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PTEN
Final classification
VUS
PTEN c.532T>G · p.Tyr178Asp
PTEN

NM_000314.8:c.532T>G (p.Tyr178Asp) is a missense variant in PTEN exon 6. This variant is absent from gnomAD v2.1 and v4.1 population databases (PM2_Supporting).

Gene
PTEN
Transcript
NM_000314.8
HGVS · transcript:coding
NM_000314.8:c.532T>G
Consequence
N/A
GRCh38
chr10:87952157 T>G
GRCh37
chr10:89711914 T>G
Basis ClinGen PTEN Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for PTEN Version 3.2 v3.2 criteria-combination framework was evaluated deterministically with applied criteria: PS3 moderate, PM2 supporting, PP2 supporting, PP3 supporting; no rule matched the adjudicated criteria.
ClinGen PTEN Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for PTEN Version 3.2 v3.2 criteria-combination framework was evaluated deterministically with applied criteria: PS3 moderate, PM2 supporting, PP2 supporting, PP3 supporting; no rule matched the adjudicated criteria.
Classification rationale
PS3PM2PP2PP3 VUS
PTEN c.532T>G

NM_000314.8:c.532T>G (p.Tyr178Asp) is a missense variant in PTEN exon 6. This variant is absent from gnomAD v2.1 and v4.1 population databases (PM2_Supporting).1 Functional assessment via saturation mutagenesis phosphatase activity assay (Mighell et al. 2018, PMID: 29706350) demonstrates a cumulative fitness score of -4.72, well below the VCEP PS3_Moderate threshold of <= -1.11, with high-confidence measurement (PS3_Moderate).2 Computational predictions support a deleterious effect: REVEL score of 0.958 exceeds the VCEP PP3 threshold of > 0.7 (PP3). PTEN has a low rate of benign missense variation and missense variants are a common disease mechanism (PP2).3 This variant has been reported in ClinVar as Uncertain significance by a single submitter (VCV000945254) and in COSMIC as a somatic variant (COSV64304856, n=1). OncoKB classifies it as Likely Oncogenic in the somatic context.4 Position 178 is outside the VCEP-defined PM1 catalytic motifs (WPD loop 90-94, P-loop 123-130, TI-loop 166-168). No alternate pathogenic missense at residue 178 was identified for PM5. No de novo, cosegregation, or case-control data are available.5 Applying the PTEN VCEP v3.2 combination rules: one moderate criterion (PS3_Moderate) and three supporting criteria (PM2_Supporting, PP2, PP3) are met. No combination rule for Likely Pathogenic is satisfied (Rule 13 requires >=3 moderate; Rule 14 requires 2 moderate + >=2 supporting; Rule 15 requires 1 moderate + >=4 supporting). The variant is classified as Uncertain Significance.6

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 applied · 15 assessed
Applied · 4
Strength Supporting Moderate Strong Very strong
PS3 moderate Pathogenic
Y178D (Tyr178Asp) has a cumulative fitness score of -4.72 in the Mighell et al. 2018 (PMID: 29706350) saturation mutagenesis phosphatase activity assay, well below the PTEN VCEP PS3_Moderate threshold of <= -1.11. The measurement is flagged as high confidence (High_conf=True). This constitutes well-established in vitro functional evidence of a damaging effect on phosphatase activity.
Mighell et al. 2018 saturation mutagenesis: Y178D Cum_score = -4.72High_conf = True. Exceeds PS3_Moderate threshold (<= -1.11) per PTEN VCEP v3.2.
PM2 supporting Pathogenic
NM_000314.8:c.532T>G is absent from gnomAD v2.1, v4.1, and gnomAD-Canada, meeting the PTEN VCEP PM2_Supporting threshold of allele frequency < 0.001% (0.00001).
Absent from gnomAD v2.1 (exomes)gnomAD v4.1 (exomes)and gnomAD-Canada v1.0. Allele frequency effectively 0
PP2 supporting Pathogenic
PTEN has a low rate of benign missense variation and missense variants are a common mechanism of disease in PTEN hamartoma tumor syndrome. This missense variant (Tyr178Asp) meets the PTEN VCEP PP2 criterion.
PTEN is a gene with low benign missense variation rate where missense variants are a common disease mechanism per VCEP v3.2.
PP3 supporting Pathogenic
REVEL score of 0.958 exceeds the PTEN VCEP PP3 threshold of > 0.7 for missense variants, indicating multiple lines of computational evidence support a deleterious effect.
REVEL score = 0.958exceeding VCEP PP3 missense threshold of > 0.7. BayesDel score = 0.593 provides additional in silico support.
Assessed · not applied
Pathogenic
PS1 PS1 requires the same amino acid change (Tyr178Asp) to have been previously established as pathogenic from a different nucleotide change.
PS2 No de novo observation data are available for this variant.
PS4 PS4 requires proband specificity scores or significantly increased prevalence in affected individuals.
PM1 The PTEN VCEP defines PM1 for residues in catalytic motifs: WPD loop (90-94), P-loop (123-130), and TI-loop (166-168).
PM5 PM5 requires a different missense change at the same residue (Tyr178) with established pathogenic or likely pathogenic classification, with the variant under assessment having an equal or lower BLOSUM62 score.
PM6 No assumed or confirmed de novo data are available for this variant.
PP1 No cosegregation data are available for this variant.
Benign
BA1 BA1 requires filtering allele frequency > 0.056% in gnomAD.
BS1 BS1 requires filtering allele frequency of 0.00043%-0.056% in gnomAD.
BS2 BS2 requires observation in the homozygous state in a healthy or PHTS-unaffected individual.
BS3 BS3_Supporting requires phosphatase activity > 0 per Mighell et al.
BS4 No lack of segregation data are available for this variant.
BP2 No evidence of this variant observed in trans with a P/LP PTEN variant or in cis with different P/LP PTEN variants.
BP4 BP4 for missense variants requires REVEL score < 0.5 per PTEN VCEP.
BP5 No evidence that this variant has been found in a case with an alternate molecular basis for disease.
N/A · 6 PVS1 · PP4 · PP5 · BP1 · BP6 · BP7
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 has been reported in ClinVar as Uncertain significance (1 clinical laboratory). (ClinVarID = 945254)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.958. BayesDel score = 0.593216.
Functional / OncoKB screenshot
Functional Likely Oncogenic
OncoKB identified variant-specific curated literature and context relevant to functional review; 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; COSV64304856, n = 1 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 · 6 PMIDs not cited in assessment
17392385 ↗ American Cancer Society guidelines for breast screening with MRI as an adjunct to mammography. CLINVAR
20301661 ↗ PTEN Hamartoma Tumor Syndrome. CLINVAR
25190698 ↗ Genetic/familial high-risk assessment: breast and ovarian, version 1.2014. CLINVAR
26389210 ↗ Genetics of Breast and Gynecologic Cancers (PDQ®): Health Professional Version. CLINVAR
26389258 ↗ Cancer Genetics Risk Assessment and Counseling (PDQ®): Health Professional Versi CLINVAR
28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR