PTEN c.1033del, p.Leu345CysfsTer7

Reasoning

NM_000314.8:c.1033del is a frameshift in exon 9 producing NP_000305.3:p.(Leu345CysfsTer7) (also p.(L345Cfs*7)). The governing PTEN PVS1 decision tree applies to nonsense or frameshift variants in the biologically relevant NM_000314.8 transcript. The premature stop occurs at approximately p.352, which is 5' of the specified p.D375 (c.1121) threshold, placing this variant on the decision-tree branch predicted to undergo NMD and assigning full PVS1. No downgrade rule applies. Searches of PVS1_DecisionTree_PTEN.pdf.txt found no variant-specific row for c.1033del, p.Leu345CysfsTer7, or p.L345Cfs*7; the call therefore follows the governing decision-tree branch applied to the case facts.

VCEP rule

Use PTEN PVS1 decision tree. ... Stop codon or disruption at or 5’ to p.D375 (c.1121) ... Exon is present in biologically-relevant transcript NM_000314.8 ... PVS1

Evidence considered

• Case consequence assessment: NM_000314.8:c.1033del, NP_000305.3:p.(Leu345CysfsTer7) / p.(L345Cfs*7), frameshift, exon 9.
• ClinGen PTEN VCEP PVS1 decision tree, PVS1_DecisionTree_PTEN.pdf, page 1: the nonsense/frameshift branch uses the p.D375 (c.1121) positional threshold; a stop codon or disruption at or 5' to that position in NM_000314.8 is assigned PVS1.
• The reported stop after seven frameshifted residues is approximately p.352, before p.D375, so the variant is on the predicted-NMD full-strength PVS1 branch; no named downgrade condition is triggered.
• Direct searches of PVS1_DecisionTree_PTEN.pdf.txt for c.1033del, p.Leu345CysfsTer7, and p.L345Cfs*7 returned no variant-specific table entry.

Still missing

• No variant-specific entry for c.1033del, p.Leu345CysfsTer7, or p.L345Cfs*7 was found in /Users/gs_agent/LYFESCI_HERMES_v11/vcep_db/PTEN/fulltext/PVS1_DecisionTree_PTEN.pdf.txt; the governing decision tree itself was sufficient for adjudication.

Sources

Reasoning

The variant begins at PTEN residue 345 (p.(Leu345CysfsTer7)). The VCEP PM1 rule includes a critical and well-established functional domain. PMID:11237521 describes the PTEN C2 domain as spanning residues 186–351 and explains that it binds phospholipids for effective membrane positioning; residue 345 therefore lies within this functional domain. The VCEP-defined catalytic motifs (90–94, 123–130, and 166–168) do not include residue 345, but the domain path is sufficient.

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

• PTEN C2 domain, residues 186–351: the domain binds phospholipids and may position PTEN at the membrane, placing residue 345 inside the functional domain (PTEN: life as a tumor suppressor, Protein domains of PTEN/Figure 2).
• The VCEP catalytic-motif list is residues 90–94, 123–130, and 166–168; residue 345 is outside those motifs, but PM1 also permits a critical functional domain.

Sources

Reasoning

The PTEN VCEP permits PM2 at Supporting strength when the variant is present at <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 <0.00002 (0.002%). The variant is absent from the default all-comers gnomAD v2.1 and v4.1 datasets, satisfying the stated frequency requirement; the VCEP rule does not require a non-cancer-only or exome-only subset.

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 v3.2 PM2 Supporting rule: allele frequency <0.00001 (0.001%) in gnomAD or another large sequenced population; if multiple alleles are present within any subpopulation, that subpopulation allele frequency must be <0.00002 (0.002%).
• gnomAD v2.1 all-comers dataset: variant absent, with no observed allele count or frequency.
• gnomAD v4.1 all-comers dataset: variant absent, with no observed allele count or frequency.
• The VCEP PM2 text specifies gnomAD generally and does not require a non-cancer-only or exome-only population subset; therefore the default all-comers gnomAD results were used.

Sources

Reasoning

The PTEN VCEP applies BA1 when the gnomAD filtering allele frequency is >0.00056 (0.056%). The variant is absent from gnomAD v2.1 and gnomAD v4.1, so the available population evidence does not meet the BA1 threshold.

VCEP rule

gnomAD Filtering allele frequency >0.00056 (0.056%)

Evidence considered

• ClinGen PTEN VCEP v3.2 BA1 rule: gnomAD filtering allele frequency >0.00056 (0.056%).
• gnomAD v2.1: NM_000314.8:c.1033del absent; no allele frequency or allele count is reported.
• gnomAD v4.1: NM_000314.8:c.1033del absent; no allele frequency or allele count is reported.

Sources

Reasoning

The PTEN VCEP applies BS1 Strong for a gnomAD filtering allele frequency from 0.000043 (0.0043%) up to 0.00056 (0.056%), and BS1 Supporting from 0.0000043 (0.00043%) up to 0.000043 (0.0043%). The variant is absent from gnomAD v2.1 and gnomAD v4.1, so neither BS1 range is met.

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 v3.2 BS1 Strong rule: gnomAD filtering allele frequency from 0.000043 (0.0043%) up to 0.00056 (0.056%).
• ClinGen PTEN VCEP v3.2 BS1 Supporting rule: allele frequency from 0.0000043 (0.00043%) up to 0.000043 (0.0043%).
• gnomAD v2.1 and gnomAD v4.1 both report the variant as absent; no frequency in either BS1 interval is observed.

Sources

Reasoning

PS2 cannot be assessed because the available case evidence does not document a proband with disease and no family history together with a confirmed de novo observation, including confirmation of both maternity and paternity.

VCEP rule

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

Evidence considered

• No proband-level de novo observation, parental testing result, maternity confirmation, paternity confirmation, or family-history assessment is documented in the available case evidence.

Still missing

• A proband-level disease phenotype and family-history assessment.
• Variant testing results for the proband and both biological parents, with maternity and paternity confirmed.
• If available, additional proven or assumed de novo observations needed for the VCEP's higher-strength PS2 paths.

Sources

Reasoning

The variant is a PTEN frameshift, NM_000314.8:c.1033del, predicted to produce NP_000305.3:p.(Leu345CysfsTer7) / p.(L345Cfs*7). The governing VCEP assay file mmc2.xlsx is declared for PS3 and BS3 but its Table S2 is a massively parallel phosphatase assay of PTEN missense variants; the VCEP requires a high-confidence Table S2 match before applying the Mighell assay path. Searches of the complete converted mmc2.xlsx text for c.1033del, p.Leu345CysfsTer7, and p.L345Cfs*7 found no entry. The two available full-text functional papers were also checked through their extracted findings: PMID:11237521 and PMID:17218262 do not mention this exact variant and provide no variant-specific functional result. Therefore the VCEP PS3 rule cannot be evaluated from the available variant-specific functional evidence; no generic frameshift functional inference is substituted.

VCEP rule

Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product; PS3_Moderate uses the Mighell et al. 2018 high-confidence phosphatase assay path.

Evidence considered

• Case normalization identifies NM_000314.8:c.1033del as a frameshift producing NP_000305.3:p.(Leu345CysfsTer7) / p.(L345Cfs*7).
• ClinGen PTEN VCEP v3.2 PS3 instructions restrict the Mighell Table S2 path to a high-confidence missense assay match and specify PS3_Moderate for phosphatase activity <= -1.11; the variant is not a missense variant and no matching notation was found in the complete converted mmc2.xlsx text.
• The complete converted file /Users/gs_agent/LYFESCI_HERMES_v11/vcep_db/PTEN/fulltext/mmc2.xlsx.txt was searched for c.1033del, p.Leu345CysfsTer7, and p.L345Cfs*7; no entry was found.
• PMID:11237521 and PMID:17218262 were reviewed through paper_extracts.json; both state that the exact variant is not mentioned and provide no variant-specific functional assay result.

Still missing

• No matching c.1033del entry was found in /Users/gs_agent/LYFESCI_HERMES_v11/vcep_db/PTEN/fulltext/mmc2.xlsx.txt.
• No matching p.Leu345CysfsTer7 entry was found in /Users/gs_agent/LYFESCI_HERMES_v11/vcep_db/PTEN/fulltext/mmc2.xlsx.txt.
• No matching p.L345Cfs*7 entry was found in /Users/gs_agent/LYFESCI_HERMES_v11/vcep_db/PTEN/fulltext/mmc2.xlsx.txt.
• No variant-specific functional assay result for this frameshift is available in the reviewed case literature.

Sources

Reasoning

The ClinGen PTEN VCEP permits PS4 through a sufficiently powered case-control study or through phenotype-specificity scores summed across independent probands. The available case evidence contains no case-control odds ratio, p-value, confidence interval, Cleveland Clinic score, pediatric phenotype score, or aggregate specificity score for this variant. Therefore no PS4 strength can be assigned. The VCEP rule also states that PS4 cannot be applied with BS1; no BS1 evidence is present here, but that does not replace the missing PS4 evidence.

VCEP rule

Probands with specificity score ≥16 (see text). ... Probands with specificity score 4-15.5 (see text) OR The prevalence of the variant in affected individuals is significantly increased compared with the prevalence in controls. ... Probands with specificity score of 2-3.5 (see text). ... Phenotype specific for disease with single genetic etiology. Proband(s) with specificity score of 1-1.5 (see text).

Evidence considered

• ClinGen PTEN VCEP specification: 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.
• Case evidence identifies the variant as NM_000314.8:c.1033del, a frameshift producing NP_000305.3:p.(Leu345CysfsTer7), but provides no PS4 case-control statistic or phenotype-specificity score.

Still missing

• Case-control odds ratio, p-value, and 95% confidence interval for the variant or a qualifying PHTS component phenotype are unavailable.
• Per-proband Cleveland Clinic scores or pediatric phenotype scores and the resulting aggregate specificity score are unavailable.

Sources

Reasoning

PM6 cannot be assessed because the available case evidence does not document an assumed de novo observation in a patient with disease and no family history, nor the number of proven or assumed de novo observations required for stronger application.

VCEP rule

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

Evidence considered

• No assumed de novo observation, parental maternity or paternity information, family-history assessment, or additional de novo observation count is documented in the available case evidence.

Still missing

• A proband-level disease phenotype and family-history assessment.
• Parental testing or other evidence establishing an assumed de novo occurrence.
• The number and confirmation status of any additional proven or assumed de novo observations.

Sources

Reasoning

PP1 cannot be assessed because the available case evidence does not document co-segregation with disease in multiple affected family members or provide an informative meiosis count.

VCEP rule

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

Evidence considered

• No affected-relative genotype or phenotype data, pedigree, family count, or meiosis count is documented in the available case evidence.

Still missing

• A pedigree identifying affected relatives and their phenotype status.
• Variant testing results for informative affected relatives.
• The number of observed meioses and the family count.

Sources

Reasoning

The PTEN VCEP requires observation of the variant in the homozygous state in a healthy or PHTS-unaffected individual, with one observation if homozygosity is confirmed or two if it is not confirmed; it also specifies supporting strength when BS1 is applied. The available gnomAD records report absence of the variant and provide no homozygote observations or clinical-status evidence, so BS2 cannot be evaluated.

VCEP rule

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

Evidence considered

• ClinGen PTEN VCEP v3.2 BS2 rule requires an observed homozygous state in a healthy or PHTS-unaffected individual; one observation is sufficient if homozygosity is confirmed and two are required if it is not confirmed.
• gnomAD v2.1 and gnomAD v4.1 report the variant as absent and contain no homozygote count or homozygote clinical-status record for this variant.

Still missing

• A documented homozygous observation in a healthy or PHTS-unaffected individual, including confirmation status, is unavailable.

Sources

Reasoning

The variant is a PTEN frameshift, NM_000314.8:c.1033del, predicted to produce NP_000305.3:p.(Leu345CysfsTer7) / p.(L345Cfs*7). The governing VCEP BS3 assay file mmc2.xlsx is declared for PS3 and BS3 but its Table S2 is a massively parallel phosphatase assay of PTEN missense variants; the VCEP requires a high-confidence Table S2 match before applying the Mighell assay path. Searches of the complete converted mmc2.xlsx text for c.1033del, p.Leu345CysfsTer7, and p.L345Cfs*7 found no entry. The two available full-text functional papers were also checked through their extracted findings: PMID:11237521 and PMID:17218262 do not mention this exact variant and provide no variant-specific normal-function result. Therefore the VCEP BS3 rule cannot be evaluated from the available variant-specific functional evidence; no benign conclusion is inferred from the absence of a result.

VCEP rule

Well-established in vitro or in vivo functional studies show no damaging effect on protein function; BS3_Supporting uses the Mighell et al. 2018 high-confidence phosphatase assay path.

Evidence considered

• Case normalization identifies NM_000314.8:c.1033del as a frameshift producing NP_000305.3:p.(Leu345CysfsTer7) / p.(L345Cfs*7).
• ClinGen PTEN VCEP v3.2 BS3 instructions restrict the Mighell Table S2 path to a high-confidence missense assay match and specify BS3_Supporting for phosphatase activity >0; the variant is not a missense variant and no matching notation was found in the complete converted mmc2.xlsx text.
• The complete converted file /Users/gs_agent/LYFESCI_HERMES_v11/vcep_db/PTEN/fulltext/mmc2.xlsx.txt was searched for c.1033del, p.Leu345CysfsTer7, and p.L345Cfs*7; no entry was found.
• PMID:11237521 and PMID:17218262 were reviewed through paper_extracts.json; both state that the exact variant is not mentioned and provide no variant-specific normal-function assay result.

Still missing

• No matching c.1033del entry was found in /Users/gs_agent/LYFESCI_HERMES_v11/vcep_db/PTEN/fulltext/mmc2.xlsx.txt.
• No matching p.Leu345CysfsTer7 entry was found in /Users/gs_agent/LYFESCI_HERMES_v11/vcep_db/PTEN/fulltext/mmc2.xlsx.txt.
• No matching p.L345Cfs*7 entry was found in /Users/gs_agent/LYFESCI_HERMES_v11/vcep_db/PTEN/fulltext/mmc2.xlsx.txt.
• No variant-specific normal-function assay result for this frameshift is available in the reviewed case literature.

Sources

Reasoning

BS4 cannot be assessed because the available case evidence does not document lack of segregation in affected members of one or more families.

VCEP rule

Lack of segregation in affected members of one family.

Evidence considered

• No affected-family-member non-segregation result, pedigree, or family count is documented in the available case evidence.

Still missing

• A pedigree with affected family members and their phenotype status.
• Variant test results for affected relatives who do not carry the variant.
• The number of families showing lack of segregation.

Sources

Reasoning

The PTEN VCEP permits BP2 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 no affected-proband observation, phase assignment, or qualifying second PTEN variant, so the rule 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

• ClinGen PTEN VCEP criterion entry for BP2: the rule requires either one trans observation with a pathogenic or likely pathogenic PTEN variant, or at least three cis and/or phase-unknown observations with different pathogenic or likely pathogenic PTEN variants.
• The case evidence contains no documented affected-proband observation, second pathogenic/likely pathogenic PTEN variant, or phase information for this variant.

Still missing

• Affected-proband observations involving this variant and a pathogenic or likely pathogenic PTEN variant are not documented.
• Phase information (trans, cis, or unknown) and the identity and classification of any second PTEN variant are not documented.

Sources

Reasoning

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

VCEP rule

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

Evidence considered

• ClinGen PTEN VCEP BP5 instructions require at least two cases, a highly penetrant alternate gene/disorder, and no overlap between the alternate disorder and PTEN in the patient's personal/family history.
• The case evidence provides no qualifying alternate molecular basis or the required clinical histories.

Still missing

• At least two cases with an alternate molecular basis for disease are needed.
• The alternate gene/disorder's high penetrance and non-overlapping personal/family histories are not documented.

Sources