PTEN c.389G>A, p.Arg130Gln

Reasoning

The PTEN VCEP applies PS1 at Strong strength when the variant has the same amino acid change as a previously established pathogenic variant, regardless of nucleotide change. NM_000314.8:c.389G>A produces NP_000305.3:p.(Arg130Gln), and ClinVar records this exact variant as Pathogenic with a PTEN Expert Panel review status; therefore the established pathogenic p.Arg130Gln change satisfies the VCEP PS1 rule.

VCEP 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.

Evidence considered

• The case variant is NM_000314.8:c.389G>A, producing NP_000305.3:p.(Arg130Gln).
• ClinVar variation 7829 records NM_000314.8:c.389G>A (p.Arg130Gln) as Pathogenic with review status reviewed by expert panel; the expert panel is the ClinGen PTEN Variant Curation Expert Panel.

Sources

Reasoning

PS3_Moderate is met for the missense variant NM_000314.8:c.389G>A (p.Arg130Gln; p.R130Q). In Mighell et al. 2018 supplementary Table S2, row R130Q / Arg130Gln, the massively parallel PTEN phosphatase-activity assay reports Cum_score = -2.04016411 and High_conf = TRUE (Pass SE Filter). The VCEP specifies PS3_Moderate for phosphatase activity ≤ -1.11 per Mighell et al. 2018 (PMID: 29706350), so the high-confidence score is below the governing threshold. The exact variant was also examined in a HEK293 cellular pAKT/AKT and stability study, but that study does not provide a separate damaging functional classification and is not needed for the assigned PS3_Moderate evidence.

VCEP rule

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.

Evidence considered

• Mighell et al. 2018 supplementary Table S2, row R130Q / Arg130Gln: Cum_score = -2.04016411; High_conf = TRUE; High_conf_nature = Pass SE Filter; Imputed_Score = NA.
• The VCEP PS3 specification directs use of Table S2 columns A or B, requires TRUE under column I (high confidence), and applies PS3_Moderate when column G cumulative score is ≤ -1.11.
• Post et al. 2020, PMID:32350270, Results section ‘HEK293 AKT assay finds 25 uncharacterized dominant negative variants,’ final paragraph: R130Q was among 6/32 variants showing >10% change in stability between parental and PTEN-knockout HEK293 cells; the quoted result does not provide a separate functional classification for R130Q.
• The variant is a missense substitution, and the exact aliases c.389G>A, p.Arg130Gln, and p.R130Q were matched in the governing functional-assay file.

Sources

Reasoning

The PTEN VCEP defines PM1 as including residues in catalytic motifs 90-94, 123-130, and 166-168 of NP_000305.3. The variant is p.Arg130Gln, so residue 130 lies within the explicitly defined 123-130 catalytic-motif interval. The vcep_materials.json domain_tables object is empty, and no hotspot route is needed for this determination.

VCEP rule

Located in a mutational hot spot and/or critical and well-established functional domain. Defined to include residues in catalytic motifs: 90-94, 123-130, 166-168 (NP_ 000305.3)

Evidence considered

• ClinGen PTEN VCEP specification v3.2, PM1 rule: catalytic motifs include residues 90-94, 123-130, and 166-168 (NP_000305.3).
• The case variant is NP_000305.3:p.(Arg130Gln), placing it at residue 130 within the defined 123-130 interval.

Sources

Reasoning

The ClinGen PTEN VCEP applies PM2 at Supporting strength when the variant is present at less than 0.00001 (0.001%) allele frequency in gnomAD or another large sequenced population, with each subpopulation below 0.00002 (0.002%) when multiple alleles are present. The all-comers gnomAD v4.1 total allele frequency is 1.23924e-06 (2/1613886), and the highest observed subpopulation allele frequency is 1.69511e-06 (2/1179864), satisfying both VCEP thresholds. No governing PTEN rule specifies a non-cancer or exome-only source, so the all-comers gnomAD v4.1 entry is the applicable default.

VCEP 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

• ClinGen PTEN VCEP v3.2 PM2 Supporting rule: population allele frequency <0.00001 (0.001%); if multiple alleles are present within any subpopulation, that subpopulation's allele frequency must be <0.00002 (0.002%).
• gnomAD v4.1 all-comers: total AF 1.23924e-06, 2/1613886 alleles, homozygotes 0; highest observed subpopulation AF 1.69511e-06 in European (non-Finnish), 2/1179864 alleles, homozygotes 0.

Sources

Reasoning

The PTEN VCEP marks PP2 as Applicable and assigns it only at Supporting strength for a missense variant in a gene with a low rate of benign missense variation where missense variants are a common disease mechanism. The case variant is missense p.Arg130Gln, so the VCEP's explicit PP2 applicability supports PP2 at Supporting strength.

VCEP 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.

Evidence considered

• The case identifies NM_000314.8:c.389G>A as the missense variant p.Arg130Gln.
• The PTEN VCEP PP2 entry is marked Applicable, with Supporting as the applicable strength, and defines the criterion as a missense variant in a gene with a low rate of benign missense variation where missense variants are a common mechanism of disease.

Sources

Reasoning

Scope first: NM_000314.8:c.389G>A is a missense variant, encoding p.(Arg130Gln), so the PTEN VCEP missense PP3 path applies; the governing rule names REVEL and requires a score > 0.7. The recorded REVEL score is 0.976, which exceeds the VCEP cutoff. SpliceAI is not used for this missense PP3 path, and the same prediction is not reused for BP4 or BP7.

VCEP rule

Multiple lines of computational evidence support a deleterious effect on the gene or gene product. * Splicing variants: Concordance of SpliceAl and VarSeak * Missense variants: REVEL score > 0.7

Evidence considered

• ClinGen PTEN VCEP Version 3.2 PP3 rule: for missense variants, REVEL score > 0.7 supports PP3.
• Local REVEL predictor lookup for NM_000314.8:c.389G>A / p.(Arg130Gln): REVEL = 0.976; this is above the VCEP cutoff of >0.7.

Sources

Reasoning

Expert panel Clingen PTEN Variant Curation Expert Panel, Clingen classified as Pathogenic.

VCEP rule

This criterion is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee.

Evidence considered

• The VCEP CSPEC entry marks PP5 'Not Applicable for this VCEP' and states that it is not for use.
• ClinVar expert panel classification

Sources

Reasoning

The ClinGen PTEN VCEP applies BA1 when the gnomAD filtering allele frequency is greater than 0.00056 (0.056%). The variant's all-comers gnomAD v4.1 total allele frequency is 1.23924e-06 (2/1613886 alleles), and the highest reported subpopulation allele frequency is 1.69511e-06 (2/1179864 alleles), both far below the VCEP BA1 threshold. No governing PTEN rule requires replacing the all-comers default with a non-cancer or exome-only subset.

VCEP rule

gnomAD Filtering allele frequency >0.00056 (0.056%)

Evidence considered

• ClinGen PTEN VCEP v3.2 BA1 rule: gnomAD filtering allele frequency >0.00056 (0.056%).
• gnomAD v4.1 all-comers: total AF 1.23924e-06, 2/1613886 alleles, homozygotes 0; highest observed subpopulation AF 1.69511e-06 in European (non-Finnish), 2/1179864 alleles, homozygotes 0.

Sources

Reasoning

The ClinGen PTEN VCEP applies BS1 Strong for a gnomAD filtering allele frequency from 0.000043 (0.0043%) up to 0.00056 (0.056%), and BS1 Supporting from 0.0000043 (0.00043%) up to 0.000043 (0.0043%). The all-comers gnomAD v4.1 total allele frequency is 1.23924e-06, below the lower BS1 Supporting boundary; the highest reported subpopulation allele frequency is also only 1.69511e-06. No governing PTEN rule requires replacing the all-comers default with a non-cancer or exome-only subset.

VCEP rule

gnomAD Filtering allele frequency from 0.000043 (0.0043%) up to 0.00056 (0.056%)...Allele frequency from 0.0000043 (0.00043%) up to 0.000043 (0.0043%).

Evidence considered

• ClinGen PTEN VCEP v3.2 BS1 Strong rule: gnomAD filtering allele frequency from 0.000043 (0.0043%) up to 0.00056 (0.056%).
• ClinGen PTEN VCEP v3.2 BS1 Supporting rule: allele frequency from 0.0000043 (0.00043%) up to 0.000043 (0.0043%).
• gnomAD v4.1 all-comers: total AF 1.23924e-06, 2/1613886 alleles; highest observed subpopulation AF 1.69511e-06 in European (non-Finnish), 2/1179864 alleles.

Sources

Reasoning

The ClinGen PTEN VCEP requires an observed homozygous state in a healthy or PHTS-unaffected individual for BS2. gnomAD v4.1 reports zero homozygotes for the variant in the all-comers dataset and zero in the highest-frequency European (non-Finnish) subpopulation; therefore no BS2 observation is present. There is no evidence of a confirmed or unconfirmed homozygous healthy individual elsewhere in the available case evidence.

VCEP 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

• ClinGen PTEN VCEP v3.2 BS2 Strong rule requires an observed 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.
• ClinGen PTEN VCEP v3.2 BS2 Supporting rule requires two homozygous observations with no clinical data, or a BS2 observation when BS1 is also applied.
• gnomAD v4.1 all-comers: 0 homozygotes, 2/1613886 alleles; European (non-Finnish) subpopulation: 0 homozygotes, 2/1179864 alleles.

Sources

Reasoning

BS3 is not met. In Mighell et al. 2018 supplementary Table S2, the high-confidence R130Q / Arg130Gln row reports Cum_score = -2.04016411, whereas the PTEN VCEP requires phosphatase activity > 0 for BS3_Supporting. The result is negative rather than positive and therefore does not support absence of damaging effect; no BS3_Strong no-damage assay result is available for this exact variant in the governing evidence.

VCEP 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.

Evidence considered

• Mighell et al. 2018 supplementary Table S2, row R130Q / Arg130Gln: Cum_score = -2.04016411; High_conf = TRUE; High_conf_nature = Pass SE Filter.
• The VCEP BS3 specification applies BS3_Supporting to Mighell et al. 2018 variants with phosphatase activity > 0; this exact variant's high-confidence score is below zero.
• The VCEP BS3_Strong rule requires well-established functional studies showing no damaging effect on protein function; the available exact-variant result instead shows a negative cumulative fitness score.

Still missing

• The governing functional file contains no exact-variant result meeting the VCEP BS3 no-damage requirement; the available high-confidence score is negative.

Sources

Reasoning

Scope first: NM_000314.8:c.389G>A is a missense variant, so the PTEN VCEP missense BP4 path applies; the governing rule names REVEL and requires a score < 0.5. The recorded REVEL score is 0.976, so the BP4 threshold is not satisfied. The SpliceAI result is not used for this missense BP4 path.

VCEP rule

Multiple lines of computational evidence suggest no impact on gene or gene product. * Splicing variants: Concordance of SpliceAl and VarSeak * Missense variants: REVEL scores < 0.5

Evidence considered

• ClinGen PTEN VCEP Version 3.2 BP4 rule: for missense variants, REVEL score < 0.5 supports BP4.
• Local REVEL predictor lookup for NM_000314.8:c.389G>A / p.(Arg130Gln): REVEL = 0.976; this does not satisfy the VCEP cutoff of <0.5.

Sources

Reasoning

The available case evidence contains ClinVar submission-trail statements that the variant was observed de novo, including a statement referring to at least one confirmed de novo case, but it does not provide a primary report with the affected proband's phenotype, documented absence of family history, and confirmation of both maternity and paternity. Therefore the VCEP PS2 rule cannot be evaluated from the available evidence.

VCEP rule

De novo (both maternity and paternity confirmed) observation in a patient with the disease and no family history.

Evidence considered

• The ClinVar audit trail reports de novo evidence for this exact variant, including a statement that it was observed in at least one confirmed de novo case, but the cited PMID is unresolved in this case and the primary case details are not available.
• No available evidence establishes all elements required by the PS2 rule for a usable strength assignment.

Still missing

• Primary case-level documentation for the de novo observation
• Affected proband phenotype and disease status
• Documented absence of family history
• Confirmation of both maternity and paternity

Sources

Reasoning

The PTEN VCEP permits PS4 through a case-control result or aggregated phenotype-specificity scores, but the available evidence supplies neither affected/control counts or an odds ratio with p-value and confidence interval nor Cleveland Clinic/pediatric scores for independent probands. The literature packet's ai_classified_papers array is empty. The two available full-text extracts do not provide PS4 evidence: PMID:32350270 studies R130Q in HEK293 functional assays, while PMID:28572459 does not mention R130Q. Therefore PS4 cannot be evaluated without variant-specific case-control data or proband phenotype scores. No PS4 numeric threshold was evaluated because the required value is unavailable.

VCEP rule

This criterion may _not_ be applied in combination with PP4. ... Phenotype specificity scores are added across independent probands and calculated as follows: ... Adults: ... * 1 point per proband with Cleveland Clinic (CC) score ≥ 30 (Tan 2011) ... * 0.5 points per proband with CC score of 25-29. ... Children: ... * 1 point per proband with pediatric phenotype score ≥ 5 (please see supplementary information in manuscript for scoring rubric). ... * 0.5 points per proband with pediatric phenotype score of 4, but autism/developmental delay/intellectual disability may not contribute to the score. ... PS4_Very Strong: Probands with specificity score ≥16. ... PS4: Probands with specificity score of 4-15.5. ... PS4_Moderate: Probands with specificity score of 2-3.5. ... PS4_Supporting: Proband(s) with specificity score of 1-1.5.

Evidence considered

• The VCEP PS4 instructions allow a sufficiently powered case-control study for a PHTS component phenotype when odds ratio >2, p<0.05, and the 95% confidence interval lower limit >1.5; no such variant-specific study result is present.
• The VCEP PS4 specificity scoring requires adult Cleveland Clinic scores or pediatric phenotype scores; no score is reported for this case or for independent probands.
• PMID:32350270, Results, section 'HEK293 AKT assay finds 25 uncharacterized dominant negative variants,' final paragraph: R130Q is among six of 32 variants with >10% stability change; this is a functional assay and not phenotype prevalence or case-control evidence.
• PMID:28572459, 'Comparison with TCGA': the paper reports cohort-level PTEN mutation frequency in breast cancer but does not mention c.389G>A or p.R130Q, so it provides no variant-specific PS4 evidence.
• gnomAD v4.1 reports 2/1,613,886 alleles overall (AF 1.23924e-06) and 2/1,179,864 European non-Finnish alleles (AF 1.69511e-06), but no affected-case frequency is available, so an enrichment comparison cannot be computed.

Still missing

• Variant-specific affected-case and matched control counts, or an odds ratio with p-value and 95% confidence interval, are unavailable.
• Independent proband Cleveland Clinic scores or pediatric phenotype scores are unavailable.

Sources

Reasoning

The PTEN VCEP requires a different missense change at the same amino-acid residue that has been determined pathogenic or likely pathogenic, and requires the interrogated variant's BLOSUM62 score to be equal to or less than the known variant. The available PM5 search found zero same-residue comparator candidates and supplies no qualifying comparator or BLOSUM62 comparison, so PM5 cannot be evaluated.

VCEP 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.

Evidence considered

• The queried variant is p.Arg130Gln at residue 130.
• The PM5 candidate artifact reports 8 candidates seen but zero same-residue candidates, zero expert-panel pathogenic/likely pathogenic same-residue candidates, and zero non-expert-majority candidates; it also reports an HTTP 429 retrieval error.

Still missing

• A different pathogenic or likely pathogenic missense variant at residue 130 and the required BLOSUM62 comparison are needed.

Sources

Reasoning

The available ClinVar submission-trail evidence mentions presumed or assumed de novo observations, but it does not establish the number of independent observations, the affected status and lack of family history for each proband, or the maternity and paternity confirmation status needed to distinguish the VCEP's very strong, strong, and moderate PM6 paths.

VCEP rule

Two proven OR four assumed OR one proven + two assumed de novo observations in a patient with the disease and no family history. ... Two probands with presumed _de novo_ occurrence (maternity/ paternity not confirmed) with the disease and no family history. ... Assumed _de novo,_ but without confirmation of paternity and maternity, in proband with the disease and no family history.

Evidence considered

• The ClinVar audit trail contains statements referring to assumed or presumed de novo observations for this exact variant, but it does not provide a verified, case-level dataset sufficient to count proven versus assumed observations.
• The available evidence does not support applying any of the VCEP PM6 strength thresholds without importing undocumented assumptions.

Still missing

• Verified count of independent de novo observations
• Affected disease status for each proband
• No family history for each proband
• Maternity and paternity confirmation status for each observation

Sources

Reasoning

No case-level segregation data are available showing the variant in multiple affected family members or documenting the number of informative meioses across families. The VCEP PP1 thresholds therefore cannot be evaluated.

VCEP rule

Co-segregation with disease in multiple affected family members, with ≥7 meioses observed across at least two families. ... Co-segregation with disease in multiple affected family members, with 5 or 6 meioses observed. ... Co-segregation with disease in multiple affected family members, with 3 or 4 meioses observed.

Evidence considered

• The available case evidence does not report cosegregation of NM_000314.8:c.389G>A with disease in affected relatives.
• No informative meiosis count or family-level segregation analysis is available.

Still missing

• Genotypes and phenotypes of affected relatives
• Family structure and phase information
• Number of informative meioses
• Evidence from at least one or more families as applicable

Reasoning

No case-level evidence documents lack of segregation in affected members of one or more families. The VCEP BS4 rule therefore cannot be evaluated at either supporting or strong strength.

VCEP rule

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

Evidence considered

• The available case evidence contains no documented affected-relative genotype that would demonstrate lack of segregation.
• There is no evidence sufficient to distinguish the VCEP's one-family supporting path from its two-or-more-family strong path.

Still missing

• Family-level segregation data
• Genotypes and affected status of relevant relatives
• Documented non-segregation in one or more families

Reasoning

The PTEN VCEP BP2 rule requires either observation of the variant in trans with a pathogenic or likely pathogenic PTEN variant, or at least three observations in cis and/or with phase unknown involving different pathogenic or likely pathogenic PTEN variants. The available case evidence does not document a second PTEN variant, affected-proband observation with phase, or sufficient cis/phase-unknown observations, so BP2 cannot be assessed.

VCEP rule

Observed in trans with a pathogenic or likely pathogenic PTEN variant OR at least three observations in cis and/or phase unknown with different pathogenic/likely pathogenic PTEN variants.

Evidence considered

• ClinGen PTEN Expert Panel specification v3.2, CSPEC criterion entry BP2: the rule requires an observation in trans with a pathogenic or likely pathogenic PTEN variant, or at least three observations in cis and/or phase unknown with different pathogenic/likely pathogenic PTEN variants.
• Case evidence for NM_000314.8:c.389G>A (NP_000305.3:p.(Arg130Gln)) contains no documented second PTEN variant with trans/cis/phase information and no qualifying count of observations.

Still missing

• Documented allelic observations identifying a pathogenic or likely pathogenic PTEN variant and its phase relative to NM_000314.8:c.389G>A are unavailable.
• A count of at least three cis and/or phase-unknown observations with different pathogenic or likely pathogenic PTEN variants is unavailable.

Sources

Reasoning

The VCEP requires at least two cases in which the variant is found with an alternate molecular basis, with the other disorder highly penetrant and the patient's personal or family history showing no overlap with PTEN. The available case and literature evidence does not establish two such cases or those clinical requirements.

VCEP rule

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.

Evidence considered

• ClinVar records the variant as pathogenic but does not provide the two qualifying alternate-molecular-basis cases or the required personal/family-history exclusions.
• The available full-text extracts concern functional testing or a non-variant-specific cancer cohort and do not establish BP5 cases.

Still missing

• At least two qualifying cases with an alternate molecular basis are not documented.
• High penetrance of the alternate disorder and non-overlapping personal/family history are not documented.

Sources