PTEN c.538del, p.(Tyr180ThrfsTer3)

Reasoning

NM_000314.8:c.538del is a frameshift predicted to cause p.(Tyr180ThrfsTer3), introducing a premature stop at residue 182. The PTEN Expert Panel PVS1 decision tree applies full-strength PVS1 to nonsense or frameshift variants at or 5′ to p.Asp375 (c.1121) in the biologically relevant transcript NM_000314.8. This variant is in exon 6 and has downstream exons, supporting NMD; its premature stop is well upstream of the PTEN-specific p.Asp375 threshold.

Rule

PTEN EP PVS1 decision tree: frameshift at or 5′ to p.Asp375 (c.1121) in NM_000314.8; predicted NMD.

Evidence considered

• Normalization on the PTEN Expert Panel's biologically relevant transcript NM_000314.8 gives p.(Tyr180ThrfsTer3) for c.538del and places the variant in exon 6.
• The PTEN Expert Panel PVS1 decision tree assigns PVS1 to frameshift or nonsense variants at or 5′ to p.Asp375 (c.1121) in NM_000314.8; c.538del is 5′ to this threshold.
• The premature stop at residue 182 occurs before downstream exon junctions, consistent with nonsense-mediated decay rather than a distal NMD-escaping truncation.

Sources

Reasoning

Under the PTEN VCEP version 3.2 specification, PM2 Supporting may be applied when a variant is present at <0.00001 (0.001%) allele frequency in gnomAD or another large sequenced population. NM_000314.8:c.538del is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0, satisfying the specified population rarity requirement.

Rule

Absent or 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%)

Evidence considered

• ClinGen PTEN Expert Panel Specification version 3.2 defines PM2 Supporting as allele frequency <0.00001 (0.001%) in gnomAD or another large sequenced population; if multiple alleles are present in a subpopulation, that subpopulation frequency must be <0.00002 (0.002%).
• The normalized variant NM_000314.8:c.538del, corresponding to NC_000010.10:g.89711920del and NC_000010.11:g.87952163del, was reported absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0.
• Because the variant is absent rather than observed at a measurable frequency, no ancestry-specific frequency exceeds the VCEP PM2 limit in the available queried datasets.

Still missing

• The queried database records provide absence rather than a numeric allele count or frequency; indel representation and calling sensitivity should be confirmed if additional population data become available.

Sources

Reasoning

The altered residue is Tyr180, which is outside the PTEN Expert Panel-defined catalytic motifs for PM1: WPD loop residues 90-94, P-loop/phosphatase core residues 123-130, and TI-loop residues 166-168 of NP_000305.3. The case hotspot search for PTEN Y180 found no statistically significant hotspot. Although a reviewed PTEN paper describes the broader phosphatase domain as extending through residue 185, the applicable PTEN specification limits PM1 to the listed catalytic motifs and/or a qualifying mutational hotspot; neither is established for this variant.

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 PTEN Expert Panel Version 3.2 PM1 specification defines qualifying catalytic motifs as residues 90-94, 123-130, and 166-168 of NP_000305.3; Tyr180 is outside these intervals.
• The case-specific Cancer Hotspots search queried PTEN Y180 and found no hotspot row, reporting that the variant does not lie in a statistically significant hotspot.
• PMID:11237521 describes the PTEN phosphatase domain as residues 1-185 and identifies the phosphatase motif at residues 123-130, providing broader domain context but not evidence that Tyr180 is within the PTEN Expert Panel PM1 motifs or a mutational hotspot.

Still missing

• No qualifying PTEN Expert Panel catalytic-motif or statistically significant hotspot evidence for residue 180.

Sources

Reasoning

This is a frameshift variant, not an in-frame insertion/deletion or stop-loss variant. It therefore does not meet the PTEN Expert Panel's PM4 scope.

Rule

PTEN EP PM4: in-frame insertion/deletion affecting a catalytic-motif residue, or protein extension only.

Evidence considered

• The PTEN Expert Panel restricts PM4 to in-frame insertions/deletions impacting at least one specified catalytic-motif residue and to variants causing protein extension.
• NM_000314.8:c.538del is predicted to cause the frameshift p.(Tyr180ThrfsTer3), not an in-frame protein length change or protein extension.

Sources

Reasoning

No exact-variant ClinVar record, and therefore no exact-variant pathogenic or likely pathogenic expert-panel assertion, was identified for NM_000314.8:c.538del.

Rule

Apply only to an exact-variant ClinVar expert-panel Pathogenic or Likely pathogenic assertion.

Evidence considered

• The ClinVar exact-variant query returned no result for PTEN c.538del.

Still missing

• An exact-variant ClinVar Pathogenic or Likely pathogenic classification reviewed by an expert panel would be required.

Sources

Reasoning

The PTEN VCEP specifies BA1 for gnomAD filtering allele frequency >0.00056 (0.056%). NM_000314.8:c.538del is absent from the queried gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada datasets, so the BA1 threshold is not reached.

Rule

gnomAD filtering allele frequency >0.00056 (0.056%)

Evidence considered

• ClinGen PTEN Expert Panel Specification version 3.2 defines BA1 as applicable only when gnomAD filtering allele frequency is >0.00056 (0.056%).
• The variant was queried using its normalized genomic representations NC_000010.10:g.89711920del and NC_000010.11:g.87952163del and was reported absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0.
• No population allele count or frequency reaches the BA1 threshold; absence is not evidence of a high-frequency benign allele.

Sources

Reasoning

The PTEN VCEP specifies BS1 Strong for gnomAD filtering allele frequency from 0.000043 to 0.00056 (0.0043% to 0.056%) and BS1 Supporting from 0.0000043 to 0.000043 (0.00043% to 0.0043%). NM_000314.8:c.538del is absent from the queried gnomAD datasets, so neither BS1 range is met.

Rule

gnomAD filtering allele frequency 0.000043-0.00056 (Strong) or 0.0000043-0.000043 (Supporting)

Evidence considered

• ClinGen PTEN Expert Panel Specification version 3.2 defines BS1 Strong as a gnomAD filtering allele frequency of 0.000043 to 0.00056 and BS1 Supporting as 0.0000043 to 0.000043.
• The variant was reported absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0; no filtering allele frequency is available in these queried datasets.
• The PTEN-specific prevalence, allelic heterogeneity, and penetrance assumptions used to derive the thresholds therefore do not produce benign population evidence for this variant.

Sources

Reasoning

No exact-variant ClinVar record, and therefore no exact-variant benign or likely benign expert-panel assertion, was identified for NM_000314.8:c.538del.

Rule

Apply only to an exact-variant ClinVar expert-panel Benign or Likely benign assertion.

Evidence considered

• The ClinVar exact-variant query returned no result for PTEN c.538del.

Still missing

• An exact-variant ClinVar Benign or Likely benign classification reviewed by an expert panel would be required.

Sources

Reasoning

No proband-level de novo observation is documented in the case-evidence bundle. The bundle contains no parental testing results, no confirmation of maternity or paternity, and no documented disease phenotype or family-history information establishing a de novo occurrence.

Rule

PTEN VCEP v3.2: Strong for de novo occurrence in a patient with disease and no family history when both maternity and paternity are confirmed; Very Strong for two proven, four assumed, or one proven plus two assumed de novo observations in patients with disease and no family history.

Evidence considered

• The applicable PTEN VCEP framework (version 3.2) defines PS2 as a de novo observation in a patient with the disease and no family history, with strong strength when both maternity and paternity are confirmed; the available case bundle provides none of these case-specific observations.
• The consolidated bundle contains only two fetched papers, both functional PTEN papers whose pre-computed extracts state that NM_000314.8:c.538del and p.(Tyr180ThrfsTer3) are not mentioned; neither supplies de novo or parental-testing evidence for this case.

Still missing

• Document the proband's disease phenotype and family history.
• Provide variant testing results for both biological parents.
• Confirm maternity and paternity and document the testing method and sensitivity.

Sources

Reasoning

The applicable ClinGen PTEN Expert Panel specification (version 3.2) permits PS3 for functional evidence, including PS3_Moderate from the Mighell et al. 2018 PTEN phosphatase assay only when the exact missense variant is present with High_conf=true and Cum_score <= -1.11. This case variant is a frameshift, NM_000314.8:c.538del, predicted to produce p.(Tyr180ThrfsTer3), not a missense variant. The bundled functional assay material contains Y180 missense substitutions but no assay result for the exact frameshift, and the fetched functional papers do not mention this variant. Therefore no validated, variant-specific damaging assay evidence is available for PS3.

Rule

ClinGen PTEN Expert Panel Specifications v3.2: PS3_Moderate requires a Mighell et al. 2018 phosphatase assay result with High_conf=true and cumulative score <= -1.11; PS3_Supporting requires qualifying damaging functional evidence, including specified assay controls where applicable.

Evidence considered

• The PTEN VCEP version 3.2 specification states that PS3_Moderate may use Mighell et al. 2018 (PMID:29706350) when the variant is listed as High_conf=true and has a cumulative phosphatase-activity score <= -1.11; its indexed assay material is for PTEN missense variants.
• The case normalization identifies NM_000314.8:c.538del as a frameshift producing NP_000305.3:p.(Tyr180ThrfsTer3).
• The bundled mmc2 assay extract lists Y180A, Y180V, and Y180I missense substitutions, not the case frameshift; no exact c.538del or p.(Y180Tfs*3) functional result is provided.
• PMID:11237521 was reviewed through its pre-computed extraction: it does not mention c.538del or p.(Y180Tfs*3) and provides only general PTEN functional context.
• PMID:17218262 was reviewed through its pre-computed extraction: it does not mention c.538del or p.(Y180Tfs*3) and reports studies of other PTEN truncating mutants, not this variant.

Still missing

• No validated functional assay result for NM_000314.8:c.538del or p.(Tyr180ThrfsTer3).
• The PTEN VCEP Mighell assay rule is specified for missense variants, whereas this variant is a frameshift.

Sources

Reasoning

The PTEN Expert Panel permits PS4 only for qualifying case-control enrichment or for an aggregate phenotype-specificity score across independent probands. No exact-variant affected-case counts, phenotype scores, or case-control data were supplied for NM_000314.8:c.538del.

Rule

PTEN EP PS4: qualifying case-control enrichment or aggregate phenotype-specificity score across independent probands; PS4_Supporting 1-1.5, PS4_Moderate 2-3.5, PS4 4-15.5, PS4_Very Strong >=16.

Evidence considered

• PTEN EP PS4 requires a specificity score of at least 1 across independent probands (with strength determined by the total score), or a sufficiently powered case-control study with odds ratio >2, p<0.05, and 95% CI lower bound >1.5 for a PHTS component phenotype.
• The supplied literature set contains only two functional-theme papers, and their precomputed extractions state that neither mentions c.538del or p.(Y180Tfs*3).

Still missing

• Independent affected probands carrying c.538del with adult Cleveland Clinic or pediatric phenotype scores, or a sufficiently powered qualifying case-control study, are needed.

Sources

Reasoning

No presumed de novo occurrence is documented in the case-evidence bundle. There are no case observations, parental testing results, phenotype details, family-history details, or counts of assumed de novo observations from which PM6 strength can be assigned.

Rule

PTEN VCEP v3.2: Moderate for an assumed de novo occurrence without confirmed maternity and paternity in a proband with disease and no family history; Strong for two presumed de novo probands or one presumed de novo observation with a highly specific phenotype; Very Strong for two proven, four assumed, or one proven plus two assumed de novo observations.

Evidence considered

• The PTEN VCEP v3.2 PM6 rule requires assumed or presumed de novo observations in a patient with disease and no family history, with strength determined by the number and confirmation status of observations; no such observations are present in the bundle.
• The available literature extracts concern PTEN mechanism or functional studies and explicitly do not mention this variant, so they do not provide presumed de novo evidence.

Still missing

• Identify the proband and document the disease phenotype and absence of family history.
• Provide parental testing results or, if unavailable, the evidence supporting presumed de novo status.
• Document the number of independent presumed or proven de novo observations and whether maternity and paternity were confirmed.

Sources

Reasoning

No affected relatives carrying the variant, pedigree, segregation data, or meiosis count is documented in the case-evidence bundle. Therefore co-segregation cannot be evaluated or assigned a PTEN VCEP strength.

Rule

PTEN VCEP v3.2: Supporting for co-segregation with disease in multiple affected family members across 3 or 4 meioses; Moderate for 5 or 6 meioses; Strong for at least 7 meioses across at least two families.

Evidence considered

• The PTEN VCEP v3.2 PP1 rule assigns Supporting for 3 or 4 observed meioses, Moderate for 5 or 6, and Strong for at least 7 meioses across at least two families; the bundle reports no informative meioses or family segregation observations.
• Neither of the two extracted full-text papers contains variant-specific family segregation or meiosis data for NM_000314.8:c.538del.

Still missing

• Provide a pedigree identifying affected and unaffected relatives.
• Provide variant and phenotype status for each informative family member.
• Provide the number of informative meioses and independent families.

Sources

Reasoning

No observation of NM_000314.8:c.538del in the homozygous state in a healthy or PHTS-unaffected individual is present in the case evidence. Population absence cannot establish BS2, and no homozygote count or individual-level clinical information is available.

Rule

Observed in the homozygous state in a healthy or PHTS-unaffected individual; one confirmed observation or two unconfirmed observations; downgrade to Supporting if BS1 also applies

Evidence considered

• ClinGen PTEN Expert Panel Specification version 3.2 requires an observed homozygous state in a healthy or PHTS-unaffected individual; one observation is sufficient only when homozygosity is confirmed, otherwise two observations are required.
• The queried gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada records report the variant as absent and provide no homozygote observations or clinical status data.
• No BS2 evidence can be inferred from the variant's absence in population databases.

Still missing

• No confirmed homozygous observation in a healthy or PHTS-unaffected individual.
• No two independent homozygous observations without parental confirmation.

Sources

Reasoning

The applicable ClinGen PTEN Expert Panel specification requires well-established functional evidence showing no damaging effect for BS3; its PTEN-specific supporting rule includes phosphatase activity >0 in the Mighell et al. 2018 assay. No benign functional assay result for the exact frameshift NM_000314.8:c.538del/p.(Tyr180ThrfsTer3) is present. The bundled missense assay rows and the reviewed papers do not test or report this exact variant. Consequently BS3 cannot be assigned.

Rule

ClinGen PTEN Expert Panel Specifications v3.2: BS3 requires well-established functional studies showing no damaging effect; BS3_Supporting includes phosphatase activity >0 per Mighell et al. 2018 (PMID:29706350).

Evidence considered

• The PTEN VCEP version 3.2 specification defines BS3 as well-established in vitro or in vivo functional evidence showing no damaging effect and specifies phosphatase activity >0 per Mighell et al. 2018 (PMID:29706350) for BS3_Supporting.
• The bundled mmc2 extract contains only Y180 missense assay rows among the displayed case-relevant material and no result for the exact c.538del frameshift.
• PMID:11237521 was reviewed through its pre-computed extraction: it does not mention c.538del or p.(Y180Tfs*3), so its general description of PTEN function cannot establish benign function for this variant.
• PMID:17218262 was reviewed through its pre-computed extraction: it does not mention c.538del or p.(Y180Tfs*3), and its experiments concern other PTEN truncating mutants rather than this exact variant.

Still missing

• No validated functional assay demonstrating preserved function for NM_000314.8:c.538del or p.(Tyr180ThrfsTer3).
• No exact-variant benign assay result with adequate controls and reproducibility is available in the case bundle.

Sources

Reasoning

No affected family members, family testing results, pedigree, or non-segregation observation is documented. Absence of segregation evidence is not evidence of lack of segregation, so BS4 cannot be applied.

Rule

PTEN VCEP v3.2: Supporting for lack of segregation in affected members of one family; Strong for lack of segregation in affected members of two or more families.

Evidence considered

• The PTEN VCEP v3.2 BS4 rule requires documented lack of segregation in affected members of one family for Supporting or two or more families for Strong; no such non-segregation data are present.
• The case bundle contains no family-level clinical or molecular observations relevant to BS4.

Still missing

• Provide a pedigree and identify affected family members evaluated for the variant.
• Provide variant test results for affected relatives and the clinical basis for affected status.
• Document whether lack of segregation occurred in one family or in two or more families.

Sources

Reasoning

The PTEN Expert Panel 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 case bundle contains no affected-proband observations, co-occurring PTEN variant, phase information, or inheritance/parental testing data for NM_000314.8:c.538del; therefore BP2 cannot be assessed.

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 Expert Panel 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.
• The consolidated case-evidence bundle provides no qualifying allelic, phase, affected-proband, parental, or pedigree observations for this variant.

Still missing

• Documented co-occurring pathogenic or likely pathogenic PTEN variant(s) in the same proband are absent.
• Phase information establishing trans, cis, or phase unknown is absent.
• Parental testing, pedigree, or other inheritance data are absent.
• At least three qualifying cis or phase-unknown observations with different pathogenic or likely pathogenic PTEN variants are not documented.

Sources

Reasoning

No patient-level observation of c.538del with a qualifying alternate molecular diagnosis was supplied.

Rule

PTEN EP BP5 Supporting: at least two qualifying cases with a highly penetrant alternate molecular diagnosis and no phenotype overlap with PTEN.

Evidence considered

• The PTEN EP requires at least two qualifying cases; the alternate disorder must be highly penetrant and the personal/family history must show no overlap with PTEN-associated disease.

Still missing

• At least two cases with c.538del, each having a highly penetrant alternate molecular diagnosis and personal/family history showing no overlap between that disorder and PTEN-associated disease, are needed.

Sources