PTEN c.383A>C, p.(Lys128Thr)

Reasoning

PS3 is met at Moderate strength under the PTEN VCEP Version 3.2 specification. The governing mmc2.xlsx Table S2 record for K128T/Lys128Thr reports a directly measured cumulative fitness score (Cum_score) of -1.97828658 with High_conf=True and Pass SE Filter. The VCEP rule specifies PS3_Moderate for phosphatase activity at or below -1.11 per Mighell et al. 2018 (PMID:29706350), and -1.97828658 is below that threshold. The independent functional study by Rodríguez-Escudero et al. explicitly tested K128T in a heterologous Saccharomyces cerevisiae PIP3-phosphatase assay and reported that it fully abrogated PTEN PIP3 phosphatase activity, supporting the biological relevance and damaging direction of the VCEP assay result. The assay evidence is variant-specific and directly measures PTEN function; no upgrade beyond the VCEP-specified Moderate level is justified.

Rule

PS3_Moderate: PTEN phosphatase activity <= -1.11 per Mighell et al. 2018 (PMID:29706350).

Evidence considered

• PTEN VCEP Version 3.2 specifies PS3_Moderate when phosphatase activity is <= -1.11 per Mighell et al. 2018 (PMID:29706350).
• The governing mmc2.xlsx Table S2 record for K128T/Lys128Thr reports Cum_score = -1.97828658, High_conf = True, and High_conf_nature = Pass SE Filter; -1.97828658 meets the <= -1.11 PS3_Moderate rule.
• Rodríguez-Escudero et al. (PMID:21828076) report: "A group of mutations (H123Y, C124N, A126D, G127N, K128T, G129D, R130A, R130K, T131I and T131L) fully abrogated the PIP3 phosphatase activity of PTEN in yeast" (Results, Functional analysis of mutations at the PTEN P-loop mimicking PTEN-like proteins; Figure 3).
• The PMID:21828076 experiment used heterologous Saccharomyces cerevisiae reconstitution with GFP-Akt1 localization and yeast growth-rescue readouts to measure in vivo PTEN PIP3 phosphatase activity.

Sources

Reasoning

The governing PTEN VCEP specification defines PM1 at moderate strength for residues in critical catalytic motifs 90-94, 123-130, and 166-168 of NP_000305.3, or a mutational hotspot. The tested variant is NP_000305.3:p.(Lys128Thr), placing residue 128 within the complete authoritative VCEP interval 123-130. PMID:21828076 independently identifies K128T in the PTEN P-loop of the phosphatase catalytic domain and reports complete loss of PIP3 phosphatase activity in its assay.

Rule

PTEN VCEP PM1 Moderate: located in a mutational hot spot and/or critical and well-established functional domain, including residues 90-94, 123-130, and 166-168 of NP_000305.3.

Evidence considered

• The PTEN VCEP PM1 rule defines critical catalytic motifs at residues 90-94, 123-130, and 166-168 of NP_000305.3 and assigns moderate strength.
• The tested protein change is NP_000305.3:p.(Lys128Thr), so residue 128 is within the authoritative 123-130 interval.
• PMID:21828076 states: "A group of mutations (H123Y, C124N, A126D, G127N, K128T, G129D, R130A, R130K, T131I and T131L) fully abrogated the PIP3 phosphatase activity of PTEN in yeast"; the study tested a heterologous Saccharomyces cerevisiae PTEN PIP3-phosphatase assay.

Sources

Reasoning

The PTEN Expert Panel Version 3.2 permits PM2 at supporting strength when the allele frequency is below 0.00001 (0.001%) in gnomAD or another large sequenced population; if multiple alleles occur in a subpopulation, that subpopulation frequency must be below 0.00002 (0.002%). NM_000314.8:c.383A>C is absent from gnomAD v2.1 and v4.1, satisfying the PTEN PM2 population requirement.

Rule

Absent in population; gnomAD or another large sequenced population allele frequency <0.00001 (0.001%), and <0.00002 (0.002%) in any subpopulation containing multiple alleles

Evidence considered

• The PTEN Expert Panel Version 3.2 specifies PM2 supporting for allele frequency <0.00001 (0.001%) in gnomAD; any subpopulation with multiple alleles must remain <0.00002 (0.002%).
• The variant is absent from gnomAD v2.1 and v4.1, which is below the PTEN PM2 frequency threshold.

Sources

Reasoning

The governing PTEN VCEP specifies PP2 at supporting strength for a missense variant in a gene with a low rate of benign missense variation where missense variants are a common disease mechanism. PTEN is covered by this gene-specific VCEP missense framework, which explicitly adopts PP2 for PTEN, and the tested variant is a missense substitution, NP_000305.3:p.(Lys128Thr).

Rule

PTEN VCEP PP2 Supporting: missense variant in a gene with a low rate of benign missense variation and where missense variants are a common mechanism of disease.

Evidence considered

• The PTEN VCEP PP2 rule is supporting strength for missense variants in a gene with a low rate of benign missense variation where missense is a common disease mechanism.
• The case variant is a PTEN missense substitution, NP_000305.3:p.(Lys128Thr), and the governing PTEN framework explicitly includes PP2 as applicable.

Sources

Reasoning

The variant is a missense substitution, so the PTEN VCEP missense computational rule applies. The ClinGen PTEN Expert Panel specification assigns PP3 at supporting strength when the REVEL score is >0.7. REVEL is 0.921, exceeding that cutoff. The available SpliceAI result is not used as an additional PP3 line because this is not a splice-region or intronic variant, avoiding double-counting computational evidence.

Rule

PTEN VCEP v3.2: PP3 supporting for missense variants with REVEL score >0.7.

Evidence considered

• ClinGen PTEN Expert Panel specification version 3.2 states for missense variants: PP3 supporting applies with REVEL score >0.7.
• The local REVEL lookup reports a score of 0.921 for NM_000314.8:c.383A>C (p.Lys128Thr).
• The variant consequence is missense; therefore splice-specific predictors are not required for this criterion and are not counted as a second computational line.

Sources

Reasoning

The PTEN Expert Panel Version 3.2 specifies BA1 when the gnomAD filtering allele frequency is greater than 0.00056 (0.056%). NM_000314.8:c.383A>C (p.Lys128Thr) is absent from both gnomAD v2.1 and gnomAD v4.1, so the BA1 threshold is not reached.

Rule

gnomAD Filtering allele frequency >0.00056 (0.056%)

Evidence considered

• The PTEN Expert Panel Version 3.2 rule defines BA1 as gnomAD filtering allele frequency >0.00056 (0.056%).
• The variant is reported absent from gnomAD v2.1 and gnomAD v4.1, with no allele-frequency observation to support BA1.

Sources

Reasoning

The PTEN Expert Panel Version 3.2 specifies BS1 strong for a gnomAD filtering allele frequency from 0.000043 through 0.00056 (0.0043% through 0.056%), and BS1 supporting from 0.0000043 through 0.000043 (0.00043% through 0.0043%). NM_000314.8:c.383A>C is absent from gnomAD v2.1 and v4.1, so neither BS1 range is met.

Rule

BS1 strong: gnomAD filtering allele frequency from 0.000043 up to 0.00056; BS1 supporting: 0.0000043 up to 0.000043

Evidence considered

• The PTEN Expert Panel Version 3.2 defines BS1 strong as 0.000043-0.00056 and BS1 supporting as 0.0000043-0.000043 filtering allele frequency in gnomAD.
• The variant is absent from gnomAD v2.1 and v4.1, so no observed frequency falls within either BS1 range.

Sources

Reasoning

BS3 is not met because the governing PTEN functional evidence shows a damaging rather than a non-damaging effect. The PTEN VCEP Version 3.2 specification allows BS3_Supporting when phosphatase activity is greater than 0 per Mighell et al. 2018 (PMID:29706350), whereas the authoritative K128T/Lys128Thr Table S2 record reports Cum_score = -1.97828658 with High_conf=True and Pass SE Filter. This value is not greater than 0 and instead meets the VCEP PS3_Moderate damaging threshold of -1.11 or lower. The independent K128T yeast assay likewise reports complete abrogation of PTEN PIP3 phosphatase activity, providing no support for a benign functional effect.

Rule

BS3_Supporting: PTEN phosphatase activity > 0 per Mighell et al. 2018 (PMID:29706350).

Evidence considered

• PTEN VCEP Version 3.2 specifies BS3_Supporting when phosphatase activity is > 0 per Mighell et al. 2018 (PMID:29706350).
• The governing mmc2.xlsx Table S2 record for K128T/Lys128Thr reports Cum_score = -1.97828658, High_conf = True, and High_conf_nature = Pass SE Filter; this is not > 0.
• The same K128T record meets the VCEP PS3_Moderate damaging threshold of <= -1.11, so it cannot support a no-damaging-effect BS3 interpretation.
• Rodríguez-Escudero et al. (PMID:21828076) report that K128T fully abrogated PTEN PIP3 phosphatase activity in yeast.

Sources

Reasoning

The variant is a missense substitution, so the PTEN VCEP missense computational rule applies. The ClinGen PTEN Expert Panel specification assigns BP4 at supporting strength when the REVEL score is <0.5. REVEL is 0.921, which does not meet the benign threshold. The available SpliceAI result is not evaluated for this missense criterion because the PTEN VCEP missense path is the applicable path, and the same computational evidence is not double-counted across PP3 and BP4.

Rule

PTEN VCEP v3.2: BP4 supporting for missense variants with REVEL score <0.5.

Evidence considered

• ClinGen PTEN Expert Panel specification version 3.2 states for missense variants: BP4 supporting applies with REVEL score <0.5.
• The local REVEL lookup reports a score of 0.921 for NM_000314.8:c.383A>C (p.Lys128Thr), so the benign computational threshold is not met.

Sources

Reasoning

The PTEN VCEP defines PS1 as a strong criterion for the same amino-acid change as a previously established pathogenic variant. The tested variant is NP_000305.3:p.(Lys128Thr), but ClinVar contains no record and the collected evidence provides no different nucleotide change producing the same Lys128Thr substitution with an established pathogenic classification. The functional paper reporting K128T cannot by itself establish PS1 because PS1 requires a previously established pathogenic comparator with the same amino-acid change.

Rule

PTEN VCEP PS1 Strong: same amino acid change as a previously established pathogenic variant regardless of nucleotide change.

Evidence considered

• The PTEN VCEP PS1 rule requires the same amino-acid change as a previously established pathogenic variant and assigns strong strength.
• The case variant is NP_000305.3:p.(Lys128Thr), and the ClinVar search found no record for NM_000314.8:c.383A>C.
• PMID:21828076 reports functional impairment of K128T but does not provide the required alternate-nucleotide established pathogenic comparator for PS1.

Still missing

• A previously established pathogenic variant producing p.Lys128Thr through a different nucleotide change is not available.

Sources

Reasoning

The PTEN Expert Panel requires a de novo observation in an affected patient with no family history and confirmed maternity and paternity for PS2 at strong strength; higher strength requires multiple proven or assumed de novo observations. The available case evidence contains no proband-level parental testing, maternity or paternity confirmation, family-history assessment, or germline de novo observation for NM_000314.8:c.383A>C (p.Lys128Thr), so PS2 cannot be assessed.

Rule

PTEN VCEP v3.2: PS2 strong requires de novo occurrence with both maternity and paternity confirmed in a patient with disease and no family history; PS2 very strong requires two proven, four assumed, or one proven plus two assumed de novo observations.

Evidence considered

• The PTEN Expert Panel Version 3.2 specifies PS2 strong for a de novo observation with both maternity and paternity confirmed in a patient with disease and no family history; it specifies very strong strength only for defined combinations of multiple proven or assumed de novo observations.
• The case materials document PTEN K128T in a somatic melanoma cohort and functional studies, but do not document a germline proband, parental testing, maternity or paternity confirmation, or family history for this variant.

Still missing

• Documented affected proband with PTEN variant
• Parental genotyping confirming or excluding the variant in both parents
• Maternity and paternity confirmation
• Family-history information relevant to de novo interpretation
• Evidence distinguishing germline from somatic tumor observation

Sources

Reasoning

The PTEN Expert Panel specifies PS4 as Very Strong for probands with specificity score ≥16, Strong for specificity score 4–15.5 or a significantly increased variant prevalence in affected individuals versus controls, Moderate for specificity score 2–3.5, and Supporting for a disease-specific phenotype or specificity score 1–1.5. No PTEN hamartoma tumor syndrome proband specificity score, germline case-control enrichment analysis, or qualifying affected-versus-control prevalence estimate is available for NM_000314.8:c.383A>C (p.Lys128Thr). The two extracted publications concern functional testing and a somatic melanoma treatment-resistance cohort, respectively, and do not establish the required germline phenotype prevalence evidence.

Rule

ClinGen PTEN Expert Panel Version 3.2 PS4 specification

Evidence considered

• The PTEN Expert Panel PS4 rule states: probands with specificity score ≥16 support Very Strong; specificity score 4-15.5 or significantly increased prevalence in affected individuals compared with controls supports Strong; specificity score 2-3.5 supports Moderate; and a phenotype specific for disease with a single genetic etiology or specificity score 1-1.5 supports Supporting.
• The available literature does not provide a PTEN hamartoma tumor syndrome proband specificity score or an exact-variant germline case-control prevalence estimate; PMID:24265153 reports PTENK128T in a metastatic melanoma tumor cohort rather than a germline PTEN syndrome cohort.

Still missing

• A qualifying germline PTEN hamartoma tumor syndrome proband phenotype or validated PTEN specificity score is not available.
• A case-control enrichment analysis or affected-versus-control prevalence estimate for this exact variant is not available.

Sources

Reasoning

The governing PTEN VCEP PM5 rule requires a different missense change at the same amino-acid residue that has been determined pathogenic or likely pathogenic, with the tested variant's BLOSUM62 score equal to or less than that comparator. The collected same-residue search found no usable comparator at Lys128, so neither the required pathogenic classification nor the BLOSUM62 comparison can be established.

Rule

PTEN VCEP PM5 Moderate: different missense change at the same amino-acid residue determined pathogenic or likely pathogenic, with tested-variant BLOSUM62 score equal to or less than the known variant.

Evidence considered

• The PTEN VCEP PM5 rule requires a different missense change at the same residue that is pathogenic or likely pathogenic and requires the interrogated variant's BLOSUM62 score to be equal to or less than the known variant.
• The collected comparator search identified four total candidates but zero same-residue candidates at Lys128, leaving no usable PM5 comparator.

Still missing

• A pathogenic or likely pathogenic different missense variant at PTEN residue Lys128 is unavailable.
• The required BLOSUM62 comparison therefore cannot be performed.

Sources

Reasoning

The PTEN Expert Panel defines PM6 for assumed de novo occurrence without confirmed maternity and paternity in an affected proband with no family history, with strong strength requiring two such probands or one presumed de novo occurrence in a highly specific phenotype. The available case evidence provides no germline proband-level de novo observations, parental testing, family-history assessment, or phenotype-specific proband documentation for NM_000314.8:c.383A>C (p.Lys128Thr), so PM6 cannot be assessed.

Rule

PTEN VCEP v3.2: PM6 moderate requires assumed de novo occurrence without confirmed maternity and paternity in a patient with disease and no family history; PM6 strong requires two such probands or one with a highly specific phenotype; PM6 very strong requires two proven, four assumed, or one proven plus two assumed observations.

Evidence considered

• The PTEN Expert Panel Version 3.2 specifies PM6 moderate for an assumed de novo variant without confirmed maternity and paternity in a patient with disease and no family history; PM6 strong requires two presumed de novo probands or one with a highly specific phenotype, and PM6 very strong requires the specified combinations of assumed and proven observations.
• The case materials do not provide a germline proband, presumed de novo parental result, family history, or phenotype-specific clinical record for this variant; the available Patient 58 report is a somatic melanoma observation and does not establish PM6.

Still missing

• One or more affected germline probands carrying the variant
• Parental testing or documentation supporting presumed de novo status
• Family-history information for each proband
• Phenotype documentation sufficient to evaluate specificity

Sources

Reasoning

The PTEN Expert Panel requires co-segregation with disease in multiple affected family members and assigns supporting strength for 3 or 4 meioses, moderate strength for 5 or 6 meioses, and strong strength for at least 7 meioses across at least two families. No affected relatives, genotypes, pedigrees, or countable meioses are documented for NM_000314.8:c.383A>C (p.Lys128Thr), so PP1 cannot be assessed.

Rule

PTEN VCEP v3.2: PP1 supporting requires 3 or 4 meioses, PP1 moderate requires 5 or 6 meioses, and PP1 strong requires at least 7 meioses across at least two families.

Evidence considered

• The PTEN Expert Panel Version 3.2 specifies PP1 supporting for 3 or 4 meioses, PP1 moderate for 5 or 6 meioses, and PP1 strong for at least 7 meioses across at least two families.
• The available case evidence contains no family pedigree, affected-relative testing, segregation data, or informative meiosis count for this variant.

Still missing

• Pedigree information with affected relatives
• Variant genotypes for affected relatives
• Disease-status definitions for each relative
• Countable informative meioses and family count

Sources

Reasoning

The PTEN Expert Panel requires the variant to be observed in the homozygous state in a healthy or PHTS-unaffected individual; one observation is sufficient when homozygosity is confirmed, otherwise two are required. The available population records report absence from gnomAD v2.1 and v4.1 and provide no homozygous observations or parental confirmation, so BS2 cannot be assessed.

Rule

Observed in the homozygous state in a healthy or PHTS-unaffected individual; one observation if homozygous status is confirmed, two if not confirmed; apply at supporting level if BS1 is also applied

Evidence considered

• The PTEN Expert Panel Version 3.2 requires one confirmed or two unconfirmed homozygous observations in a healthy or PHTS-unaffected individual; BS2 is supporting if BS1 is also applied.
• The available gnomAD v2.1 and v4.1 records report the variant as absent and contain no homozygote or parental-confirmation data.

Still missing

• A confirmed homozygous observation in a healthy or PHTS-unaffected individual, or two unconfirmed homozygous observations, is required for BS2.

Sources

Reasoning

The PTEN Expert Panel defines BS4 supporting as lack of segregation in affected members of one family and BS4 strong as lack of segregation in affected members of two or more families, while cautioning that phenocopies and multiple pathogenic variants can confound interpretation. No affected non-carriers, family genotypes, pedigrees, or non-segregation observations are documented for NM_000314.8:c.383A>C (p.Lys128Thr), so BS4 cannot be assessed.

Rule

PTEN VCEP v3.2: BS4 supporting requires lack of segregation in affected members of one family; BS4 strong requires lack of segregation in affected members of two or more families.

Evidence considered

• The PTEN Expert Panel Version 3.2 specifies BS4 supporting for lack of segregation in affected members of one family and BS4 strong for lack of segregation in affected members of two or more families, with potential confounding by phenocopies and multiple pathogenic variants.
• The available case evidence contains no family-level genotype and phenotype data, affected non-carrier observations, or documented lack of segregation for this variant.

Still missing

• Affected relatives tested for the variant
• Documented non-segregation result in at least one family
• Family-level genotype and phenotype data
• Assessment for phenocopies or multiple pathogenic variants

Sources

Reasoning

The PTEN Expert Panel Specification Version 3.2 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 or phase unknown with different pathogenic or likely pathogenic PTEN variants. The available case evidence documents no affected-proband observation, second PTEN variant, phase assignment, or qualifying cis/unknown-phase observations for NM_000314.8:c.383A>C (p.Lys128Thr). Therefore BP2 cannot be assessed from the available evidence.

Rule

PTEN VCEP Version 3.2: Supporting BP2 requires observation 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.

Evidence considered

• The PTEN Expert Panel Specification Version 3.2 defines BP2 as supporting when the variant is observed in trans with a pathogenic or likely pathogenic PTEN variant.
• The PTEN Expert Panel Specification Version 3.2 also allows BP2 for at least three observations in cis or phase unknown with different pathogenic or likely pathogenic PTEN variants.
• No qualifying affected-proband, phase, cis, trans, or repeated unknown-phase observation is documented in the reviewed case evidence.

Still missing

• Affected-proband or family-level data identifying another pathogenic or likely pathogenic PTEN variant are needed.
• Phase information is needed to establish trans, or at least three qualifying cis/unknown-phase observations are needed.

Sources

Reasoning

The PTEN Expert Panel defines BP5 Supporting as a variant found in a case with an alternate molecular basis for disease, requiring the other gene/disorder to be highly penetrant and the patient's personal or family history to demonstrate no overlap with PTEN. PMID:24265153 reports PTENK128T in a metastatic melanoma tumor cohort and describes an acquired MITF amplification after treatment, but this is somatic oncology evidence and does not establish a germline PTEN hamartoma tumor syndrome case, a highly penetrant alternate germline disorder, or non-overlapping personal/family history. The BP5 requirements therefore cannot be adjudicated from the available evidence.

Rule

ClinGen PTEN Expert Panel Version 3.2 BP5 Supporting: alternate disorder must be highly penetrant and personal/family history must show no overlap with PTEN

Evidence considered

• The PTEN Expert Panel BP5 rule requires a highly penetrant alternate gene/disorder and personal or family history showing no overlap with PTEN.
• PMID:24265153 explicitly reports a pre-treatment PTENK128T missense mutation in a metastatic melanoma patient and later acquired MITF amplification; the study is a somatic tumor-treatment cohort and does not provide the germline clinical information required by the PTEN BP5 rule.

Still missing

• No qualifying germline case documents a highly penetrant alternate molecular diagnosis.
• No personal or family history demonstrates absence of overlap between the alternate disorder and PTEN hamartoma tumor syndrome.

Sources