PTEN c.1082G>T, p.Ser361Ile

Reasoning

The PTEN VCEP applies PM2 at Supporting strength when a variant is absent in population databases, with allele frequency <0.00001 (0.001%) in gnomAD or another large sequenced population; if multiple alleles are present in a subpopulation, that subpopulation frequency must be <0.00002 (0.002%). The variant is absent from the default all-comers gnomAD v2.1 and gnomAD v4.1 datasets, satisfying the VCEP PM2 threshold.

VCEP rule

Absent in population * Databases present at <0.00001 (0.001%) allele frequency in gnomAD or another large sequenced population.  If multiple alleles are present within any subpopulation, allele frequency in that subpopulation must be <0.00002 (0.002%).

Evidence considered

• ClinGen PTEN VCEP Version 3.2, PM2 Supporting rule: databases present at <0.00001 (0.001%) allele frequency in gnomAD or another large sequenced population; if multiple alleles are present within any subpopulation, that subpopulation allele frequency must be <0.00002 (0.002%).
• gnomAD v2.1 all-comers query for NM_000314.8:c.1082G>T: absent.
• gnomAD v4.1 all-comers query for NM_000314.8:c.1082G>T: absent.

Sources

Reasoning

The variant is a missense change in PTEN, and the PTEN VCEP provides PP2 as an applicable pathogenic supporting criterion for this gene without marking it Not Applicable. Applying the VCEP's gene-specific PP2 rule, the criterion is met at Supporting strength.

VCEP rule

Missense variant in a gene that has a low rate of benign missense variation and where missense variants are a common mechanism of disease.

Evidence considered

• ClinGen PTEN VCEP Version 3.2 lists PP2 with default strength Pathogenic Supporting and the rule for a missense variant in a gene with a low rate of benign missense variation where missense variants are a common disease mechanism.
• Case normalization identifies NM_000314.8:c.1082G>T as NP_000305.3:p.(Ser361Ile), a missense variant.

Sources

Reasoning

The PTEN VCEP permits BS3_Supporting for the Mighell et al. 2018 massively parallel phosphatase assay when the Table S2 variant is listed as high confidence and has phosphatase activity (Cum_score) > 0. The exact variant was found in Table S2 as S361I / Ser361Ile, with High_conf=True and Cum_score=0.154237354. The high-confidence positive activity value satisfies the VCEP's BS3_Supporting threshold.

VCEP rule

_In vitro_ or _in vivo_ functional study or studies showing no damaging effect on protein function. * Phosphatase activity >0 per Mighell et al. 2018, PMID: 29706350.

Evidence considered

• Mighell et al. 2018 supplementary data mmc2, Table S2, row S361I / Ser361Ile: Cum_score=0.154237354; High_conf=True; High_conf_nature=Pass SE Filter; type=missense.
• The VCEP's Table S2 instruction requires High_conf=True and applies BS3_Supporting to phosphatase activity values > 0; the observed value 0.154237354 is greater than zero.

Sources

Reasoning

The PTEN VCEP BP4 rule applies to this missense variant through its missense path, which requires a REVEL score < 0.5. The available REVEL score is 0.438, satisfying that cutoff, so BP4 is met at Supporting strength. SpliceAI is not required for this missense path and is not additionally counted.

VCEP rule

Multiple lines of computational evidence suggest no impact on gene or gene product. * Splicing variants: Concordance of SpliceAl and VarSeak * Missense variants: REVEL scores < 0.5

Evidence considered

• ClinGen PTEN VCEP CSPEC BP4 rule, missense-variant path: REVEL scores < 0.5.
• Local REVEL predictor lookup: PTEN NM_000314.8:c.1082G>T (p.Ser361Ile), REVEL score 0.438; 0.438 is < 0.5.
• SpliceAI result was not additionally counted because the VCEP BP4 missense path is evaluated with REVEL and the same prediction must not be double-counted across criteria.

Sources

Reasoning

The variant is NP_000305.3:p.(Ser361Ile). The available ClinVar record for this exact variant is Uncertain significance with one single-submitter laboratory and no expert-panel submission; no previously established pathogenic variant producing the same amino-acid change was identified in the collected evidence. Therefore the PTEN VCEP PS1 condition is not met.

VCEP rule

Same amino acid change as a previously established pathogenic variant regardless of nucleotide change OR different variant at same nucleotide position as a pathogenic splicing variant, where in silico models predict impact equal to or greater than the known pathogenic variant.

Evidence considered

• ClinVar variation 1786821, NM_000314.8(PTEN):c.1082G>T (p.Ser361Ile): Uncertain significance, criteria provided, single submitter, one submission; no expert-panel submission.
• The collected evidence contains no previously established pathogenic variant producing p.Ser361Ile.

Sources

Reasoning

The PTEN VCEP permits PS3_Moderate for the Mighell et al. 2018 massively parallel phosphatase assay when the Table S2 variant is listed as high confidence and has phosphatase activity (Cum_score) <= -1.11. The exact variant was found in Table S2 as S361I / Ser361Ile, with High_conf=True and Cum_score=0.154237354. Although the result is high confidence, 0.154237354 does not meet the VCEP threshold for PS3_Moderate. No other qualifying damaging functional result for this variant was identified in the governing functional file.

VCEP rule

Well-established _in vitro_ or _in vivo_ functional studies supportive of a damaging effect on the gene or gene product. * Phosphatase activity ≤ -1.11 per Mighell et al. 2018, PMID: 29706350.

Evidence considered

• Mighell et al. 2018 supplementary data mmc2, Table S2, row S361I / Ser361Ile: Cum_score=0.154237354; High_conf=True; High_conf_nature=Pass SE Filter; type=missense.
• The variant was searched in the governing PTEN mmc2 full-text conversion under c.1082G>T, p.Ser361Ile, p.S361I, S361I, and Ser361Ile; the exact functional match is keyed as S361I / Ser361Ile in Table S2.
• The VCEP's Table S2 instruction requires High_conf=True and applies PS3_Moderate to phosphatase activity values <= -1.11; the observed value 0.154237354 is above that threshold.

Sources

Reasoning

The PTEN VCEP defines PM1 to include residues in catalytic motifs 90-94, 123-130, and 166-168 of NP_000305.3. The variant affects residue 361, outside all three specified regions. The collected Cancer Hotspots result for PTEN S361 reported no statistically significant hotspot, and the VCEP PM1 rule does not provide an additional named hotspot-source route. Therefore PM1 is not met.

VCEP rule

Located in a mutational hot spot and/or critical and well-established functional domain. Defined to include residues in catalytic motifs: 90-94, 123-130, 166-168 (NP_ 000305.3)

Evidence considered

• ClinGen PTEN VCEP Version 3.2 PM1 definition: catalytic motifs are residues 90-94, 123-130, and 166-168 (NP_000305.3); the variant is p.Ser361Ile.
• Cancer Hotspots query PTEN S361: no result; evidence sentence states that the variant does not lie in a statistically significant hotspot.

Sources

Reasoning

The PTEN VCEP requires a different missense change at the same amino-acid residue that has been determined pathogenic or likely pathogenic, plus a BLOSUM62 score for the interrogated variant equal to or less than that known variant. The collected comparator search found zero same-residue candidates meeting the pathogenic/likely pathogenic requirement. Mighell et al. supplementary Table S2 contains S361A and S361V assay rows, but those rows are functional-assay data rather than determinations that either comparator is pathogenic or likely pathogenic. Thus PM5 is not met.

VCEP rule

Missense change at an amino acid residue where a different missense change determined to be pathogenic or likely pathogenic has been seen before. In addition, variant being interrogated must have BLOSUM62 score equal to or less than the known variant.

Evidence considered

• PM5 comparator candidate collection: total candidates seen 5, same-residue candidates 0, expert-panel pathogenic/likely pathogenic candidates 0, non-expert-majority pathogenic/likely pathogenic candidates 0, conflicted candidates 0.
• Mighell et al. 2018 Supplementary Table S2, rows S361I, S361A, and S361V: saturation-mutagenesis assay rows; the table excerpt does not designate S361A or S361V as pathogenic or likely pathogenic.
• Because no qualifying known pathogenic or likely pathogenic same-residue comparator exists, the VCEP-required BLOSUM62 comparison has no eligible comparator.

Sources

Reasoning

The PTEN VCEP PP3 rule applies to this missense variant through its missense path, which requires a REVEL score > 0.7. The available REVEL score is 0.438, so the named missense predictor does not meet the pathogenic-supporting cutoff. SpliceAI is not used for PP3 here because the VCEP assigns splicing predictors to its splicing-variant path, while this variant is missense; no other computational predictor is named by the governing rule for this situation.

VCEP rule

Multiple lines of computational evidence support a deleterious effect on the gene or gene product. * Splicing variants: Concordance of SpliceAl and VarSeak * Missense variants: REVEL score > 0.7

Evidence considered

• ClinGen PTEN VCEP CSPEC PP3 rule, missense-variant path: REVEL score > 0.7.
• Local REVEL predictor lookup: PTEN NM_000314.8:c.1082G>T (p.Ser361Ile), REVEL score 0.438; 0.438 is not > 0.7.
• SpliceAI result was not counted for PP3 because the variant is missense and the VCEP rule names SpliceAl and VarSeak only under its splicing-variant path.

Sources

Reasoning

The PTEN VCEP specifies BA1 when the gnomAD filtering allele frequency is >0.00056 (0.056%). This variant is absent from gnomAD v2.1 and gnomAD v4.1, so its observed filtering allele frequency is not above the BA1 threshold.

VCEP rule

gnomAD Filtering allele frequency >0.00056 (0.056%)

Evidence considered

• ClinGen PTEN VCEP Version 3.2, BA1 rule: gnomAD Filtering allele frequency >0.00056 (0.056%).
• gnomAD v2.1 all-comers query for NM_000314.8:c.1082G>T: absent.
• gnomAD v4.1 all-comers query for NM_000314.8:c.1082G>T: absent.

Sources

Reasoning

The PTEN VCEP specifies BS1 Strong for a gnomAD filtering allele frequency from 0.000043 (0.0043%) up to 0.00056 (0.056%), and BS1 Supporting from 0.0000043 (0.00043%) up to 0.000043 (0.0043%). This variant is absent from gnomAD v2.1 and gnomAD v4.1, so no observed allele frequency falls in either BS1 interval.

VCEP rule

gnomAD Filtering allele frequency from 0.000043 (0.0043%) up to 0.00056 (0.056%)...Allele frequency from 0.0000043 (0.00043%) up to 0.000043 (0.0043%).

Evidence considered

• ClinGen PTEN VCEP Version 3.2, BS1 Strong rule: gnomAD Filtering allele frequency from 0.000043 (0.0043%) up to 0.00056 (0.056%).
• ClinGen PTEN VCEP Version 3.2, BS1 Supporting rule: Allele frequency from 0.0000043 (0.00043%) up to 0.000043 (0.0043%).
• gnomAD v2.1 all-comers query for NM_000314.8:c.1082G>T: absent.
• gnomAD v4.1 all-comers query for NM_000314.8:c.1082G>T: absent.

Sources

Reasoning

The available case evidence documents no de novo observation for NM_000314.8:c.1082G>T, no parental maternity and paternity testing, and no family-history assessment. Therefore the VCEP requirements for a proven de novo observation cannot be evaluated.

VCEP rule

De novo (both maternity and paternity confirmed) observation in a patient with the disease and no family history.

Evidence considered

• No proband-level de novo, parental-testing, or family-history evidence is present in the reviewed case materials.
• The only fetched paper, PMID:25394175, does not mention NM_000314.8:c.1082G>T or p.(Ser361Ile) and provides no de novo evidence.

Still missing

• Documented proband disease phenotype
• Documented absence of family history
• Parental testing confirming both maternity and paternity
• Number of proven or assumed de novo observations

Sources

Reasoning

The PTEN VCEP allows PS4 for a sufficiently powered case-control study with odds ratio >2, p<0.05, and a 95% confidence-interval lower limit >1.5, or for summed phenotype-specificity scores across independent probands. No affected/control counts, odds ratio, confidence interval, p-value, Cleveland Clinic scores, pediatric scores, or qualifying proband set are available for this variant. The only literature lead, PMID:25394175, was verified in its full text and does not mention c.1082G>T or p.(S361I); it therefore provides neither variant-specific case-control evidence nor a qualifying variant-specific phenotype score. The VCEP also states that PS4 may not be applied in combination with PP4, and PP4 is not applicable. PS4 cannot be evaluated with the available evidence.

VCEP rule

**PTEN EP Commentary:** This criterion is unlikely to be used in this manner for a condition as rare as PHTS. However, if sufficiently powered, a case-control study finding an odds ratio >2 for a PHTS component phenotype with p<0.05 and 95% confidence interval with lower limit >1.5, this criteria may be applied. However, this criterion may _not_ be applied in combination with PP4. ... **PTEN EP Specifications:** This criterion may not be applied if BS1 applies. ... Phenotype specificity scores are added across independent probands and calculated as follows: ... PS4\_Very Strong: Probands with specificity score ≥16. ... PS4: Probands with specificity score of 4-15.5. ... PS4\_Moderate: Probands with specificity score of 2-3.5. ... PS4\_Supporting: Proband(s) with specificity score of 1-1.5.

Evidence considered

• ClinGen PTEN VCEP specification v3.2, PS4 instructions: a case-control study requires odds ratio >2, p<0.05, and a 95% confidence-interval lower limit >1.5; alternatively, phenotype-specificity scores are summed across independent probands.
• ClinGen PTEN VCEP specification v3.2, PS4 strength rules: PS4 Very Strong requires specificity score ≥16; PS4 Strong requires 4-15.5 or significantly increased prevalence in affected individuals versus controls; PS4 Moderate requires 2-3.5; PS4 Supporting requires 1-1.5.
• No affected/control counts, odds ratio, confidence interval, p-value, Cleveland Clinic score, pediatric score, or qualifying proband-level specificity evidence is present in the case materials.
• A full-text review of PMID:25394175 found the paper does not mention PTEN c.1082G>T or p.(S361I); its PTEN syndrome phenotype discussion is not variant-specific and does not provide a case-control comparison for this variant.

Still missing

• Variant-specific affected and control counts or a reported odds ratio, p-value, and 95% confidence interval for a qualifying PHTS component phenotype.
• Independent proband-level Cleveland Clinic scores or pediatric phenotype scores sufficient to calculate the VCEP specificity score.

Sources

Reasoning

The available case evidence documents no presumed or assumed de novo observation, no proband phenotype or family-history information, and no maternity or paternity testing. The VCEP PM6 thresholds therefore cannot be evaluated.

VCEP rule

Assumed _de novo,_ but without confirmation of paternity and maternity, in proband with the disease and no family history.

Evidence considered

• No proband-level de novo observations, phenotype description, family-history assessment, or parental-testing results are present in the reviewed case materials.
• The only fetched paper, PMID:25394175, does not mention NM_000314.8:c.1082G>T or p.(Ser361Ile) and provides no de novo evidence.

Still missing

• Documented proband disease phenotype
• Documented absence of family history
• Maternity and paternity confirmation status
• Count of proven and assumed de novo observations

Sources

Reasoning

The available case evidence contains no affected relatives, familial genotype-phenotype relationships, or observed meioses. Consequently, the VCEP co-segregation thresholds of 3–4, 5–6, or at least 7 meioses cannot be assessed.

VCEP rule

Co-segregation with disease in multiple affected family members, with 3 or 4 meioses observed.

Evidence considered

• No family segregation data, affected relatives, relative genotypes, or meiosis count is present in the reviewed case materials.
• The only fetched paper, PMID:25394175, does not mention NM_000314.8:c.1082G>T or p.(Ser361Ile) and provides no segregation evidence.

Still missing

• Affected relatives and their clinical phenotypes
• Variant testing results in relatives
• Phase and inheritance information
• Number of informative meioses across families

Sources

Reasoning

The PTEN VCEP requires the variant to be observed in the homozygous state in a healthy or PHTS-unaffected individual, with one observation if homozygous status is confirmed and two if it is not confirmed; two homozygous observations without clinical data support BS2 Supporting. The available gnomAD results report absence of the variant and provide no homozygous observations or individual-level confirmation, so BS2 cannot be evaluated.

VCEP rule

Observed in the homozygous state in a healthy or PHTS-unaffected individual. One observation if homozygous status confirmed, two if not confirmed. To be applied at supporting evidence level if BS1 is also applied.

Evidence considered

• ClinGen PTEN VCEP Version 3.2, BS2 rule requires observation in the homozygous state in a healthy or PHTS-unaffected individual; one observation if confirmed and two if not confirmed; two homozygous observations without clinical data support BS2 Supporting.
• gnomAD v2.1 and v4.1 report the variant as absent and do not provide a homozygous observation or individual-level confirmation for this variant.

Still missing

• Homozygous observation count and confirmation status in healthy or PHTS-unaffected individuals are unavailable.

Sources

Reasoning

The available case evidence contains no affected family members with genotype data and no documented non-segregation. Therefore neither the VCEP one-family supporting rule nor the two-or-more-family strong rule can be evaluated.

VCEP rule

Lack of segregation in affected members of one family.

Evidence considered

• No affected-family genotype data or non-segregation observations are present in the reviewed case materials.
• The only fetched paper, PMID:25394175, does not mention NM_000314.8:c.1082G>T or p.(Ser361Ile) and provides no non-segregation evidence.

Still missing

• Affected family members and clinical status
• Genotype results for affected relatives
• Documented non-segregation in one family or two or more families

Sources

Reasoning

The PTEN VCEP permits BP2 at supporting strength when the variant is observed in trans with a pathogenic or likely pathogenic PTEN variant, or when there are at least three observations in cis and/or phase unknown with different pathogenic or likely pathogenic PTEN variants. No qualifying trans observation or three-observation cis/unknown-phase series is documented for NM_000314.8:c.1082G>T, so BP2 cannot be assessed.

VCEP rule

Observed in trans with a pathogenic or likely pathogenic PTEN variant OR at least three observations in cis and/or phase unknown with different pathogenic/likely pathogenic PTEN variants.

Evidence considered

• No affected-proband, phase, cis/trans, or pathogenic/likely pathogenic-in-trans partner observation is documented for NM_000314.8:c.1082G>T in the available case evidence.

Still missing

• Documented phase with a pathogenic or likely pathogenic PTEN variant in trans, or three observations with different pathogenic or likely pathogenic PTEN variants in cis or unknown phase.

Sources

Reasoning

The PTEN VCEP permits BP5 only when the variant is found in a case with an alternate molecular basis for disease, with at least two such cases, a highly penetrant alternate gene/disorder, and personal/family history demonstrating no overlap between that disorder and PTEN. The available evidence contains no qualifying alternate molecular diagnosis, no two qualifying cases, and no documented non-overlapping personal or family histories. BP5 therefore cannot be evaluated.

VCEP rule

Variant found in a case with an alternate molecular basis for disease. Other gene/disorder must be considered highly penetrant AND patient’s personal/family history must demonstrate no overlap between other gene and PTEN.

Evidence considered

• ClinGen PTEN VCEP specification v3.2 BP5 instruction requires at least two such cases, a highly penetrant alternate gene/disorder, and no overlap between the other gene/disorder and PTEN in the patient's personal/family history.
• No qualifying alternate molecular basis, case count, penetrance documentation, or non-overlapping personal/family history is available in the case evidence.

Still missing

• At least two variant-positive cases with a documented alternate molecular basis for disease.
• Evidence that the alternate gene/disorder is highly penetrant and that each patient's personal/family history has no overlap with PTEN.

Sources