS1 is not applicable: the PTEN PVS1 decision tree is restricted to null variants (nonsense, frameshift, canonical splice site disruptions, exon deletions); missense substitutions are not within scope.6 Remaining pathogenic criteria (PS1, PS2, PS4, PS5, PM5, PM6, PP1, PP4, PP5) and benign criteria (BA1, BS1-BS4, BP1-BP7) are either not met, not assessed due to absent data, or not applicable per PTEN VCEP v3.2.0.7 Total evidence: PM2_Supporting + PP2_Supporting + PP3_Supporting. Per the PTEN VCEP classification rules (Richards et al. 2015 combination framework), this does not meet any pathogenic or likely pathogenic rule: Rule 4 requires one very strong criterion plus ≥2 supporting, which is not satisfied. The evidence is insufficient for classification beyond Variant of Uncertain Significance.8

PM2 + PP2 + PP3 VUS
3 revelcspec ↗
4 vcep_mmc2
6 vcep_pvs1_decisiontree_pten
8 cspec ↗final_classification_framework
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
      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 = 0.05). REVEL score = 0.868. BayesDel score = 0.341906.
      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; COSV64295816, n = 1 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