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PTEN
Final classification
VUS
PTEN c.722T>C · p.Phe241Ser
PTEN

The PTEN c.722T>C (p.Phe241Ser) variant has been observed in somatic cancers in COSMIC (COSV64294827, 5 occurrences) and has not been reported in the current ClinVar record set.

Gene
PTEN
Transcript
NM_000314.8
HGVS · transcript:coding
NM_000314.8:c.722T>C
Consequence
N/A
GRCh38
chr10:87957940 T>C
GRCh37
chr10:89717697 T>C
Basis PTEN CSPEC/VCEP cspec_ruleset v3.2.0 final-classification framework (Richards et al. 2015 combining rules) from final_classification_framework.json; applied criteria were PS3_Moderate, PM2_Supporting, PP2, and PP3.
PTEN CSPEC/VCEP cspec_ruleset v3.2.0 final-classification framework (Richards et al. 2015 combining rules) from final_classification_framework.json; applied criteria were PS3_Moderate, PM2_Supporting, PP2, and PP3.
Classification rationale
PS3PM2PP2PP3 VUS
PTEN c.722T>C

The PTEN c.722T>C (p.Phe241Ser) variant has been observed in somatic cancers in COSMIC (COSV64294827, 5 occurrences) and has not been reported in the current ClinVar record set.1 This variant is absent from gnomAD v2.1 and gnomAD v4.1, with an observed allele frequency of 0, which is below the PTEN Expert Panel PM2_Supporting threshold of <0.00001 (0.001%).2 Functional studies support a damaging effect on PTEN, including a Mighell et al. phosphatase assay result of Cum_score -2.399 with High_conf=True, which is below the PTEN Expert Panel PS3_Moderate threshold of <= -1.11; OncoKB also describes the variant as Likely Oncogenic with a likely loss-of-function effect.3 Computational evidence supports a deleterious effect for the missense change because the REVEL score is 0.858, above the PTEN Expert Panel PP3 threshold of >0.7, while SpliceAI predicts no significant splice effect with a maximum delta score of 0.01.4

PS3 + PM2 + PP2 + PP3 VUS
Gene diagram · NM_000314.8 · variants mapped to exon structure
PTEN NM_000314.8
Fetching transcript structure from UCSC…
Applied criteria · 4 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.
      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.
      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 = 0.01).
      Functional / OncoKB screenshot
      Functional Likely Oncogenic
      OncoKB classifies this variant as Likely Oncogenic; biological effect: Likely Loss-of-function.
      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; COSV64294827, n = 5 times).
      Hotspots
      This variant does not lie in a statistically significant hotspot.
      Literature · how each cited paper was used
      4papers cited
      Each card is an audit: what was searched, what was found, whether it names the variant, which criteria it fed, and why.
      PMID PMID:21828076
      Found
      Structured finding pending for this record — see source link.
      Applied to
      PS3 supports · met
      PMID PMID:25527629
      Found
      Structured finding pending for this record — see source link.
      Applied to
      PS3 supports · met
      PMID PMID:29706350
      Found
      Structured finding pending for this record — see source link.
      Applied to
      PS3 supports · met
      PMID PMID:32350270
      Found
      Structured finding pending for this record — see source link.
      Applied to
      PS3 supports · met
      Sources & reference links
      8Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots