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PTEN
Final classification
Likely Pathogenic
PTEN c.368A>G · p.His123Arg
PTEN

c.368A>G (p.His123Arg) is a missense variant in exon 5 of PTEN, within the phosphatase catalytic motif (residues 123-130).

Gene
PTEN
Transcript
NM_000314.8
HGVS · transcript:coding
NM_000314.8:c.368A>G
Consequence
N/A
GRCh38
chr10:87933127 A>G
GRCh37
chr10:89692884 A>G
Basis Richards et.al., 2015 - Combining rules v3.2.0 criteria-combination framework: matched Rule13 (Pathogenic.Moderate >=3) with applied criteria: PS3 moderate, PM1 moderate, PM2 supporting, PM6 moderate, PP2 supporting, PP3 supporting, PP5 supporting; maps to Likely Pathogenic.
Richards et.al., 2015 - Combining rules v3.2.0 criteria-combination framework: matched Rule13 (Pathogenic.Moderate >=3) with applied criteria: PS3 moderate, PM1 moderate, PM2 supporting, PM6 moderate, PP2 supporting, PP3 supporting, PP5 supporting; maps to Likely Pathogenic.
Classification rationale
PS3PM1PM2PM6PP2PP3PP5 Likely Pathogenic
PTEN c.368A>G

c.368A>G (p.His123Arg) is a missense variant in exon 5 of PTEN, within the phosphatase catalytic motif (residues 123-130).1 The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada, meeting PM2_Supporting under PTEN VCEP rules.2 His123 is located within the VCEP-defined catalytic motif, meeting PM1_Moderate.3 The variant has been classified as Pathogenic by the ClinGen PTEN Variant Curation Expert Panel (ClinVar SCV000863477, reviewed by expert panel).4 In the Mighell et al. 2018 (PMID:29706350) saturation mutagenesis phosphatase activity assay, H123R has a cumulative fitness score of -3.83 (High_conf = True), meeting the PTEN VCEP threshold for PS3_Moderate (Cum_score <= -1.11).5 The ClinGen PTEN VCEP applied PM6_Moderate, noting an assumed de novo occurrence (parentage unconfirmed) in a patient with Cowden syndrome (Nelen et al. 1999, PMID:10234502).6 Computational evidence supports pathogenicity: REVEL score 0.985 meets PP3_Supporting; PTEN's low rate of benign missense variation supports PP2_Supporting.7 The ClinGen PTEN VCEP classification as Pathogenic supports PP5_Supporting, applied per user directive to override VCEP Not Applicable when expert panel classification exists.8

PS3 + PM1 + PM2 + PM6 + PP2 + PP3 + PP5 Likely Pathogenic
Gene diagram · NM_000314.8 · variants mapped to exon structure
PTEN NM_000314.8
Fetching transcript structure from UCSC…
Applied criteria · 7 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 · supports pathogenic
      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 has been reported in ClinVar as Pathogenic (4 clinical laboratories) and as Pathogenic by Clingen PTEN Variant Curation Expert Panel, Clingen (expert panel). (ClinVarID = 7816)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01). REVEL score = 0.985. BayesDel score = 0.61462.
      Functional / OncoKB screenshot
      Functional Likely Oncogenic
      OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Loss-of-function; curated oncogenicity label: Likely Oncogenic.
      OncoKB ↗
      COSMIC screenshot
      COSMIC
      Cancer hotspots screenshot
      Cancer hotspots
      Somatic evidence Hotspot
      COSMIC
      This variant lies in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV64309701, n = 4 times).
      Hotspots
      This variant lies 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
      Triaged references · 8 PMIDs not cited in assessment
      10555148 ↗ Crystal structure of the PTEN tumor suppressor: implications for its phosphoinositide phosphatase activity and membrane association. CLINVAR
      10772829 ↗ Cell cycle arrest by the PTEN tumor suppressor is target cell specific and may require protein phosphatase activity. CLINVAR
      16619501 ↗ Tumour suppressor PTEN regulates cell cycle and protein kinase B/Akt pathway in breast cancer cells. CLINVAR
      21828076 ↗ A comprehensive functional analysis of PTEN mutations: implications in tumor- and autism-related syndromes. CLINVAR
      23161105 ↗ A new insight into structural and functional impact of single-nucleotide polymorphisms in PTEN gene. CLINVAR
      25527629 ↗ Functionally distinct groups of inherited PTEN mutations in autism and tumour syndromes. CLINVAR
      25741868 ↗ Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. CLINVAR
      26800850 ↗ Prediction of functionally significant single nucleotide polymorphisms in PTEN tumor suppressor gene: An in silico approach. CLINVAR