PTEN c.527A>G, p.(Tyr176Cys)

Reasoning

The PTEN VCEP specification assigns PS3_Moderate when Mighell et al. 2018 phosphatase-assay Cum_score is <= -1.11. In Table S2 of mmc2.xlsx, the exact protein substitution Y176C (Tyr176Cys; corresponding to c.527A>G) has a directly measured Cum_score of -1.291488163, below the VCEP cutoff; the value is not imputed. The same variant was independently tested in a recombinant PTEN biochemical PIP3 phosphatase assay and showed 32% of wild-type catalytic activity, supporting a damaging functional effect, although that study did not provide a VCEP-specific strength rule. The Table S2 High_conf flag is False with High_conf_nature Fail Both, so the assay result is clinically relevant but carries some reproducibility/calibration uncertainty; the VCEP's explicit Cum_score rule nevertheless supports PS3 at Moderate strength.

Rule

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

Evidence considered

• The PTEN VCEP index declares mmc2.xlsx as governing PS3 and states that PS3_Moderate applies when Cum_score <= -1.11 per Mighell et al. 2018 (PMID:29706350).
• Table S2 lists Y176C/Tyr176Cys as a missense variant with directly measured Cum_score -1.291488163, Cum_SE 0.631849906, High_conf False, High_conf_nature Fail Both, and Imputed_Score NA.
• The PTEN-specific CSPEC rule states that phosphatase activity <= -1.11 per Mighell et al. 2018 supports PS3 at Moderate strength.
• Johnston and Raines measured recombinant Y176C PTEN in a continuous PIP3 phosphatase assay and reported kcat/KM of 55 ± 10 µM−1min−1, 32% of wild-type activity, with modestly reduced stability.
• The Y176C result is concordant with a damaging effect in the biologically relevant PTEN lipid-phosphatase function, while the failed high-confidence filter is retained as a calibration limitation rather than ignored.

Sources

Reasoning

The PTEN VCEP permits PM6 Moderate for an assumed de novo variant without confirmed maternity and paternity in a patient with disease and no family history. The p.Y176C report states that the variant was absent from both tested parents, confirms alleged paternity by molecular testing, and describes a clearly affected child with severe autism-range findings, speech delay, absent social interaction, and macrocephaly. The paper reports c.530A.G rather than the case input c.527A>G, although p.Y176C matches.

Rule

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

Evidence considered

• The PTEN VCEP defines PM6 Moderate as an assumed de novo observation without confirmed maternity and paternity in a patient with disease and no family history.
• The publication states that the mutations were not found in the respective parents and that alleged paternities were confirmed by molecular testing.
• The p.Y176C proband was a 9-year-old male with significant speech delay, absent social interaction, macrocephaly, and a severe-autism-range CARS score.
• The paper reports c.530A.G for p.Y176C, whereas the case input is c.527A>G; this nucleotide discrepancy limits confidence in direct variant identity.

Still missing

• Maternity was not confirmed by molecular testing in the publication.
• The publication reports c.530A.G rather than the case input c.527A>G, requiring identity confirmation.
• The publication does not explicitly state the absence of a family history.

Sources

Reasoning

The 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. This variant is a confirmed PTEN missense substitution, and the governing PTEN framework recognizes germline PTEN disease with missense-specific interpretation criteria; clinical and functional studies document disease-associated PTEN missense variation. PP2 is met at supporting strength under the VCEP specification.

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 PTEN VCEP specifies PP2 at supporting strength for missense variants in a gene with a low rate of benign missense variation and in which missense variants are a common disease mechanism.
• The governing PTEN framework recognizes germline PTEN disease and includes missense-specific interpretation criteria, establishing missense variation as an applicable disease mechanism for this gene.
• A prospective cohort of 3,042 probands included 85 pathogenic missense PTEN mutations, supporting the established role of PTEN missense variation in disease.
• A PTEN functional study evaluated inherited missense mutations associated with autism/developmental delay and PTEN hamartoma tumor syndrome, documenting disease-associated missense variation.

Sources

Reasoning

The ClinGen PTEN VCEP Version 3.2 specifies BS1 Strong for gnomAD Filtering allele frequency from 0.000043 (0.0043%) up to 0.00056 (0.056%). The variant's maximum reported all-comers gnomAD Filtering allele frequency is 7.354e-05 in gnomAD v2.1; gnomAD v4.1 reports 5.79e-05. These values fall within the PTEN VCEP BS1 Strong interval, so BS1 is met at Strong strength.

Rule

gnomAD Filtering allele frequency from 0.000043 (0.0043%) up to 0.00056 (0.056%)

Evidence considered

• The PTEN VCEP Version 3.2 specifies BS1 Strong for gnomAD Filtering allele frequency from 0.000043 (0.0043%) up to 0.00056 (0.056%).
• gnomAD v2.1 reports a maximum population Filtering allele frequency of 7.354e-05 and gnomAD v4.1 reports 5.79e-05.
• The observed maximum is above 0.000043 and below 0.00056, meeting the PTEN-specific BS1 Strong range.

Sources

Reasoning

The PTEN p.Y176C report states that the variant was absent from both tested parents and that alleged paternity was confirmed by molecular testing. However, maternal identity was not confirmed, so the evidence does not satisfy the PTEN VCEP PS2 Strong requirement for confirmed maternity and paternity. The report uses c.530A.G notation rather than the case input c.527A>G, although the protein change p.Y176C matches.

Rule

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

Evidence considered

• The PTEN VCEP defines PS2 Strong as a de novo observation with both maternity and paternity confirmed in a patient with disease and no family history.
• The publication states that the three mutations were not found in the respective parents and that alleged paternities were confirmed by molecular testing.
• The reported patient carrying p.Y176C had severe autism-range findings, significant speech delay, absent social interaction, and macrocephaly.
• The paper reports c.530A.G for p.Y176C, whereas the case input is c.527A>G; the protein-level match is documented but the nucleotide-level identity remains a review point.

Still missing

• Molecular confirmation of maternity is not reported.
• The publication reports c.530A.G rather than the case input c.527A>G, requiring identity confirmation.
• No additional proven de novo observations are available to meet the VCEP PS2 Very Strong rule.

Sources

Reasoning

The governing PTEN VCEP specifies PM1 at moderate strength for a mutational hotspot and/or critical well-established functional domain, defining catalytic motifs at residues 90-94, 123-130, and 166-168 of NP_000305.3. The variant is NP_000305.3:p.(Tyr176Cys), so residue 176 lies outside every specified interval. The case-specific domain_tables object contains no PTEN entry adding approved domain intervals. Therefore PM1 is not met.

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, and 166-168 (NP_000305.3).

Evidence considered

• The PTEN VCEP PM1 rule defines the critical catalytic-motif intervals as residues 90-94, 123-130, and 166-168 on NP_000305.3.
• The variant is NP_000305.3:p.(Tyr176Cys), placing the altered residue at position 176 outside all three VCEP-specified intervals.
• The case-specific domain_tables data has no PTEN entry supplying any additional approved domain interval.

Sources

Reasoning

The ClinGen PTEN VCEP Version 3.2 permits PM2 Supporting when the variant is present at less than 0.00001 (0.001%) allele frequency in a large population database and, if multiple alleles occur in a subpopulation, that subpopulation frequency is less than 0.00002 (0.002%). Although the all-comers gnomAD v4.1 total allele frequency is 4.95943e-06, the East Asian subpopulation frequency is 0.000133761, and gnomAD v2.1 likewise reports an East Asian frequency of 0.000250601. These exceed the VCEP subpopulation limit, so PM2 is not met.

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

• The PTEN VCEP Version 3.2 specifies PM2 Supporting below 0.00001 (0.001%) overall, with a less-than-0.00002 (0.002%) limit for any subpopulation containing multiple alleles.
• gnomAD v4.1 reports total allele frequency 4.95943e-06 but East Asian allele frequency 0.000133761 from 6/44856 alleles.
• gnomAD v2.1 reports East Asian allele frequency 0.000250601 from 5/19952 alleles, independently exceeding the PTEN VCEP subpopulation limit.

Sources

Reasoning

The variant is a missense substitution, so PP3 must be assessed through the REVEL path only. The ClinGen PTEN VCEP specification assigns PP3 supporting when the REVEL score is >0.7. The observed REVEL score is 0.695, which does not meet that threshold; SpliceAI is not used for this missense PP3 assessment.

Rule

Multiple lines of computational evidence support a deleterious effect on the gene or gene product; missense variants: REVEL score > 0.7.

Evidence considered

• The PTEN VCEP Version 3.2 specification defines PP3 supporting for missense variants as a REVEL score >0.7.
• The case-specific REVEL score is 0.695, below the PTEN VCEP threshold.
• Because this is a missense variant, SpliceAI was not used for PP3 and its score was not double-counted.

Sources

Reasoning

The ClinGen PTEN VCEP Version 3.2 BA1 threshold is gnomAD Filtering allele frequency >0.00056 (0.056%). The variant's highest reported all-comers gnomAD Filtering allele frequency is 7.354e-05 in gnomAD v2.1, with 5.79e-05 in gnomAD v4.1; both are below the BA1 threshold. Therefore BA1 is not met.

Rule

gnomAD Filtering allele frequency >0.00056 (0.056%)

Evidence considered

• The PTEN VCEP Version 3.2 specifies BA1 only when gnomAD Filtering allele frequency is greater than 0.00056 (0.056%).
• gnomAD v2.1 reports a maximum population Filtering allele frequency of 7.354e-05; gnomAD v4.1 reports 5.79e-05.
• Both all-comers gnomAD values are below the PTEN-specific BA1 threshold.

Sources

Reasoning

The ClinGen PTEN VCEP Version 3.2 requires the variant to be observed in the homozygous state in a healthy or PHTS-unaffected individual for BS2. The variant has zero reported homozygotes in gnomAD v2.1 and gnomAD v4.1, and the available non-cancer population records also report zero homozygotes. No qualifying homozygous healthy individual is documented, so BS2 is not met.

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

• The PTEN VCEP Version 3.2 requires an observed homozygous state in a healthy or PHTS-unaffected individual for BS2.
• gnomAD v2.1 reports homozygotes = 0 and gnomAD v4.1 reports homozygotes = 0.
• No qualifying homozygous healthy observation is present in the available population evidence.

Sources

Reasoning

The PTEN VCEP specification assigns BS3_Supporting only when Mighell et al. 2018 phosphatase activity is >0. The exact Y176C Table S2 row has a directly measured Cum_score of -1.291488163, not >0, and the independent biochemical study measured only 32% of wild-type catalytic activity. These functional data do not show absence of damaging effect and therefore do not support BS3.

Rule

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

Evidence considered

• The PTEN VCEP specification states that BS3_Supporting requires phosphatase activity >0 per Mighell et al. 2018 (PMID:29706350).
• Table S2 lists the exact Y176C/Tyr176Cys Cum_score as -1.291488163, which is below rather than above zero.
• The independent recombinant-protein assay reported Y176C catalytic activity at 32% of wild type, inconsistent with a no-damaging-effect interpretation.

Sources

Reasoning

The variant is a missense substitution, so BP4 must be assessed through the REVEL path only. The ClinGen PTEN VCEP specification assigns BP4 supporting when the REVEL score is <0.5. The observed REVEL score is 0.695, which does not meet that threshold; the SpliceAI score is not substituted for the missense REVEL result.

Rule

Multiple lines of computational evidence suggest no impact on gene or gene product; missense variants: REVEL scores < 0.5.

Evidence considered

• The PTEN VCEP Version 3.2 specification defines BP4 supporting for missense variants as a REVEL score <0.5.
• The case-specific REVEL score is 0.695, above the PTEN VCEP threshold.
• Because this is a missense variant, SpliceAI was not used for BP4 and its score was not substituted for the applicable REVEL result.

Sources

Reasoning

The PTEN VCEP requires the same amino-acid change to be a previously established pathogenic variant. Y176C is reported in clinical and research publications, including descriptions as a novel or deleterious missense variant, but the reviewed evidence does not establish an expert-panel or otherwise clearly established pathogenic classification for Y176C. The criterion cannot be adjudicated definitively from the available comparator evidence.

Rule

Same amino acid change as a previously established pathogenic variant regardless of nucleotide change.

Evidence considered

• The PTEN VCEP defines PS1 as the same amino-acid change as a previously established pathogenic variant, regardless of nucleotide change.
• p.Tyr176Cys is explicitly reported in a neurodevelopmental cohort, but that report calls it a novel missense variant and does not establish a pathogenic classification.
• p.Tyr176Cys is listed in a clinical PTEN-testing cohort among previously reported deleterious missense variants, but the available record does not provide the established pathogenic classification required by PS1.
• Functional and clinical papers report Y176C, including biochemical characterization and disease-associated observations, but those observations do not by themselves establish the prior pathogenic comparator required for PS1.

Still missing

• A clearly established pathogenic classification for PTEN p.Tyr176Cys, sufficient for the VCEP PS1 rule, remains unverified.

Sources

Reasoning

The PTEN VCEP permits PS4 from a sufficiently powered case-control study with odds ratio >2, p<0.05, and a 95% confidence-interval lower limit >1.5, or from phenotype-specificity scores: >=16 for very strong, 4-15.5 for strong, 2-3.5 for moderate, and 1-1.5 for supporting. No case-control enrichment statistics or computable PTEN phenotype score are provided. The literature documents p.Y176C in individual patients with macrocephaly, autism, speech delay, and social impairment, but the pediatric scoring rubric and complete score inputs are unavailable; therefore these observations do not establish a PS4 strength. The PTEN specification also states that PS4 may not be combined with PP4 and may not be applied if BS1 applies; BS1 is not assessed in this group.

Rule

PTEN VCEP PS4: case-control odds ratio >2 with p<0.05 and 95% confidence-interval lower limit >1.5; phenotype specificity score >=16 is PS4_Very Strong, 4-15.5 is PS4, 2-3.5 is PS4_Moderate, and 1-1.5 is PS4_Supporting. PS4 may not be combined with PP4 or applied if BS1 applies.

Evidence considered

• The PTEN VCEP PS4 specification states: case-control use requires an odds ratio >2 for a PHTS component phenotype, p<0.05, and a 95% confidence-interval lower limit >1.5.
• The PTEN VCEP assigns phenotype-specificity points of 1 for an adult Cleveland Clinic score >=30 or a pediatric phenotype score >=5, 0.5 for adult scores 25-29 or pediatric score 4, and maps totals of >=16, 4-15.5, 2-3.5, and 1-1.5 to very strong, strong, moderate, and supporting PS4 respectively.
• PMID:18759867 reports p.Y176C in a 9-year-old male with significant speech delay, absent social interaction, macrocephaly of 56.5 cm at the 95th centile, and a flat profile; the report does not provide the PTEN pediatric specificity score.
• PMID:21659347 lists p.Tyr176Cys (Y176C) in one patient in an 802-subject PTEN testing cohort, without a variant-specific clinical score or case-control enrichment analysis.
• PMID:21828076 includes Y176C among PTEN mutations associated with ASD/developmental delay and PHTS, but does not provide a separate Y176C phenotype score.
• PMID:25647146 describes Y176C in an autistic boy with delayed speech and inhibited social interactions, but does not provide a PTEN phenotype specificity score or case-control enrichment statistic.

Still missing

• No sufficiently powered case-control odds ratio, p-value, or 95% confidence interval for p.Y176C.
• No complete adult Cleveland Clinic score or pediatric phenotype score with the PTEN scoring rubric for the relevant probands.
• The PMID:18759867 report uses c.530A.G rather than the supplied c.527A>G, although both identify p.Y176C; variant-level normalization should be confirmed by a reviewer.

Sources

Reasoning

The PTEN VCEP requires a different missense change at the same amino-acid residue that is pathogenic or likely pathogenic and has a BLOSUM62 score equal to or less than the interrogated variant. The available PM5 candidate collection contains no same-residue candidates for Tyr176, and no reviewed paper extract establishes a qualifying alternate pathogenic or likely pathogenic Tyr176 substitution or the required BLOSUM62 comparison. The criterion cannot be adjudicated definitively.

Rule

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

Evidence considered

• The PTEN VCEP PM5 rule requires a different pathogenic or likely pathogenic missense change at the same residue and a BLOSUM62 score equal to or less than the known variant.
• The PM5 candidate collection reports zero same-residue candidates, zero expert-panel pathogenic or likely pathogenic candidates, and zero non-expert majority pathogenic or likely pathogenic candidates for residue 176.
• The reviewed literature extracts report Y176C itself but do not establish a qualifying alternate pathogenic or likely pathogenic substitution at Tyr176.

Still missing

• A qualifying pathogenic or likely pathogenic alternate missense variant at PTEN Tyr176 with a documented BLOSUM62 comparison remains unverified.

Sources

Reasoning

No qualifying co-segregation data from multiple affected family members or a documented number of informative meioses were identified for this variant. The single reported p.Y176C proband and parental testing provide de novo evidence, not PP1 segregation evidence.

Rule

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

Evidence considered

• The PTEN VCEP requires co-segregation in multiple affected family members and assigns strength according to the number of observed meioses: 3 or 4 supporting, 5 or 6 moderate, and at least 7 across at least two families strong.
• The available report describes one affected child and parental variant testing but does not provide affected-relative segregation data or an informative meiosis count.

Still missing

• Affected relatives with genotype and phenotype data are not reported.
• The number of informative meioses is not reported.

Sources

Reasoning

No affected family members carrying an alternate allele or other documented lack of segregation were identified. The report documents parental absence of the variant in the proband, which is relevant to de novo assessment but does not establish BS4 lack of segregation in affected relatives.

Rule

Lack of segregation in affected members of one family.

Evidence considered

• The PTEN VCEP defines BS4 as lack of segregation in affected members of one family at supporting strength or two or more families at strong strength.
• The available report contains parental testing for the proband but no affected-relative non-segregation analysis.

Still missing

• No affected family members with variant-negative testing are reported.
• No non-segregation data from one or more families are available.

Sources

Reasoning

The PTEN VCEP specifies 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. The available reports document Y176C in individual patients but do not establish an accompanying pathogenic or likely pathogenic PTEN variant, phase, or three qualifying observations; therefore BP2 cannot be assessed from the available evidence.

Rule

PTEN VCEP BP2 supporting: 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 or likely pathogenic PTEN variants.

Evidence considered

• The PTEN VCEP Version 3.2 BP2 rule requires either 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.
• PMID:21659347 reports p.Tyr176Cys in one patient, but provides no variant-specific segregation or phase data and does not document a qualifying second PTEN variant.
• PMID:18759867 reports a p.Y176C patient and states the variant was absent from the parents, but does not document an accompanying pathogenic or likely pathogenic PTEN variant in trans or the three observations required by the PTEN BP2 specification.

Still missing

• Parental or other phasing data showing NM_000314.8:c.527A>G in trans with a pathogenic or likely pathogenic PTEN variant.
• Alternatively, at least three independent observations of c.527A>G in cis or phase unknown with different pathogenic or likely pathogenic PTEN variants.

Sources

Reasoning

The PTEN VCEP requires at least two cases with an alternate molecular basis, the alternate gene/disorder to be highly penetrant, and personal or family history showing no overlap with PTEN. The available reports describe p.Y176C-associated neurodevelopmental phenotypes but do not establish two qualifying cases with a documented alternate highly penetrant molecular diagnosis and non-overlapping history. Therefore BP5 cannot be applied from the available evidence.

Rule

PTEN VCEP BP5: at least two cases with an alternate molecular basis; the other gene/disorder must be highly penetrant and the patient's personal/family history must demonstrate no overlap between the other gene and PTEN.

Evidence considered

• The PTEN VCEP BP5 specification requires at least two such cases and additionally requires a highly penetrant alternate gene/disorder plus personal or family history with no overlap between that disorder and PTEN.
• The reviewed p.Y176C reports describe PTEN-associated clinical findings and do not document two cases meeting the alternate-molecular-basis, penetrance, and non-overlap requirements.

Still missing

• No two qualifying p.Y176C cases with a documented alternate molecular basis for disease.
• No evidence that an alternate gene/disorder is highly penetrant in those cases.
• No documented personal or family histories demonstrating no phenotype overlap with PTEN.

Sources