PTEN c.165-10_209+6del, p.?

Reasoning

The governing PTEN PVS1 decision tree applies to NM_000314.8 and assigns PVS1_Strong when a single-exon deletion preserves the reading frame, the deleted exon is exon 3, and the altered region is critical to protein function. NM_000314.8:c.165-10_209+6del spans exon 3 and its flanking splice regions; the deleted coding interval c.165_209 is 45 nucleotides, consistent with an in-frame exon-3 deletion. SpliceAI predicts a strong splice effect (maximum delta 0.996), supporting exon loss or altered splicing. The variant is well 5-prime of p.D375/c.1121, and exon 3 is present in the biologically relevant transcript. The searched PVS1_DecisionTree_PTEN.pdf contains no variant-specific row for c.165-10_209+6del or p.?, so the assigned strength comes from the named PTEN decision-tree branch rather than a pre-assigned variant entry.

Rule

PTEN PVS1 decision tree: single exon deletion preserving the reading frame; exon 3 is a critical altered region; assign PVS1_Strong.

Evidence considered

• The PTEN-specific decision tree states that a single exon 3 deletion preserving the reading frame, with exon 3 critical to protein function, receives PVS1_Strong.
• The normalized variant is NM_000314.8:c.165-10_209+6del, spanning exon 3 and flanking intronic sequence; c.165_209 is a 45-nucleotide coding interval.
• SpliceAI reports DS_AL 0.976 and DS_DL 0.996, with maximum delta score 0.996, consistent with substantial splice impact.
• The PTEN VCEP framework uses NM_000314.8 as the preferred transcript and directs PVS1 assessment to the PTEN decision tree.

Still missing

• PVS1_DecisionTree_PTEN.pdf was searched for c.165-10_209+6del and p.?; no variant-specific entry was found.
• No RNA or minigene assay directly confirms the transcript-level splice product or NMD behavior for this variant.

Sources

Reasoning

The ClinGen PTEN Expert Panel Version 3.2 specifies PM2 at supporting strength when the variant is absent or has allele frequency below 0.00001 (0.001%) in gnomAD or another large sequenced population; if multiple alleles occur in a subpopulation, that subpopulation frequency must be below 0.00002 (0.002%). The variant is absent from the default all-comers gnomAD v2.1 and gnomAD v4.1 datasets, satisfying the PTEN PM2 supporting rule. The failed non-cancer subset queries do not prevent assessment because the PTEN specification does not require a non-cancer subset or an exome-only source for PM2.

Rule

PTEN VCEP v3.2: PM2 supporting when absent or <0.00001 (0.001%) allele frequency; subpopulation with multiple alleles <0.00002 (0.002%)

Evidence considered

• PTEN Expert Panel Version 3.2 specifies PM2 supporting for absence or allele frequency <0.00001 (0.001%) in gnomAD or another large sequenced population; any subpopulation with multiple alleles must be <0.00002 (0.002%).
• The variant was reported absent from the default all-comers gnomAD v2.1 and gnomAD v4.1 datasets, satisfying the PTEN PM2 supporting threshold.
• The gnomAD v2.1 and v3.1 non-cancer queries failed, but the PTEN PM2 specification does not require those subsets; the default all-comers datasets were therefore used.

Sources

Reasoning

The PTEN VCEP PM4 rule permits in-frame insertions or deletions only when they affect at least one residue in a defined catalytic motif, or when they cause a protein extension. The coding segment removed by this exon 3 deletion is 45 nucleotides and is predicted to be in-frame, but exon 3 corresponds to the N-terminal region before the PTEN catalytic motifs at residues 90-94, 123-130, and 166-168. The variant is not a stop-loss or protein-extension event, and no evidence places the deleted region in a repeat region or any listed catalytic motif. Therefore the VCEP-specific PM4 requirement is not met.

Rule

PTEN VCEP PM4: in-frame deletion must affect a residue in catalytic motifs 90-94, 123-130, or 166-168, or cause protein extension; neither condition is met.

Evidence considered

• The PTEN VCEP PM4 specification restricts in-frame deletions to those affecting at least one residue in a listed catalytic motif or causing protein extension.
• The deleted coding interval c.165_209 is 45 nucleotides and lies in exon 3, before the PTEN catalytic motifs at residues 90-94, 123-130, and 166-168.
• SpliceAI predicts splice impact with maximum delta 0.996, but this does not establish a catalytic-motif deletion or protein extension for PM4.

Sources

Reasoning

The ClinGen PTEN Expert Panel Version 3.2 BA1 rule requires a gnomAD filtering allele frequency greater than 0.00056 (0.056%). The variant is absent from the default all-comers gnomAD v2.1 and gnomAD v4.1 datasets, so its observed allele frequency is 0 and does not meet BA1. The failed non-cancer subset queries were not used because the PTEN specification does not require a non-cancer subset for BA1.

Rule

PTEN VCEP v3.2: gnomAD filtering allele frequency >0.00056 (0.056%)

Evidence considered

• PTEN Expert Panel Version 3.2 specifies BA1 only when gnomAD filtering allele frequency is >0.00056 (0.056%).
• The variant was reported absent from the default all-comers gnomAD v2.1 and gnomAD v4.1 datasets; therefore the observed frequency is 0.
• The gnomAD v2.1 and v3.1 non-cancer queries failed, but those subsets are not required by the PTEN BA1 specification and were not treated as evidence.

Sources

Reasoning

The ClinGen PTEN Expert Panel Version 3.2 defines BS1 as a gnomAD filtering allele frequency from 0.000043 (0.0043%) up to 0.00056 (0.056%) for strong evidence, or 0.0000043 (0.00043%) up to 0.000043 (0.0043%) for supporting evidence. The variant is absent from the default all-comers gnomAD v2.1 and gnomAD v4.1 datasets, with observed frequency 0, so neither BS1 range is met. The failed non-cancer subset queries were not used because the PTEN specification does not require a non-cancer subset for BS1.

Rule

PTEN VCEP v3.2: BS1 strong at 0.000043–0.00056; BS1 supporting at 0.0000043–0.000043

Evidence considered

• PTEN Expert Panel Version 3.2 defines BS1 strong as 0.000043–0.00056 and BS1 supporting as 0.0000043–0.000043 allele frequency.
• The variant was reported absent from the default all-comers gnomAD v2.1 and gnomAD v4.1 datasets; therefore the observed frequency is 0 and below both BS1 ranges.
• The gnomAD v2.1 and v3.1 non-cancer queries failed, but those subsets are not required by the PTEN BS1 specification and were not treated as evidence.

Sources

Reasoning

The ClinGen PTEN Expert Panel Version 3.2 BS2 rule requires the variant to be observed in the homozygous state in a healthy or PHTS-unaffected individual, with one observation if homozygosity is confirmed or two if it is not confirmed. The variant is absent from the default all-comers gnomAD v2.1 and gnomAD v4.1 datasets, so there is no population observation supporting homozygosity and BS2 is not met.

Rule

PTEN VCEP v3.2: homozygous in a healthy or PHTS-unaffected individual; one confirmed or two unconfirmed observations

Evidence considered

• PTEN Expert Panel Version 3.2 requires a confirmed homozygous observation in a healthy or PHTS-unaffected individual for BS2 strong, or two unconfirmed homozygous observations for BS2 strong.
• The variant was reported absent from the default all-comers gnomAD v2.1 and gnomAD v4.1 datasets, so no homozygous population observation is available.

Sources

Reasoning

The PTEN Expert Panel specification requires a documented de novo observation with both maternity and paternity confirmed for PS2 at strong strength, or defined combinations of proven and assumed de novo observations for very strong strength. The available case evidence does not document a proband, parental testing, maternity or paternity confirmation, family history, or any qualifying de novo observation. Therefore, PS2 cannot be assessed.

Rule

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

Evidence considered

• The PTEN Expert Panel specifies strong PS2 for a de novo observation with both maternity and paternity confirmed in a patient with the disease and no family history.
• No case-level proband, parental-testing, maternity, paternity, family-history, or de novo observation data are documented in the available case evidence.

Still missing

• Documented proband with the disease phenotype
• Parental testing results for the variant
• Maternity and paternity confirmation
• Family history sufficient to establish absence of familial disease
• Number and quality of proven or assumed de novo observations

Sources

Reasoning

The ClinGen PTEN VCEP permits PS3 for RNA, mini-gene, or other assays demonstrating abnormal splicing, and permits PS3_Moderate from Mighell et al. 2018 only when the variant is a high-confidence Table S2 missense entry with Cum_score <= -1.11. The queried variant is the intronic deletion NM_000314.8:c.165-10_209+6del (NP_000305.3:p.?), and the governing mmc2.xlsx full-text table contains no entry for c.165-10_209+6del, p.?, or this intronic deletion; no case RNA or other variant-specific functional assay is present in the supplied evidence. Therefore PS3 cannot be assigned from the available functional evidence.

Rule

PTEN VCEP PS3: RNA, mini-gene, or other assay demonstrating an impact on splicing; PS3_Moderate for Mighell et al. 2018 Table S2 high-confidence variants with Cum_score <= -1.11.

Evidence considered

• The ClinGen PTEN VCEP PS3 specification allows strong evidence for an assay showing splicing impact and PS3_Moderate for Mighell et al. 2018 Table S2 high-confidence missense variants with cumulative score <= -1.11.
• The governing mmc2.xlsx full-text file was searched for c.165-10_209+6del, p.?, and the corresponding intronic coordinates; no matching variant entry was found.
• Case normalization identifies NM_000314.8:c.165-10_209+6del as an intronic deletion with predicted protein consequence NP_000305.3:p.?, and the case evidence contains no variant-specific RNA, mini-gene, or other functional assay result.

Still missing

• No entry for c.165-10_209+6del or p.? was found in the governing mmc2.xlsx full-text file; the file is restricted to PTEN missense functional-assay data.
• No variant-specific RNA, mini-gene, or other functional assay demonstrating abnormal splicing was available in the case evidence.

Sources

Reasoning

The ClinGen PTEN Expert Panel specification permits PS4 from a sufficiently powered case-control study when the odds ratio is >2, p<0.05, and the 95% confidence interval lower limit is >1.5; it also permits phenotype-specific scoring across independent probands: 1 point per adult with Cleveland Clinic score ≥30, 0.5 points for score 25-29, 1 point per child with pediatric phenotype score ≥5, or 0.5 points for score 4 subject to the stated exclusions. The available case evidence contains no proband phenotype or family-history scores, no independent-proband specificity score, and no case-control enrichment results for this variant, so PS4 cannot be assessed.

Rule

PTEN EP Commentary: This criterion is unlikely to be used in this manner for a condition as rare as PHTS. However, if sufficiently powered, a case-control study finding an odds ratio >2 for a PHTS component phenotype with p<0.05 and 95% confidence interval with lower limit >1.5, this criteria may be applied. Use 2: Patient’s phenotype or family history is highly specific for a disease with a single genetic etiology. Phenotype specificity scores are added across independent probands. 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 PTEN VCEP source states that a sufficiently powered case-control study may support PS4 when odds ratio >2, p<0.05, and the 95% confidence interval lower limit >1.5.
• The PTEN VCEP source defines phenotype-specific scoring as 1 point for an adult Cleveland Clinic score ≥30, 0.5 points for 25-29, 1 point for a pediatric phenotype score ≥5, and 0.5 points for score 4 with exclusions.
• The case evidence reports no proband phenotype scores, family-history specificity scores, or case-control enrichment statistics for this variant.

Still missing

• Obtain phenotype and family-history data for independent probands, including Cleveland Clinic or pediatric phenotype scores.
• If using case-control evidence, obtain odds ratio, p-value, and 95% confidence interval for the exact variant or qualifying PHTS phenotype.

Sources

Reasoning

The PTEN Expert Panel specification permits PM6 for presumed de novo occurrence without confirmed maternity and paternity in a patient with the disease and no family history, with higher strengths requiring specified numbers of proven or assumed observations. The available case evidence contains no documented proband, phenotype, parental testing, family history, or presumed de novo observation. Therefore, PM6 cannot be assessed.

Rule

Assumed de novo, but without confirmation of paternity and maternity, in a proband with the disease and no family history; higher strengths require the specified combinations of proven and assumed de novo observations.

Evidence considered

• The PTEN Expert Panel specifies moderate PM6 for an assumed de novo variant without confirmed maternity and paternity in a patient with the disease and no family history.
• No case-level presumed de novo, parental-testing, phenotype, or family-history data are documented in the available case evidence.

Still missing

• Documented proband with the disease phenotype
• Evidence that the variant is presumed de novo
• Parental testing or explicit lack of parental confirmation
• Family history showing no relevant disease
• Additional proven or assumed de novo observations if increased strength is considered

Sources

Reasoning

The PTEN Expert Panel specification requires co-segregation with disease in multiple affected family members and assigns supporting strength for 3 or 4 observed meioses, moderate strength for 5 or 6 meioses, and strong strength for at least 7 meioses across at least two families. No affected relatives, segregation results, family structure, or meioses are documented in the available case evidence. Therefore, PP1 cannot be assessed.

Rule

Co-segregation with disease in multiple affected family members: supporting for 3 or 4 observed meioses, moderate for 5 or 6 observed meioses, and strong for at least 7 meioses across at least two families.

Evidence considered

• The PTEN Expert Panel specifies PP1 supporting for 3 or 4 meioses, moderate for 5 or 6 meioses, and strong for at least 7 meioses across at least two families.
• No case-level affected-relative, pedigree, variant-status, segregation, or meiosis data are documented in the available case evidence.

Still missing

• Affected family members with phenotype documentation
• Variant status in each informative relative
• Pedigree or family structure
• Number of informative meioses
• Evidence from one or more families

Sources

Reasoning

The ClinGen PTEN VCEP requires an RNA, mini-gene, or other assay demonstrating no splicing impact for BS3 in intronic variants; its BS3_Supporting phosphatase-assay pathway applies to high-confidence missense entries in Mighell et al. 2018 Table S2 with phosphatase activity score >0. The queried variant is the intronic deletion NM_000314.8:c.165-10_209+6del (NP_000305.3:p.?), and the governing mmc2.xlsx full-text table contains no entry for c.165-10_209+6del, p.?, or this intronic deletion; no case assay demonstrates preserved splicing. Therefore BS3 cannot be assigned from the available functional evidence.

Rule

PTEN VCEP BS3: for intronic or synonymous variants, RNA, mini-gene, or other assay demonstrating no impact on splicing; BS3_Supporting for Mighell et al. 2018 high-confidence variants with phosphatase activity score >0.

Evidence considered

• The ClinGen PTEN VCEP BS3 specification requires an RNA, mini-gene, or other assay showing no splicing impact for intronic variants; BS3_Supporting from Mighell et al. 2018 is limited to high-confidence missense functional results with phosphatase activity score >0.
• The governing mmc2.xlsx full-text file was searched for c.165-10_209+6del, p.?, and the corresponding intronic coordinates; no matching variant entry was found.
• Case normalization identifies NM_000314.8:c.165-10_209+6del as an intronic deletion with predicted protein consequence NP_000305.3:p.?, and the case evidence contains no variant-specific assay demonstrating preserved splicing.

Still missing

• No entry for c.165-10_209+6del or p.? was found in the governing mmc2.xlsx full-text file; the file is restricted to PTEN missense functional-assay data.
• No variant-specific RNA, mini-gene, or other functional assay demonstrating no splicing impact was available in the case evidence.

Sources

Reasoning

The PTEN Expert Panel specification requires lack of segregation in affected members of one family for BS4 at supporting strength and two or more families for strong strength, while recognizing phenocopies and multiple pathogenic variants as confounders. No affected relatives, variant-negative affected individuals, family pedigrees, or non-segregation observations are documented in the available case evidence. Therefore, BS4 cannot be assessed.

Rule

Lack of segregation in affected members of one family supports BS4 at supporting strength; lack of segregation in affected members of two or more families supports strong strength.

Evidence considered

• The PTEN Expert Panel specifies BS4 supporting for lack of segregation in one family and BS4 strong for lack of segregation in two or more families, with phenocopies and multiple pathogenic variants as confounders.
• No case-level affected-relative, variant-negative, pedigree, family-count, or non-segregation data are documented in the available case evidence.

Still missing

• Affected relatives evaluated for the variant
• Variant-negative status in affected relatives
• Family pedigrees and number of families
• Phenotype specificity and assessment of phenocopy risk
• Assessment for additional pathogenic variants that could confound segregation

Sources

Reasoning

The PTEN Expert Panel specification permits BP2 at supporting strength when the variant is observed in trans with a pathogenic or likely pathogenic PTEN variant, or in at least three observations in cis and/or phase unknown with different pathogenic or likely pathogenic PTEN variants. The available case evidence contains no affected-proband observations, allelic phase information, co-occurring PTEN variants, or documented pathogenic/likely pathogenic variants in cis or trans; therefore BP2 cannot be assessed.

Rule

PTEN VCEP BP2 Supporting: observed in trans with a pathogenic or likely pathogenic PTEN variant, or at least three observations in cis and/or phase unknown with different pathogenic/likely pathogenic PTEN variants.

Evidence considered

• The governing PTEN Expert Panel rule requires either 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 or likely pathogenic PTEN variants.
• No qualifying co-occurring PTEN variant, affected-proband observation, or cis/trans phase observation is documented in the reviewed case evidence.

Still missing

• Documented affected-proband observations with a qualifying second PTEN pathogenic or likely pathogenic variant.
• Reliable phase information establishing trans, or at least three qualifying cis/phase-unknown observations.

Sources

Reasoning

The PTEN VCEP allows BP5 at supporting strength only when the variant is found in at least two cases with an alternate molecular basis, the other gene or disorder is highly penetrant, and the personal or family history shows no overlap between that disorder and PTEN. The available evidence contains no qualifying cases, alternate molecular diagnosis, penetrance assessment, or non-overlapping phenotype/family-history documentation, so BP5 cannot be assessed.

Rule

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.

Evidence considered

• The PTEN VCEP requires at least two BP5 cases and requires the alternate gene or disorder to be highly penetrant with no overlap between the patient's personal or family history and PTEN.
• The case evidence provides no qualifying BP5 cases or alternate molecular diagnosis.

Still missing

• Identify at least two cases carrying the exact variant with a documented alternate molecular basis for disease.
• Verify high penetrance of the alternate disorder and absence of phenotype or family-history overlap with PTEN.

Sources