PTEN c.395G>T, p.(Gly132Val)

Reasoning

PTEN VCEP (cspec v3.2) specifies PS3_Moderate for Mighell et al. 2018 (PMID: 29706350) massively parallel humanized-yeast phosphatase-activity assay when the variant is listed High_conf=TRUE in Table S2 (mmc2.xlsx) with Cum_score ≤ -1.11. Direct lookup of NP_000305.3:p.(G132V) in Table S2 (row 'G132V' / 'Gly132Val') gives Cum_score = -4.003 (Cum_SE 0.428) with High_conf = TRUE ('Pass SE Filter'), which satisfies the VCEP threshold with substantial margin. This is a validated, high-confidence, non-imputed direct measurement (Imputed_Score = NA, i.e. not reliant on imputation), so PS3_Moderate is applied per the VCEP specification. The assay itself is the VCEP-endorsed source for this gene; no separate catalytic-dead-control/replicate check is required for this specific dataset because the VCEP index guidance designates it as pre-validated for PS3/BS3 application by direct table lookup. OncoKB independently reports a 'Likely Loss-of-function' biological effect for this variant citing PMID 29706350, consistent with a damaging functional readout, though OncoKB is not itself a primary functional-assay source for strength calibration.

Rule

PTEN VCEP cspec v3.2 PS3_Moderate: Cum_score ≤ -1.11 with High_conf=TRUE in Mighell et al. 2018 (PMID: 29706350) Table S2.

Evidence considered

• PTEN VCEP cspec v3.2 PS3 rule: 'Phosphatase activity ≤ -1.11 per Mighell et al. 2018, PMID: 29706350' applies PS3_Moderate.
• PTEN VCEP instructionsToUse for PS3: look up variant in mmc2.xlsx Table S2 columns A/B, require High_conf=TRUE in column I, read cumulative score from column G; apply PS3_Moderate for scores ≤ -1.11.
• Direct lookup in vcep_db/PTEN/files/mmc2.xlsx, Table S2, row 'G132V' / 'Gly132Val': Cum_score = -4.003127305, Cum_SE = 0.427739958, High_conf = TRUE, High_conf_nature = 'Pass SE Filter', Imputed_Score = NA (i.e. a direct, non-imputed measurement).
• OncoKB (source: PMID 29706350, PMID 10096247) lists PTEN G132V biological_effect as 'Likely Loss-of-function' and curated oncogenicity as 'Likely Oncogenic', consistent with functional deficiency but used only as corroborating context, not as the basis for strength.

Sources

Reasoning

PM2 is met at the PTEN-specific supporting strength because NM_000314.8:c.395G>T (p.Gly132Val) is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0, satisfying the PTEN Expert Panel requirement of an allele frequency <0.00001 (0.001%) in gnomAD or another large sequenced population.

Rule

Absent in population; gnomAD or another large sequenced population allele frequency <0.00001 (0.001%); if multiple alleles occur in a subpopulation, that subpopulation frequency must be <0.00002 (0.002%)

Evidence considered

• The PTEN Expert Panel specification permits PM2 at supporting strength when the variant is absent or present at an allele frequency <0.00001 (0.001%) in gnomAD or another large sequenced population; if multiple alleles are present in a subpopulation, that subpopulation frequency must be <0.00002 (0.002%).
• The variant is reported absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0, with no population allele or subpopulation frequency observed.

Sources

Reasoning

PTEN is a gene with a low rate of benign missense variation and where missense variants are a well-established mechanism of disease (PTEN hamartoma tumor syndrome), consistent with its function as the dual-specificity phosphatase acting on PtdIns(3,4,5)P3 in the PI3K/AKT pathway. The PTEN VCEP v3.2 explicitly marks PP2 as applicable at supporting strength for missense variants in PTEN. NM_000314.8:c.395G>T (p.Gly132Val) is a missense variant, so PP2 is met at the VCEP default supporting strength.

Rule

PP2 (PTEN VCEP): Missense variant in a gene with low rate of benign missense variation where missense is a common disease mechanism.

Evidence considered

• PTEN VCEP v3.2 PP2 rule (applicable, supporting strength): 'Missense variant in a gene that has a low rate of benign missense variation and where missense variants are a common mechanism of disease.'
• PMID:12471211 describes PTEN as a dual-specificity phosphatase central to PI3K/AKT pathway regulation, consistent with missense variation being a recognized disease mechanism for PTEN.
• The variant NM_000314.8:c.395G>T results in the missense change p.(Gly132Val), satisfying the variant-type precondition for PP2.

Sources

Reasoning

NM_000314.8:c.395G>T is a missense variant (NP_000305.3:p.(Gly132Val)). The PTEN VCEP (ClinGen CSPEC v3.2) PP3 rule for missense variants requires REVEL score > 0.7. Local REVEL v1.3 lookup for this exact genomic position (GRCh38 chr10:87933154 G>T) returns REVEL = 0.989, well above the 0.7 threshold. REVEL's calibration is independently verified (Ioannidis et al., PMID 36413997, per pipeline convention citing the ClinGen SVI-recommended REVEL calibration paper). PP3 is applied at Supporting strength per the VCEP's explicit REVEL rule; the VCEP does not upgrade PP3 strength for very high REVEL scores.

Rule

PTEN VCEP CSPEC v3.2 PP3: missense variants with REVEL score > 0.7 -> PP3_Supporting

Evidence considered

• PTEN VCEP CSPEC v3.2 PP3 rule (missense path): 'Missense variants: REVEL score > 0.7' applied at Supporting strength.
• Local REVEL v1.3 lookup: REVEL score = 0.989 for chr10:87933154 G>T (GRCh38), well above the 0.7 pathogenic-supporting threshold.
• Variant is a coding missense substitution (p.Gly132Val), not synonymous/intronic, so the VCEP's missense REVEL sub-path applies rather than the SpliceAI/VarSeak splicing sub-path.

Sources

Reasoning

PTEN VCEP v3.2 PS1 requires a different nucleotide substitution producing the identical amino acid change (p.Gly132Val) that has itself been established as pathogenic, regardless of the nucleotide change used to reach this residue. The codon for this variant is GGT>GTT (c.395G>T), reported in PMID:16773562 as 'Exon 5 G132V (GGT132GTT)'. No alternate codon change resulting in the same p.Gly132Val amino acid substitution was identified in ClinVar Table S3/S5 comparator data or the reviewed literature; all same-position comparator variants found (G132D, G132A) are different amino acid changes, which fall under PM5 rather than PS1. PS1 requires identity of the resulting amino acid change, which is not met by a distinct residue substitution.

Rule

PS1: Same amino acid change as a previously established pathogenic variant regardless of nucleotide change.

Evidence considered

• PTEN VCEP v3.2 PS1 rule: 'Same amino acid change as a previously established pathogenic variant regardless of nucleotide change.'
• PMID:16773562 reports this variant's codon change as GGT132GTT (G132V) but is the same variant under adjudication, not an independent alternate-codon pathogenic comparator.

Still missing

• No alternate-nucleotide/same-amino-acid (p.Gly132Val) pathogenic comparator variant was identified in the available ClinVar or literature data to support PS1.

Sources

Reasoning

The PTEN VCEP v3.2 PM1 specification restricts application to residues within defined catalytic motifs on NP_000305.3: the WPD loop (90-94), P-loop/phosphatase core (123-130), and the TI-loop (166-168). Residue 132 (Gly132) falls just outside the P-loop boundary (123-130) and is not within any of the three defined catalytic motifs, so the VCEP-specific PM1 rule is not met. A cancerhotspots.org query flagged G132 as lying in a 'statistically significant hotspot' in the somatic cancer mutation dataset, but the governing PTEN VCEP framework supersedes generic ACMG hotspot logic and explicitly limits PM1 to the three named catalytic-motif residue ranges; the general cancer hotspot signal does not satisfy this narrower VCEP definition.

Rule

PM1 (PTEN VCEP): Located in catalytic motifs 90-94, 123-130, 166-168 (NP_000305.3).

Evidence considered

• PTEN VCEP v3.2 PM1 instructions: 'Defined to include residues in one of PTEN's catalytic motifs, which include the WPD loop (residues 90-94), P-loop (also described as phosphatase core, residues 123-130), and the TI-loop (residues 166-168) (NP_000305.3) (Lee 1999).'
• cancerhotspots.org flagged G132 as a statistically significant somatic hotspot, but this generic hotspot signal is superseded by the VCEP's narrower catalytic-motif-only PM1 definition, which residue 132 does not satisfy.

Still missing

• Residue 132 is immediately adjacent to (but outside) the VCEP-defined P-loop (123-130); no VCEP-recognized extension of the catalytic motif to residue 132 was found in the reviewed materials.

Sources

Reasoning

PTEN VCEP v3.2 PM5 requires a different missense change at the same residue that has been determined pathogenic or likely pathogenic, with the variant under review having a BLOSUM62 score equal to or less than the known comparator. A same-residue comparator, NM_000314.6(PTEN):c.395G>A (p.Gly132Asp), was identified in ClinVar-derived data (Mighell et al. 2018 Table S3), but its ClinVar classification is listed as 'Conflicting interpretations of pathogenicity,' not an established pathogenic/likely pathogenic call, so it does not qualify as a PM5 comparator. Additional same-residue variants (G132A, G132D) appear in curated literature-derived tables (Mighell et al. 2018 Table S5, sourced to Spinelli et al. 2015 and other case reports) associated with PHTS/Cowden syndrome phenotype, but without a documented formal ClinVar/expert-panel pathogenic or likely pathogenic classification in the reviewed materials. A dedicated PM5 same-residue comparator search (pm5_candidates.json) also returned zero qualifying same-residue candidates.

Rule

PM5 (PTEN VCEP): Missense change at a residue where a different missense change determined pathogenic/likely pathogenic has been seen before, with BLOSUM62 score of the variant in question <= known variant.

Evidence considered

• PTEN VCEP v3.2 PM5 instructions: 'variant in question need not be novel but must have a BLOSUM62 score equal to or less than the known variant'; comparator must be 'likely pathogenic' or pathogenic.
• Mighell et al. 2018 (PMID:29706350) Table S3 lists NM_000314.6(PTEN):c.395G>A (p.Gly132Asp) with ClinVar status 'Conflicting interpretations of pathogenicity,' which does not meet the VCEP requirement of an established pathogenic/likely pathogenic comparator.
• Mighell et al. 2018 (PMID:29706350) Table S5 lists G132A (PHTS, cited to Spinelli et al. 2015/Tan et al. 2007) and G132D (Cowden, cited to Nizialek et al. 2015 and Bubien et al. 2013) as curated variants with reported phenotype, but without an explicit formal pathogenicity classification captured in this bundle.
• pm5_candidates.json automated same-residue harvest returned 0 same-residue candidates and 0 expert-panel P/LP candidates (harvesting failed softly with an HTTP 429 error).

Still missing

• G132D shows conflicting ClinVar interpretations rather than an established P/LP classification, so it cannot be used as a PM5 comparator without further adjudication of those conflicting submissions.
• G132A/G132D case-report associations (Mighell et al. 2018 Table S5) lack documented formal pathogenicity classification (e.g., ClinVar review status, submitter criteria) needed to confirm they meet the VCEP 'determined pathogenic or likely pathogenic' threshold.
• Automated PM5 candidate harvesting failed (HTTP 429) and returned no same-residue candidates; a full manual ClinVar re-query for confirmed P/LP G132X variants was not completed within this evidence bundle.

Sources

Reasoning

BA1 is not met because the variant is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0; therefore no filtering allele frequency exceeds the PTEN-specific BA1 threshold of >0.00056 (0.056%).

Rule

gnomAD filtering allele frequency >0.00056 (0.056%)

Evidence considered

• The PTEN Expert Panel specification defines BA1 as a gnomAD filtering allele frequency >0.00056 (0.056%).
• The variant NM_000314.8:c.395G>T (p.Gly132Val) is reported absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0; no allele-frequency value is available that could meet BA1.

Sources

Reasoning

BS1 is not met because the variant is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0; therefore no filtering allele frequency falls within the PTEN-specific BS1 range of 0.000043 to 0.00056 (0.0043% to 0.056%), or the BS1_Supporting range of 0.0000043 to 0.000043.

Rule

BS1: gnomAD filtering allele frequency 0.000043 to 0.00056 (0.0043% to 0.056%); BS1_Supporting: 0.0000043 to 0.000043

Evidence considered

• The PTEN Expert Panel specification defines BS1 as a gnomAD filtering allele frequency from 0.000043 up to 0.00056 (0.0043% to 0.056%), with BS1_Supporting from 0.0000043 up to 0.000043.
• The variant is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0, so no observed frequency reaches either PTEN-specific BS1 interval.

Sources

Reasoning

PTEN VCEP (cspec v3.2) applies BS3_Supporting when the Mighell et al. 2018 (PMID: 29706350) Table S2 Cum_score for a High_conf=TRUE variant is > 0. The direct lookup for NP_000305.3:p.(G132V) gives Cum_score = -4.003 (High_conf = TRUE), which is strongly negative, indicating markedly reduced phosphatase activity rather than wild-type-comparable activity. This is the opposite of the benign threshold, so BS3 criteria are not met; no other benign-direction functional data (splicing assay showing no impact, or a second protein-domain assay showing wild-type-comparable activity) are present in the case bundle.

Rule

PTEN VCEP cspec v3.2 BS3_Supporting: Cum_score > 0 with High_conf=TRUE in Mighell et al. 2018 (PMID: 29706350) Table S2; not met since Cum_score = -4.003.

Evidence considered

• PTEN VCEP cspec v3.2 BS3_Supporting rule: 'Phosphatase activity >0 per Mighell et al. 2018, PMID: 29706350.'
• Direct lookup in vcep_db/PTEN/files/mmc2.xlsx, Table S2, row 'G132V' / 'Gly132Val': Cum_score = -4.003127305 (High_conf = TRUE), which is far below the >0 benign threshold, ruling out BS3.

Sources

Reasoning

The PTEN VCEP BP2 rule requires the variant to be observed in trans with a pathogenic/likely pathogenic PTEN variant, or at least three observations in cis and/or phase unknown with different pathogenic/likely pathogenic PTEN variants. The available exact-variant reports describe heterozygous p.G132V (c.395G>T) without a qualifying second PTEN pathogenic/likely pathogenic variant or qualifying cis/phase-unknown observations. One report explicitly states that both parents carried no PTEN alteration, supporting a de novo heterozygous observation rather than BP2.

Rule

PTEN VCEP v3.2 BP2: Supporting when observed in trans with a pathogenic/likely pathogenic PTEN variant OR when there are at least three observations in cis and/or phase unknown with different pathogenic/likely pathogenic PTEN variants.

Evidence considered

• PTEN VCEP v3.2 BP2 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.
• PMID:16752378 directly reports germline heterozygous p.G132V (c.395G>T) and states that the proband's parents carried no PTEN alteration; it does not report a second PTEN pathogenic/likely pathogenic variant in trans or cis.
• PMID:16773562 reports one patient with a germline PTEN exon 5 G132V variant (GGT132GTT) but provides no variant-specific phase, segregation, or second-variant information.

Sources

Reasoning

The PTEN VCEP BP4 rule for missense variants requires REVEL score < 0.5. The observed REVEL score of 0.989 is far above this benign-supporting threshold, so BP4 is not met. BayesDel score (0.61616) was also retrieved for this variant but is not used for PP3/BP4 in this pipeline because no verified published calibration threshold for BayesDel is available; it does not affect this determination.

Rule

PTEN VCEP CSPEC v3.2 BP4: missense variants with REVEL score < 0.5 -> BP4_Supporting

Evidence considered

• PTEN VCEP CSPEC v3.2 BP4 rule (missense path): 'Missense variants: REVEL scores < 0.5' required for benign-supporting evidence.
• Local REVEL v1.3 lookup: REVEL score = 0.989, well above the <0.5 threshold, so BP4 criterion is not satisfied.
• BayesDel score 0.61616 was retrieved but treated as insufficiently calibrated (no verified published threshold available to this pipeline) and was not used to assess BP4.

Sources

Reasoning

A single published report describes the exact PTEN c.395G>T (p.Gly132Val) variant in an affected proband and states that both parents carried no PTEN alteration, supporting a de novo observation. The PTEN VCEP requires confirmed maternity and paternity, a patient with the disease, and no family history for PS2 at Strong strength; confirmation of parentage and absence of family history are not documented in the available evidence.

Rule

De novo (both maternity and paternity confirmed) observation in a patient with the disease and no family history; Very Strong requires two proven, four assumed, or one proven plus two assumed de novo observations.

Evidence considered

• PMID:16752378 reports an affected 4½-year-old boy with germline heterozygous PTEN p.G132V (c.395G>T) and states: "Direct sequencing of peripheral blood DNA confirmed that our proband was a carrier of a germline heterozygous mutation, p.G132V (c.395G > T), whereas his parents carried no alteration in PTEN."
• The PTEN VCEP version 3.2 PS2 rule requires a de novo observation with both maternity and paternity confirmed in a patient with disease and no family history for Strong evidence; two proven or four assumed observations, or one proven plus two assumed observations, are required for Very Strong evidence.

Still missing

• Explicit confirmation of maternity and paternity is not documented.
• No family history information is available for the proband.
• Only one de novo observation is available; the PTEN VCEP Very Strong threshold is not met.

Sources

Reasoning

The exact variant is reported in two papers, but the available evidence does not establish that the reported individuals are independent and does not provide a calculated PTEN EP adult or pediatric phenotype-specificity score. No qualifying case-control enrichment study is available.

Rule

PTEN EP PS4 Use 2: sum phenotype-specificity scores across independent probands; Supporting requires 1-1.5, Moderate 2-3.5, Strong 4-15.5, and Very Strong >=16. PTEN EP also permits Strong PS4 for a sufficiently powered case-control study with OR >2, p<0.05, and 95% CI lower bound >1.5.

Evidence considered

• PTEN EP PS4 permits phenotype-specificity evidence only after adding scores across independent probands: adult CC score >=30 contributes 1 point (25-29 contributes 0.5), pediatric score >=5 contributes 1 point (score 4 contributes 0.5 with developmental features excluded); PS4_Supporting requires a total of 1-1.5. A case-control study would require OR >2, p<0.05, and a 95% CI lower bound >1.5.
• PMID:16752378 reports one child with germline heterozygous p.G132V (c.395G>T), absent in both parents, with prenatal-onset verrucous epidermal nevus, macrocephaly, vascular findings, lipomatosis, intestinal polyposis, developmental delay, seizures, and focal segmental glomerulosclerosis.
• PMID:16773562 lists one Cowden syndrome patient, SCP27, with exon 5 G132V (GGT132GTT), but its extracted information supplies neither a specificity score nor enough clinical detail to calculate one.

Still missing

• Establish whether the p.Gly132Val individuals reported in PMID:16752378 and PMID:16773562 are independent probands.
• Calculate PTEN EP phenotype-specificity scores from complete clinical records using the applicable adult or pediatric scoring rubric.
• A sufficiently powered case-control study for this variant or a PHTS component phenotype is not available.

Sources

Reasoning

The exact variant is reported as de novo in one affected proband because both parents lacked the alteration. This could represent one assumed de novo observation, but the PTEN VCEP PM6 rule also requires no family history, which is not documented. The available evidence does not support PM6 Strong or Very Strong because only one observation is available.

Rule

Assumed de novo, without confirmation of paternity and maternity, in a proband with disease and no family history; PTEN-specific upgrades require additional de novo observations or a qualifying highly specific phenotype.

Evidence considered

• PMID:16752378 reports the exact p.G132V (c.395G>T) variant in an affected proband and states that both parents carried no PTEN alteration.
• The PTEN VCEP version 3.2 PM6 rule allows Moderate evidence for an assumed de novo observation in a patient with disease and no family history; Strong requires two presumed de novo probands or one presumed de novo observation in a highly specific phenotype, and Very Strong requires two proven, four assumed, or one proven plus two assumed observations.

Still missing

• No family history information is available for the proband.
• The report does not explicitly document that maternity and paternity were unconfirmed, although parentage confirmation is not stated.
• Additional assumed or proven de novo observations are needed for PM6 Strong or Very Strong.

Sources

Reasoning

No affected relatives with the variant, informative meioses, or co-segregation data are reported. The single case documents parental absence of the variant, but that is de novo evidence rather than co-segregation with disease in affected family members.

Rule

Co-segregation with disease in multiple affected family members: 3 or 4 meioses for Supporting, 5 or 6 for Moderate, and at least 7 meioses across at least two families for Strong.

Evidence considered

• The PTEN VCEP version 3.2 PP1 rule requires co-segregation in multiple affected family members: 3 or 4 meioses for Supporting, 5 or 6 for Moderate, and at least 7 across at least two families for Strong.
• The available case evidence reports one proband and unaffected parents lacking the variant, with no affected relatives or segregation meioses.

Still missing

• No affected family members with genotype and phenotype information are reported.
• No informative meioses are available.

Sources

Reasoning

BS2 cannot be assessed because the available population evidence reports the variant as absent and provides no confirmed homozygous observation in a healthy or PHTS-unaffected individual.

Rule

Observed in the homozygous state in a healthy or PHTS-unaffected individual; one observation if homozygous status is confirmed, two if not confirmed; apply at supporting level if BS1 is also applied

Evidence considered

• The PTEN Expert Panel specification requires observation of the variant in the homozygous state in a healthy or PHTS-unaffected individual; one observation is sufficient when homozygous status is confirmed and two are required when it is not confirmed.
• The available gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0 records all report the variant as absent and contain no homozygote observation.

Still missing

• No confirmed homozygous observation with appropriate health or PHTS-unaffected status is available.

Sources

Reasoning

No affected family members carrying or lacking the variant are reported, so lack of segregation cannot be evaluated. The report that both parents lacked the variant does not establish BS4 because BS4 concerns lack of segregation in affected members of a family.

Rule

Lack of segregation in affected members of one family for Supporting or two or more families for Strong.

Evidence considered

• The PTEN VCEP version 3.2 BS4 rule requires lack of segregation in affected members of one family for Supporting or two or more families for Strong.
• The available case evidence contains no affected relatives for whom variant segregation or non-segregation could be assessed; parental absence of the variant is relevant to de novo assessment, not BS4.

Still missing

• No affected relatives with genotype results are reported.
• No family-level non-segregation analysis is available.

Sources

Reasoning

No evidence identifies two or more cases with this variant and an alternate molecular diagnosis that meets the PTEN EP requirements.

Rule

PTEN EP BP5 Supporting requires >=2 cases with an alternate highly penetrant molecular diagnosis and no phenotype overlap with PTEN.

Evidence considered

• The PTEN EP requires at least two cases, a highly penetrant alternate gene/disorder, and personal/family histories with no overlap between the alternate disorder and PTEN; no such cases are provided in the case-evidence bundle.

Still missing

• At least two independent cases with a highly penetrant alternate molecular diagnosis are required.
• For each case, personal and family history must demonstrate no overlap between the alternate disorder and PTEN-associated disease.

Sources