PTEN c.127dup, p.Glu43GlyfsTer9

Reasoning

NM_000314.8:c.127dup is a frameshift, NP_000305.3:p.(Glu43GlyfsTer9), in exon 2. The resulting premature stop is at codon 51, well 5' of p.D375 (c.1121), and exon 2 is present in the biologically relevant transcript NM_000314.8; therefore the PTEN VCEP decision tree assigns full PVS1 for a frameshift predicted to undergo NMD. The exact variant notations c.127dup, p.Glu43GlyfsTer9, and p.E43Gfs*9 were not present as individual rows in PVS1_DecisionTree_PTEN.pdf.txt, so the governing frameshift path was applied to the documented consequence and transcript facts.

VCEP rule

Nonsense or frameshift | Predicted to undergo NMD: stop codon or disruption at or 5' to p.D375 (c.1121) -> exon is present in biologically-relevant transcript NM_000314.8 | PVS1

Evidence considered

• Case variant facts: NM_000314.8:c.127dup; NP_000305.3:p.(Glu43GlyfsTer9)/p.(E43Gfs*9); frameshift; exon 2.
• PVS1_DecisionTree_PTEN.pdf, page 1, row 'Nonsense or frameshift | Predicted to undergo NMD: stop codon or disruption at or 5' to p.D375 (c.1121) -> exon is present in biologically-relevant transcript NM_000314.8 | PVS1': c.127dup produces a premature stop at p.51, 5' of p.D375, and exon 2 is present in NM_000314.8.
• The required searches for c.127dup, p.Glu43GlyfsTer9, and p.E43Gfs*9 returned no exact variant row in the PTEN fulltext directory.

Still missing

• No exact c.127dup, p.Glu43GlyfsTer9, or p.E43Gfs*9 entry was found in PVS1_DecisionTree_PTEN.pdf.txt; the applicable frameshift decision-tree row was present and used.

Sources

Reasoning

The PTEN VCEP permits 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; if multiple alleles occur in a subpopulation, that subpopulation frequency must be less than 0.00002 (0.002%). NM_000314.8:c.127dup is absent from gnomAD v2.1, gnomAD v4.1, gnomAD v2.1 non-cancer, and gnomAD v3.1 non-cancer, satisfying the stated population-frequency requirement.

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 applies when databases show <0.00001 (0.001%) allele frequency in gnomAD or another large sequenced population; if multiple alleles are present within any subpopulation, that subpopulation allele frequency must be <0.00002 (0.002%).
• gnomAD v2.1: NM_000314.8:c.127dup absent.
• gnomAD v4.1: NM_000314.8:c.127dup absent.
• GNOMAD_V2_1_NON_CANCER, exomes-only figures: NM_000314.8:c.127dup absent.
• GNOMAD_V3_1_NON_CANCER, genomes-only figures: NM_000314.8:c.127dup absent.

Sources

Reasoning

The PTEN VCEP limits PM1 to residues in catalytic motifs 90-94, 123-130, and 166-168 of NP_000305.3. This variant alters residue 43 and is outside all three specified regions. The case's authoritative PTEN domain_tables entry is empty, and no VCEP-approved hotspot route is specified in the governing PM1 rule.

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

• PTEN VCEP PM1 specification: catalytic motifs are residues 90-94, 123-130, and 166-168 in NP_000305.3; the variant protein consequence begins at Glu43.
• vcep_materials.json domain_tables for PTEN is an empty object; no additional authoritative domain entry is available.
• Hotspot evidence reports that the variant does not lie in a statistically significant hotspot, and the VCEP PM1 rule does not name a somatic hotspot source or route.

Sources

Reasoning

The PTEN VCEP defines BA1 as a gnomAD filtering allele frequency greater than 0.00056 (0.056%). NM_000314.8:c.127dup is absent from gnomAD v2.1 and gnomAD v4.1, so no allele frequency exceeding the BA1 threshold is present.

VCEP rule

gnomAD Filtering allele frequency >0.00056 (0.056%)

Evidence considered

• ClinGen PTEN VCEP Version 3.2: BA1 requires gnomAD filtering allele frequency >0.00056 (0.056%).
• gnomAD v2.1: NM_000314.8:c.127dup absent; no allele frequency or homozygote count reported.
• gnomAD v4.1: NM_000314.8:c.127dup absent; no allele frequency or homozygote count reported.

Sources

Reasoning

The PTEN VCEP defines BS1 Strong as a gnomAD filtering allele frequency from 0.000043 (0.0043%) up to 0.00056 (0.056%) and BS1 Supporting as 0.0000043 (0.00043%) up to 0.000043 (0.0043%). NM_000314.8:c.127dup is absent from gnomAD v2.1 and gnomAD v4.1, so neither BS1 frequency interval is 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 requires gnomAD filtering allele frequency from 0.000043 (0.0043%) up to 0.00056 (0.056%).
• ClinGen PTEN VCEP Version 3.2: BS1 Supporting requires allele frequency from 0.0000043 (0.00043%) up to 0.000043 (0.0043%).
• gnomAD v2.1: NM_000314.8:c.127dup absent; no allele frequency reported.
• gnomAD v4.1: NM_000314.8:c.127dup absent; no allele frequency reported.

Sources

Reasoning

The available case evidence does not document a de novo observation for NM_000314.8:c.127dup, parental testing, confirmation of both maternity and paternity, or absence of family history. Therefore, the PTEN VCEP PS2 rule cannot be evaluated.

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

Evidence considered

• No proband-level de novo, parental-testing, or family-history result for NM_000314.8:c.127dup is present in the available case evidence.

Still missing

• Documented proband-level de novo observation is missing.
• Parental testing with confirmation of both maternity and paternity is missing.
• Family-history information is missing.

Sources

Reasoning

The PTEN VCEP permits PS4 from a sufficiently powered case-control study with odds ratio >2, p<0.05, and a 95% confidence-interval lower limit >1.5, or from independent probands meeting its phenotype-specificity score thresholds; it also states PS4 may not be applied if BS1 applies. The available literature does not report this exact variant, c.127dup/p.(Glu43GlyfsTer9), in affected patients with an unaffected/control comparison or patient-level Cleveland Clinic/pediatric specificity scores. Tan et al. (PMID:21194675) reports 290/3042 probands with pathogenic PTEN mutations but does not identify c.127dup and is not an exact-variant case-control comparison. The other reviewed papers likewise do not report this variant. Therefore the VCEP PS4 rule cannot be evaluated from the available evidence; no odds ratio or 95% CI was computable.

VCEP 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. However, this criterion may _not_ be applied in combination with PP4. ... **PTEN EP Specifications:** This criterion may not be applied if BS1 applies.  Phenotype specificity scores are added across independent probands and calculated as follows: ... 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

• ClinGen PTEN VCEP PS4 rule: the case-control route requires an odds ratio >2, p<0.05, and a 95% confidence-interval lower limit >1.5; the specificity-score route uses independent probands and the listed adult/child score thresholds.
• Tan et al. 2011 (PMID:21194675), Results, PTEN Mutation Spectrum in Patients: 290 of 3,042 probands had germline pathogenic PTEN mutations, but the paper does not identify c.127dup or p.(Glu43GlyfsTer9) and supplies no exact-variant control comparison.
• Zelcer et al. 2013 (PMID:23519317), Page 4, Single-gene disorders: reports 3/18 and 15/318 PTEN-positive ASD cases, but does not mention c.127dup or provide exact-variant data.
• ACMG incidental-findings recommendations (PMID:23788249) do not mention PTEN c.127dup or p.(Glu43GlyfsTer9).
• NCCN/ACMG/NSGC referral guideline (PMID:25394175) discusses PTEN hamartoma tumor syndrome generally but does not mention the exact variant or provide variant-level case-control or specificity-score evidence.
• Marsh et al. 1998 (PMID:9467011), Results/Table 1: reports PTEN mutation distributions in Cowden/Bannayan-Zonana families, including insertions, but does not report c.127dup or an exact-variant control comparison.

Still missing

• An exact-variant case-control dataset with affected and unaffected/control counts, or an exact-variant case frequency with an appropriate matched-ancestry control frequency, is needed to compute the odds ratio and 95% CI.
• Patient-level Cleveland Clinic scores or pediatric phenotype scores for independent probands carrying this exact variant are needed to evaluate the VCEP specificity-score route.

Sources

Reasoning

The available case evidence does not document a presumed or assumed de novo observation of NM_000314.8:c.127dup in a proband with PTEN hamartoma tumor syndrome, the number of de novo observations, parental confirmation status, or family history. Therefore, the PTEN VCEP PM6 rule cannot be evaluated.

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. * May also be used for a proband with presumed de novo occurrence for an individual with a highly specific phenotype (meets criteria to count towards PS4) ... Assumed _de novo,_ but without confirmation of paternity and maternity, in proband with the disease and no family history.

Evidence considered

• No proband-level presumed or assumed de novo observation, observation count, parental-confirmation status, or family-history result for NM_000314.8:c.127dup is present in the available case evidence.

Still missing

• Proband-level presumed or assumed de novo observation is missing.
• The number of independent de novo observations is missing.
• Maternity and paternity confirmation status is missing.
• Family-history information is missing.

Sources

Reasoning

The available case evidence contains no affected relatives carrying NM_000314.8:c.127dup, no informative meioses, and no family-level segregation data. Therefore, the PTEN VCEP PP1 rule cannot be evaluated at supporting, moderate, or strong strength.

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

• No family members, genotype-phenotype pairs, informative meioses, or co-segregation results for NM_000314.8:c.127dup are present in the available case evidence.

Still missing

• Affected relatives with genotype and phenotype data are missing.
• Informative meiosis count is missing.
• Segregation results across families are missing.

Sources

Reasoning

The PTEN VCEP requires an observation in the homozygous state in a healthy or PHTS-unaffected individual for BS2. The available gnomAD records report the variant as absent and provide no homozygote observations; absence from gnomAD cannot establish the required homozygous observation or its clinical status.

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. ... Two homozygous observations with no clinical data provided, or meets criteria for BS2 but BS1 is also applied.

Evidence considered

• ClinGen PTEN VCEP Version 3.2: BS2 Strong requires one confirmed homozygous observation in a healthy or PHTS-unaffected individual, or two observations if homozygous status is not confirmed; BS2 is Supporting when there are two homozygous observations with no clinical data or when BS1 is also applied.
• gnomAD v2.1 and gnomAD v4.1 both report NM_000314.8:c.127dup as absent, with no homozygote observations or clinical-status data.

Still missing

• A confirmed homozygous observation in a healthy or PHTS-unaffected individual, or two unconfirmed homozygous observations, is not available.

Sources

Reasoning

The available case evidence contains no affected family members who lack NM_000314.8:c.127dup and no documented non-segregation in one or more families. Therefore, the PTEN VCEP BS4 rule cannot be evaluated.

VCEP rule

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

Evidence considered

• No affected relative tested negative for NM_000314.8:c.127dup and no family-level non-segregation result is present in the available case evidence.

Still missing

• Affected relatives tested negative for the variant are missing.
• Family-level non-segregation data are missing.

Sources

Reasoning

The ClinGen PTEN VCEP BP2 rule requires either observation of this variant 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 contains no documented affected-proband observation, paired pathogenic/likely pathogenic PTEN variant, phase result, cis/trans relationship, or qualifying count of observations. Therefore 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 VCEP Version 3.2 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."
• Case evidence documents NM_000314.8:c.127dup (NP_000305.3:p.(Glu43GlyfsTer9)) but provides no qualifying second PTEN variant, cis/trans phase, or three qualifying observations.

Still missing

• Documented affected-proband observations involving this variant and another pathogenic or likely pathogenic PTEN variant are unavailable.
• Cis/trans or phase information and a qualifying observation count are unavailable.

Sources

Reasoning

The PTEN VCEP requires at least two cases with an alternate molecular basis for disease, with the other gene/disorder considered highly penetrant and the patient's personal/family history demonstrating no overlap between that disorder and PTEN. The available case, ClinVar, population, and literature materials do not document two such cases for PTEN c.127dup, an alternate pathogenic molecular diagnosis, or the required non-overlapping histories. BP5 therefore cannot be evaluated.

VCEP rule

**PTEN EP Specifications:** 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_. ... 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

• ClinGen PTEN VCEP BP5 instructions require at least two such cases, a highly penetrant other gene/disorder, and no overlap between the patient's personal/family history and PTEN.
• No available exact-variant case record documents the alternate molecular basis and the required personal/family-history exclusions.

Still missing

• Two independent exact-variant cases with the alternate molecular diagnosis, evidence that the alternate disorder is highly penetrant, and documented non-overlapping personal/family histories are required.

Sources