PTEN c.392C>T, p.Thr131Ile

Reasoning

PS3_Moderate is met under the PTEN VCEP specification. In mmc2.xlsx, Table S2, the exact variant row T131I / Thr131Ile has High_conf=True and Cum_score=-1.91132903. The VCEP requires a high-confidence Table S2 result and applies PS3_Moderate when phosphatase activity is ≤ -1.11; -1.91132903 meets that threshold. The independently extracted PMID:21828076 functional study also reports that T131I fully abrogated PTEN PIP3 phosphatase activity in yeast, consistent with a damaging effect, but the assigned strength here is determined by the VCEP Table S2 rule.

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 mmc2.xlsx, Table S2, row T131I / Thr131Ile: High_conf=True; Cum_score=-1.91132903; assay status=missense.
• ClinGen PTEN VCEP specification v3.2: Table S2 variants must be high confidence, and PS3_Moderate applies for phosphatase activity ≤ -1.11.
• Rodríguez-Escudero et al. 2011, PMID:21828076: the exact p.T131I mutant fully abrogated PTEN PIP3 phosphatase activity in a heterologous S. cerevisiae assay.

Sources

Reasoning

The PTEN VCEP permits PM2 at Supporting strength when a variant is present at less than 0.00001 (0.001%) allele frequency in gnomAD or another large sequenced population; if multiple alleles occur in a subpopulation, that subpopulation frequency must be less than 0.00002 (0.002%). NM_000314.8:c.392C>T (p.Thr131Ile) is absent from the default all-comers gnomAD v2.1 and v4.1 datasets, satisfying an allele frequency of zero and therefore both thresholds. The VCEP rule does not specify a non-cancer or exome-only source, and the non-cancer searches are also absent.

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 specification v3.2, 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, the allele frequency in that subpopulation must be <0.00002 (0.002%).
• gnomAD v2.1: NM_000314.8:c.392C>T is absent, corresponding to no observed allele and an allele frequency of 0 in the reported dataset.
• gnomAD v4.1: NM_000314.8:c.392C>T is absent, corresponding to no observed allele and an allele frequency of 0 in the reported dataset.
• gnomAD v2.1 non-cancer and gnomAD v3.1 non-cancer searches also report the variant absent; these datasets are not separately registered source keys.

Sources

Reasoning

The ClinGen PTEN Expert Panel submission audit records two probands with presumed de novo occurrence, unconfirmed maternity/paternity, disease, and no family history. This matches the VCEP PM6 Strong rule for two presumed de novo probands. The underlying case-level pedigree and parental-test records are not provided, so human review is warranted.

VCEP rule

Two probands with presumed _de novo_ occurrence (maternity/ paternity not confirmed) with the disease and no family history.

Evidence considered

• The ClinGen PTEN Expert Panel submission audit states: two probands with presumed de novo occurrence, maternity/paternity not confirmed, in a patient with the disease and no family history.
• This evidence meets the VCEP PM6 Strong threshold of two probands with presumed de novo occurrence when maternity and paternity are not confirmed.

Still missing

• Primary case reports or laboratory records confirming the two individual observations, phenotypes, family histories, and parental testing are not available.

Sources

Reasoning

NM_000314.8:c.392C>T, NP_000305.3:p.(Thr131Ile), is a missense variant. The PTEN VCEP PP3 rule names REVEL for missense variants and requires a REVEL score > 0.7. The exact-variant REVEL score is 0.965, which exceeds the VCEP threshold; the available SpliceAI result was not used because SpliceAI is named by this rule only for splicing variants, not for this missense situation. PP3 is met at supporting strength.

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 v3.2 PP3 rule: for missense variants, the named predictor is REVEL and the cutoff is >0.7.
• Local REVEL predictor lookup for NM_000314.8:c.392C>T / NP_000305.3:p.(Thr131Ile): REVEL score = 0.965; this exceeds the VCEP PP3 missense cutoff.
• SpliceAI max delta score = 0.004 was not used for PP3 because the VCEP rule assigns SpliceAI to its splicing-variant path, whereas this variant is missense.

Sources

Reasoning

Expert panel Clingen PTEN Variant Curation Expert Panel, Clingen classified as Pathogenic.

VCEP rule

This criterion is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee.

Evidence considered

• ClinGen PTEN VCEP specification v3.2 marks PP5 not applicable for this VCEP; the ClinVar expert-panel pathogenic classification was not used as PP5.
• ClinVar expert panel classification

Sources

Reasoning

The variant affects residue 131. The VCEP defines PM1 to include catalytic-motif residues 90-94, 123-130, and 166-168 of NP_000305.3; residue 131 is outside all three specified intervals. The case hotspot search found no statistically significant hotspot, and vcep_materials.json contains no PTEN domain_tables entry requiring an additional authoritative domain interval check. Thus the VCEP PM1 location requirement 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

• The variant is NP_000305.3:p.(Thr131Ile), so the affected residue is 131.
• The VCEP PM1 rule defines catalytic-motif residues 90-94, 123-130, and 166-168 in NP_000305.3; residue 131 is not in any interval.
• The case hotspot result reports no statistically significant hotspot for PTEN T131.
• The vcep_materials.json domain_tables object is empty, so there is no gene-specific authoritative domain-table entry to extend the listed VCEP intervals.

Sources

Reasoning

The PTEN VCEP defines BA1 as a gnomAD Filtering allele frequency greater than 0.00056 (0.056%). NM_000314.8:c.392C>T (p.Thr131Ile) is reported absent from the default all-comers gnomAD v2.1 and v4.1 datasets, so no allele frequency exceeding the BA1 threshold is present. The VCEP rule does not specify a non-cancer or exome-only source for BA1, and the available non-cancer searches are also absent.

VCEP rule

gnomAD Filtering allele frequency >0.00056 (0.056%)

Evidence considered

• ClinGen PTEN VCEP specification v3.2, BA1 rule: gnomAD Filtering allele frequency >0.00056 (0.056%).
• gnomAD v2.1: NM_000314.8:c.392C>T is absent; no allele frequency or allele count is reported.
• gnomAD v4.1: NM_000314.8:c.392C>T is absent; no allele frequency or allele count is reported.
• gnomAD v2.1 non-cancer and gnomAD v3.1 non-cancer searches also report the variant absent; these datasets are not separately registered source keys.

Sources

Reasoning

The PTEN VCEP defines BS1 Strong as a gnomAD Filtering allele frequency from 0.000043 (0.0043%) up to 0.00056 (0.056%), and BS1 Supporting as 0.0000043 (0.00043%) up to 0.000043 (0.0043%). NM_000314.8:c.392C>T (p.Thr131Ile) is absent from gnomAD v2.1 and v4.1, so the available data do not show an allele frequency in either BS1 interval. The VCEP rule does not specify a non-cancer or exome-only source for BS1, and the available non-cancer searches are also absent.

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 specification v3.2, BS1 Strong rule: gnomAD Filtering allele frequency from 0.000043 (0.0043%) up to 0.00056 (0.056%).
• ClinGen PTEN VCEP specification v3.2, BS1 Supporting rule: allele frequency from 0.0000043 (0.00043%) up to 0.000043 (0.0043%).
• gnomAD v2.1: NM_000314.8:c.392C>T is absent; no allele frequency or allele count is reported.
• gnomAD v4.1: NM_000314.8:c.392C>T is absent; no allele frequency or allele count is reported.
• gnomAD v2.1 non-cancer and gnomAD v3.1 non-cancer searches also report the variant absent; these datasets are not separately registered source keys.

Sources

Reasoning

BS3 is not met. The governing PTEN VCEP BS3_Supporting rule requires phosphatase activity >0 in the Mighell et al. 2018 Table S2 assay, whereas the exact high-confidence T131I / Thr131Ile row has Cum_score=-1.91132903. The independently extracted PMID:21828076 study likewise reports complete loss of PIP3 phosphatase activity for T131I rather than absence of a damaging effect.

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 mmc2.xlsx, Table S2, row T131I / Thr131Ile: High_conf=True; Cum_score=-1.91132903, which does not satisfy the VCEP BS3 threshold >0.
• ClinGen PTEN VCEP specification v3.2: BS3_Supporting applies to phosphatase activity >0 per Mighell et al. 2018; no BS3 strength is assigned because this variant's measured activity is damaging.
• Rodríguez-Escudero et al. 2011, PMID:21828076: the exact p.T131I mutant fully abrogated PTEN PIP3 phosphatase activity in yeast, not a no-damage result.

Sources

Reasoning

NM_000314.8:c.392C>T, NP_000305.3:p.(Thr131Ile), is a missense variant. The PTEN VCEP BP4 rule names REVEL for missense variants and requires a REVEL score < 0.5. The exact-variant REVEL score is 0.965, so the VCEP BP4 missense condition is not met. The available SpliceAI result was not used because SpliceAI is named by this rule only for splicing variants, not for this missense situation.

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 v3.2 BP4 rule: for missense variants, the named predictor is REVEL and the cutoff is <0.5.
• Local REVEL predictor lookup for NM_000314.8:c.392C>T / NP_000305.3:p.(Thr131Ile): REVEL score = 0.965; this does not satisfy the VCEP BP4 missense cutoff.
• SpliceAI max delta score = 0.004 was not used for BP4 because the VCEP rule assigns SpliceAI to its splicing-variant path, whereas this variant is missense.

Sources

Reasoning

The variant is NP_000305.3:p.(Thr131Ile). The governing rule requires the same amino acid change as a previously established pathogenic variant, regardless of nucleotide change, or an alternative variant at the same nucleotide position as a pathogenic splicing variant with equivalent or greater predicted impact. The available evidence includes a functional study mentioning T131L and T131I, but it does not establish an alternate T131 missense change as pathogenic, and no pathogenic splicing comparator at c.392 was provided. Therefore PS1 cannot be assessed from the available VCEP-governed evidence.

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

• The variant is NP_000305.3:p.(Thr131Ile).
• ClinGen PTEN VCEP PS1 requires the same amino acid change as a previously established pathogenic variant, regardless of nucleotide change, or a different variant at the same nucleotide position as a pathogenic splicing variant with equal or greater predicted impact.
• Rodríguez-Escudero et al. report T131I and T131L in a yeast PIP3 phosphatase assay, but the extracted paper finding does not establish an alternate T131 missense variant as pathogenic.

Still missing

• A previously established pathogenic variant producing the same p.Thr131Ile amino acid change through a different nucleotide change, or a qualifying pathogenic-splicing comparator at c.392, is required.

Sources

Reasoning

The available evidence describes presumed de novo observations without confirmation of maternity and paternity. The PTEN VCEP PS2 rule requires both maternity and paternity to be confirmed for the Strong level, and no evidence establishes the Very Strong PS2 observation counts.

VCEP rule

Strong: De novo (both maternity and paternity confirmed) observation in a patient with the disease and no family history. Very Strong: Two proven OR four assumed OR one proven + two assumed de novo observations in a patient with the disease and no family history.

Evidence considered

• The ClinGen PTEN Expert Panel submission audit records a signal for presumed de novo occurrence but does not provide confirmed maternity and paternity; it therefore does not satisfy the VCEP PS2 Strong rule.
• The available literature extraction for PMID:23160955 reports a de novo PTEN mutation burden in an autism cohort but does not explicitly report PTEN c.392C>T (p.Thr131Ile).

Still missing

• Confirmation of both maternity and paternity for a qualifying affected proband is not available.
• The number of proven or assumed de novo observations qualifying for PS2 Very Strong is not independently documented.

Sources

Reasoning

The PTEN VCEP permits PS4 from a case-control result with odds ratio >2, p<0.05, and a 95% confidence-interval lower limit >1.5, or from independent proband phenotype-specificity scores. The available evidence provides no case-control odds ratio, p-value, confidence interval, Cleveland Clinic score, pediatric phenotype score, or aggregate specificity score for this variant. The reviewed literature describes PTEN-associated cohorts or phenotypes but does not provide the required variant-specific PS4 metric. Therefore PS4 cannot be evaluated under the VCEP rule.

VCEP rule

This criterion may not be applied if BS1 applies. Phenotype specificity scores are added across independent probands and calculated as follows: ... PS4: Probands with specificity score of 4-15.5. ... PS4_Supporting: Proband(s) with specificity score of 1-1.5.

Evidence considered

• ClinGen PTEN VCEP specification v3.2: PS4 may use a sufficiently powered case-control study with odds ratio >2, p<0.05, and 95% confidence-interval lower limit >1.5, or phenotype-specificity scores summed across independent probands.
• ClinVar record for NM_000314.8:c.392C>T (p.Thr131Ile) lists disease conditions including macrocephaly-autism syndrome, diffuse pediatric-type high-grade glioma, and PTEN hamartoma tumor syndrome, but supplies no PS4 specificity score or case-control statistic.
• PMID:23160955 reports macrocephaly in individuals with PTEN mutations but does not explicitly report c.392C>T/p.(T131I) or a qualifying variant-specific PS4 metric.
• PMID:22748663 reports pediatric glioma PTEN mutation/deletion frequencies but does not mention c.392C>T/p.(T131I) or provide the VCEP-required variant-specific case-control statistic.
• PMID:23335809 reports a 146-person PTEN cohort and genotype-phenotype analyses but does not mention c.392C>T/p.(T131I) or provide a qualifying specificity score for this variant.

Still missing

• Variant-specific case-control odds ratio, p-value, and 95% confidence interval, or qualifying independent-proband Cleveland Clinic/pediatric phenotype scores, are unavailable.

Sources

Reasoning

The variant is p.Thr131Ile. The VCEP PM5 rule 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 queried variant equal to or lower than that known variant. The available PM5 candidate collection found no same-residue candidates and supplies no qualifying comparator or BLOSUM62 comparison; therefore PM5 is not assessed.

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

• The variant is NP_000305.3:p.(Thr131Ile), affecting residue 131.
• The VCEP PM5 rule requires a different missense change at the same residue that is pathogenic or likely pathogenic and requires the queried variant's BLOSUM62 score to be equal to or lower than the known variant's score.
• The PM5 candidate artifact reports zero same-residue candidates, zero expert-panel pathogenic/likely pathogenic candidates, and zero non-expert majority pathogenic/likely pathogenic candidates; it provides no BLOSUM62 comparator calculation.

Still missing

• A different p.Thr131 missense variant determined pathogenic or likely pathogenic and its applicable BLOSUM62 score are required.

Sources

Reasoning

No case-level segregation observations, affected relatives, or meiosis count are available for this variant. The literature extraction does not report variant-specific segregation, so none of the VCEP PP1 thresholds can be evaluated.

VCEP rule

Strong: Co-segregation with disease in multiple affected family members, with ≥7 meioses observed across at least two families. Moderate: Co-segregation with disease in multiple affected family members, with 5 or 6 meioses observed. Supporting: Co-segregation with disease in multiple affected family members, with 3 or 4 meioses observed.

Evidence considered

• The available evidence contains no variant-specific co-segregation results or meiosis count for PTEN c.392C>T (p.Thr131Ile).

Still missing

• Variant-level segregation data in affected family members are not available.
• The number of observed meioses across families is not available.

Sources

Reasoning

The VCEP PP2 rule requires both a low rate of benign missense variation in the gene and missense variants being a common disease mechanism. The available VCEP-governed evidence does not provide a gene-level benign-missense-rate assessment or an explicit VCEP determination that missense variation is a common PTEN disease mechanism. The criterion therefore cannot be assessed without importing a non-VCEP threshold or assumption.

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

• The VCEP PP2 rule requires a low rate of benign missense variation and missense variants to be a common mechanism of disease.
• The available case evidence does not contain a VCEP-specific benign-missense-rate value or an explicit VCEP statement satisfying both PP2 conditions.

Still missing

• A VCEP-governed assessment of PTEN benign missense variation rate and missense disease-mechanism prevalence is required.

Sources

Reasoning

The PTEN VCEP requires observation of the variant in the homozygous state in a healthy or PHTS-unaffected individual. The available population evidence reports the variant as absent from gnomAD v2.1, v4.1, v2.1 non-cancer, and v3.1 non-cancer, and provides no homozygote observations, parental confirmation, or clinical-status information. Therefore 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 specification v3.2, BS2 Strong rule: observed in the homozygous state in a healthy or PHTS-unaffected individual; one observation if homozygous status is confirmed and two if not confirmed; apply at supporting level if BS1 is also applied.
• gnomAD v2.1, gnomAD v4.1, gnomAD v2.1 non-cancer, and gnomAD v3.1 non-cancer all report the variant absent and provide no homozygote observation or clinical-status record.

Still missing

• A confirmed or appropriately documented homozygous observation in a healthy or PHTS-unaffected individual is required.

Sources

Reasoning

No affected family members carrying the variant are described as non-segregating, and no family-level segregation data are available. Therefore, the VCEP BS4 thresholds for one or two or more families cannot be evaluated.

VCEP rule

Strong: Lack of segregation in affected members of two or more families. Supporting: Lack of segregation in affected members of one family.

Evidence considered

• The available evidence contains no affected-family non-segregation observation for PTEN c.392C>T (p.Thr131Ile).

Still missing

• Family-level non-segregation data are not available.

Sources

Reasoning

The VCEP BP2 rule requires either observation of the queried variant in trans with a pathogenic or likely pathogenic PTEN variant, or at least three observations in cis and/or phase unknown with different pathogenic or likely pathogenic PTEN variants. The available case evidence does not document a qualifying trans observation, three qualifying cis or phase-unknown observations, or the relevant phase and partner-variant details. The criterion therefore cannot be evaluated.

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 case-level report in the reviewed evidence documents NM_000314.8:c.392C>T in trans with a pathogenic or likely pathogenic PTEN variant.
• No set of at least three observations in cis and/or phase unknown with different pathogenic or likely pathogenic PTEN variants is documented; ClinVar classification and functional observations do not establish this allelic evidence.

Still missing

• A qualifying pathogenic or likely pathogenic PTEN partner variant and its phase relative to NM_000314.8:c.392C>T are not documented.
• There are not three documented cis and/or phase-unknown observations involving different pathogenic or likely pathogenic PTEN variants.

Sources

Reasoning

The PTEN VCEP requires a variant found in a case with an alternate molecular basis, at least two such cases, a highly penetrant other gene/disorder, and personal or family history showing no overlap between that disorder and PTEN. The available case bundle contains no qualifying alternate-gene diagnoses, two-case series, or documented non-overlapping personal/family histories for NM_000314.8:c.392C>T. Therefore BP5 cannot be evaluated.

VCEP rule

At least two such cases are required for criteria to apply. In addition, the other gene/disorder must be considered highly penetrant AND the patient’s personal/family history must demonstrate no overlap between the other gene and PTEN. ... 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 requires at least two cases, a highly penetrant alternate gene/disorder, and personal/family history demonstrating no overlap between the alternate disorder and PTEN.
• No case-level alternate molecular basis or qualifying non-overlapping personal/family history is provided for this variant.

Still missing

• At least two qualifying cases with an alternate highly penetrant molecular diagnosis and documented absence of phenotype overlap with PTEN are unavailable.

Sources