PTEN c.209T>G, p.(Leu70Arg)

Reasoning

The governing framework is the ClinGen PTEN Expert Panel VCEP specification v3.2 (cspec doc 135637575; framework_mode=vcep), which defines PS3_Moderate as 'Phosphatase activity ≤ -1.11 per Mighell et al. 2018, PMID: 29706350'. The variant is a missense change, p.(Leu70Arg) (NP_000305.3), so the relevant functional evidence is the PTEN saturation-mutagenesis lipid phosphatase activity assay of Mighell et al. 2018 rather than splicing assays. Direct lookup in the VCEP-supplied assay data (vcep_mmc2, mmc2.xlsx, Table S2) for variant code L70R yields a cumulative fitness score (Cum_score) of -4.645 (Cum_SE 0.449), which is well below the -1.11 PS3_Moderate threshold and also below the truncation-like threshold (-2.13, the upper 95th percentile of nonsense mutations), indicating a severe loss of lipid phosphatase activity. The measurement is high-confidence (High_conf = True, 'Pass SE Filter') and directly measured (Imputed_score = NA, i.e., not an imputed value). The paper itself (PMID:29706350) defines the score scale: scores ≤ -1.11 correspond to 'less than wild-type' (lower 95th percentile, two-tailed, for synonymous variants; Table 1 footnote c, p. 947). PS3_Moderate is therefore met. PS3_Strong (RNA/mini-gene/other assay showing splicing impact) does not apply: this is a missense variant, SpliceAI predicts no significant splice impact (max delta 0.15), and no RNA/minigene assay evidence is present. PS3_Supporting is superseded by the Moderate call.

Rule

PS3_Moderate: Phosphatase activity ≤ -1.11 per Mighell et al. 2018, PMID: 29706350 (ClinGen PTEN VCEP v3.2).

Evidence considered

• PTEN VCEP v3.2 PS3 rule (cspec doc 135637575): PS3_Moderate when 'Phosphatase activity ≤ -1.11 per Mighell et al. 2018, PMID: 29706350'.
• mmc2.xlsx Table S2 row L70R: Cum_score = -4.645, Cum_SE = 0.449, High_conf = True (Pass SE Filter), Imputed_score = NA (directly measured). Cum_score -4.645 ≤ -1.11, so the variant meets the VCEP PS3_Moderate threshold.
• PMID:29706350 Table 1 footnote c: 'Total < WT: less than wild-type; variants with scores less than or equal to −1.11, the lower 95th percentile (two-tailed) for synonymous variants.' Confirms score scale and threshold semantics.
• SpliceAI max delta score 0.15 (no significant splice impact) - excludes PS3_Strong splicing-based rule for this missense variant.

Still missing

• The Mighell 2018 assay measures yeast-based in vivo lipid phosphatase activity (artificial humanized yeast model); no orthogonal mammalian-cell functional assay (e.g., AKT phosphorylation readout) was reviewed for this variant.
• The paper's full text does not mention L70R by name; the variant-level score comes from the assay supplement (Table S2), which is the data source endorsed by the PTEN VCEP.

Sources

Reasoning

PTEN VCEP v3.2 PM2 (Supporting) requires the variant to be absent or present at <0.00001 (0.001%) allele frequency in gnomAD or another large sequenced population, with any subpopulation AF <0.00002 (0.002%) if multiple alleles are present. The variant is entirely absent (AF = 0) from gnomAD v2.1 exomes, gnomAD v4.1 exomes, and gnomAD-Canada v1.0 genomes; because no alleles exist in any subpopulation, the subpopulation cap is not triggered. PM2 is met at Supporting strength per the PTEN VCEP (the VCEP downgrades PM2 from the generic Moderate to Supporting).

Rule

ClinGen PTEN Expert Panel v3.2 PM2 (Supporting): '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

• gnomAD v2.1 exome lookup (10-89685314-T-G, GRCh37): variant absent (AF = 0)
• gnomAD v4.1 exome lookup (chr10-87925557-T-G, GRCh38): variant absent (AF = 0)
• gnomAD-Canada v1.0 (HostSeq genomes) lookup: variant absent (AF = 0)
• ClinGen PTEN VCEP v3.2 PM2 rule: absent or AF <0.00001 (0.001%) in gnomAD or another large sequenced population; subpopulation AF <0.00002 (0.002%) if multiple alleles present

Still missing

• Per-subpopulation allele counts were not captured (gnomAD records report only 'absent' status with empty source_data); absence across three independent large databases mitigates this, but numeric counts would strengthen the audit trail.

Sources

Reasoning

Missense variant NM_000314.8:c.209T>G (p.Leu70Arg) in PTEN. Governing framework is ClinGen PTEN Expert Panel Specifications v3.2 (cspec doc 135637575), which pre-assigns the missense sub-path of PP3: REVEL score > 0.7. Local REVEL v1.3 lookup returns 0.985, well above the VCEP cutoff, so PP3 is met at the VCEP default strength of Supporting. Corroborating: 0.985 also exceeds the SVI-calibrated REVEL PP3_Strong threshold (>= 0.965) per Pejaver et al. 2022 (PMID 36413997, Table 2), but the VCEP-assigned supporting strength governs and is not upgraded. SpliceAI (max delta 0.15, DS_DL) predicts no splice impact; the VCEP splice-concordance sub-path (SpliceAI + VarSeak) does not apply to a missense variant and VarSeak is not available in this case, so it was not used for PP3. BayesDel score 0.595825 was retrieved but is excluded: no verified published threshold is available, so it cannot support PP3.

Rule

Multiple lines of computational evidence support a deleterious effect on the gene or gene product. Missense variants: REVEL score > 0.7 (ClinGen PTEN EP v3.2, PP3 rule)

Evidence considered

• REVEL v1.3 local lookup (source_registry key 'revel'): REVEL score 0.985 for NM_000314.8:c.209T>G (p.Leu70Arg).
• ClinGen PTEN Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for PTEN Version 3.2 (cspec doc 135637575): PP3 rule for missense variants = 'REVEL score > 0.7', default strength Pathogenic Supporting.
• Pejaver et al. 2022, Am J Hum Genet, PMID 36413997, Table 2: SVI-calibrated REVEL PP3_Strong threshold >= 0.965; score 0.985 exceeds it (corroborating only; VCEP strength applied).
• SpliceAI lookup (source_registry key 'spliceai'): max delta score 0.15 (DS_AG 0.02, DS_DL 0.15), no splice impact predicted; contextual only, not counted toward PP3/BP4.
• BayesDel local lookup (source_registry key 'bayesdel'): score 0.595825 retrieved but NOT used - no verified published threshold can be named, treated as insufficiently calibrated for PP3 per group policy.

Still missing

• VarSeak absent from case evidence bundle - VCEP splice-concordance sub-path (SpliceAI + VarSeak) not evaluable; irrelevant to the call because the variant is missense and the REVEL sub-path governs.
• BayesDel 0.595825 not used - no published threshold verifiable to this pipeline (group calibration policy), insufficiently calibrated for PP3.

Sources

Reasoning

PTEN VCEP v3.2 BA1 requires a gnomAD Filtering allele frequency >0.00056 (0.056%). This variant is absent (AF = 0) from gnomAD v2.1 exomes, gnomAD v4.1 exomes, and gnomAD-Canada v1.0 genomes, so the BA1 frequency threshold is not approached. A frequency of zero cannot meet a stand-alone benign frequency criterion.

Rule

ClinGen PTEN Expert Panel v3.2 BA1: 'gnomAD Filtering allele frequency >0.00056 (0.056%)' (Benign Stand Alone).

Evidence considered

• gnomAD v2.1 exome lookup (10-89685314-T-G, GRCh37): variant absent, search_status 'absent'
• gnomAD v4.1 exome lookup (chr10-87925557-T-G, GRCh38): variant absent, search_status 'absent'
• gnomAD-Canada v1.0 (HostSeq genomes) lookup: variant absent, search_status 'absent'
• ClinGen PTEN VCEP v3.2 BA1 rule: gnomAD Filtering allele frequency >0.00056 (0.056%) required for BA1

Still missing

• Numeric allele counts and per-subpopulation frequencies were not captured in the evidence bundle (gnomAD records returned 'absent' with empty source_data); absence status from three independent large population databases was used instead.

Sources

Reasoning

PTEN VCEP v3.2 BS1 requires gnomAD Filtering allele frequency of at least 0.0000043 (0.00043%) for the Supporting band and 0.000043-0.00056 for Strong. The variant is absent (AF = 0) from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0, below even the lowest BS1 band; BS1 is not met.

Rule

ClinGen PTEN Expert Panel v3.2 BS1: 'gnomAD Filtering allele frequency from 0.000043 (0.0043%) up to 0.00056 (0.056%)' (Strong); 'Allele frequency from 0.0000043 (0.00043%) up to 0.000043 (0.0043%)' (Supporting).

Evidence considered

• gnomAD v2.1 exome lookup (10-89685314-T-G, GRCh37): variant absent
• gnomAD v4.1 exome lookup (chr10-87925557-T-G, GRCh38): variant absent
• gnomAD-Canada v1.0 (HostSeq genomes) lookup: variant absent
• ClinGen PTEN VCEP v3.2 BS1 rule: Strong band 0.000043-0.00056, Supporting band 0.0000043-0.000043

Still missing

• Numeric allele counts per population were not captured in the bundle; 'absent' status across three large databases is sufficient to conclude AF = 0 for BS1 purposes.

Sources

Reasoning

PTEN VCEP v3.2 BS2 requires observation of the variant in the homozygous state in a healthy or PHTS-unaffected individual (one observation if homozygosity confirmed, two if not). The variant is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0, so no homozygous (or any) population observations exist. No clinical or case-level homozygote data were found in the evidence bundle. BS2 is not met.

Rule

ClinGen PTEN Expert Panel v3.2 BS2: '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

• gnomAD v2.1 exome lookup: variant absent, no homozygous carriers
• gnomAD v4.1 exome lookup: variant absent, no homozygous carriers
• gnomAD-Canada v1.0 genome lookup: variant absent, no homozygous carriers
• ClinGen PTEN VCEP v3.2 BS2 rule: homozygous observation(s) in healthy or PHTS-unaffected individual required

Still missing

• No case-level homozygote observations for this variant were found in the bundle; if any PHTS-unaffected homozygous carrier is identified in clinical records, BS2 should be re-evaluated under the VCEP rule.

Sources

Reasoning

Under the governing ClinGen PTEN VCEP v3.2 framework, BS3_Supporting requires 'Phosphatase activity >0 per Mighell et al. 2018, PMID: 29706350', and BS3_Strong requires well-established in vitro/in vivo functional studies showing no damaging effect on protein function (for intronic/synonymous variants, a splicing assay demonstrating no splicing impact). The functional evidence shows the opposite: the directly measured high-confidence cumulative fitness score for L70R in the Mighell saturation-mutagenesis assay is -4.645, which is not greater than 0 and indicates a damaging (severely reduced) lipid phosphatase activity. BS3_Strong is inapplicable because the variant is a missense with demonstrated damaging effect, not a variant with demonstrated lack of effect; the SpliceAI result (max delta 0.15) is a computational prediction, not a functional study showing no damaging effect, and BS3 cannot be based on it. Therefore BS3 is not met.

Rule

BS3_Supporting: Phosphatase activity >0 per Mighell et al. 2018, PMID: 29706350; BS3_Strong: well-established in vitro/in vivo functional studies show no damaging effect (ClinGen PTEN VCEP v3.2).

Evidence considered

• PTEN VCEP v3.2 BS3 rule (cspec doc 135637575): BS3_Supporting = 'Phosphatase activity >0 per Mighell et al. 2018, PMID: 29706350'; BS3_Strong = well-established functional studies showing no damaging effect on protein function.
• mmc2.xlsx Table S2 row L70R: Cum_score = -4.645 (High_conf = True). Since Cum_score is not > 0, the BS3_Supporting threshold is not met.
• PMID:29706350 score scale (Table 1 footnotes c-f, p. 947): WT-like scores range between -1.11 and 0.89; L70R at -4.645 falls in the truncation-like range, not the neutral/WT-like range.

Still missing

• No assay demonstrating wild-type-like function for L70R exists; all available functional data indicate loss of function, so no BS3-supporting evidence is anticipated unless an orthogonal assay reports preserved activity.

Sources

Reasoning

PTEN VCEP v3.2 defines BP2 (Benign Supporting) as: '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.' No source in the evidence bundle reports c.209T>G (p.Leu70Arg) in trans with a pathogenic/likely pathogenic PTEN variant, and no cis or phase-unknown observations with different P/LP PTEN variants exist. The ClinVar germline submissions (SCV002730363 Ambry, LP; SCV007391075 Labcorp, VUS) carry no phase or segregation data, and their own evidence signals (PS3/PP3 for Ambry; PM2 for Labcorp) contain nothing allelic. The variant is absent from gnomAD v2.1/v4.1/Canada, so no population-based cis/trans observations are possible. A targeted screen of all 5 retrieved full-text papers found no mention of the variant and no trans/cis/compound-heterozygote/homozygous content. BP2 cannot be met on the available evidence.

Rule

ClinGen PTEN Expert Panel v3.2 BP2 (Benign 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.'

Evidence considered

• ClinGen PTEN VCEP v3.2 (cspec doc 135637575) BP2 rule (Supporting): requires observation in trans with a pathogenic/likely pathogenic PTEN variant OR at least three cis and/or phase-unknown observations with different P/LP PTEN variants
• ClinVar VCV001785871: submissions SCV002730363 (Ambry, germline, LP) and SCV007391075 (Labcorp, germline, VUS); neither reports phase, parental origin, or a second PTEN variant; submission evidence signals are PS3/PP3 (Ambry) and PM2 (Labcorp) - none allelic
• gnomAD v2.1 exome lookup: variant absent (AF = 0), no observations of any phase
• gnomAD v4.1 exome lookup: variant absent (AF = 0), no observations of any phase
• gnomAD-Canada v1.0 genome lookup: variant absent (AF = 0), no observations of any phase
• Full-text screen of 5 retrieved papers (PMID:29706350, 28492532, 25645574, 17392385, 25394175): zero occurrences of c.209T>G / Leu70Arg / L70R / L70 and zero trans/cis/compound-heterozygote/homozygous content

Still missing

• No phase/allelism data for c.209T>G in any consulted source (no parental testing results, no trans/cis observations, no reports of a second pathogenic PTEN variant in the same proband). BP2 (Supporting) should be re-evaluated if family/phase data or a documented trans observation with a P/LP PTEN variant becomes available.

Sources

Reasoning

VCEP PTEN v3.2 BP4 rule for missense variants requires REVEL score < 0.5. REVEL = 0.985 for this variant, so BP4 is not met. The VCEP BP4 splice-concordance line (SpliceAI + VarSeak agreement) does not apply to missense variants, and SpliceAI (max delta 0.15) cannot substitute for the REVEL line without double-counting predictions already considered under PP3; SpliceAI was therefore not used for BP4. BayesDel 0.595825 is excluded for the same calibration reason as for PP3.

Rule

Multiple lines of computational evidence suggest no impact on gene or gene product. Missense variants: REVEL scores < 0.5 (ClinGen PTEN EP v3.2, BP4 rule)

Evidence considered

• REVEL v1.3 local lookup (source_registry key 'revel'): REVEL score 0.985 for NM_000314.8:c.209T>G (p.Leu70Arg); VCEP BP4 cutoff is < 0.5, therefore not met.
• ClinGen PTEN Expert Panel Specifications v3.2 (cspec doc 135637575): BP4 rule for missense variants = 'REVEL scores < 0.5'.
• BayesDel local lookup (source_registry key 'bayesdel'): score 0.595825 retrieved but NOT used - no verified published threshold, insufficiently calibrated for BP4 per group policy.

Still missing

• VarSeak absent - VCEP BP4 splice-concordance sub-path not evaluable; not applicable to this missense variant and does not affect the call.

Sources

Reasoning

PS1 could not be assessed because its agent did not produce valid output.

Still missing

• attempt 1: evidence_refs must contain only source_registry keys
• attempt 2: evidence_refs must contain only source_registry keys
• attempt 3: evidence_refs must contain only source_registry keys

Reasoning

Governing framework is the ClinGen PTEN Expert Panel (VCEP) specification v3.2 (CSPEC doc 135637575, precedence rank 1), which defines PS2 as requiring a de novo observation with BOTH maternity and paternity confirmed in a patient with the disease and no family history (Strong), with Very Strong reserved for two proven / four assumed / one proven + two assumed de novo observations. No source in the case bundle documents any de novo occurrence, parental testing result, maternity/paternity confirmation, or family-history status for c.209T>G (p.Leu70Arg). The ClinVar record VCV001785871 (2 single-submitter clinical labs: Ambry LP citing PMID:29706350 functional data with PS3/PP3 signals; Labcorp VUS with a PM2 signal) contains no de novo assertion and no parental testing data; no expert panel submission exists. Targeted full-text search of all five available publications found zero mentions of the variant and zero de novo/parental-testing content. Because there is no positive evidence of a confirmed de novo occurrence (nor of inheritance), PS2 cannot be met or excluded; the criterion is not assessed pending parental/family testing data.

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. (ClinGen PTEN VCEP v3.2)

Still missing

• No parental testing results (maternity and paternity confirmation) for any proband carrying c.209T>G; de novo status unknown
• No proband-level family history data (required: patient with disease and no family history)
• No literature report documents a confirmed de novo occurrence of p.Leu70Arg

Sources

Reasoning

PS4 is applicable under the ClinGen PTEN VCEP v3.2 (CSPEC doc 135637575): either a sufficiently powered case-control study (OR >2, p<0.05, 95% CI lower limit >1.5 for a PHTS component phenotype) or the phenotype specificity-score model (1 pt per adult proband with Cleveland Clinic score >=30, 0.5 pt for 25-29; children 1 pt pediatric score >=5, 0.5 pt for score 4 excluding autism/DD/ID; Supporting 1-1.5, Moderate 2-3.5, Strong 4-15.5, Very Strong >=16). No evidence in the case bundle permits either calculation: ClinVar submissions for VCV001785871 (Ambry LP, Labcorp VUS) carry no proband phenotype or specificity scores; no case-control study exists; the five retrieved full-text publications and the GeneReviews PHTS entry contain no mention of c.209T>G/p.Leu70Arg (variant-absence screen performed on all five full texts); COSMIC COSV109700563 (n=1) is a somatic observation and is not germline case evidence. Evidence is insufficient, so the criterion is returned not_assessed rather than met.

Rule

PTEN VCEP v3.2 PS4: case-control study with OR >2 for a PHTS component phenotype, p<0.05 and 95% CI lower limit >1.5; OR phenotype specificity scores summed across independent probands (adults: 1 pt CC score >=30, 0.5 pt CC 25-29 per Tan 2011 PMID 21194675; children: 1 pt pediatric score >=5, 0.5 pt score 4 with autism/DD/ID excluded) - Supporting 1-1.5, Moderate 2-3.5, Strong 4-15.5, Very Strong >=16; not to be applied if BS1 applies.

Evidence considered

• ClinGen PTEN VCEP v3.2 PS4 rule (case-control OR>2 p<0.05 CI>1.5 OR specificity-score model) from CSPEC doc 135637575
• ClinVar VCV001785871 submission audit: 2 single-submitter clinical laboratory submissions (Ambry LP SCV002730363; Labcorp VUS SCV007391075), no expert panel, no phenotype detail provided
• Full-text screen of 5 retrieved publications for c.209T>G/p.Leu70Arg/Leu70/L70R: zero variant mentions
• COSMIC COSV109700563 somatic count n=1 excluded as non-germline case evidence

Still missing

• No proband-level phenotype data (Cleveland Clinic score or pediatric phenotype score) for any carrier of c.209T>G to compute the PTEN VCEP specificity score
• No case-control or prevalence-enrichment data for c.209T>G in PHTS or PHTS component phenotypes
• No variant-specific case reports identified in retrieved literature (all five full texts and GeneReviews screened; variant absent)

Sources

Reasoning

PM1 could not be assessed because its agent did not produce valid output.

Still missing

• attempt 1: evidence_refs must contain only source_registry keys
• attempt 2: evidence_refs must contain only source_registry keys
• attempt 3: evidence_refs must contain only source_registry keys

Reasoning

PM5 could not be assessed because its agent did not produce valid output.

Still missing

• attempt 1: evidence_refs must contain only source_registry keys
• attempt 2: evidence_refs must contain only source_registry keys
• attempt 3: evidence_refs must contain only source_registry keys

Reasoning

Under the ClinGen PTEN VCEP v3.2 (CSPEC doc 135637575), PM6 applies to an assumed de novo occurrence (maternity/paternity NOT confirmed) in a proband with the disease and no family history (Moderate), escalating to Strong with two presumed-de-novo probands or one presumed-de-novo proband with a highly specific phenotype meeting PS4 criteria. The evidence bundle contains no proband-level assertion of assumed de novo origin, no parental testing data, and no family history documentation for any carrier of c.209T>G (p.Leu70Arg). The two ClinVar submissions (SCV002730363 Ambry LP, SCV007391075 Labcorp VUS) cite only functional (PS3), in silico (PP3), and population (PM2) signals; neither records a de novo observation. None of the seven retrieved publications mention the variant, and targeted full-text search found no de novo/segregation/parental-testing content. With no data on which to base an assumed-de-novo determination, PM6 is not assessed.

Rule

PM6 (Moderate): 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 a proband with presumed de novo occurrence for an individual with a highly specific phenotype (meets criteria to count towards PS4). PM6_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. (ClinGen PTEN VCEP v3.2)

Still missing

• No proband identified as having assumed de novo occurrence of c.209T>G; parental testing not performed or not reported
• No family history documentation to confirm 'no family history' requirement
• No multiple-proband de novo series for this variant in the literature

Sources

Reasoning

Under the ClinGen PTEN VCEP v3.2 (CSPEC doc 135637575), PP1 requires co-segregation with disease in multiple affected family members, with 3-4 meioses (Supporting), 5-6 meioses (Moderate), or >=7 meioses across at least two families (Strong). No segregation data exists anywhere in the case bundle: no pedigrees, no affected-family-member testing, and no meiosis counts are reported for c.209T>G (p.Leu70Arg) in ClinVar VCV001785871, in any of the seven retrieved publications, or in any other case source. The literature triage (literature_pass.json) screened papers for functional/splicing/segregation/case-observation themes, and no paper was flagged as bearing segregation evidence; targeted full-text search of the five available publications confirmed zero variant mentions and zero segregation content. Without any observed meioses, PP1 cannot be applied at any strength and is not assessed.

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. (ClinGen PTEN VCEP v3.2)

Still missing

• No family segregation studies or pedigrees reported for this variant
• No meiosis counts across affected relatives in any source
• No multi-family segregation data (required for PP1_Strong)

Sources

Reasoning

PP2 could not be assessed because its agent did not produce valid output.

Still missing

• attempt 1: evidence_refs must contain only source_registry keys
• attempt 2: evidence_refs must contain only source_registry keys
• attempt 3: evidence_refs must contain only source_registry keys

Reasoning

Under the ClinGen PTEN VCEP v3.2 (CSPEC doc 135637575), BS4 requires POSITIVE evidence of lack of segregation in affected members of one family (Supporting) or two or more families (Strong). The case bundle contains no family testing data at all for c.209T>G (p.Leu70Arg): no affected relative tested, no non-segregating affected individuals documented, and no pedigrees in ClinVar VCV001785871 or in any of the retrieved publications (full-text search returned zero variant mentions and zero segregation/parental-testing content). Absence of segregation data is not evidence of non-segregation, so BS4 must not be applied; the criterion is not assessed until family-based studies demonstrate lack of segregation.

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. (ClinGen PTEN VCEP v3.2)

Still missing

• No family studies demonstrating an affected member who does not carry the variant
• No non-segregation data in one family (BS4_Supporting) or two or more families (BS4_Strong)
• No pedigree data in ClinVar submissions or literature for this variant

Sources

Reasoning

BP1 could not be assessed because its agent did not produce valid output.

Still missing

• attempt 1: evidence_refs must contain only source_registry keys
• attempt 2: evidence_refs must contain only source_registry keys
• attempt 3: evidence_refs must contain only source_registry keys

Reasoning

BP5 is applicable under the ClinGen PTEN VCEP v3.2 at Supporting strength but requires at least two cases in which the variant is found together with an alternate molecular basis for disease, where the other gene/disorder is highly penetrant AND the patient's personal/family history shows no overlap between the other gene and PTEN. The case bundle contains no case-level data for any c.209T>G carrier demonstrating an alternate molecular diagnosis (ClinVar submissions contain no such information; none of the retrieved publications mention the variant). Evidence is insufficient, so the criterion is returned not_assessed rather than met.

Rule

PTEN VCEP 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 must be highly penetrant AND patient's personal/family history must demonstrate no overlap between the other gene and PTEN.

Evidence considered

• ClinGen PTEN VCEP v3.2 BP5 rule (>=2 cases with alternate molecular basis; other gene highly penetrant; no PTEN phenotype overlap) from CSPEC doc 135637575
• ClinVar VCV001785871 submissions: no alternate-molecular-basis information provided
• Full-text screen of 5 retrieved publications for variant-specific case data: no variant mentions

Still missing

• No case with a documented alternate molecular basis (e.g., pathogenic variant in another highly penetrant gene) available for any c.209T>G carrier
• PTEN VCEP requires at least two such cases plus demonstration of no personal/family history overlap between the other gene and PTEN

Sources