PTEN c.165-1_185del, p.?

Reasoning

NM_000314.8:c.165-1_185del is a canonical acceptor splice-site variant affecting exon 3. The case evidence identifies exon 3 as 45 coding nucleotides and predicts exon skipping with preservation of the reading frame; the PTEN decision tree specifically identifies a preserved-frame splice outcome involving a critical region including entire exon 3 as PVS1. The variant is in the biologically relevant NM_000314.8 transcript, and the resulting protein annotation is p.?. This is an un-downgraded PVS1 assignment; the applicable decision-tree branch is the critical exon 3 branch, not the non-NMD stop-codon downgrade branch.

VCEP rule

Use PTEN PVS1 decision tree. ... Exon skipping or use of a cryptic splice site preserves reading frame ... Truncated/altered region is critical to protein function (entire exon 3, 8 OR 9) ... PVS1

Evidence considered

• Case consequence assessment: NM_000314.8:c.165-1_185del; NP_000305.3:p.?; canonical splice acceptor (-1), affected exon 3, exon range c.165_209, 45 coding nucleotides, and predicted exon skipping preserving the reading frame.
• PVS1_DecisionTree_PTEN.pdf.txt: the splice-site branch states that exon skipping or cryptic-site use can preserve the reading frame and identifies a truncated/altered region as critical to protein function when it is entire exon 3, 8, or 9, with the resulting assignment PVS1.
• PVS1_DecisionTree_PTEN.pdf.txt was searched for c.165-1_185del, c.165-1, and p.?; no variant-specific row was present.

Still missing

• No variant-specific row for c.165-1_185del or p.? was found in PVS1_DecisionTree_PTEN.pdf.txt; the assignment therefore uses the governing decision-tree branch and case consequence facts.

Sources

Reasoning

The ClinGen PTEN VCEP permits PM2 at Supporting strength when the variant is absent or present at <0.00001 (0.001%) allele frequency in gnomAD or another large sequenced population, with a <0.00002 (0.002%) requirement if multiple alleles are present within a subpopulation. The variant was absent from gnomAD v2.1, gnomAD v4.1, gnomAD v2.1 non-cancer, and gnomAD v3.1 non-cancer, corresponding to allele frequency 0 and satisfying the VCEP threshold.

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 Version 3.2, PM2 Supporting rule: absent in population; databases present at <0.00001 (0.001%) allele frequency in gnomAD or another large sequenced population, and if multiple alleles are present within any subpopulation, the subpopulation allele frequency must be <0.00002 (0.002%).
• gnomAD v2.1: variant absent, allele frequency 0.
• gnomAD v4.1: variant absent, allele frequency 0.
• GNOMAD_V2_1_NON_CANCER: variant absent, allele frequency 0.
• GNOMAD_V3_1_NON_CANCER: variant absent, allele frequency 0.

Sources

Reasoning

The ClinGen PTEN VCEP applies BA1 only when the gnomAD filtering allele frequency is >0.00056 (0.056%). The variant was absent from gnomAD v2.1 and gnomAD v4.1, with no allele frequency exceeding this threshold; therefore BA1 is not met.

VCEP rule

gnomAD Filtering allele frequency >0.00056 (0.056%)

Evidence considered

• ClinGen PTEN VCEP Version 3.2, BA1 rule: gnomAD Filtering allele frequency >0.00056 (0.056%).
• gnomAD v2.1: variant absent; no filtering allele frequency reported.
• gnomAD v4.1: variant absent; no filtering allele frequency reported.

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 variant was absent from gnomAD v2.1 and v4.1, so no allele frequency falls within either BS1 interval; BS1 is not met.

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 Version 3.2, BS1 Strong rule: gnomAD Filtering allele frequency from 0.000043 (0.0043%) up to 0.00056 (0.056%).
• ClinGen PTEN VCEP Version 3.2, BS1 Supporting rule: Allele frequency from 0.0000043 (0.00043%) up to 0.000043 (0.0043%).
• gnomAD v2.1: variant absent; no filtering allele frequency reported.
• gnomAD v4.1: variant absent; no filtering allele frequency reported.

Sources

Reasoning

The ClinGen PTEN VCEP requires observation of the variant 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 available population records show the variant is absent from gnomAD v2.1 and v4.1, with no homozygous observations; BS2 is not met.

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 Version 3.2, BS2 rule: observed in the homozygous state in a healthy or PHTS-unaffected individual; one observation if homozygous status confirmed, two if not confirmed.
• gnomAD v2.1: variant absent; no homozygous observations reported.
• gnomAD v4.1: variant absent; no homozygous observations reported.

Sources

Reasoning

Scope: the PTEN VCEP applies BP4 to synonymous or intronic variants when both SpliceAI and VarSeak predict no splicing impact; SpliceAI scores 0-0.2 are benign evidence, and the criterion is supporting strength. NM_000314.8:c.165-1_185del is a canonical intronic splice-acceptor variant and is not excluded by the VCEP's intron 1 caution. The available SpliceAI max delta is 0.976, outside the VCEP benign range and strongly predicts splice impact rather than no impact. Therefore BP4 is not met; the absent VarSeak result is an additional missing component, but it cannot convert the available contrary SpliceAI result into evidence of no impact.

VCEP rule

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

Evidence considered

• ClinGen PTEN VCEP v3.2 BP4 rule: synonymous or intronic variants require concordant SpliceAI and VarSeak no-impact predictions; SpliceAI scores 0-0.2 are benign evidence and the criterion is supporting strength.
• SpliceAI Lookup for NM_000314.8:c.165-1_185del: max delta score 0.976 (DS_AL 0.976; DS_DL 0.912), outside the VCEP BP4 benign range and predicting splice impact.
• No VarSeak result is present for this variant.

Still missing

• VarSeak prediction class is unavailable, so complete two-predictor concordance cannot be assessed; the available SpliceAI result already contradicts BP4.

Sources

Reasoning

The ClinGen PTEN VCEP PS1 rule requires either the same amino acid change as a previously established pathogenic variant or a different variant at the same nucleotide position as a pathogenic splicing variant with in-silico evidence equal to or greater than the known pathogenic variant. This variant is a canonical splice variant, NM_000314.8:c.165-1_185del, with protein consequence p.?; the case evidence contains no established pathogenic comparator at the same amino-acid or nucleotide position and no comparator in-silico result. Therefore PS1 cannot be evaluated from the available evidence.

Evidence considered

• ClinGen PTEN VCEP v3.2 PS1 entry: the rule requires the same amino-acid change as a previously established pathogenic variant, or a different variant at the same nucleotide position as a pathogenic splicing variant with in-silico impact equal to or greater than the known pathogenic variant.
• Variant assessment: NM_000314.8:c.165-1_185del is a canonical splice acceptor variant with protein consequence NP_000305.3:p.?.
• ClinVar evidence states that this variant is absent from ClinVar; no pathogenic comparator was supplied in the case evidence.

Still missing

• A previously established pathogenic PTEN variant at the same amino-acid change or same nucleotide position is not available.
• Comparative in-silico evidence for a pathogenic splicing comparator is not available.

Sources

Reasoning

The available case evidence contains no proband-level de novo observation, parental testing, disease status, or family-history information; therefore the VCEP PS2 rule cannot be evaluated.

VCEP rule

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

Evidence considered

• ClinGen PTEN VCEP specification v3.2 provides the PS2 rule, but the case evidence contains no proband, parental-testing, de novo, or family-history observations.
• The case literature packet contains 0 PMIDs and no paper-extraction findings relevant to PS2.

Still missing

• Proband disease phenotype and family-history information
• Confirmed maternity and paternity or other parental testing
• Documented de novo observation

Sources

Reasoning

The PTEN VCEP permits PS3 for an RNA, mini-gene, or other assay showing an impact on splicing, and permits PS3_Moderate from Mighell et al. 2018 only when the Table S2 variant is listed as high confidence and has phosphatase activity <= -1.11. This variant is the canonical splice/deletion NM_000314.8:c.165-1_185del (NP_000305.3:p.?), not a missense variant represented by the phosphatase assay table. Searches of mmc2.xlsx converted full text found no entry for c.165-1_185del or p.?, and the case evidence contains no variant-specific RNA, mini-gene, or other functional assay demonstrating splice impact. PS3 therefore cannot be assessed from the available evidence.

VCEP rule

Well-established _in vitro_ or _in vivo_ functional studies supportive of a damaging effect on the gene or gene product. * RNA, mini-gene, or other assay shows impact on splicing

Evidence considered

• ClinGen PTEN VCEP Version 3.2 PS3 rule: RNA, mini-gene, or other assay shows impact on splicing; PS3_Moderate uses Mighell et al. 2018 Table S2 only for a high-confidence variant with cumulative phosphatase score <= -1.11.
• Mighell et al. 2018 supplementary file mmc2.xlsx, Table S2: searched the full converted text for c.165-1_185del and p.?; no matching row was found. The table is indexed for PTEN missense assay variants.
• Case evidence identifies NM_000314.8:c.165-1_185del as a canonical splice deletion with predicted protein consequence NP_000305.3:p.? and contains no variant-specific functional assay result.

Still missing

• No entry for c.165-1_185del was found in /Users/gs_agent/LYFESCI_HERMES_v11/vcep_db/PTEN/fulltext/mmc2.xlsx.txt.
• No entry for p.? was found in /Users/gs_agent/LYFESCI_HERMES_v11/vcep_db/PTEN/fulltext/mmc2.xlsx.txt.
• A variant-specific RNA, mini-gene, or other assay demonstrating splice impact is not available in the reviewed case evidence.

Sources

Reasoning

The ClinGen PTEN VCEP permits PS4 from a sufficiently powered case-control study with odds ratio >2 for a PHTS component phenotype, p<0.05, and a 95% confidence-interval lower limit >1.5, or from phenotype-specificity scores accumulated across independent probands. The available evidence contains no case-control odds ratio, p-value, confidence interval, Cleveland Clinic scores, pediatric phenotype scores, or independent-proband specificity total for this variant. Therefore the PS4 rule cannot be evaluated. No numeric comparison was performed because the required PS4 value and threshold evidence are absent.

VCEP rule

Probands with specificity score 4-15.5 (see text) OR The prevalence of the variant in affected individuals is significantly increased compared with the prevalence in controls.

Evidence considered

• The case evidence contains no case-control study result for NM_000314.8:c.165-1_185del.
• The case evidence contains no Cleveland Clinic score, pediatric phenotype score, or accumulated independent-proband specificity score for this variant.

Still missing

• Case-control odds ratio, p-value, and 95% confidence interval for a PHTS component phenotype are unavailable.
• Independent-proband Cleveland Clinic scores or pediatric phenotype scores and the resulting specificity total are unavailable.

Sources

Reasoning

The available case evidence contains no presumed or assumed de novo observation, proband disease status, parental confirmation status, or family-history information; therefore the VCEP PM6 rule cannot be evaluated.

VCEP rule

Assumed _de novo,_ but without confirmation of paternity and maternity, in proband with the disease and no family history.

Evidence considered

• ClinGen PTEN VCEP specification v3.2 provides PM6 thresholds for assumed and presumed de novo observations, but the case evidence contains none of the required observations or parental-confirmation details.
• The case literature packet contains 0 PMIDs and no paper-extraction findings relevant to PM6.

Still missing

• Number of relevant de novo observations
• Proband disease phenotype and family-history information
• Maternity and paternity confirmation status for each observation

Sources

Reasoning

The available case evidence contains no affected family members, phase information, or informative meioses; therefore the VCEP PP1 co-segregation thresholds cannot be evaluated.

VCEP rule

Co-segregation with disease in multiple affected family members, with 3 or 4 meioses observed.

Evidence considered

• ClinGen PTEN VCEP specification v3.2 defines PP1 using 3 or 4, 5 or 6, or at least 7 observed meioses, but the case evidence documents no segregation observations or meioses.
• The case literature packet contains 0 PMIDs and no paper-extraction findings relevant to PP1.

Still missing

• Affected family-member genotypes and phenotypes
• Informative meiosis count
• Segregation and phase data across families

Sources

Reasoning

Scope: the PTEN VCEP applies PP3 to synonymous or intronic variants when both SpliceAI and VarSeak predict a splicing impact; the named SpliceAI pathogenic range is 0.5-1, and the rule assigns supporting strength. NM_000314.8:c.165-1_185del is a canonical intronic splice-acceptor variant. SpliceAI is available and predicts splice impact with max delta 0.976, within the VCEP's pathogenic range. However, no VarSeak result is available, so concordance of the two predictors cannot be established. The criterion therefore cannot be evaluated to the VCEP's required two-predictor rule and is not assessed; the SpliceAI result must not be 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

Evidence considered

• ClinGen PTEN VCEP v3.2 PP3 rule: synonymous or intronic variants require concordant SpliceAI and VarSeak splicing-impact predictions; SpliceAI scores 0.5-1 are pathogenic evidence and the criterion is supporting strength.
• SpliceAI Lookup for NM_000314.8:c.165-1_185del: max delta score 0.976 (DS_AL 0.976; DS_DL 0.912), predicting splice impact.
• No VarSeak result is present for this variant, so the required predictor concordance cannot be confirmed.

Still missing

• VarSeak prediction class for NM_000314.8:c.165-1_185del is unavailable; both named predictors are required for PP3.

Sources

Reasoning

The PTEN VCEP requires an RNA, mini-gene, or other splicing assay demonstrating no splicing impact for BS3 in intronic or synonymous variants. This variant is a canonical splice deletion, and the case evidence contains no variant-specific assay showing preserved splicing. The VCEP's Mighell et al. 2018 BS3_Supporting phosphatase rule is restricted to high-confidence Table S2 assay variants with phosphatase activity >0; searches of mmc2.xlsx converted full text found no entry for c.165-1_185del or p.?. BS3 therefore cannot be assessed from the available evidence.

VCEP 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.

Evidence considered

• ClinGen PTEN VCEP Version 3.2 BS3 rule: for intronic or synonymous variants, RNA, mini-gene, or other splicing assay must demonstrate no splicing impact; BS3_Supporting phosphatase evidence uses a high-confidence Mighell et al. 2018 Table S2 variant with activity >0.
• Mighell et al. 2018 supplementary file mmc2.xlsx, Table S2: searched the full converted text for c.165-1_185del and p.?; no matching row was found. The table is indexed for PTEN missense assay variants.
• Case evidence identifies NM_000314.8:c.165-1_185del as a canonical splice deletion with predicted protein consequence NP_000305.3:p.? and contains no assay demonstrating no splicing impact.

Still missing

• No entry for c.165-1_185del was found in /Users/gs_agent/LYFESCI_HERMES_v11/vcep_db/PTEN/fulltext/mmc2.xlsx.txt.
• No entry for p.? was found in /Users/gs_agent/LYFESCI_HERMES_v11/vcep_db/PTEN/fulltext/mmc2.xlsx.txt.
• A variant-specific RNA, mini-gene, or other assay demonstrating no splicing impact is not available in the reviewed case evidence.

Sources

Reasoning

The available case evidence contains no affected relatives or family-level non-segregation observations; therefore the VCEP BS4 one-family or two-family rule cannot be evaluated.

VCEP rule

Lack of segregation in affected members of one family.

Evidence considered

• ClinGen PTEN VCEP specification v3.2 defines BS4 from lack of segregation in affected members of one family or two or more families, but the case evidence contains no such observations.
• The case literature packet contains 0 PMIDs and no paper-extraction findings relevant to BS4.

Still missing

• Affected family-member genotypes and phenotypes
• Documented lack of segregation in one or more families
• Number of families with informative non-segregation

Sources

Reasoning

BP2 is applicable at the supporting level under the PTEN VCEP rule, requiring 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. The available case evidence documents no affected-proband, family, or laboratory observation establishing trans, cis, or phase-unknown occurrence with another pathogenic or likely pathogenic PTEN variant; therefore the criterion 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 VCEP specification v3.2, BP2 supporting 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."
• Case evidence contains no documented affected-proband, family, or laboratory observation establishing this variant in trans, in cis, or in phase unknown with another pathogenic or likely pathogenic PTEN variant.

Still missing

• Documented phase and pairing information for this variant with another pathogenic or likely pathogenic PTEN variant is unavailable.
• No qualifying set of at least three cis and/or phase-unknown observations with different pathogenic or likely pathogenic PTEN variants is documented.

Sources

Reasoning

The PTEN VCEP requires at least two cases in which the variant is found with an alternate molecular basis for disease, with the other gene/disorder highly penetrant and the patient's personal or family history showing no overlap between that disorder and PTEN. The available evidence provides no such cases, alternate molecular diagnosis, penetrance assessment, or non-overlapping phenotype/family-history documentation. Therefore BP5 cannot be evaluated.

VCEP 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 case evidence contains no alternate molecular diagnosis associated with this variant and no qualifying case series.
• The case evidence contains no documentation of highly penetrant alternate disease or non-overlapping personal/family history.

Still missing

• At least two cases with an alternate molecular basis for disease are unavailable.
• Evidence that the alternate disorder is highly penetrant and has no phenotype or family-history overlap with PTEN is unavailable.

Sources