PTEN c.722_723dup, p.(Glu242LeufsTer15)

Reasoning

NM_000314.8:c.722_723dup (p.Glu242LeufsTer15; p.E242Lfs*15) is a frameshift null variant in the biologically relevant PTEN transcript. The PTEN VCEP PVS1 decision tree assigns PVS1 to frameshift variants predicted to undergo NMD when the stop codon or disruption is at or 5' to p.D375 (c.1121), and this variant disrupts the coding sequence at c.722, well 5' of that threshold. The resulting premature termination at p.E242LeufsTer15 is therefore an early truncation expected to undergo NMD; no named VCEP downgrade rule applies. The searched file PVS1_DecisionTree_PTEN.pdf.txt contains the governing decision-tree rules but no separate variant-specific row for c.722_723dup, p.Glu242LeufsTer15, or p.E242Lfs*15.

Rule

PTEN VCEP PVS1 decision tree: frameshift; biologically relevant NM_000314.8; disruption 5' to p.D375/c.1121; predicted NMD -> PVS1 very strong.

Evidence considered

• The case normalization identifies NM_000314.8:c.722_723dup as a frameshift producing NP_000305.3:p.(Glu242LeufsTer15), also represented as p.(E242Lfs*15).
• The PTEN VCEP decision tree states that a nonsense or frameshift variant with a stop codon or disruption at or 5' to p.D375 (c.1121), in biologically relevant transcript NM_000314.8 and predicted to undergo NMD, receives PVS1.
• The PTEN VCEP specification explicitly directs reviewers to use the PTEN PVS1 decision tree for PVS1 strength assignment.

Still missing

• PVS1_DecisionTree_PTEN.pdf.txt was searched for c.722_723dup, p.Glu242LeufsTer15, and p.E242Lfs*15; no variant-specific row was found.
• The case evidence does not provide a direct RNA assay demonstrating NMD for this variant; the NMD conclusion follows the governing PTEN VCEP decision tree.

Sources

Reasoning

The ClinGen PTEN Expert Panel Version 3.2 specifies PM2 at supporting strength for variants absent from gnomAD or another large sequenced population, with allele frequency below 0.00001 (0.001%) and below 0.00002 (0.002%) in any subpopulation when multiple alleles are present. The variant is absent from gnomAD v2.1, gnomAD v4.1, GNOMAD_V2_1_NON_CANCER, and GNOMAD_V3_1_NON_CANCER, satisfying the PTEN PM2 rule.

Rule

PTEN VCEP PM2: absent in gnomAD or another large sequenced population; frequency <0.00001 (0.001%), and <0.00002 (0.002%) in any subpopulation with multiple alleles.

Evidence considered

• The governing ClinGen PTEN Expert Panel Version 3.2 defines PM2 supporting as absent from gnomAD or another large sequenced population, with allele frequency <0.00001 (0.001%); if multiple alleles occur in a subpopulation, that subpopulation frequency must be <0.00002 (0.002%).
• The variant is reported absent from gnomAD v2.1 and gnomAD v4.1.
• The variant is also reported absent from GNOMAD_V2_1_NON_CANCER and GNOMAD_V3_1_NON_CANCER, including the specified non-cancer cohort views.

Sources

Reasoning

The governing PTEN VCEP specifies PM1 at moderate strength for a variant in a mutational hotspot or critical, well-established functional domain, defined in its rule as residues 90-94, 123-130, or 166-168 (NP_000305.3). The variant affects residue 242 and is not in any of those listed critical motifs; the vcep_materials.json domain_tables object contains no PTEN entry requiring additional domain intervals to be checked. The hotspot source also reports no statistically significant hotspot at PTEN E242.

Rule

PTEN VCEP PM1 moderate: located in a mutational hotspot and/or critical, well-established functional domain; defined to include residues 90-94, 123-130, and 166-168 (NP_000305.3).

Evidence considered

• The PTEN VCEP PM1 rule defines critical functional residues as 90-94, 123-130, and 166-168 on NP_000305.3.
• The variant consequence is p.(Glu242LeufsTer15), placing the altered residue at 242, outside all three VCEP-defined critical motifs.
• The case hotspot review reports that PTEN E242 is not in a statistically significant hotspot.
• The authoritative vcep_materials.json domain_tables object has no PTEN entry, so there are no additional VCEP domain-table intervals to apply.

Sources

Reasoning

The PTEN VCEP PM4 rule is limited to protein-length changes caused by in-frame insertions or deletions in a non-repeat region, including in-frame changes affecting a catalytic motif, and to stop-loss protein extensions. NM_000314.8:c.722_723dup is a frameshift producing a premature stop (p.E242Lfs*15), not an in-frame insertion/deletion or stop-loss variant, so PM4 is not met.

Rule

PTEN VCEP PM4: in-frame insertion/deletion in a non-repeat region or stop-loss protein extension; frameshift premature-stop variants do not meet the rule.

Evidence considered

• The PTEN VCEP PM4 rule applies to in-frame insertions/deletions in a non-repeat region and protein extensions caused by stop-loss variants.
• The case variant is a frameshift, NM_000314.8:c.722_723dup, producing p.E242Lfs*15 rather than an in-frame length change or stop-loss extension.

Sources

Reasoning

The ClinGen PTEN Expert Panel Version 3.2 specifies BA1 when the gnomAD filtering allele frequency is greater than 0.00056 (0.056%). The variant is absent from gnomAD v2.1 and gnomAD v4.1, and is also absent from the available non-cancer gnomAD v2.1 and v3.1 datasets; therefore, the BA1 frequency threshold is not met.

Rule

PTEN VCEP BA1: gnomAD filtering allele frequency >0.00056 (0.056%).

Evidence considered

• The governing ClinGen 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.
• The variant is also reported absent from GNOMAD_V2_1_NON_CANCER and GNOMAD_V3_1_NON_CANCER; no population frequency approaches the BA1 threshold.

Sources

Reasoning

The ClinGen PTEN Expert Panel Version 3.2 specifies BS1 as strong for a gnomAD filtering allele frequency from 0.000043 (0.0043%) up to 0.00056 (0.056%), or supporting from 0.0000043 (0.00043%) up to 0.000043 (0.0043%). The variant is absent from gnomAD v2.1 and v4.1 and from the available non-cancer datasets, so neither BS1 frequency interval is met.

Rule

PTEN VCEP BS1: supporting at allele frequency 0.0000043–0.000043; strong at 0.000043–0.00056.

Evidence considered

• The governing ClinGen PTEN Expert Panel Version 3.2 rule defines BS1 supporting as allele frequency 0.0000043–0.000043 and BS1 strong as 0.000043–0.00056.
• The variant is reported absent from gnomAD v2.1 and gnomAD v4.1.
• The variant is also reported absent from GNOMAD_V2_1_NON_CANCER and GNOMAD_V3_1_NON_CANCER; no observed frequency falls within a PTEN BS1 interval.

Sources

Reasoning

The PTEN VCEP specifies PS2 strong for a de novo observation with both maternity and paternity confirmed and no family history, and very strong for two proven, four assumed, or one proven plus two assumed observations. The available evidence does not document a proband carrying NM_000314.8:c.722_723dup with confirmed parental relationships, parental variant testing, or absence of family history. The reviewed case literature does not mention this exact variant, so PS2 cannot be applied.

Rule

De novo (both maternity and paternity confirmed) observation in a patient with the disease and no family history; higher strengths require the specified numbers of proven or assumed de novo observations.

Evidence considered

• The PTEN VCEP Version 3.2 rule requires confirmed maternity and paternity for PS2 strong and defines higher-strength PS2 using multiple proven or assumed de novo observations.
• No case-level parental testing, confirmed de novo status, or family-history assessment for NM_000314.8:c.722_723dup is documented in the available evidence.
• PMID:21194675 reports a prospective PTEN cohort but the exact c.722_723dup / p.(E242Lfs*15) variant was not mentioned, so it cannot establish PS2 for this variant.

Still missing

• A proband carrying NM_000314.8:c.722_723dup must be identified.
• Maternal and paternal identity and testing must be documented, including whether both parents tested negative for the variant.
• Family history and phenotype consistency must be documented.

Sources

Reasoning

The PTEN VCEP specifies PS3_Moderate for Mighell et al. 2018 Table S2 missense variants only when the exact one-letter or three-letter protein variant is listed with High_conf=TRUE and Cum_score <= -1.11. The queried variant is a frameshift, NM_000314.8:c.722_723dup / p.(Glu242LeufsTer15), not a missense substitution, and searches of mmc2.xlsx.txt found no c.722_723dup, p.Glu242LeufsTer15, or p.E242Lfs*15 entry. No variant-specific RNA, mini-gene, or other functional assay result is available in the reviewed evidence, so PS3 cannot be assigned.

Rule

PTEN VCEP v3.2: PS3_Moderate requires Mighell et al. 2018 Table S2, High_conf=TRUE, and Cum_score <= -1.11; PS3_Supporting requires an applicable abnormal functional study that does not meet PS3_Moderate.

Evidence considered

• The PTEN VCEP PS3 specification permits PS3_Moderate from Mighell et al. 2018 Table S2 only for an exact listed variant with High_conf=TRUE and Cum_score <= -1.11.
• The governing mmc2.xlsx material describes Table S2 as a saturation-mutagenesis phosphatase-activity table for PTEN protein-level missense variants.
• The case variant is a frameshift, NM_000314.8:c.722_723dup producing p.(Glu242LeufsTer15) / p.(E242Lfs*15), and none of the three requested notations occurs in mmc2.xlsx.txt.
• The reviewed paper extracts contain no exact-variant functional assay result applicable to PS3.

Still missing

• No c.722_723dup entry was found in the governing mmc2.xlsx full-text table.
• No p.Glu242LeufsTer15 entry was found in the governing mmc2.xlsx full-text table.
• No p.E242Lfs*15 entry was found in the governing mmc2.xlsx full-text table.
• A variant-specific RNA, mini-gene, or other validated functional assay result was not available in the reviewed case evidence.

Sources

Reasoning

The PTEN Expert Panel specification permits PS4 from a case-control study with odds ratio >2, p<0.05, and a 95% confidence-interval lower limit >1.5, or from accumulated phenotype-specific proband scores: very strong at >=16, strong at 4-15.5, moderate at 2-3.5, and supporting at 1-1.5. The available records provide no odds ratio, p value, confidence interval, Cleveland Clinic score, pediatric phenotype score, or per-proband specificity score for this exact frameshift variant. PMID:21194675 reports a 3042-proband PTEN testing cohort and 290 (9.5%) pathogenic PTEN findings, but the exact c.722_723dup variant and a variant-specific phenotype score are not reported; therefore PS4 cannot be assigned from that study. The specification also states PS4 may not be applied with BS1; BS1 is not established here, but the required PS4 evidence itself is absent.

Rule

PTEN PS4: case-control odds ratio >2 with p<0.05 and 95% confidence-interval lower limit >1.5, or phenotype specificity score >=16 (very strong), 4-15.5 (strong), 2-3.5 (moderate), or 1-1.5 (supporting); PS4 may not be combined with BS1.

Evidence considered

• The PTEN Expert Panel source states that a case-control PS4 result requires odds ratio >2, p<0.05, and a 95% confidence-interval lower limit >1.5.
• The same source assigns PS4 strength by cumulative phenotype-specific proband score: >=16 very strong, 4-15.5 strong, 2-3.5 moderate, and 1-1.5 supporting.
• Tan et al. studied 3042 probands and found 290 (9.5%) with germline pathogenic PTEN mutations, but the paper extract does not report this exact variant or a variant-specific phenotype score.
• Marsh et al. reported germline PTEN mutations in Cowden and Bannayan-Zonana syndrome families, but the exact c.722_723dup variant was not mentioned and no qualifying PS4 metric was provided.

Still missing

• Variant-specific clinical phenotype and family-history data sufficient to calculate the PTEN specificity score are unavailable.
• No qualifying case-control odds ratio, p value, or 95% confidence interval was provided.

Sources

Reasoning

The PTEN VCEP specifies PM6 moderate for an assumed de novo occurrence without confirmed maternity and paternity in a proband with disease and no family history; strong requires two presumed de novo probands or one presumed de novo proband with a highly specific phenotype, and very strong requires the specified combinations of observations. The available evidence contains no documented presumed de novo proband observation for this exact variant, parental testing result, or family-history assessment. The exact variant is not reported in the reviewed literature, so PM6 cannot be applied.

Rule

Assumed de novo without confirmation of paternity and maternity in a proband with disease and no family history; stronger levels require the specified numbers of observations or a highly specific phenotype.

Evidence considered

• The PTEN VCEP Version 3.2 defines PM6 as assumed de novo without confirmed maternity and paternity, with strength determined by the number of observations and phenotype specificity.
• No exact-variant presumed de novo observation, parental testing result, or no-family-history statement is documented in the available evidence.
• PMID:9467011 and PMID:21194675 provide gene-level or cohort-level PTEN information but do not mention NM_000314.8:c.722_723dup and therefore do not establish PM6.

Still missing

• A proband with disease carrying NM_000314.8:c.722_723dup must be documented.
• Parental testing or a clearly documented unconfirmed-parentage de novo observation is needed.
• Family history and, for strong PM6, phenotype specificity must be documented.
• Additional independent presumed or proven de novo observations are needed for upgraded PM6 strength.

Sources

Reasoning

The PTEN VCEP requires co-segregation with disease in multiple affected family members: 3–4 meioses for PP1 supporting, 5–6 for PP1 moderate, and at least 7 across at least two families for PP1 strong. The available evidence provides no exact-variant pedigree, affected relatives, informative meioses, or phenotype-confirmed segregation data. PMID:9467011 describes segregation of PTEN mutations generally but does not mention c.722_723dup, so it cannot support PP1 for this variant.

Rule

Co-segregation with disease in multiple affected family members: 3–4 meioses supporting, 5–6 meioses moderate, and at least 7 meioses across at least two families strong.

Evidence considered

• The PTEN VCEP Version 3.2 requires 3–4 meioses for PP1 supporting, 5–6 for PP1 moderate, and at least 7 meioses across at least two families for PP1 strong.
• No exact-variant family segregation observations, affected relatives, or informative meiosis count are documented.
• PMID:9467011 reports segregation assessment in available family members for PTEN mutations generally, but its extracted finding states that NM_000314.8:c.722_723dup was not explicitly mentioned.

Still missing

• An exact-variant pedigree with affected and tested relatives is needed.
• The number of informative meioses must be documented.
• Affected relatives should have phenotype consistency and variant status confirmed.
• Independent families are required for PP1 strong.

Sources

Reasoning

The ClinGen PTEN Expert Panel Version 3.2 permits BS2 when the variant is observed homozygously in a healthy or PHTS-unaffected individual, with strong or supporting strength depending on confirmation and concurrent BS1. The available population records report absence of the variant but provide no homozygote observations or individual-level health status, so BS2 cannot be assessed.

Rule

PTEN VCEP BS2: observed homozygously in a healthy or PHTS-unaffected individual; one confirmed observation supports strong, two unconfirmed observations support supporting, and BS2 is supporting if BS1 is also applied.

Evidence considered

• The governing ClinGen PTEN Expert Panel Version 3.2 rule requires observation in the homozygous state in a healthy or PHTS-unaffected individual for BS2.
• The available gnomAD records report the variant as absent and contain no homozygote or health-status observation for this variant.

Still missing

• No confirmed homozygous observation with healthy or PHTS-unaffected status is available.

Sources

Reasoning

The PTEN VCEP specifies BS3_Supporting for phosphatase activity >0 in Mighell et al. 2018, while BS3 generally requires a well-established functional study showing no damaging effect. The queried variant is a frameshift rather than a missense variant, and searches of mmc2.xlsx.txt found no c.722_723dup, p.Glu242LeufsTer15, or p.E242Lfs*15 entry. No variant-specific benign functional assay result is available, so BS3 cannot be assigned.

Rule

PTEN VCEP v3.2: BS3_Supporting may be applied for phosphatase activity >0 per Mighell et al. 2018; BS3_Strong requires a well-established in vitro or in vivo study showing no damaging effect.

Evidence considered

• The PTEN VCEP BS3 specification requires a functional study showing no damaging effect and specifically identifies phosphatase activity >0 in Mighell et al. 2018 as BS3_Supporting.
• The governing mmc2.xlsx material describes a saturation-mutagenesis phosphatase-activity table for PTEN protein-level missense variants, not this frameshift.
• The case variant is NM_000314.8:c.722_723dup, p.(Glu242LeufsTer15) / p.(E242Lfs*15), and none of the three requested notations occurs in mmc2.xlsx.txt.
• The reviewed paper extracts contain no exact-variant benign functional assay result applicable to BS3.

Still missing

• No c.722_723dup entry was found in the governing mmc2.xlsx full-text table.
• No p.Glu242LeufsTer15 entry was found in the governing mmc2.xlsx full-text table.
• No p.E242Lfs*15 entry was found in the governing mmc2.xlsx full-text table.
• A variant-specific functional result demonstrating no damaging effect was not available in the reviewed case evidence.

Sources

Reasoning

The PTEN VCEP specifies BS4 supporting for lack of segregation in one family and BS4 strong for lack of segregation in two or more families, while cautioning that phenocopies and multiple pathogenic variants can confound interpretation. No exact-variant affected relatives, non-carrier testing results, or family-level non-segregation observations are documented. Therefore, absence of segregation evidence cannot be interpreted as BS4.

Rule

Lack of segregation in affected members of one family is supporting; lack of segregation in affected members of two or more families is strong.

Evidence considered

• The PTEN VCEP Version 3.2 defines BS4 supporting as lack of segregation in one family and BS4 strong as lack of segregation in two or more families, with phenocopy and multiple-variant caveats.
• No exact-variant family testing or documented non-segregation in affected relatives is available.
• The absence of reported segregation data is not itself evidence that the variant fails to segregate.

Still missing

• A family with affected relatives and documented testing for NM_000314.8:c.722_723dup is needed.
• The affected relatives who lack the variant and their phenotype assessments must be identified.
• Potential phenocopies and additional pathogenic variants must be evaluated.
• Two or more independent families are required for BS4 strong.

Sources

Reasoning

The ClinGen PTEN Expert Panel Version 3.2 specification 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. The available case evidence documents the queried PTEN c.722_723dup variant and its pathogenic ClinVar classification, but provides no paired PTEN variant, affected-proband observation with another PTEN variant, or cis/trans/phase information. Consequently, BP2 cannot be assessed from the available evidence.

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

• The PTEN VCEP BP2 rule 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.
• Case records identify PTEN NM_000314.8:c.722_723dup, but do not document a second PTEN variant, affected-proband allelic pairing, or cis/trans/phase information.
• The queried variant's ClinVar pathogenic classification does not establish an allelic relationship with another PTEN variant and was not used as BP2 evidence.

Still missing

• A paired pathogenic or likely pathogenic PTEN variant is not documented for this case.
• Cis, trans, or phase-unknown status is not documented for any additional PTEN variant in an affected proband.
• The minimum three observations required for the VCEP's cis/phase-unknown alternative are not documented.

Sources

Reasoning

The PTEN Expert Panel permits BP5 at supporting strength only when the variant is found in at least two cases with an alternate molecular basis, the alternate gene/disorder is highly penetrant, and the patients' personal or family histories show no overlap with PTEN-related disease. The available evidence contains no such two-case series, alternate pathogenic molecular diagnoses, penetrance documentation, or non-overlapping clinical histories for c.722_723dup. The variant's somatic COSMIC observations and OncoKB context do not establish the required germline alternate molecular basis for BP5.

Rule

PTEN BP5 supporting: at least two cases with an alternate molecular basis; the other gene/disorder must be highly penetrant and the patients' personal/family histories must show no overlap with PTEN.

Evidence considered

• The PTEN Expert Panel requires at least two BP5 cases, a highly penetrant alternate gene/disorder, and personal/family histories without overlap with PTEN disease.
• COSMIC reports nine somatic cancer observations, but somatic occurrence is not evidence of the required germline alternate molecular basis.
• OncoKB provides variant-specific likely loss-of-function/likely oncogenic context, not an alternate germline diagnosis in qualifying cases.

Still missing

• At least two cases with an alternate molecular basis for disease are not documented.
• The alternate diagnosis, its penetrance, and non-overlapping personal/family histories are unavailable.

Sources