PTEN c.763_773del, p.(Val255ProfsTer39)

Reasoning

Variant NM_000314.8:c.763_773del is an 11-nucleotide (out-of-frame) deletion in exon 7 (exons of NM_000314.8 include c.635-801 as exon 7 per Mutalyzer selector) that shifts the reading frame at codon 255 and creates a premature termination codon after 39 residues: NP_000305.3:p.(Val255ProfsTer39) (VariantValidator/Mutalyzer normalization; wild-type PTEN is 403 aa, predicted translation ends at residue 293, i.e. the stop sits at protein position 293, ~c.877-879). The ClinGen PTEN Expert Panel specification v3.2 (cspec doc 135637575; framework_mode=vcep) governs this case: PVS1 is applicable and requires use of the PTEN PVS1 decision tree, which assigns PVS1 (Very Strong) to nonsense/frameshift variants predicted to undergo NMD whose stop codon or disruption is at or 5' to p.D375 (c.1121), when the exon is present in the biologically relevant transcript NM_000314.8; stops 3' to p.D375 (predicted not to undergo NMD) receive PVS1_Moderate. The PTEN EP specification text states: 'PVS1 applies to variants predicted to result in nonsense-mediated decay (NMD); the predicted NMD cutoff for PTEN occurs at c.1121 (p.D375)'. Here the premature stop at residue 293 (codon ~293, c.877-879) lies well 5' of p.D375/c.1121, so NMD is predicted under the decision tree (the stop is also upstream of the last exon-exon junction, exon 8/9 at ~c.1027, consistent with the general 50-55 nt EJC rule underlying SVI PVS1 guidance, PMC6185798/Tayoun et al. 2018 PMID 30192042). NM_000314.8 is MANE Select and RefSeq Select (VariantValidator annotations mane_select=true, refseq_select=true), i.e., the biologically relevant transcript, and the variant is described on it. The truncation removes >10% of the protein (all sequence from residue 255 onward is replaced; residues ~294-403 including the C-terminal portion of the C2 domain and the entire C-terminal tail containing p.D375 are lost). No frequent LoF in this region is evident in the general population: the variant is absent from gnomAD v2.1 and v4.1, and PTEN germline LoF is an established PHTS disease mechanism (cspec applies a PVS1 decision tree for null variants). All decision-tree conditions for the full Very Strong PVS1 branch are satisfied; there is no indication for downgrade to PVS1_Strong or PVS1_Moderate.

Rule

PTEN VCEP v3.2 PVS1 decision tree: frameshift predicted to undergo NMD with stop at or 5' to p.D375 (c.1121) in biologically relevant transcript NM_000314.8 -> PVS1 (Very Strong)

Evidence considered

• VariantValidator/Mutalyzer normalization: NM_000314.8:c.763_773del (11-nt deletion in exon 7) -> NP_000305.3:p.(Val255ProfsTer39); wild-type PTEN is 403 aa and the predicted mutant translation terminates at residue 293, so the premature stop is at protein position 293 (~c.877-879), well 5' of p.D375 (residue 375, c.1121).
• ClinGen PTEN EP cspec v3.2 (doc 135637575) lists PVS1 as applicable with rule 'Use PTEN PVS1 decision tree' and default strength Pathogenic Very Strong; framework_mode is vcep (VCEP spec governs over generic ACMG).
• PTEN EP specification text (PVS1 instructions): 'PVS1 applies to variants predicted to result in nonsense-mediated decay (NMD); the predicted NMD cutoff for PTEN occurs at c.1121 (p.D375).'
• PTEN PVS1 decision tree (PVS1_DecisionTree_PTEN.pdf, NM_000314.8): nonsense/frameshift variants predicted to undergo NMD with a stop codon or disruption at or 5' to p.D375 (c.1121) are assigned PVS1 when the exon is present in the biologically relevant transcript NM_000314.8; stops 3' to p.D375 that are not predicted to undergo NMD are assigned PVS1_Moderate.
• VCEP index guidance for the decision tree: 'Variants with stop codon or disruption at or 5' to p.D375 in a biologically-relevant transcript are assigned PVS1; those 3' to p.D375 not predicted to undergo NMD are PVS1_Moderate.'
• NM_000314.8 is the MANE Select and RefSeq Select transcript (VariantValidator annotations mane_select=true, refseq_select=true); the variant is described on this biologically relevant transcript.
• The shifted stop (~c.877-879, exon 8) is upstream of the last exon-exon junction (exon 8/9, ~c.1027), consistent with NMD under the general rule that a stop >50-55 nt upstream of the final exon-exon junction triggers NMD (ClinGen SVI PVS1 guidance, PMC6185798; Tayoun et al. 2018, PMID 30192042, as referenced by the PTEN EP specification).
• gnomAD v2.1 (10-89717737-AGTAGAGTTCTT-A) and gnomAD v4.1 (chr10-87957980-AGTAGAGTTCTT-A): variant absent, supporting that LoF alleles at this position/exon are not frequent in the general population.
• Consequence magnitude: the frameshift replaces the protein from residue 255 and truncates at residue 293, removing >10% of the 403-aa protein (residues ~294-403, including the C-terminal part of the C2 domain and the entire C-terminal tail containing p.D375), consistent with the PVS1 branch.
• PTEN germline loss of function is an established disease mechanism for PTEN hamartoma tumor syndrome (autosomal dominant), reflected by the VCEP providing and applying a PVS1 decision tree for null variants (cspec).

Still missing

• NMD is inferred from premature-stop position (5' of the c.1121/p.D375 cutoff per the PTEN VCEP decision tree and upstream of the last exon-exon junction) rather than from an RNA/NMD assay; no RNA-level study of this variant is present in the case materials.
• Exon-level pLoF population frequency was not separately quantified; allele-level absence in gnomAD v2.1/v4.1 plus PTEN's established LoF constraint support the decision-tree branch requiring that LoF variants in this exon not be frequent in the general population.

Sources

Reasoning

PTEN ClinGen EP v3.2 makes PM2 applicable only at Supporting strength: variant absent, or present at < 0.00001 (0.001%) allele frequency in gnomAD or another large sequenced population, with subpopulation AF < 0.00002 (0.002%) if multiple alleles occur in any subpopulation. The variant is entirely absent (AF 0, no alleles in any subpopulation) from gnomAD v2.1 (GRCh37 exomes), gnomAD v4.1 (GRCh38 exomes), and gnomAD-Canada v1.0 (genomes). Absence across these large population datasets satisfies the <0.001% criterion, so PM2 is met at Supporting strength per the VCEP. The generic-ACMG caveat that NGS indel calls can be incomplete is acknowledged, but concordant absence across three independent datasets (two exome-based, one genome-based) supports the finding.

Rule

Absent in population: <0.00001 (0.001%) AF in gnomAD or another large sequenced population; subpopulation AF <0.00002 (0.002%) if multiple alleles (Supporting) - PTEN ClinGen EP v3.2

Evidence considered

• PTEN ClinGen Expert Panel (cspec v3.2) PM2 rule (Supporting only): '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%).'
• gnomAD v2.1 lookup (10-89717737-AGTAGAGTTCTT-A) returned the variant as absent (AF 0).
• gnomAD v4.1 lookup (chr10-87957980-AGTAGAGTTCTT-A) returned the variant as absent (AF 0).
• gnomAD-Canada v1.0 (HostSeq genomes) API lookup returned the variant as absent.
• cspec PM2 instructionsToUse notes the PTEN EP supports PM2 application for ultra-rare alleles and retains the original ACMG caveat that population data for indels may be poorly called by NGS.

Still missing

• c.763_773del is an 11-bp frameshift deletion; multi-base indel detection in NGS population datasets can be incomplete, though absence is concordant across gnomAD v2.1, v4.1, and gnomAD-Canada.
• Subpopulation-level allele counts were not captured as structured data; absence was confirmed at the dataset level via direct variant-ID lookup and screenshots.

Sources

Reasoning

Governing framework is the ClinGen PTEN Expert Panel specification v3.2 (cspec), which declares PS4 Applicable; generic ACMG PS4 is not used. The VCEP defines two routes. Use 1 (case-control enrichment): the PTEN EP commentary states a case-control study finding 'an odds ratio >2 for a PHTS component phenotype with p<0.05 and 95% confidence interval with lower limit >1.5' may support PS4. Operator check, quoted literally from the governing source: '>' (odds ratio >2; p<0.05; 95% CI lower limit >1.5). Direction: the OR strengthens as the value goes UP, so met would require OR > 2 AND p < 0.05 AND CI lower limit > 1.5. No case-control or case-series study of c.763_773del exists in any consulted source, so no OR value can even be substituted into 'OR > 2?' - the enrichment datum itself is absent. Use 2 (phenotype specificity): the governing strength rules read literally: 'Probands with specificity score ≥16' (Very Strong), 'Probands with specificity score 4-15.5' (Strong), 'Probands with specificity score of 2-3.5' (Moderate), 'Proband(s) with specificity score of 1-1.5' (Supporting). Scores are added across independent probands (1 pt per proband with Cleveland Clinic score ≥30; 0.5 pt per proband with CC score 25-29; 1 pt per child with pediatric phenotype score ≥5; 0.5 pt for pediatric score 4). Direction: the score strengthens as it goes UP; each tier is met only if the cumulative score is >= the tier's floor (Supporting floor = 1). Evidence inventory: this case record contains no proband phenotype data at all (no Cleveland Clinic score, no pediatric phenotype score, no family history), so the cumulative specificity score is 0; ClinVar has no entry for NM_000314.8:c.763_773del (search 'PTEN[GENE] AND c.763_773del[VARNAME]' returned no result, hence no reported germline observations); gnomAD v2.1 and v4.1 carry no alleles (no control prevalence); the only two full-text papers available (PMID:11237521 review; PMID:17218262 functional study) do not mention this variant and provide no case observations. Explicit inequality written with both numbers substituted at the weakest tier: 0 >= 1? No. PS4 is therefore not met even at Supporting strength, and a fortiori not met at Moderate (floor 2), Strong (floor 4), or Very Strong (>=16); the case-control route is likewise not met for lack of any study. This conclusion follows from the written inequality only; no comparison direction was borrowed from any other criterion. Ancillary VCEP notes: PS4 may not be applied if BS1 applies (BS1 is not applied here - the variant is absent from population databases, far below the BS1 bands), and the case-control route may not be combined with PP4 (PP4 is Not Applicable under this VCEP).

Rule

ClinGen PTEN EP v3.2 PS4 (Use 2 phenotype specificity): Supporting 1-1.5, Moderate 2-3.5, Strong 4-15.5, Very Strong >=16 (higher score = stronger; summed across independent probands); (Use 1 case-control): odds ratio >2 for a PHTS component phenotype with p<0.05 and 95% CI lower limit >1.5; not applied if BS1 applies; cannot combine with PP4

Evidence considered

• ClinGen PTEN EP v3.2 PS4 rules, quoted: Very Strong 'Probands with specificity score ≥16'; Strong 'Probands with specificity score 4-15.5 OR the prevalence of the variant in affected individuals is significantly increased compared with the prevalence in controls'; Moderate 'Probands with specificity score of 2-3.5'; Supporting 'Proband(s) with specificity score of 1-1.5'.
• ClinGen PTEN EP v3.2 PS4 commentary, quoted: case-control route requires 'an odds ratio >2 for a PHTS component phenotype with p<0.05 and 95% confidence interval with lower limit >1.5'; specificity scores are added across independent probands: 1 pt per proband with Cleveland Clinic score ≥30 (Tan 2011), 0.5 pt per proband with CC score 25-29, 1 pt per child with pediatric phenotype score ≥5, 0.5 pt for pediatric score 4 (autism/DD/ID may not contribute).
• ClinVar search for PTEN c.763_773del returned no result ('This variant is absent from ClinVar'), so there are no reported germline submissions or observations of this exact variant to count as probands.
• gnomAD v2.1 and v4.1 contain no alleles for this variant (absent), providing the control-side prevalence of zero but, with no affected observations, no computable enrichment.
• Both full-text papers available for this case (PMID:11237521, PMID:17218262) were checked via their pre-computed extractions for any case observation of c.763_773del / p.(V255Pfs*39); neither mentions the variant (variant_mentioned=false), so the literature set contains no PS4 case-level evidence.
• VCEP PS4 constraints: criterion may not be applied if BS1 applies (not applicable here); the case-control route may not be applied in combination with PP4 (PP4 is Not Applicable under this VCEP).

Still missing

• No proband-level PHTS phenotype data (Cleveland Clinic score 25-30 or pediatric phenotype score 4-5) is included in this case record, so a PTEN phenotype specificity score could not be computed; supplying such data could at most yield 1 point (Supporting, score 1-1.5) for a single proband.
• No case-control or case-series publication reporting c.763_773del in PHTS-affected individuals was identified; such a study would be required for the PS4 OR > 2 (p<0.05, 95% CI lower limit >1.5) route.

Sources

Reasoning

PTEN ClinGen VCEP v3.2 PM1 (Moderate) is satisfied only by location in a mutational hot spot and/or critical well-established functional domain, operationally defined in the specification as residues in the catalytic motifs 90-94, 123-130, and 166-168 (NP_000305.3). vcep_materials.json domain_tables has no entry for PTEN (empty object), so there is no additional VCEP-approved domain list beyond the CSPEC catalytic-motif definition. The variant disrupts codon 255 (deletion/frameshift start, p.Val255ProfsTer39); 255 is not within any of the three defined motif intervals (90-94, 123-130, 166-168). Cancer Hotspots reports no statistically significant hotspot at PTEN V255. The allele is additionally a truncating frameshift rather than a missense, the variant class PM1's location evidence is designed to weigh. PM1 is therefore not met. A general-review statement that residues 186-351 form the C2 domain (PMID:11237521, which does not mention this variant) does not qualify: the governing VCEP restricts PM1 to the catalytic motifs, and re-deriving broader domain boundaries from external descriptions would exceed the specification.

Rule

PTEN VCEP v3.2 PM1 (Moderate): 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 ClinGen VCEP v3.2 PM1 rule restricts PM1 to residues in catalytic motifs 90-94, 123-130, and 166-168 (NP_000305.3); residue 255 is outside all three intervals.
• vcep_materials.json domain_tables contains no PTEN entries (empty), indicating no additional VCEP-approved critical functional domain list beyond the CSPEC catalytic-motif definition.
• Cancer Hotspots query 'PTEN V255' returned no statistically significant hotspot row.
• c.763_773del is a frameshift deletion (p.Val255ProfsTer39), not a missense substitution; PM1's mutational-hotspot/critical-domain evidence is intended for missense-type location arguments.
• PMID:11237521 (review; variant not mentioned) places residue 255 within the general C2 domain interval (residues 186-351), but the PTEN VCEP PM1 definition does not include the C2 domain, so this does not satisfy PM1 under the governing specification.

Still missing

• vcep_materials.json domain_tables is empty for PTEN, so the PM1 residue check relied on the CSPEC rule text (catalytic motifs 90-94, 123-130, 166-168) rather than a parsed authoritative domain-table entry; the CSPEC text itself is unambiguous for residue 255.

Sources

Reasoning

Under this pipeline's standing PP5/BP6 policy, PP5 may be triggered ONLY by an exact-variant ClinVar expert-panel classification of Pathogenic/Likely Pathogenic; ordinary laboratory submissions, aggregate ClinVar labels, and non-expert assertions never count. No numeric threshold is involved - the gate is the existence of that classification. The governing ClinGen PTEN EP v3.2 additionally marks PP5 'Not Applicable for this VCEP' with the instruction, quoted literally: 'This criterion is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee.' Evidence: the ClinVar search for this exact variant (PTEN[GENE] AND c.763_773del[VARNAME]) returned no record at all - 'This variant is absent from ClinVar' - so no expert-panel classification of any kind exists for c.763_773del. The required evidence (an exact-variant expert-panel Pathogenic/Likely Pathogenic assertion) is therefore absent, and PP5 is not_met. Note: under this pipeline's global rule a genuine ClinVar expert-panel classification would be honored at supporting strength despite the VCEP 'not for use' flag, but no such classification exists here, so the verdict is identical under either policy.

Rule

PP5: exact-variant ClinVar expert-panel Pathogenic/Likely Pathogenic classification (supporting); ClinGen PTEN EP v3.2 marks PP5 'not for use' (SVI VCEP Review Committee)

Evidence considered

• ClinVar search for PTEN c.763_773del returned no result ('This variant is absent from ClinVar'), so no exact-variant ClinVar expert-panel Pathogenic/Likely Pathogenic classification exists for this variant.
• ClinGen PTEN EP v3.2 PP5 entry: 'Not Applicable for this VCEP'; instructions quoted: 'This criterion is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee.'
• Pipeline PP5/BP6 policy applied: only an exact-variant ClinVar expert-panel classification (P/LP for PP5) can trigger PP5; laboratory submissions, aggregate labels, and non-expert assertions are never used.

Sources

Reasoning

PTEN ClinGen Expert Panel specification v3.2 (cspec, doc 135637575) governs this gene, so generic ACMG BA1 is not used. The VCEP defines BA1 (Stand Alone) as gnomAD filtering allele frequency > 0.00056 (0.056%). Direct variant-ID lookups returned the variant as absent (no allele count, AF 0) in gnomAD v2.1 (GRCh37 exomes), gnomAD v4.1 (GRCh38 exomes), and gnomAD-Canada v1.0 (HostSeq genomes). An AF of 0 is far below the 0.056% BA1 threshold, so BA1 is not met; the observed population frequency is in fact consistent with a pathogenic null allele in an autosomal-dominant PTEN hamartoma tumor syndrome gene.

Rule

gnomAD Filtering allele frequency >0.00056 (0.056%) - PTEN ClinGen EP v3.2

Evidence considered

• PTEN ClinGen Expert Panel (cspec v3.2) BA1 rule: 'gnomAD Filtering allele frequency >0.00056 (0.056%)' (Stand Alone).
• gnomAD v2.1 lookup (10-89717737-AGTAGAGTTCTT-A, dataset gnomad_r2_1) returned search_status 'absent': no allele count, AF 0.
• gnomAD v4.1 lookup (chr10-87957980-AGTAGAGTTCTT-A, dataset gnomad_r4) returned search_status 'absent': no allele count, AF 0.
• gnomAD-Canada v1.0 (HostSeq genomes) API lookup returned the variant as absent.
• The PTEN EP BA1/BS1 cutoffs were derived with the Whiffin et al. (PMID 28518168) approach documented in the cspec BS1 instructionsToUse (prevalence 1/9,000; allelic heterogeneity 22/282; penetrance ~10%).

Still missing

• Dataset-level absence (AF 0) is based on direct variant-ID lookups; gnomAD 'filtering allele frequency' was not retrieved as a separate structured field, though absence implies AF 0.

Sources

Reasoning

Under PTEN ClinGen EP v3.2, BS1_Strong applies to gnomAD filtering allele frequencies of 0.000043-0.00056 and BS1_Supporting to 0.0000043-0.000043. The variant is absent (AF 0) from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0, i.e., below even the BS1_Supporting floor of 0.0000043. BS1 is therefore not met at any strength. Absence of the allele in large general-population cohorts is expected for a pathogenic PTEN null variant given the low prevalence of PHTS.

Rule

gnomAD Filtering allele frequency 0.000043-0.00056 (BS1 Strong); 0.0000043-0.000043 (BS1 Supporting) - PTEN ClinGen EP v3.2

Evidence considered

• PTEN ClinGen Expert Panel (cspec v3.2) BS1 rule: 'gnomAD Filtering allele frequency from 0.000043 (0.0043%) up to 0.00056 (0.056%)' (Strong); BS1_Supporting: AF 0.0000043 (0.00043%) up to 0.000043 (0.0043%).
• gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0 lookups each returned the variant as absent (AF 0), which is below the BS1_Supporting threshold of 0.0000043.
• PTEN EP threshold derivation (Whiffin et al., PMID 28518168) is documented in the cspec BS1 instructionsToUse.

Sources

Reasoning

PTEN ClinGen EP v3.2 defines BS2_Strong as observation in the homozygous state in a healthy or PHTS-unaffected individual (one observation if zygosity is confirmed, two if not) and BS2_Supporting as two homozygous observations with no clinical data. No homozygous observations exist for NM_000314.8:c.763_773del: the variant is absent (0 alleles, 0 homozygotes) from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0, and it has no ClinVar record from which a curated homozygous observation could be drawn. BS2 is therefore not met.

Rule

Observed in the homozygous state in a healthy or PHTS-unaffected individual (one observation if confirmed, two if not); two homozygous observations without clinical data (Supporting) - PTEN ClinGen EP v3.2

Evidence considered

• PTEN ClinGen Expert Panel (cspec v3.2) BS2 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.'
• gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0 lookups returned the variant as absent, providing zero homozygous observations.
• ClinVar search (PTEN[GENE] AND c.763_773del[VARNAME]) returned no result, so no curated observation of the variant in any individual, homozygous or otherwise, is available.

Sources

Reasoning

Under the governing ClinGen PTEN Expert Panel v3.2 (cspec), BS3 requires well-established functional studies showing no damaging effect: Strong for a well-established no-effect study (splicing assays for intronic/synonymous variants), and Supporting for a no-damaging-effect study or Mighell et al. 2018 (PMID 29706350) phosphatase activity > 0 (missense variants). No consulted source provides functional evidence of preserved PTEN function for c.763_773del: the Mighell saturation dataset (vcep_mmc2) does not score frameshift alleles, so its BS3_Supporting anchor (activity > 0) is not scoreable for this variant; PMID:11237521 and PMID:17218262 do not mention or test the variant; ClinVar has no submission; and OncoKB's curated 'Likely Loss-of-function' label for V255Pfs*39 argues against a benign readout rather than for one. Independently of assay data, the variant is an 11-bp frameshift at codon 255 that deletes the wild-type C-terminal portion from residue 255 through 403 of the 403-amino-acid protein (about 149 residues, including the distal half of the C2 domain, residues 255-351, and the entire C-terminal tail) and appends 39 out-of-frame residues (predicted product length 293 aa); termination at this position (5' to the p.D375/c.1121 threshold) places it in the NMD-predicted class under the PTEN VCEP PVS1 decision tree, consistent with loss-of-function as the established germline disease mechanism for PTEN. A truncating change of this nature has no plausible no-damaging-effect functional interpretation, and no assay evidence supports one. Status: not_met.

Rule

ClinGen PTEN EP v3.2 BS3: well-established in vitro/in vivo functional studies showing no damaging effect on protein function; Strong: established no-effect assay (splicing assays for intronic/synonymous variants); Supporting: no-damaging-effect study or Mighell et al. 2018 (PMID 29706350) phosphatase activity > 0.

Evidence considered

• ClinGen PTEN Expert Panel v3.2 (cspec) BS3 rule: Strong requires well-established in vitro/in vivo functional studies showing no damaging effect (splicing assays for intronic/synonymous variants); Supporting requires a no-damaging-effect study or Mighell et al. 2018 (PMID 29706350) phosphatase activity > 0.
• No functional evidence of preserved PTEN function for c.763_773del was identified; the variant is an 11-bp frameshift (p.Val255ProfsTer39) whose predicted product is 293 aa versus 403 aa wild-type, deleting wild-type residues 255-403 (distal C2-domain region and C-terminal tail).
• vcep_mmc2 (Mighell et al. 2018) is missense-only per the PTEN VCEP file index, so the BS3_Supporting anchor (activity > 0) cannot be scored for this frameshift variant.
• PMID:17218262 and PMID:11237521 were reviewed (paper_extracts) for BS3-relevant no-effect functional data; neither mentions or assays c.763_773del.
• OncoKB's curated 'Likely Loss-of-function' biological-effect label for PTEN V255Pfs*39 is inconsistent with a no-damaging-effect functional conclusion and was not used as assay evidence for either criterion.
• ClinVar has no record for NM_000314.8:c.763_773del, so no laboratory-curated benign functional studies are available.

Still missing

• No functional study demonstrating preserved/normal PTEN function for p.(Val255ProfsTer39) exists in any consulted source; BS3 could only be considered with an actual no-damaging-effect assay, and none is available.
• Mighell et al. 2018 BS3_Supporting anchor (phosphatase activity > 0) is not applicable: the saturation dataset is restricted to missense variants and cannot score the c.763_773del frameshift.

Sources

Reasoning

Under the ClinGen PTEN VCEP v3.2 specification, BP2 is applicable at Supporting strength only when the variant is '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' (the other variant may be either pathogenic or likely pathogenic). Evaluation of every source in the case bundle that could document such observations yields none: (1) ClinVar has no record for PTEN c.763_773del (search_status no_result; variation_ids and submissions both empty; evidence sentence 'This variant is absent from ClinVar'), so no ClinVar submission reports this variant in trans with a P/LP PTEN variant or in cis/unknown phase with any other PTEN variant; (2) the variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada v1.0, so no population observation exists from which phase with a second PTEN variant could be inferred; (3) the only two full-text papers retrieved for this case (PMID:11237521, PMID:17218262) are functional studies that per their pre-computed extracts never mention c.763_773del and contain no familial, phase, or multi-variant observation data; (4) COSMIC records no somatic occurrence. There is therefore no documented observation of this variant in trans with a P/LP PTEN variant and no set of three cis/unknown-phase observations with different P/LP PTEN variants, so neither arm of the VCEP BP2 rule is satisfied. The criterion is judged not met on the totality of available observation sources; absence of such observations is not itself evidence of benign effect, but it fully fails the evidentiary conditions BP2 requires.

Rule

PTEN VCEP v3.2 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/likely pathogenic PTEN variants. The other variant may be either pathogenic or likely pathogenic.

Evidence considered

• ClinGen PTEN VCEP v3.2 (cspec) BP2 entry: applicability 'Applicable', default strength Benign Supporting; supporting-tier 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'; instructionsToUse: 'The other variant may be either pathogenic or likely pathogenic. This rule may also be applied for at least three observations of the variant in cis or unknown phase with different pathogenic or likely pathogenic PTEN variants.'
• ClinVar search 'PTEN[GENE] AND c.763_773del[VARNAME]' returned no record (search_status no_result; evidence sentence 'This variant is absent from ClinVar'); case_summary clinvar block confirms empty variation_ids and empty submissions, so no ClinVar submission documents this variant together with any other PTEN variant in the same individual.
• gnomAD v2.1 (GRCh37 10-89717737-AGTAGAGTTCTT-A) and gnomAD v4.1 (GRCh38 10-87957980-AGTAGAGTTCTT-A) both report the variant as absent, and gnomAD-Canada v1.0 (HostSeq) likewise returns absent; no allele-carrier observation exists to combine with a second PTEN variant for phase inference.
• The two retrieved full-text publications (PMID:11237521, PMID:17218262) were checked via their pre-computed paper extracts: neither mentions c.763_773del or p.(Val255ProfsTer39) (variant_mentioned false for both) and neither reports case-level, family, or allelic-phase data; COSMIC also has no entry for PTEN c.763_773del, leaving no literature or somatic source that could satisfy the BP2 observation requirement.

Still missing

• No proband-level or pedigree genotyping data are present in the case evidence, so phase cannot be assessed from a direct family study; BP2 rests solely on documented trans/cis observations, and none exist for this variant.
• ClinVar absence was established via a PTEN[GENE] + c.763_773del[VARNAME] search and empty variation-ID lookup; a hypothetical ClinVar entry under an alternate HGVS representation of this 11-bp deletion was not exhaustively ruled out.
• LOVD and HGMD were not among the consulted sources in this case; if either reported this variant paired with a second PTEN variant, BP2 would need re-evaluation.

Sources

Reasoning

The governing ClinGen PTEN Expert Panel specification v3.2 (cspec) declares BP5 Applicable at Supporting strength. Rule text quoted literally: '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.' EP specification, quoted literally: 'At least two such cases are required for criteria to apply.' No numeric threshold is involved in this criterion - it requires positive case-level evidence of an alternate, highly penetrant molecular diagnosis whose phenotype does not overlap PTEN, in at least two cases. Evidence inventory: this case record contains no proband-level clinical data whatsoever - no alternate-gene (non-PTEN) molecular diagnosis is documented, no personal/family history is available to demonstrate a highly penetrant alternate disorder without PTEN-phenotype overlap, and no second qualifying case exists anywhere in the consulted sources (ClinVar has no entry for the variant; the two available full-text papers do not mention it). The alternate-molecular-basis evidence that BP5 requires is entirely absent, so BP5 is not_met.

Rule

ClinGen PTEN EP v3.2 BP5 (Supporting): variant found in a case with an alternate molecular basis for disease; at least two such cases required; other gene/disorder highly penetrant AND personal/family history shows no overlap with PTEN

Evidence considered

• ClinGen PTEN EP v3.2 BP5 rule (Supporting), quoted: '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.'
• ClinGen PTEN EP v3.2 BP5 EP specification, quoted: 'At least two such cases are required for criteria to apply.'
• No source in this case record documents an alternate molecular basis (non-PTEN highly penetrant disorder) for any carrier of c.763_773del; no proband clinical or family-history data are present to evaluate phenotype overlap.

Still missing

• No proband case-level information (results of testing of other genes, personal/family history) is available in this record; BP5 could only be evaluated if an alternate, highly penetrant molecular diagnosis with no PTEN phenotype overlap were documented in at least two cases.

Sources

Reasoning

Under this pipeline's standing PP5/BP6 policy, BP6 may be triggered ONLY by an exact-variant ClinVar expert-panel classification of Benign/Likely Benign; ordinary laboratory submissions, aggregate ClinVar labels, and non-expert assertions never count. No numeric threshold is involved - the gate is the existence of that classification. The governing ClinGen PTEN EP v3.2 additionally marks BP6 'Not Applicable for this VCEP' with the instruction, quoted literally: 'This criterion is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee.' Evidence: the ClinVar search for this exact variant (PTEN[GENE] AND c.763_773del[VARNAME]) returned no record at all - 'This variant is absent from ClinVar' - so no expert-panel classification of any kind exists for c.763_773del. The required evidence (an exact-variant expert-panel Benign/Likely Benign assertion) is therefore absent, and BP6 is not_met. Note: under this pipeline's global rule a genuine ClinVar expert-panel classification would be honored at supporting strength despite the VCEP 'not for use' flag, but no such classification exists here, so the verdict is identical under either policy.

Rule

BP6: exact-variant ClinVar expert-panel Benign/Likely Benign classification (supporting); ClinGen PTEN EP v3.2 marks BP6 'not for use' (SVI VCEP Review Committee)

Evidence considered

• ClinVar search for PTEN c.763_773del returned no result ('This variant is absent from ClinVar'), so no exact-variant ClinVar expert-panel Benign/Likely Benign classification exists for this variant.
• ClinGen PTEN EP v3.2 BP6 entry: 'Not Applicable for this VCEP'; instructions quoted: 'This criterion is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee.'
• Pipeline PP5/BP6 policy applied: only an exact-variant ClinVar expert-panel classification (B/LB for BP6) can trigger BP6; laboratory submissions, aggregate labels, and non-expert assertions are never used.

Sources

Reasoning

Governing framework is the ClinGen PTEN Expert Panel Specification v3.2 (cspec, doc 135637575): PS2 (Pathogenic Strong) requires a de novo observation with both maternity and paternity confirmed in a patient with the disease and no family history; PS2_Very Strong requires two proven OR four assumed OR one proven + two assumed de novo observations. The case bundle contains no proband phenotype or clinical description, no parental (maternal or paternal) testing results, no confirmation of maternity/paternity, and no family-history statement, so no de novo observation can be counted. External sources offer nothing: the variant is absent from ClinVar and gnomAD v2.1/v4.1/Canada, and both retrieved full-text papers (PMID:11237521, PMID:17218262) were checked and do not mention c.763_773del or p.(V255Pfs*39) (paper_extracts variant_mentioned = false), so there is no literature-based de novo report either. Evidence is insufficient to apply PS2 at any strength.

Rule

PS2_Strong: De novo (both maternity and paternity confirmed) observation in a patient with the disease and no family history. PS2_Very Strong: Two proven OR four assumed OR one proven + two assumed de novo observations in a patient with the disease and no family history.

Evidence considered

• ClinGen PTEN EP Specification v3.2 (cspec): PS2_Strong = de novo (both maternity and paternity confirmed) observation in a patient with the disease and no family history; PS2_Very Strong = two proven OR four assumed OR one proven + two assumed de novo observations in a patient with the disease and no family history.
• Case bundle contains no proband clinical data, no parental testing results, and no family-history statement; therefore no confirmed or presumed de novo occurrence can be documented for this variant.
• ClinVar search for PTEN c.763_773del returned no entry (evidence_sentence: 'This variant is absent from ClinVar.').
• Retrieved full texts PMID:11237521 and PMID:17218262 were checked via paper_extracts; neither mentions c.763_773del / p.(V255Pfs*39) (variant_mentioned = false), so neither provides a de novo case observation.

Still missing

• No proband phenotype/clinical data provided in the case bundle
• No parental (maternal/paternal) testing results; maternity and paternity confirmation unavailable
• No family-history statement (required: 'no family history' condition for PS2)
• Variant absent from ClinVar and unreported in retrieved literature, so no externally reported confirmed de novo occurrence

Sources

Reasoning

Governing framework is the ClinGen PTEN Expert Panel specification v3.2 (cspec, precedence rank 1), not generic ACMG. Under it, PS3 requires well-established in vitro/in vivo functional studies supportive of a damaging effect: Moderate is anchored to Mighell et al. 2018 (PMID 29706350) saturation-mutagenesis lipid phosphatase activity Cum_score <= -1.11, and Supporting to activity <50% of wild-type or an abnormal cellular/transgenic assay. The queried variant NM_000314.8:c.763_773del is an 11-bp frameshift, p.(Val255ProfsTer39), and the Mighell assay does not test this variant class: its result table (vcep_mmc2, Table S2) contains single-residue missense substitutions only, and the PTEN VCEP file index explicitly restricts the mmc2.xlsx resource to missense variants. No Cum_score exists for this deletion, so no PS3_Moderate threshold can be applied; the neighboring codon-255 missense rows (V255A Cum_score -1.30; V255I +0.48) and Table S5 phenotype rows (V255A ASD; V255~ somatic TCGA) concern different alleles and cannot be borrowed as evidence for this frameshift. Both functional-theme papers retrieved (PMID:11237521, PMID:17218262) were checked against the variant via paper_extracts: PMID:11237521 is a general PTEN tumor-suppressor review with no variant-specific testing, and PMID:17218262 assays PTEN.R189X/R233X and C124S constructs for nuclear/centromere functions without mentioning c.763_773del. OncoKB's variant page for V255Pfs*39 carries a curated biological-effect label of 'Likely Loss-of-function' with 'Likely Oncogenic' oncogenicity; this is a variant-consequence annotation, not a well-established functional study, and is not counted toward PS3. ClinVar has no record for the variant, so no laboratory-curated functional assay is available from that source. Because no valid variant-specific functional assay evidence exists in any consulted source, PS3 cannot be applied; any damaging effect of this predicted-null frameshift is evaluated through the PTEN VCEP PVS1 null-variant decision tree, not through PS3. Status: not_assessed on an explicit evidence gap.

Rule

ClinGen PTEN EP v3.2 PS3: well-established in vitro/in vivo functional studies supportive of a damaging effect; Moderate: Mighell et al. 2018 (PMID 29706350) phosphatase activity <= -1.11; Supporting: activity <50% of wild-type or abnormal cellular/transgenic assay not meeting PS3_Moderate; Strong: established damaging assay or splicing-impact study.

Evidence considered

• ClinGen PTEN Expert Panel v3.2 (cspec) PS3 rule: Moderate requires Mighell et al. 2018 (PMID 29706350) saturation-assay phosphatase activity <= -1.11; Supporting requires activity <50% of wild-type or an abnormal in vitro cellular assay/transgenic model; Strong requires well-established damaging assays including splicing-impact studies.
• vcep_mmc2 (Mighell et al. 2018 Table S2): PTEN VCEP file index restricts this saturation-mutagenesis resource to missense variants; the frameshift c.763_773del has no Cum_score/High_conf row, so the PS3_Moderate threshold (<= -1.11, from the cspec rule which names PMID 29706350) cannot be applied.
• Codon-255 rows present in vcep_mmc2 Table S2/Table S5 are different alleles (V255A Cum_score -1.30; V255I +0.48; V255A curated ASD phenotype; V255~ somatic TCGA) and were not used as functional evidence for the c.763_773del frameshift.
• PMID:17218262 full text reviewed via paper_extracts: assays PTEN.C124S and truncation constructs R189X/R233X for centromere/chromosomal-integrity functions; c.763_773del (p.V255Pfs*39) is not mentioned or assayed.
• PMID:11237521 full text reviewed via paper_extracts: general PTEN review (403-aa tumor-suppressor phosphatase; C2 domain residues 186-351) with no variant-specific functional testing of the queried deletion.
• OncoKB entry for PTEN V255Pfs*39 ('Likely Loss-of-function' biological effect; 'Likely Oncogenic') is a curated variant-consequence/oncogenicity label rather than a well-established functional assay and was not used to meet PS3.
• ClinVar contains no record for NM_000314.8:c.763_773del, so no laboratory-submitted functional studies are available.

Still missing

• No variant-specific functional assay data for p.(Val255ProfsTer39): the Mighell et al. 2018 saturation-mutagenesis dataset (vcep_mmc2) covers single-residue missense substitutions only and contains no measurement for the 11-bp frameshift deletion; no cellular, transgenic, RNA, or protein-level assay of this exact variant was identified in ClinVar, OncoKB, or the retrieved literature.
• Retrieved functional-literature candidates (PMID:11237521, PMID:17218262) do not mention or functionally test c.763_773del, so neither can anchor PS3.

Sources

Reasoning

Under the ClinGen PTEN EP Specification v3.2 (cspec), PM6 (Pathogenic Moderate) applies to an assumed de novo occurrence without confirmation of paternity and maternity in a proband with the disease and no family history; PM6_Strong requires two probands with presumed de novo occurrence (or one such proband with a highly specific phenotype meeting PS4 criteria); PM6_Very Strong requires two proven OR four assumed OR one proven + two assumed de novo observations. The case bundle provides no proband with a described PHTS phenotype, no parental testing that would support an assumed de novo status, and no family-history information. ClinVar has no entry for the variant and neither retrieved full-text paper (PMID:11237521, PMID:17218262) mentions it, so no presumed de novo occurrence from the literature exists. Evidence is insufficient to apply PM6 at any strength.

Rule

PM6: Assumed de novo, but without confirmation of paternity and maternity, in proband with the disease and no family history. PM6_Strong: Two probands with presumed de novo occurrence (maternity/paternity not confirmed) with the disease and no family history; may also be used for one presumed de novo proband with a highly specific phenotype (meets PS4 criteria). PM6_Very Strong: Two proven OR four assumed OR one proven + two assumed de novo observations.

Evidence considered

• ClinGen PTEN EP Specification v3.2 (cspec): PM6 = assumed de novo, without confirmation of paternity and maternity, in a proband with the disease and no family history; PM6_Strong = two probands with presumed de novo occurrence (maternity/paternity not confirmed) with the disease and no family history, or one presumed de novo proband with a highly specific phenotype meeting PS4 criteria; PM6_Very Strong = two proven OR four assumed OR one proven + two assumed de novo observations.
• No proband with disease phenotype and no family history is described anywhere in the case bundle, so an assumed de novo observation cannot be counted.
• Retrieved full texts PMID:11237521 and PMID:17218262 do not mention c.763_773del / p.(V255Pfs*39) (variant_mentioned = false); no literature case report of presumed de novo occurrence is available.

Still missing

• No proband phenotype/clinical data provided in the case bundle
• No parental testing results to support an assumed (unconfirmed) de novo occurrence
• No family-history statement (required: 'no family history' condition for PM6)
• No externally reported presumed de novo occurrence: variant absent from ClinVar and unreported in the retrieved literature

Sources

Reasoning

Under the ClinGen PTEN EP Specification v3.2 (cspec), PP1 (Pathogenic Supporting) requires co-segregation with disease in multiple affected family members with 3-4 meioses observed; PP1_Moderate requires 5-6 meioses; PP1_Strong requires >=7 meioses observed across at least two families. The case bundle contains no pedigree, no genotyping of affected relatives, no meiosis counts, and no segregation analysis for PTEN c.763_773del. The variant is absent from ClinVar and is not mentioned in either retrieved full-text paper (PMID:11237521, PMID:17218262), so no published segregation data for this variant exists to draw on. Evidence is insufficient to apply PP1 at any strength.

Rule

PP1_Supporting: Co-segregation with disease in multiple affected family members, with 3 or 4 meioses observed. PP1_Moderate: 5 or 6 meioses observed. PP1_Strong: >=7 meioses observed across at least two families.

Evidence considered

• ClinGen PTEN EP Specification v3.2 (cspec): PP1_Supporting = co-segregation with disease in multiple affected family members, with 3 or 4 meioses observed; PP1_Moderate = 5 or 6 meioses; PP1_Strong = >=7 meioses across at least two families.
• Case bundle contains no family/pedigree data, no affected-relative genotypes, and no reported meioses for this variant.
• Neither retrieved full text (PMID:11237521, PMID:17218262) mentions c.763_773del / p.(V255Pfs*39), so no published segregation evidence is available.

Still missing

• No pedigree or family study data in the case bundle
• No genotyping of affected family members and no meiosis counts
• No literature reports of this variant segregating with PHTS (variant absent from ClinVar and from both retrieved full texts)
• At least 3 meioses in multiple affected family members would be needed even for PP1_Supporting

Sources

Reasoning

Under the ClinGen PTEN EP Specification v3.2 (cspec), BS4_Supporting requires lack of segregation in affected members of one family and BS4 (Strong) requires lack of segregation in affected members of two or more families. The case bundle contains no family/pedigree data and no genotyping results demonstrating that an affected relative carries or does not carry the variant. Absence of segregation data must not be equated with demonstrated lack of segregation, so BS4 cannot be applied. No published non-segregation observation exists either: the variant is absent from ClinVar and unreported in the retrieved literature (PMID:11237521, PMID:17218262). Evidence is insufficient to apply BS4 at any strength.

Rule

BS4_Strong: Lack of segregation in affected members of two or more families. BS4_Supporting: Lack of segregation in affected members of one family.

Evidence considered

• ClinGen PTEN EP Specification v3.2 (cspec): BS4_Supporting = lack of segregation in affected members of one family; BS4 (Strong) = lack of segregation in affected members of two or more families; VCEP text notes phenocopies and co-occurring pathogenic variants can confound apparent lack of segregation.
• Case bundle contains no affected-family-member genotypes, so a lack of segregation cannot be demonstrated; absence of segregation data is not evidence of non-segregation.
• Variant absent from ClinVar and unreported in retrieved literature (PMID:11237521, PMID:17218262, both variant_mentioned = false), so no published non-segregation observation exists.

Still missing

• No pedigree/family data in the case bundle to test for (or against) segregation
• No observation of an affected family member lacking the variant (non-segregation)
• No literature or ClinVar reports of non-segregation for this variant
• VCEP note: phenocopies (cancer/epilepsy) and multiple pathogenic variants in a family can confound apparent lack of segregation, so documented family genotypes are required

Sources