PTEN c.46T>G, p.(Tyr16Asp)

Reasoning

Variant is missense NM_000314.8:c.46T>G (p.Tyr16Asp; TAT>GAT) in PTEN. The ClinGen PTEN Expert Panel Specification v3.2 (cspec doc 135637575) is the governing framework; PS3_moderate applies when the Mighell et al. 2018 saturation-mutagenesis lipid phosphatase assay (PMID 29706350) Table S2 cumulative fitness score (Cum_score) is <= -1.11 for a variant flagged high confidence (High_conf TRUE). The exact variant was directly assayed: Table S2 row Y16D shows Cum_score = -2.205 (Cum_SE 0.373), High_conf = TRUE ('Pass SE Filter'), Imputed_Score = NA (directly measured, not imputed), with all six biological replicate scores <= -1.88 (A1 -3.26, B1 -2.02, A2 -3.39, B2 -2.30, A3 -2.73, B3 -1.88). Since -2.205 <= -1.11, PS3_moderate is met. The -1.11 cutoff is published in the paper itself (Table 1 footnote c: variants with scores less than or equal to -1.11, the lower 95th percentile two-tailed for synonymous variants), and -2.205 also falls within the paper's 'truncation-like' range (<= -2.13, the upper 95th percentile of nonsense mutations at positions 1-349, Table 1 footnote d), indicating damage as severe as typical truncating variants. PS3_strong (RNA/mini-gene/splicing assay demonstrating splicing impact) is not met: no RNA assay exists for this variant and SpliceAI max delta is 0.03. The supporting-strength tier (<50% wild-type activity) is superseded because the moderate tier is met. Confidence is high: direct high-confidence measurement with replicate concordance and exact variant identity (Wt codon TAT / Mut codon GAT; the paper's own Table S3 lists NM_000314.6(PTEN):c.46T>G (p.Tyr16Asp), VariationID 422899, matching this case).

Rule

ClinGen PTEN EP Specification v3.2, PS3_moderate: 'Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product. Phosphatase activity <= -1.11 per Mighell et al. 2018, PMID: 29706350.' (applied only when Table S2 High_conf = TRUE)

Evidence considered

• ClinGen PTEN EP Specification v3.2 (cspec doc 135637575), PS3_moderate rule: 'Phosphatase activity <= -1.11 per Mighell et al. 2018, PMID: 29706350.' Instructions require the variant to be listed TRUE under Table S2 column I (high confidence) and state 'Apply PS3_moderate for all variants with scores <= -1.11.'
• Mighell et al. 2018, Am J Hum Genet 102:943-955, PMID 29706350, Table 1 footnote c: 'variants with scores less than or equal to -1.11, the lower 95th percentile (two-tailed) for synonymous variants' - published calibration of the less-than-wild-type (likely damaging) threshold used by the VCEP.
• Mighell et al. 2018 Table S2 (source_registry key vcep_mmc2, mmc2.xlsx), row Y16D: Cum_score = -2.205 (Cum_SE 0.373), High_conf = TRUE ('Pass SE Filter'), Imputed_Score = NA (directly measured); biological replicates A1 -3.26, B1 -2.02, A2 -3.39, B2 -2.30, A3 -2.73, B3 -1.88 (all <= -1.88).
• Cum_score -2.205 <= -1.11 satisfies PS3_moderate; it is also <= -2.13, i.e. within the paper's truncation-like category (Table 1 footnote d: 'scores less than or equal to -2.13, the upper 95th percentile (two-tailed) of nonsense mutations at positions 1-349').
• OncoKB (source_registry key oncokb) variant-specific annotation for PTEN Y16D: 'Likely Oncogenic', biological-effect context 'Likely Loss-of-function'; used as context and literature lead (pointed to PMID 29706350) but not as a validated functional assay.

Still missing

• No RNA/mini-gene/splicing assay data for this missense variant, so PS3_strong (splicing impact) cannot be applied; PS3 is capped at Moderate per the PTEN VCEP specification.

Sources

Reasoning

ClinGen PTEN VCEP CSPEC v3.2 PM2 (Supporting): variant absent in population databases 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. NM_000314.8:c.46T>G (p.Tyr16Asp) is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0 (AF = 0 in all), satisfying the absence criterion with no subpopulation alleles to trigger the stricter subpopulation check. Consistent with PHTS prevalence (~1:200,000) and autosomal dominant inheritance. PM2 met at Supporting strength per the PTEN VCEP rule (the CSPEC combination rules reference PM2_Supporting as a Pathogenic.Supporting code, confirming this strength).

Rule

Absent in population. Databases present at <0.00001 (0.001%) allele frequency in gnomAD or another large sequenced population. If multiple alleles are present within any subpopulation, allele frequency in that subpopulation must be <0.00002 (0.002%).

Evidence considered

• gnomAD v2.1 (exome) variant lookup 10-89624272-T-G: variant absent; AF=0 < 0.001%
• gnomAD v4.1 (exome) variant lookup chr10-87864515-T-G: variant absent; AF=0 < 0.001%
• gnomAD-Canada v1.0 (HostSeq genomes) variant lookup 10-87864515-T-G: variant absent; AF=0 < 0.001%
• ClinGen PTEN Expert Panel Specifications v3.2 (cspec doc 135637575): PM2 rule threshold <0.00001 (0.001%) overall and <0.00002 (0.002%) per subpopulation

Still missing

• gnomAD source_data did not include numeric allele counts (absence recorded by variant-page status); subpopulation AF check not applicable because zero alleles were observed in every queried population.

Sources

Reasoning

PTEN VCEP v3.2 lists PP2 as Applicable (default Supporting) for missense variants in PTEN, a gene with a low rate of benign missense variation in which missense variants are a common mechanism of PTEN hamartoma tumor syndrome. The variant under assessment is a missense change (p.Tyr16Asp, NP_000305.3), so the gene-level PP2 condition is satisfied. This is corroborated by the Mighell et al. 2018 (PMID:29706350) saturation mutagenesis of PTEN lipid phosphatase activity, in which the majority of assayed PTEN missense variants impaired function (2,273 of 7,244 assayed single-amino-acid variants with reduced activity, including 1,789 missense changes), indicating low tolerance to benign missense variation. PP2 met at Supporting.

Rule

Missense variant in a gene that has a low rate of benign missense variation and where missense variants are a common mechanism of disease. (ClinGen PTEN VCEP v3.2, PP2 Supporting)

Evidence considered

• PTEN VCEP v3.2 (cspec doc 135637575) PP2 rule: 'Missense variant in a gene that has a low rate of benign missense variation and where missense variants are a common mechanism of disease' - Applicable, default strength Supporting
• Mighell et al. 2018 (PMID:29706350): 'We identified 2,273 mutations with reduced cellular lipid phosphatase activity, which includes 1,789 missense mutations' - gene-level evidence of low PTEN missense tolerance (humanized yeast saturation assay)

Sources

Reasoning

Variant NM_000314.8:c.46T>G is a missense substitution (p.Tyr16Asp) in exon 1 of PTEN. Governing framework is the ClinGen PTEN Expert Panel Specifications v3.2 (cspec doc 135637575; framework_mode=vcep, precedence_rank=1), which pre-assigns PP3 (Supporting) for missense variants with REVEL score > 0.7. REVEL score for this variant is 0.844 (> 0.7), so PP3 is met at Supporting strength. The splice-impact path was also evaluated: SpliceAI max delta = 0.03 (DS_AG 0.00, DS_AL 0.02, DS_DG 0.03, DS_DL 0.02), far below the VCEP PP3 splice threshold of 0.5, so the splice path contributes no additional PP3 evidence (and the VCEP splice path is specified for synonymous/intronic variants only). BayesDel score 0.518836 is treated as not_available for PP3 because no verified published calibration threshold can be named (pipeline policy); aGVGD data are absent from the evidence bundle. The VCEP pre-assignment based on REVEL alone is applied directly per group instructions; no double-counting with BP4/BP7 (REVEL is used only for PP3).

Rule

ClinGen PTEN EP v3.2 (cspec doc 135637575): PP3 Supporting - missense variants with REVEL score > 0.7; splicing path (SpliceAI 0.5-1 + VarSeak class 4/5 concordance) applies to synonymous/intronic variants only

Evidence considered

• REVEL score 0.844 (source_registry key 'revel'; local REVEL v1.3 lookup, GRCh38 chr10:87864515 T>G) exceeds the ClinGen PTEN Expert Panel Specifications v3.2 (cspec doc 135637575) missense PP3 threshold of > 0.7 -> PP3 Supporting
• SpliceAI max delta score 0.03 (DS_AG 0.00, DS_AL 0.02, DS_DG 0.03, DS_DL 0.02; source_registry key 'spliceai', SpliceAI Lookup for NM_000314.8:c.46T>G) is well below the VCEP PP3 splice threshold of 0.5; no splice-impact evidence for PP3
• ClinGen PTEN Expert Panel Specifications v3.2 (source_registry key 'cspec', doc 135637575): PP3 Supporting rule 'Missense variants: REVEL score > 0.7'; VCEP commentary cites Bayesian adaptation of the ACMG/AMP framework (Tavtigian et al., 2018, PMID 29300386, referenced within the cspec document) as the calibration basis
• BayesDel score 0.518836 (source_registry key 'bayesdel') consulted but treated as not_available for PP3: no verified published threshold can be named in the same entry as the score, per pipeline calibration policy

Still missing

• VarSeak splice predictor not present in evidence bundle - VCEP splice path nominally requires SpliceAI+VarSeak concordance, but that path applies to synonymous/intronic variants and is not needed for this missense variant (REVEL missense path is independent and satisfied)
• BayesDel score 0.518836 treated as not_available for PP3/BP4: no verified published calibration threshold available to this pipeline
• aGVGD prediction not present in evidence bundle

Sources

Reasoning

Variant is NM_000314.8:c.46T>G, predicted p.(Tyr16Asp) (NP_000305.3). PS1 (PTEN VCEP v3.2, Strong) requires the same amino acid change as a previously established pathogenic variant arising from a DIFFERENT nucleotide change, or an alternate nucleotide at a pathogenic splicing-variant position. Codon 16 is TAT: only c.46T>G (TAT>GAT) can produce p.Tyr16Asp — no alternate single-nucleotide change yields Asp at this residue, so the same-amino-acid/different-nucleotide condition cannot be satisfied by any variant. The splicing clause is inapplicable: c.46 is a coding (exon 1) position and SpliceAI predicts no splice impact (max delta 0.03). The ClinVar Pathogenic (GeneDx) and Likely pathogenic (Great Ormond Street GOSH) submissions for VCV000422899 apply to this exact nucleotide change (c.46T>G) and do not constitute a distinct established-pathogenic variant producing the same amino acid change; per the no-inference-from-final-classification rule they cannot satisfy PS1.

Rule

Same amino acid change as a previously established pathogenic variant regardless of nucleotide change OR different variant at same nucleotide position as a pathogenic splicing variant, where in silico models predict impact equal to or greater than the known pathogenic variant. (ClinGen PTEN VCEP v3.2, PS1 Strong)

Evidence considered

• PTEN VCEP v3.2 (cspec doc 135637575) PS1 rule: 'Same amino acid change as a previously established pathogenic variant regardless of nucleotide change OR different variant at same nucleotide position as a pathogenic splicing variant, where in silico models predict impact equal to or greater than the known pathogenic variant'
• Mutalyzer/VariantValidator normalization (prefetch): NM_000314.8:c.46T>G -> NP_000305.3:p.(Tyr16Asp); codon TAT at c.46-48 permits Asp only via c.46T>G, so no alternate-nucleotide same-amino-acid variant exists
• ClinVar VCV000422899: Pathogenic (SCV000572492, GeneDx, 2025-11-14) and Likely pathogenic (SCV007334851, GOSH, 2025-11-25) are for c.46T>G itself; not an alternate-nucleotide comparator
• SpliceAI max delta score 0.03: no splicing impact; splicing clause of PS1 not applicable

Sources

Reasoning

The PTEN VCEP v3.2 PM1 rule (Moderate) operationally defines PM1 residues for PTEN as the catalytic motifs WPD loop (residues 90-94), P-loop/phosphatase core (123-130), and TI-loop (166-168) of NP_000305.3 (instructions cite Lee 1999). p.Tyr16 is not within any of these motifs (it lies near the N-terminus, outside the defined catalytic regions), so PM1 is not met under the governing VCEP specification. Prefetch flagged Y16 as a 'statistically significant hotspot' in CANCERHOTSPOTS (screenshot with partial-parse warning; source not registered in source_registry) and OncoKB labels Y16D Likely Oncogenic/Likely Loss-of-function, but these are somatic/functional signals and the PTEN VCEP defines PM1 strictly by the catalytic-motif residues; the generic ACMG 'mutational hot spot' clause does not extend PM1 to residue 16.

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). (ClinGen PTEN VCEP v3.2, PM1 Moderate)

Evidence considered

• PTEN VCEP v3.2 (cspec doc 135637575) PM1 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)'
• PTEN VCEP v3.2 PM1 instructions: catalytic motifs are the WPD loop (90-94), P-loop/phosphatase core (123-130), and TI-loop (166-168); residue 16 is outside all three

Still missing

• CANCERHOTSPOTS flagged Y16 as a statistically significant somatic hotspot (partial-parse warning on screenshot; CANCERHOTSPOTS is not a source_registry key). Not used because PTEN VCEP v3.2 defines PM1 residues as catalytic motifs 90-94, 123-130, 166-168 only; if the review team considers somatic hotspot status to warrant PM1 beyond the VCEP definition, this is a spec-level question for human review.

Sources

Reasoning

ClinGen PTEN VCEP CSPEC v3.2 sets BA1 (Stand Alone) at gnomAD Filtering allele frequency >0.00056 (0.056%). NM_000314.8:c.46T>G (p.Tyr16Asp) is absent from gnomAD v2.1 (GRCh37 10-89624272-T-G), gnomAD v4.1 (GRCh38 10-87864515-T-G), and gnomAD-Canada v1.0; AF = 0 in all queried populations, far below the 0.056% stand-alone threshold. No threshold-boundary artifact applies because the variant is entirely absent. BA1 not met.

Rule

gnomAD Filtering allele frequency >0.00056 (0.056%)

Evidence considered

• gnomAD v2.1 (exome) variant lookup 10-89624272-T-G: variant absent (AF=0)
• gnomAD v4.1 (exome) variant lookup chr10-87864515-T-G: variant absent (AF=0)
• gnomAD-Canada v1.0 (HostSeq genomes) variant lookup 10-87864515-T-G: variant absent (AF=0)
• ClinGen PTEN Expert Panel Specifications v3.2 (cspec doc 135637575): BA1 rule threshold gnomAD FAF >0.00056 (0.056%)

Still missing

• gnomAD lookups recorded variant-page 'absent' status without numeric allele counts in source_data; absence is the operative datum and is corroborated by screenshots.

Sources

Reasoning

ClinGen PTEN VCEP CSPEC v3.2 sets BS1 Strong at gnomAD Filtering allele frequency 0.000043-0.00056 (0.0043%-0.056%) and BS1 Supporting at 0.0000043-0.000043 (0.00043%-0.0043%). The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada v1.0 (AF = 0), which is below the lower bound of even the Supporting frequency band. BS1 not met at any strength.

Rule

gnomAD Filtering allele frequency from 0.000043 (0.0043%) up to 0.00056 (0.056%); Supporting: allele frequency from 0.0000043 (0.00043%) up to 0.000043 (0.0043%)

Evidence considered

• gnomAD v2.1 (exome) variant lookup 10-89624272-T-G: variant absent (AF=0)
• gnomAD v4.1 (exome) variant lookup chr10-87864515-T-G: variant absent (AF=0)
• gnomAD-Canada v1.0 (HostSeq genomes) variant lookup 10-87864515-T-G: variant absent (AF=0)
• ClinGen PTEN Expert Panel Specifications v3.2 (cspec doc 135637575): BS1 rule bands 0.000043-0.00056 (Strong) and 0.0000043-0.000043 (Supporting)

Still missing

• No allele count data beyond absence status was captured; not material to the not-met determination since AF=0 is unambiguous.

Sources

Reasoning

ClinGen PTEN VCEP CSPEC v3.2 BS2 requires observation 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, v4.1, and gnomAD-Canada v1.0, so no homozygous (or any) observations exist in these population datasets. No evidence of homozygous carriers in unaffected individuals is available from any reviewed source. BS2 not met. Note PTEN hamartoma tumor syndrome is autosomal dominant, so homozygous carrier observations would be exceptionally unlikely.

Rule

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

Evidence considered

• gnomAD v2.1 (exome) variant lookup 10-89624272-T-G: variant absent; no homozygous observations
• gnomAD v4.1 (exome) variant lookup chr10-87864515-T-G: variant absent; no homozygous observations
• gnomAD-Canada v1.0 (HostSeq genomes) variant lookup 10-87864515-T-G: variant absent; no homozygous observations
• ClinGen PTEN Expert Panel Specifications v3.2 (cspec doc 135637575): BS2 requires homozygous state in healthy or PHTS-unaffected individual

Still missing

• No population homozygous observations exist to evaluate; no clinical cohort data bearing on homozygous state in unaffected individuals was identified in this case bundle.

Sources

Reasoning

BS3 was adjudicated against the PTEN VCEP v3.2 specification. BS3_supporting requires 'Phosphatase activity >0 per Mighell et al. 2018, PMID: 29706350' (Table S2 Cum_score > 0 with High_conf TRUE). The exact variant Y16D was directly assayed with high confidence and its Cum_score is -2.205 - severely reduced, not > 0 - so BS3_supporting is not met; the same validated assay that supports PS3_moderate affirmatively excludes a benign functional effect. BS3_strong is not applicable to this variant: the VCEP restricts BS3_strong to intronic or synonymous variants with RNA, mini-gene, or other splicing assays demonstrating no splicing impact, and p.Tyr16Asp is a missense change with no benign splicing evidence (SpliceAI max delta 0.03 is not a functional assay). No alternative benign functional evidence exists for this variant (no assay showing wild-type-comparable activity plus a second appropriate assay). Therefore BS3 is not met, based on direct functional evidence rather than absence of data.

Rule

ClinGen PTEN EP Specification v3.2, BS3_supporting: 'Phosphatase activity >0 per Mighell et al. 2018, PMID: 29706350.' - NOT satisfied (Cum_score -2.205); BS3_strong restricted to intronic/synonymous splicing evidence - not applicable

Evidence considered

• ClinGen PTEN EP Specification v3.2 (cspec doc 135637575), BS3_supporting rule: 'In vitro or in vivo functional study or studies showing no damaging effect on protein function. Phosphatase activity >0 per Mighell et al. 2018, PMID: 29706350.'
• Mighell et al. 2018 Table S2 (vcep_mmc2), row Y16D: Cum_score = -2.205, High_conf = TRUE - the score is not > 0, so the BS3_supporting threshold fails.
• ClinGen PTEN EP Specification v3.2, BS3_strong rule: 'Well-established in vitro or in vivo functional studies shows no damaging effect on protein function. To be applied to intronic or synonymous variants, RNA, mini-gene or other splicing assay demonstrating no splicing impact.' - not applicable to missense p.Tyr16Asp.
• Mighell et al. 2018, PMID 29706350, Table 1 footnote f ('WT-like: variants with scores between -1.11 and 0.89, the 95th percentile (two-tailed) of synonymous variants') confirms -2.205 falls far outside the wild-type-like score range.

Still missing

• No benign functional assay data for Y16D exist; the only validated assay covering this variant (Mighell 2018 saturation mutagenesis) shows severe loss of lipid phosphatase activity, which directly excludes BS3.
• No RNA/mini-gene assay available, so BS3_strong (intronic/synonymous splicing no-impact evidence) could not apply even in principle for this missense variant.

Sources

Reasoning

BP2 under the ClinGen PTEN VCEP v3.2 (Benign Supporting) requires the variant to be 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 such observation exists in any case source: ClinVar VCV000422899 contains two clinical-laboratory submissions (GeneDx: Pathogenic; Great Ormond Street Hospital: Likely pathogenic) with review status 'criteria provided' only - no expert panel curation, no criterion leads, and no phase, allelism, or co-occurring-variant data; the variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada (no homozygous or compound observations); and none of the seven papers in the literature packet mention c.46T>G/p.Tyr16Asp or report trans/cis observations. The criterion requires positive evidence of the specified allelic configuration, which is entirely absent, so BP2 is not met (absence of this evidence must not be read as a benign signal).

Rule

BP2: 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 (ClinGen PTEN VCEP v3.2, Benign Supporting)

Evidence considered

• ClinVar VCV000422899: 2 submissions (GeneDx Pathogenic; Great Ormond Street Hospital NHS Foundation Trust Likely pathogenic); review status 'criteria provided'; no expert panel, no criterion leads, no phase/allelism or co-occurring variant data
• gnomAD v2.1, gnomAD v4.1, gnomAD-Canada v1.0: variant absent from all three (no homozygotes, no allelic observations)
• Literature packet (7 papers; PMIDs 28481359, 29706350, 17392385, 20301661, 23788249, 25645574, 26389333): none mention c.46T>G or provide trans/cis observations relevant to BP2

Still missing

• No phase (trans/cis) determination available - parental genotyping or haplotyping would be required to ever meet BP2
• No reports of the variant co-occurring in trans with a pathogenic/likely pathogenic PTEN variant
• ClinVar submissions for VCV000422899 provide no allelic-context data (no co-occurring PTEN variants listed)

Sources

Reasoning

The VCEP BP4 (Supporting) missense rule requires REVEL score < 0.5; the variant's REVEL score is 0.844, so the missense BP4 path is not met. The BP4 splice path (SpliceAI 0-0.2 + VarSeak class 1-2 concordance) is specified by the VCEP for synonymous or intronic variants only and is not applied to this exonic missense variant; in any case SpliceAI max delta 0.03 is a single splice prediction and cannot by itself establish BP4 for a missense variant. BayesDel 0.518836 is treated as not_available (no verified published threshold). No BP4-grade computational evidence exists for this variant; the sole calibrated missense prediction (REVEL 0.844) points in the pathogenic direction and was counted once for PP3 only (no double-counting).

Rule

ClinGen PTEN EP v3.2 (cspec doc 135637575): BP4 Supporting - missense variants with REVEL score < 0.5; synonymous/intronic variants with SpliceAI 0-0.2 + VarSeak class 1-2 concordance

Evidence considered

• REVEL score 0.844 (source_registry key 'revel'; local REVEL v1.3 lookup, GRCh38 chr10:87864515 T>G) does not meet the ClinGen PTEN EP v3.2 (cspec doc 135637575) BP4 missense threshold of < 0.5 -> BP4 not met
• SpliceAI max delta score 0.03 (source_registry key 'spliceai') would fall in the VCEP benign range (0-0.2 is benign, 0.03 < 0.2) for the synonymous/intronic splice path, but that path is not applied to missense variants per the VCEP; not used as BP4 evidence here
• ClinGen PTEN Expert Panel Specifications v3.2 (source_registry key 'cspec', doc 135637575): BP4 Supporting rule 'Missense variants: REVEL scores < 0.5'; variant fails threshold
• BayesDel score 0.518836 (source_registry key 'bayesdel') consulted but treated as not_available for BP4: no verified published threshold can be named in the same entry as the score, per pipeline calibration policy

Still missing

• No BP4-grade evidence: REVEL 0.844 fails the VCEP benign missense threshold (< 0.5)
• VCEP BP4 splice path not applicable to exonic missense variants (reserved for synonymous/intronic variants)
• BayesDel treated as not_available (no verified published threshold); aGVGD absent from evidence bundle

Sources

Reasoning

No proband-level de novo evidence is available in this case bundle. The ClinGen PTEN VCEP v3.2 PS2 rule requires a proven de novo occurrence (maternity and paternity confirmed) in a patient with the disease and no family history (Strong), or multiple proven/assumed de novo observations (Very Strong). The ClinVar record (VCV000422899) is classified Pathogenic/Likely pathogenic by two clinical laboratories (GeneDx SCV000572492, GOSH SCV007334851) but neither submission provides any de novo, parental-testing, or family-history detail in the bundle (submission audit: 0 criterion-lead submissions, 0 usable_for_criterion_leads). No publication among the retrieved full-text papers is a de novo case report. Because there is no documented de novo observation and no parental testing data, PS2 cannot be evaluated.

Rule

De novo (both maternity and paternity confirmed) observation in a patient with the disease and no family history (Strong). Two proven OR four assumed OR one proven + two assumed de novo observations in a patient with the disease and no family history (Very Strong). ClinGen PTEN VCEP v3.2.

Evidence considered

• cspec: PTEN VCEP v3.2 PS2 rule (proven de novo, maternity+paternity confirmed, patient with disease and no family history) - no applicable data found
• clinvar: VCV000422899 submissions reviewed; no de novo or parental testing information reported in case bundle

Still missing

• No proband phenotype/family-history documentation in case bundle
• No parental testing results (maternity/paternity confirmation) for any proband
• ClinVar submissions lack criterion-level de novo evidence (no usable criterion leads)
• No de novo case-report literature retrieved for c.46T>G

Sources

Reasoning

Governing framework is ClinGen PTEN Expert Panel v3.2 (CSPEC doc 135637575). PS4 requires either (a) a sufficiently powered case-control study showing odds ratio >2 for a PHTS component phenotype with p<0.05 and 95% CI lower limit >1.5, or (b) summed phenotype specificity scores across independent probands (adults: Cleveland Clinic score >=30 = 1 point, 25-29 = 0.5 points; children: pediatric phenotype score >=5 = 1 point, score of 4 = 0.5 points, autism/DD/ID excluded). No case-control study for c.46T>G is present in the evidence bundle, and no CC or pediatric phenotype specificity scores are available for any proband. The two ClinVar submissions (GeneDx Pathogenic; Great Ormond Street Hospital Likely pathogenic) are single-submitter laboratory classifications without phenotype scores, and their classifications cannot be used as PS4 evidence (no inference of criteria from another source's final classification). The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada, so no control-frequency enrichment can be computed in either direction. The single COSMIC observation is somatic (n=1), not germline proband phenotype evidence. PS4 therefore cannot be applied at any strength level from available data.

Rule

PS4 (PTEN EP v3.2): Probands with specificity score >=16 (Very Strong); 4-15.5 (Strong) OR prevalence of the variant in affected individuals significantly increased vs controls; 2-3.5 (Moderate); 1-1.5 (Supporting). Scoring: 1 point per adult proband with Cleveland Clinic score >=30 (0.5 if 25-29); 1 point per child proband with pediatric phenotype score >=5 (0.5 if score of 4, autism/DD/ID excluded). May not be applied if BS1 applies.

Evidence considered

• PTEN EP v3.2 PS4 rule: 'Probands with specificity score >=16 (Very Strong); 4-15.5 (Strong); 2-3.5 (Moderate); 1-1.5 (Supporting)' and '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'
• ClinVar variation 422899: two germline clinical-testing submissions (Pathogenic by GeneDx, SCV000572492; Likely pathogenic by Great Ormond Street Hospital, SCV007334851, condition 'PTEN Hamartoma Tumor Syndrome'); no phenotype specificity scores reported
• gnomAD v2.1 (10-89624272-T-G): absent; gnomAD v4.1 (chr10-87864515-T-G): absent; gnomAD-Canada v1.0: absent - no control allele frequency available for case-control enrichment assessment
• COSMIC COSV64294593: somatic count 1 - somatic observation, not germline proband phenotype evidence

Still missing

• No case-control study of c.46T>G reporting OR/CI for any PHTS component phenotype
• No Cleveland Clinic (Tan 2011) or pediatric phenotype specificity scores for any proband carrying c.46T>G
• ClinVar submissions lack detailed proband phenotypes (one condition label 'PTEN Hamartoma Tumor Syndrome', one 'Not Provided') insufficient to compute specificity scores
• Proband counts and family-history detail needed for PS4 Use 2 scoring are not available in this case file

Sources

Reasoning

PM5 (PTEN VCEP v3.2, Moderate) requires a DIFFERENT missense change at residue Tyr16 previously determined Pathogenic or Likely pathogenic, with BLOSUM62 score of the interrogated variant (p.Tyr16Asp, BLOSUM62 Y>D = -3) equal to or less than that of the known variant. The pipeline's PM5 comparator harvest (pm5_candidates.json, classic same-residue mode) failed with HTTP 429 Too Many Requests and returned 0 same-residue candidates (total 10 candidates seen, none at Tyr16); no ClinVar comparator at residue 16 (e.g., p.Tyr16Cys/Asn/His/Phe) was collected. Full-text search of the two available functional papers (PMID:29706350, PMID:28481359) found no Y16/Tyr16/c.46T variant mention. Evidence is therefore insufficient to determine whether a pathogenic same-residue comparator exists; PM5 is not assessed pending a successful ClinVar query or manual review.

Rule

Missense change at an amino acid residue where a different missense change determined to be pathogenic or likely pathogenic has been seen before. In addition, variant being interrogated must have BLOSUM62 score equal to or less than the known variant. (ClinGen PTEN VCEP v3.2, PM5 Moderate)

Evidence considered

• pm5_candidates.json: pm5_mode 'classic_same_residue_missense', candidate_summary same_residue_candidates = 0, errors = 'HTTP Error 429: Too Many Requests' - harvest failed softly, no Tyr16 comparator collected
• PTEN VCEP v3.2 (cspec) PM5 rule: different missense at a residue where a P/LP different missense has been seen, with BLOSUM62 of interrogated variant <= known variant; comparator must be established P/LP (LP acceptable unless it would upgrade classification)
• PMID:29706350 and PMID:28481359 full texts searched for 'Y16', 'Tyr16', 'c.46T', '46T' - no variant mention, no same-residue comparator identified

Still missing

• ClinVar PM5 comparator query failed with HTTP 429 (Too Many Requests); re-run ClinVar query for PTEN p.Tyr16* (e.g., PTEN[GENE] AND Tyr16[VARNAME]) or perform manual ClinVar review for pathogenic/likely pathogenic missense variants at residue 16
• If a same-residue comparator is identified, confirm BLOSUM62 comparison per VCEP PM5 rule (p.Tyr16Asp Y>D = -3 must be <= comparator's BLOSUM62 score)

Sources

Reasoning

No proband with a documented presumed de novo occurrence is available. The ClinGen PTEN VCEP v3.2 PM6 rule requires an assumed de novo occurrence (paternity/maternity not confirmed) in a proband with the disease and no family history (Moderate), with Strong/Very Strong tiers for multiple presumed de novo probands. The case bundle contains no proband-level data whatsoever: no trio testing, no parental testing, no family-history statement, and no de novo segregation case report among retrieved publications. ClinVar submissions (VCV000422899) do not report any presumed de novo observation. PM6 cannot be evaluated.

Rule

Assumed de novo, but without confirmation of paternity and maternity, in proband with the disease and no family history (Moderate). Two probands with presumed de novo occurrence with the disease and no family history (Strong). ClinGen PTEN VCEP v3.2.

Evidence considered

• cspec: PTEN VCEP v3.2 PM6 rule (assumed de novo without paternity/maternity confirmation, proband with disease and no family history) - no applicable data found
• clinvar: VCV000422899 submissions reviewed; no presumed de novo occurrence reported in case bundle

Still missing

• No proband with documented presumed de novo occurrence
• No parental testing or trio data (even unconfirmed-parentage assumed de novo requires a proband observation)
• No family-history documentation (PM6 requires 'no family history')
• No de novo case-report literature retrieved for c.46T>G

Sources

Reasoning

No segregation data are available. The ClinGen PTEN VCEP v3.2 PP1 rule requires co-segregation with disease in multiple affected family members: 3-4 meioses (Supporting), 5-6 meioses (Moderate), or >=7 meioses across at least two families (Strong). The consolidated evidence bundle contains no family/pedigree information, no segregation counts, and no affected relative testing for c.46T>G; the literature_pass.json criteria index covers only PP5 and PS4 and no segregation-themed paper was retrieved. With zero observed meioses, PP1 cannot be evaluated.

Rule

Co-segregation with disease in multiple affected family members, with 3 or 4 meioses observed (Supporting); 5 or 6 meioses (Moderate); >=7 meioses across at least two families (Strong). ClinGen PTEN VCEP v3.2.

Evidence considered

• cspec: PTEN VCEP v3.2 PP1 rule (co-segregation in multiple affected family members, 3-4/5-6/>=7 meioses) - no segregation data found
• clinvar: VCV000422899 submissions reviewed; no segregation information reported in case bundle

Still missing

• No segregation data / meiosis counts for c.46T>G in any source
• No affected-family-member testing results in case bundle
• No segregation-themed literature retrieved for this variant

Sources

Reasoning

No non-segregation (lack-of-segregation) observations are available. The ClinGen PTEN VCEP v3.2 BS4 rule requires documented lack of segregation in affected members of one family (Supporting) or two or more families (Strong). The case bundle contains no family testing data, no unaffected affected-member results, and no report that the variant failed to segregate with disease; the ClinVar record provides no segregation detail, and no segregation-themed publication was retrieved. BS4 cannot be evaluated.

Rule

Lack of segregation in affected members of two or more families (Strong). Lack of segregation in affected members of one family (Supporting). ClinGen PTEN VCEP v3.2.

Evidence considered

• cspec: PTEN VCEP v3.2 BS4 rule (lack of segregation in affected members of one or two+ families) - no non-segregation data found
• clinvar: VCV000422899 submissions reviewed; no segregation/non-segregation information reported in case bundle

Still missing

• No documented non-segregation observations in any family
• No affected-member testing results showing absence of the variant
• No segregation-themed literature retrieved for this variant

Sources

Reasoning

ClinGen PTEN Expert Panel v3.2 BP5 (supporting) requires at least two cases in which the variant was found in a case with an alternate molecular basis for disease, where the other gene/disorder is considered highly penetrant AND the patient's personal/family history demonstrates no overlap between the other gene and PTEN. No proband-level information on an alternate molecular basis (co-occurring pathogenic/likely pathogenic variants in other highly penetrant genes, with non-overlapping phenotype) is present anywhere in the evidence bundle. Without such case data, BP5 cannot be evaluated.

Rule

BP5 (PTEN EP v3.2, Supporting): 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. At least two such cases required.

Evidence considered

• PTEN EP v3.2 BP5 instructions: 'At least two such cases are required for criteria to apply. In addition, the other gene/disorder must be considered highly penetrant AND the patient's personal/family history must demonstrate no overlap between the other gene and PTEN.'

Still missing

• No proband-level data on an alternate molecular basis (pathogenic/likely pathogenic variants in other highly penetrant genes) for any carrier of c.46T>G
• No personal/family history data to demonstrate absence of phenotype overlap between any other gene/disorder and PTEN
• At least two such cases are required per PTEN EP specification; zero cases with alternate-basis documentation are available

Sources