PTEN c.30_32del, p.(Ser10del)

Reasoning

PM2 is met at Supporting strength under the PTEN-specific VCEP. The exact variant NM_000314.8:c.30_32del is reported as absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0. This satisfies the PTEN rule requiring a frequency below 0.00001 (0.001%) in gnomAD or another large sequenced population; when multiple alleles are present in a subpopulation, the subpopulation frequency must be below 0.00002 (0.002%).

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 Expert Panel specifications version 3.2 define PM2 at Supporting strength for absence or allele frequency <0.00001 (0.001%) in gnomAD or another large sequenced population; if multiple alleles occur within a subpopulation, that subpopulation frequency must be <0.00002 (0.002%).
• The exact variant is reported as absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0.
• Absence in all three reported population resources is below the specified PM2 frequency thresholds.

Still missing

• The supplied records do not provide explicit allele-number denominators or per-ancestry frequency estimates; they report absence only.

Sources

Reasoning

One exact-match ClinVar clinical-laboratory record reports presumed de novo occurrence in an individual with a PTEN-consistent phenotype. Maternity and paternity are not confirmed in the available evidence, so this supports PM6 at the PTEN-specific Moderate level, but not PS2. The record is a secondary submission summary rather than primary case documentation and mentions possible germline mosaicism, warranting human review.

Rule

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

Evidence considered

• The PTEN Expert Panel specification defines PM6 Moderate as assumed de novo without confirmation of paternity and maternity in a proband with the disease and no family history.
• The exact-match ClinVar submission reports the variant as de novo or due to germline mosaicism in one individual with epilepsy, developmental delay with regression, and macrocephaly; the available record does not provide confirmed parental testing.
• Only one presumed de novo observation is available, so the PTEN-specific thresholds for PM6 Strong or PM6 Very Strong are not met.

Still missing

• Primary report or laboratory case data documenting the de novo testing result are not provided.
• Confirmation status for maternity and paternity is not provided.
• The bundle does not establish whether there was no family history for the individual beyond the ClinVar criterion wording.

Sources

Reasoning

NM_000314.8:c.30_32del is an in-frame three-nucleotide deletion predicted to remove Ser10 only (p.(Ser10del)); it does not introduce a premature termination codon, frameshift, canonical splice-site alteration, initiation-codon alteration, or exon deletion. Therefore, it is outside the PTEN EP PVS1 decision tree for null variants and no NMD-mediated loss-of-function mechanism is predicted.

Rule

PTEN EP PVS1: apply the PTEN-specific PVS1 decision tree to eligible null variants; this in-frame single-residue deletion is not an eligible null-variant mechanism.

Evidence considered

• Normalization on the PTEN EP preferred transcript NM_000314.8 predicts NP_000305.3:p.(Ser10del), with protein length reduced by one residue and no frameshift or premature stop.
• The PTEN EP PVS1 specification limits its PVS1 workflow to null-variant mechanisms, including nonsense, frameshift, canonical splice-site, initiation-codon, and exon-deletion events; its PTEN-specific decision tree assigns strength using NMD and the p.Asp375/c.1121 threshold only for eligible null variants.

Sources

Reasoning

The variant is not in the statistically significant hotspot set and residue 10 is outside the PTEN Expert Panel-defined catalytic motifs: WPD loop residues 90-94, P-loop/phosphatase core residues 123-130, and TI-loop residues 166-168. A published PTEN study describes a PIP2-binding motif spanning residues 6-15, but the governing PTEN PM1 specification defines the qualifying motifs as the three catalytic regions above; therefore residue 10 does not meet PM1.

Rule

Located in a mutational hotspot and/or critical and well-established functional domain; for PTEN, defined to include residues in the WPD loop (90-94), P-loop/phosphatase core (123-130), or TI-loop (166-168) of NP_000305.3.

Evidence considered

• The PTEN Expert Panel Version 3.2 PM1 specification defines qualifying catalytic motifs as WPD loop residues 90-94, P-loop/phosphatase core residues 123-130, and TI-loop residues 166-168 in NP_000305.3.
• The case hotspot assessment reports that the variant does not lie in a statistically significant hotspot.
• Mighell et al. describe a PIP2-binding motif in the phosphatase domain spanning residues 6-15, but this does not replace the narrower PTEN-specific PM1 motif definition.

Sources

Reasoning

Although the in-frame deletion shortens PTEN by one residue (p.(Ser10del)), the PTEN EP permits PM4 for an in-frame insertion/deletion only when it affects at least one residue in a defined catalytic motif, or for a protein-extension variant. Ser10 is outside the defined catalytic motifs at residues 90-94, 123-130, and 166-168, and the variant does not cause protein extension.

Rule

PTEN EP PM4 Moderate: in-frame insertions/deletions must impact at least one residue in a defined catalytic motif; protein-extension variants also qualify.

Evidence considered

• Normalization predicts an in-frame single-residue deletion, NP_000305.3:p.(Ser10del), rather than a frameshift or stop-loss/protein-extension consequence.
• The PTEN EP PM4 specification requires an in-frame insertion/deletion to affect at least one residue in a PM1-defined catalytic motif; the defined motifs are residues 90-94, 123-130, and 166-168.

Sources

Reasoning

BA1 is not met. The PTEN-specific VCEP threshold is a gnomAD filtering allele frequency greater than 0.00056 (0.056%). NM_000314.8:c.30_32del is reported as absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0, so no allele frequency reaches the BA1 threshold.

Rule

gnomAD Filtering allele frequency >0.00056 (0.056%)

Evidence considered

• ClinGen PTEN Expert Panel specifications version 3.2 define BA1 as gnomAD filtering allele frequency >0.00056 (0.056%).
• The case evidence bundle reports the exact variant as absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0.
• Because the variant is absent in each reported population resource, the BA1 frequency threshold is not reached.

Still missing

• The supplied population records provide absence statements rather than explicit allele-number denominators or ancestry-stratified frequency values.

Sources

Reasoning

BS1 is not met. The PTEN-specific VCEP defines BS1 as a gnomAD filtering allele frequency from 0.000043 (0.0043%) up to 0.00056 (0.056%) for strong evidence, or from 0.0000043 (0.00043%) up to 0.000043 (0.0043%) for supporting evidence. The exact variant is reported as absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0, with no observed frequency in either BS1 interval.

Rule

gnomAD Filtering allele frequency from 0.000043 (0.0043%) up to 0.00056 (0.056%) for strong evidence; allele frequency from 0.0000043 (0.00043%) up to 0.000043 (0.0043%) for supporting evidence.

Evidence considered

• ClinGen PTEN Expert Panel specifications version 3.2 define BS1 frequency intervals of 0.000043 to 0.00056 for strong evidence and 0.0000043 to 0.000043 for supporting evidence.
• The case evidence bundle reports the exact variant as absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0.
• No population frequency falls within either PTEN-specific BS1 interval.

Still missing

• The supplied population records provide absence statements rather than explicit allele-number denominators or ancestry-stratified frequency values.

Sources

Reasoning

A ClinVar clinical-laboratory submission reports the variant as de novo or due to germline mosaicism in one individual with epilepsy, developmental delay with regression, and macrocephaly, but the available case evidence does not document confirmed maternity and paternity. The PTEN-specific PS2 rule requires both maternity and paternity confirmation for PS2 Strong; the evidence therefore cannot establish PS2.

Rule

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

Evidence considered

• The PTEN Expert Panel specification (version 3.2) defines PS2 Strong as a de novo observation in a patient with disease and no family history with both maternity and paternity confirmed; PS2 Very Strong requires two proven, four assumed, or one proven plus two assumed de novo observations.
• The exact-match ClinVar submission for NM_000314.8:c.30_32del includes a criterion signal stating that the variant was determined to result from a de novo mutation or germline mosaicism in one individual with epilepsy, developmental delay with regression, and macrocephaly.
• Because the available record does not confirm both maternity and paternity and allows germline mosaicism, it is insufficient for PS2.

Still missing

• Primary case documentation is needed to distinguish de novo occurrence from germline mosaicism.
• Maternity and paternity confirmation is not provided.
• The individual's family history and complete phenotype documentation are not available in the bundle.

Sources

Reasoning

The PTEN-specific framework is applicable to this variant group only through the listed functional assay calibration for missense variants: PS3_Moderate requires phosphatase activity <= -1.11 in Mighell et al. 2018. The variant is an in-frame deletion, and the available extraction from that study confirms that single-codon deletions were included in the library but does not provide a variant-specific result for p.(Ser10del). Therefore, a damaging functional effect cannot be assigned from the available evidence.

Rule

PTEN VCEP v3.2 PS3: strong for well-established functional studies showing a damaging effect, moderate for phosphatase activity <= -1.11 per Mighell et al. 2018, and supporting for phosphatase activity <50% of wild type or an abnormal assay not meeting PS3_Moderate; no variant-specific result is available here.

Evidence considered

• The PTEN Expert Panel specification defines PS3_Moderate for phosphatase activity <= -1.11 per Mighell et al. 2018 (PMID:29706350), and defines PS3_Supporting for phosphatase activity <50% of wild type or an abnormal functional assay that does not meet the moderate threshold.
• Mighell et al. 2018 used a massively parallel humanized-yeast lipid-phosphatase assay and included programmed single-codon amino-acid deletions, but the pre-computed extraction does not report the assay result for deletion of Ser10 and does not explicitly name c.30_32del or p.(Ser10del).
• The PTEN local framework index specifies the mmc2 calibration for missense variants; this case is an in-frame deletion rather than a missense variant.

Still missing

• No variant-specific phosphatase activity or other validated functional assay result for PTEN p.(Ser10del) was available.
• No calibrated PS3 strength rule for this in-frame deletion was identified in the applicable PTEN framework.

Sources

Reasoning

The PTEN Expert Panel requires either a sufficiently powered case-control result (odds ratio >2, p<0.05, and 95% CI lower bound >1.5) or independent probands totaling a phenotype-specificity score of at least 1. The available record supplies neither a case-control analysis nor independently documented proband phenotypes/scores for this exact variant.

Rule

PTEN EP v3.2 PS4: case-control OR >2 with p<0.05 and 95% CI lower bound >1.5, or independent-proband phenotype-specificity score >=1; PS4 cannot be combined with PP4.

Evidence considered

• ClinGen PTEN Expert Panel Specification v3.2 defines PS4 phenotype-specificity scoring: adult Cleveland Clinic score >=30 contributes 1 point (25-29 contributes 0.5); pediatric score >=5 contributes 1 point (score 4 contributes 0.5 subject to the specified restriction). PS4_Supporting requires a total of 1-1.5, Moderate 2-3.5, Strong 4-15.5, and Very Strong >=16. It also permits a sufficiently powered case-control study with OR >2, p<0.05, and 95% CI lower bound >1.5.
• ClinVar variation 428224 is an exact match for NM_000314.8:c.30_32del (p.Ser10del). Its included single-submitter narrative reports one individual with epilepsy, developmental delay with regression, and macrocephaly, but provides no PTEN Expert Panel phenotype-specificity score, sufficient clinical detail to calculate one, independent-proband count, or case-control enrichment statistics.

Still missing

• A case-control study for PTEN c.30_32del with the specified effect estimate, p value, and confidence interval, or independent proband-level phenotype documentation sufficient to calculate the PTEN Expert Panel specificity score.

Sources

Reasoning

The case bundle contains no documented affected relatives, informative meioses, or family-level co-segregation data for NM_000314.8:c.30_32del. The PTEN-specific PP1 thresholds require at least 3 meioses for supporting strength, with higher strengths requiring 5–6 or at least 7 meioses across at least two families.

Rule

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

Evidence considered

• The PTEN Expert Panel specification requires 3 or 4 meioses for PP1 Supporting, 5 or 6 meioses for PP1 Moderate, and at least 7 meioses across at least two families for PP1 Strong.
• No primary paper extraction or case-level evidence in the bundle reports segregation or informative meioses for this exact variant.

Still missing

• Affected family members and their variant/phenotype status are not documented.
• The number of informative meioses is not available.
• Independent family structure and segregation results are not available.

Sources

Reasoning

PP3 cannot be applied. The PTEN VCEP requires concordant SpliceAI and VarSeak predictions for the splicing path; SpliceAI alone has a maximum delta score of 0.037, but no VarSeak result is available. REVEL is inapplicable because this is an in-frame deletion (p.(Ser10del)), not a missense SNV.

Rule

PTEN VCEP v3.2 PP3: splicing variants require concordance of SpliceAI and VarSeak; missense variants require REVEL >0.7.

Evidence considered

• ClinGen PTEN Expert Panel Specifications v3.2 assigns PP3_Supporting for splicing variants only with concordance of SpliceAI and VarSeak; its missense route requires REVEL >0.7.
• For NM_000314.8:c.30_32del, SpliceAI reports DS_AG 0.032, DS_AL 0.032, DS_DG 0.037, DS_DL 0.005 (maximum delta 0.037), predicting no significant splice impact.
• The variant is an in-frame three-nucleotide deletion encoding p.(Ser10del); REVEL was not available because it is not an SNV.

Still missing

• A VarSeak prediction is required to assess the PTEN VCEP splicing computational-evidence rule.
• No PTEN VCEP computational rule specific to in-frame deletions was provided beyond assessment for splice impact.

Sources

Reasoning

BS2 cannot be assessed from the supplied evidence. The PTEN-specific VCEP requires the variant to be observed in the homozygous state in a healthy or PHTS-unaffected individual; the bundle contains no homozygous observation, zygosity confirmation, or clinical status for an individual carrying this variant.

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

• ClinGen PTEN Expert Panel specifications version 3.2 require an observed homozygous state in a healthy or PHTS-unaffected individual for BS2; they specify strong evidence for one confirmed homozygote or two unconfirmed observations, and supporting evidence for two homozygous observations without clinical data.
• The case evidence bundle reports the variant as absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0, but reports no homozygous carrier or clinical status.

Still missing

• No confirmed homozygous observation is provided.
• No individual-level health or PHTS-unaffected status is provided.
• The absence of the variant from population databases does not establish or exclude a homozygous observation.

Sources

Reasoning

The PTEN-specific framework permits BS3_Supporting when phosphatase activity is >0 per Mighell et al. 2018, and BS3_Strong for well-established functional studies showing no damaging effect. Although the cited saturation assay included single-codon deletions, the available extraction does not report a result for p.(Ser10del). No validated benign functional result is therefore available for this variant.

Rule

PTEN VCEP v3.2 BS3: strong for well-established functional studies showing no damaging effect, and supporting for phosphatase activity >0 per Mighell et al. 2018; no variant-specific result is available here.

Evidence considered

• The PTEN Expert Panel specification defines BS3_Supporting for phosphatase activity >0 per Mighell et al. 2018 (PMID:29706350), and BS3_Strong for well-established in vitro or in vivo functional studies showing no damaging effect on protein function.
• Mighell et al. 2018 used a massively parallel humanized-yeast lipid-phosphatase assay and included programmed single-codon amino-acid deletions, but the pre-computed extraction does not report the assay result for deletion of Ser10 and does not explicitly name c.30_32del or p.(Ser10del).
• The PTEN local framework index specifies the mmc2 calibration for missense variants; this case is an in-frame deletion rather than a missense variant.

Still missing

• No variant-specific phosphatase activity result demonstrating activity >0 or otherwise showing no damaging effect for PTEN p.(Ser10del) was available.
• No calibrated BS3 strength rule for this in-frame deletion was identified in the applicable PTEN framework.

Sources

Reasoning

The case bundle contains no documented affected relatives who lack the variant and no family-level non-segregation analysis. Therefore lack of segregation cannot be established at either the PTEN-specific Supporting level for one family or Strong level for two or more families.

Rule

Lack of segregation in affected members of one family.

Evidence considered

• The PTEN Expert Panel specification defines BS4 Supporting as lack of segregation in one family and BS4 Strong as lack of segregation in affected members of two or more families.
• The PTEN specification cautions that phenocopies and more than one pathogenic variant in an autosomal-dominant family can mimic lack of segregation.
• No affected-relative testing or non-segregation data for this exact variant are present in the case bundle.

Still missing

• Variant testing results for affected relatives are not available.
• The number of families with potential non-segregation is not available.
• Phenocopy risk and the possibility of more than one pathogenic variant in a family cannot be evaluated.

Sources

Reasoning

The PTEN VCEP specifies BP2 at Supporting strength when the variant is observed in trans with a pathogenic or likely pathogenic PTEN variant, or when there are at least three observations in cis and/or phase unknown with different pathogenic or likely pathogenic PTEN variants. The case-evidence bundle contains no affected-proband, family, parental, phase, cis, or trans observations establishing either condition for NM_000314.8:c.30_32del.

Rule

PTEN VCEP v3.2 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 ClinGen PTEN Expert Panel Version 3.2 BP2 rule requires 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 supplied case-evidence bundle provides no qualifying phase, allelic, parental, or affected-proband observation for this variant.

Still missing

• No documented affected-proband or family observations with a second pathogenic or likely pathogenic PTEN variant.
• No parental testing, haplotyping, or other evidence establishing trans or cis phase.
• No three qualifying cis or phase-unknown observations with different pathogenic or likely pathogenic PTEN variants.

Sources

Reasoning

BP4 cannot be applied. The PTEN VCEP requires concordant SpliceAI and VarSeak predictions for the splicing path. Although SpliceAI predicts no significant splice impact (maximum delta 0.037), VarSeak is unavailable. The VCEP missense route (REVEL <0.5) does not apply to this in-frame deletion.

Rule

PTEN VCEP v3.2 BP4: splicing variants require concordance of SpliceAI and VarSeak; missense variants require REVEL <0.5.

Evidence considered

• ClinGen PTEN Expert Panel Specifications v3.2 assigns BP4_Supporting for splicing variants only with concordance of SpliceAI and VarSeak; its missense route requires REVEL <0.5.
• For NM_000314.8:c.30_32del, SpliceAI reports DS_AG 0.032, DS_AL 0.032, DS_DG 0.037, DS_DL 0.005 (maximum delta 0.037), predicting no significant splice impact.
• The variant is an in-frame three-nucleotide deletion encoding p.(Ser10del); REVEL was not available because it is not an SNV.

Still missing

• A VarSeak prediction is required to assess the PTEN VCEP splicing computational-evidence rule.
• No PTEN VCEP computational rule specific to in-frame deletions was provided beyond assessment for splice impact.

Sources

Reasoning

No evidence identifies two affected cases with a separate highly penetrant molecular diagnosis and personal/family histories demonstrating no overlap between that disorder and PTEN-associated disease.

Rule

PTEN EP v3.2 BP5: supporting only after >=2 cases meeting the alternate highly penetrant diagnosis and non-overlapping phenotype/family-history requirements.

Evidence considered

• ClinGen PTEN Expert Panel Specification v3.2 requires at least two such cases for BP5; the alternate gene/disorder must be highly penetrant and the patient's personal/family history must demonstrate no overlap with PTEN.
• The available exact-variant ClinVar record provides no alternate molecular diagnosis or the required case-level phenotype and family-history documentation.

Still missing

• At least two case-level reports documenting an alternate molecular diagnosis that is highly penetrant and clinical/family-history evidence showing no phenotype overlap with PTEN hamartoma tumor syndrome.

Sources