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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 applied · 16 assessed
Applied · 3
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
This variant is absent from gnomAD v2.1 (exomes), gnomAD v4.1 (exomes), and gnomAD-Canada v1.0 (genomes). Allele frequency is below the PTEN VCEP PM2_Supporting threshold of <0.00001 (0.001%).
Absent from gnomAD v2.1Absent from gnomAD v4.1Absent from gnomAD-Canada v1.0
PP2 supporting Pathogenic
PTEN has a low rate of benign missense variation and missense variants are a common mechanism of disease (PHTS, autosomal dominant). This is a missense variant (Pro213Arg). Per PTEN VCEP v3.2.0, PP2_Supporting applies to missense variants in PTEN.
Missense variant (Pro213Arg) in PTENPTEN has low rate of benign missense variation per VCEP specificationMissense variants are a common mechanism of disease in PTEN
PP3 supporting Pathogenic
REVEL score is 0.868, exceeding the PTEN VCEP PP3 threshold of >0.7 for missense variants. This represents multiple lines of computational evidence (conservation, biochemical properties, and ensemble prediction) supporting a deleterious effect.
REVEL score 0.868 (>0.7 per VCEP PP3 threshold for missense variants)
Assessed · not applied
Pathogenic
PS1 PS1 requires the same amino acid change (Pro213Arg) to have been previously established as pathogenic regardless of nucleotide change.
PS2 No de novo observation data were identified for this variant.
PS3 PTEN VCEP PS3 criteria require either (a) RNA/mini-gene splicing impact (not applicable; SpliceAI max delta 0.05), (b) PS3_Moderate: phosphatase activity ≤ −1.11 per Mighell et al.
PS4 No proband count or phenotype specificity data are available for this variant.
PM1 PTEN VCEP defines PM1 as limited to residues in catalytic motifs: WPD loop (90-94), P-loop (123-130), and TI-loop (166-168) per NP_000305.3.
PM5 PM5 requires a different missense change at the same amino acid residue (codon 213) to have been previously classified as pathogenic or likely pathogenic.
PM6 No assumed or confirmed de novo observations were identified for this variant.
PP1 No co-segregation data are available for this variant.
Benign
BA1 This variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada.
BS1 This variant is absent from gnomAD.
BS2 BS2 requires observation in the homozygous state in a healthy or PHTS-unaffected individual.
BS3 BS3 per PTEN VCEP requires functional studies showing no damaging effect.
BS4 No segregation data are available to assess lack of segregation in affected family members.
BP2 BP2 requires observation in trans with a pathogenic/likely pathogenic PTEN variant, or at least three observations in cis/phase unknown with different pathogenic/likely pathogenic PTEN variants.
BP4 PTEN VCEP BP4_Supporting for missense variants requires REVEL score <0.5.
BP5 BP5 requires the variant to be found in a case with an alternate molecular basis for disease (at least two such cases per PTEN VCEP).
N/A · 9 PVS1 · PM3 · PM4 · PP4 · PP5 · BP1 · BP3 · 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 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