PTEN c.922_923insT, p.(Arg308LeufsTer4)

Reasoning

NM_000314.8:c.922_923insT is a frameshift producing NP_000305.3:p.(Arg308LeufsTer4) / p.(R308Lfs*4). The PTEN VCEP PVS1 workflow applies PVS1 to frameshift variants predicted to undergo NMD and places the PTEN NMD cutoff at c.1121 (p.D375). This variant disrupts the coding sequence at c.922_923, 5' of c.1121, and the decision-tree diagram explicitly assigns PVS1 to a nonsense or frameshift variant predicted to undergo NMD when the stop codon or disruption is at or 5' to p.D375 in the biologically relevant NM_000314.8 transcript. No exact variant row was found in PVS1_DecisionTree_PTEN.pdf.txt under c.922_923insT, p.Arg308LeufsTer4, or p.R308Lfs*4; the result is therefore based on the governing decision-tree branch rather than a pre-assigned variant-specific row.

VCEP rule

PVS1 applies to variants predicted to result in nonsense-mediated decay (NMD); the predicted NMD cutoff for PTEN occurs at c.1121 (p.D375).

Evidence considered

• Variant normalization: NM_000314.8:c.922_923insT produces NP_000305.3:p.(Arg308LeufsTer4) / p.(R308Lfs*4), and the consequence class is frameshift.
• ClinGen PTEN VCEP PVS1 instructions: PVS1 applies to variants predicted to result in NMD, with the predicted PTEN NMD cutoff at c.1121 (p.D375).
• PVS1_DecisionTree_PTEN.pdf, page 1: the frameshift/nonsense branch places variants predicted to undergo NMD with a stop codon or disruption at or 5' to p.D375 on the PVS1 branch; the biologically relevant transcript is NM_000314.8.
• Searches of PVS1_DecisionTree_PTEN.pdf.txt for c.922_923insT, p.Arg308LeufsTer4, and p.R308Lfs*4 returned no exact variant-specific row.

Still missing

• No exact variant entry was found in PVS1_DecisionTree_PTEN.pdf.txt for c.922_923insT, p.Arg308LeufsTer4, or p.R308Lfs*4.

Sources

Reasoning

The ClinGen PTEN VCEP PM2 rule applies at supporting strength when a variant is absent from population databases or is present at less than 0.00001 (0.001%) allele frequency in gnomAD or another large sequenced population; if multiple alleles are present in a subpopulation, that subpopulation frequency must be less than 0.00002 (0.002%). The variant was absent from gnomAD v2.1 and v4.1. The VCEP does not specify a non-cancer or exome-only source for PM2, so the default all-comers gnomAD results were used.

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, with <0.00002 (0.002%) required in a subpopulation if multiple alleles are present.
• gnomAD v2.1 result for NM_000314.8:c.922_923insT: search_status=absent.
• gnomAD v4.1 result for NM_000314.8:c.922_923insT: search_status=absent.
• No PTEN VCEP PM2 instruction in the governing criterion requires a non-cancer or exome-only population source; all-comers gnomAD v2.1 and v4.1 were used as the default sources.

Sources

Reasoning

The PTEN VCEP PM1 rule assigns moderate evidence for a variant in a mutational hotspot or critical, well-established functional domain and specifically defines catalytic motifs at residues 90-94, 123-130, and 166-168. The variant changes residue 308 and vcep_materials.json contains no PTEN domain_tables entry adding another approved domain, so residue 308 is outside every VCEP-listed catalytic motif and no VCEP hotspot evidence is present.

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 Version 3.2 CSPEC PM1 rule: critical functional regions include catalytic-motif residues 90-94, 123-130, and 166-168 of NP_000305.3.
• Variant normalization places the frameshift at protein residue Arg308: NP_000305.3:p.(Arg308LeufsTer4).
• vcep_materials.json domain_tables for PTEN is empty; therefore no additional authoritative PTEN domain-table interval is available to include.
• Cancer Hotspots search for PTEN R308 returned no statistically significant hotspot row.

Sources

Reasoning

The ClinGen PTEN VCEP BA1 threshold is a gnomAD filtering allele frequency greater than 0.00056 (0.056%). The variant was absent from gnomAD v2.1 and gnomAD v4.1, so no allele frequency exceeding the BA1 threshold was observed. The VCEP does not specify a non-cancer or exome-only source for BA1; the default all-comers gnomAD results were therefore used.

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 result for NM_000314.8:c.922_923insT: search_status=absent; no allele-frequency or homozygote record was returned.
• gnomAD v4.1 result for NM_000314.8:c.922_923insT: search_status=absent; no allele-frequency or homozygote record was returned.
• No PTEN VCEP BA1 instruction in the governing criterion requires a non-cancer or exome-only population source; all-comers gnomAD v2.1 and v4.1 were used as the default sources.

Sources

Reasoning

The ClinGen PTEN VCEP defines BS1 Strong as a gnomAD filtering allele frequency from 0.000043 (0.0043%) up to 0.00056 (0.056%), with a supporting range from 0.0000043 (0.00043%) up to 0.000043 (0.0043%). The variant was absent from gnomAD v2.1 and gnomAD v4.1, so neither BS1 frequency range is met. The VCEP does not specify a non-cancer or exome-only source for BS1; the default all-comers gnomAD results were used.

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 result for NM_000314.8:c.922_923insT: search_status=absent; no allele-frequency record was returned.
• gnomAD v4.1 result for NM_000314.8:c.922_923insT: search_status=absent; no allele-frequency record was returned.
• No PTEN VCEP BS1 instruction in the governing criterion requires a non-cancer or exome-only population source; all-comers gnomAD v2.1 and v4.1 were used as the default sources.

Sources

Reasoning

The ClinGen PTEN VCEP requires observation of the variant in the homozygous state in a healthy or PHTS-unaffected individual. The variant was absent from gnomAD v2.1 and v4.1, and therefore there is no homozygous observation supporting BS2. The BS1-dependent supporting downgrade is not relevant because BS1 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 is confirmed and two if not confirmed; apply at supporting level if BS1 is also applied.
• gnomAD v2.1 result for NM_000314.8:c.922_923insT: search_status=absent; no homozygous observation was returned.
• gnomAD v4.1 result for NM_000314.8:c.922_923insT: search_status=absent; no homozygous observation was returned.

Sources

Reasoning

No proband-level de novo observation, parental maternity/paternity testing, family history, or phenotype-specific proband evidence is documented for NM_000314.8:c.922_923insT. Therefore, the PTEN VCEP PS2 thresholds cannot be evaluated.

Evidence considered

• The case materials contain no documented proband-level de novo observation or parental testing result for NM_000314.8:c.922_923insT.
• The PTEN VCEP PS2 rule requires de novo observations in a patient with the disease and no family history, with strength depending on proven versus assumed observations.

Still missing

• Proband disease status and phenotype-specific documentation
• Confirmed maternity and paternity testing
• Family-history status
• Additional proven or assumed de novo observations, if any

Sources

Reasoning

The variant is a frameshift, NP_000305.3:p.(Arg308LeufsTer4), not a missense variant. The governing mmc2.xlsx file was searched in full for c.922_923insT, p.Arg308LeufsTer4, and p.R308Lfs*4; no entry was found. Therefore the Mighell et al. 2018 phosphatase-activity pathway cannot be evaluated for this variant. The case evidence contains no qualifying RNA, mini-gene, splicing, cellular, or other functional assay result demonstrating a damaging effect, so PS3 is not assessed rather than inferred from the predicted truncation.

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

• ClinGen PTEN VCEP v3.2 PS3 specification: PS3 may use RNA, mini-gene, or other assays demonstrating splicing impact; PS3_Moderate uses Mighell et al. 2018 Table S2 with high-confidence status and phosphatase activity <= -1.11.
• Mighell et al. 2018 supplementary file mmc2.xlsx, converted full text: searches for c.922_923insT, p.Arg308LeufsTer4, and p.R308Lfs*4 returned no matching row; the indexed assay is specified for missense variants.
• The available case evidence identifies the variant as a frameshift, NP_000305.3:p.(Arg308LeufsTer4), and provides no variant-specific qualifying functional assay result.

Still missing

• No matching c.922_923insT, p.Arg308LeufsTer4, or p.R308Lfs*4 entry was found in /Users/gs_agent/LYFESCI_HERMES_v11/vcep_db/PTEN/fulltext/mmc2.xlsx.txt.
• No qualifying variant-specific functional assay result is available for PS3 assessment.

Sources

Reasoning

The 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 case evidence contains no qualifying case-control odds ratio, p-value, confidence interval, Cleveland Clinic score, pediatric phenotype score, or independent-proband specificity total. Therefore PS4 cannot be assessed.

VCEP rule

Probands with specificity score ≥16 (see text). ... 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. ... Probands with specificity score of 2-3.5 (see text). ... Phenotype specific for disease with single genetic etiology. Proband(s) with specificity score of 1-1.5 (see text).

Evidence considered

• ClinGen PTEN VCEP specification v3.2: PS4 requires either a qualifying case-control result or a specificity score derived from independent probands; no such case-specific values are present in the available evidence.

Still missing

• Qualifying case-control odds ratio, p-value, and 95% confidence interval are unavailable.
• Independent proband phenotype scores and the resulting PS4 specificity total are unavailable.

Sources

Reasoning

No assumed de novo observation, proband disease status, parental maternity/paternity information, or family-history information is documented for NM_000314.8:c.922_923insT. Therefore, the PTEN VCEP PM6 thresholds cannot be evaluated.

Evidence considered

• The case materials contain no documented presumed de novo proband observation or parental testing result for NM_000314.8:c.922_923insT.
• The PTEN VCEP PM6 rule requires an assumed de novo observation in a patient with the disease and no family history, with stronger levels requiring multiple observations or a highly specific phenotype.

Still missing

• Assumed de novo observation in a proband
• Proband disease and phenotype documentation
• Maternity and paternity testing status
• Family-history status
• Any additional PM6 or PS2 observations

Sources

Reasoning

No affected relatives, variant-positive relatives, co-segregation observations, family count, or meiosis count is documented for NM_000314.8:c.922_923insT. Therefore, the PTEN VCEP PP1 strength thresholds cannot be evaluated.

Evidence considered

• The case materials contain no documented family segregation results or observed meioses for NM_000314.8:c.922_923insT.
• The PTEN VCEP PP1 rule requires co-segregation in multiple affected family members and assigns supporting, moderate, or strong evidence according to 3-4, 5-6, or at least 7 observed meioses, respectively.

Still missing

• Affected family members tested for the variant
• Co-segregation results and phenotype status for each relative
• Number of observed meioses
• Number of families represented

Sources

Reasoning

The variant is a frameshift, NP_000305.3:p.(Arg308LeufsTer4), not a missense variant. The governing mmc2.xlsx file was searched in full for c.922_923insT, p.Arg308LeufsTer4, and p.R308Lfs*4; no entry was found. Therefore the Mighell et al. 2018 phosphatase-activity pathway cannot be evaluated for this variant. No qualifying functional study showing no damaging effect on protein function is available, so BS3 is not assessed and no benign functional evidence is assigned.

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

• ClinGen PTEN VCEP v3.2 BS3 specification: BS3_Supporting may use an in vitro or in vivo functional study showing no damaging effect on protein function; Mighell et al. 2018 Table S2 requires high-confidence status and phosphatase activity > 0.
• Mighell et al. 2018 supplementary file mmc2.xlsx, converted full text: searches for c.922_923insT, p.Arg308LeufsTer4, and p.R308Lfs*4 returned no matching row; the indexed assay is specified for missense variants.
• The available case evidence identifies the variant as a frameshift, NP_000305.3:p.(Arg308LeufsTer4), and provides no variant-specific qualifying benign functional assay result.

Still missing

• No matching c.922_923insT, p.Arg308LeufsTer4, or p.R308Lfs*4 entry was found in /Users/gs_agent/LYFESCI_HERMES_v11/vcep_db/PTEN/fulltext/mmc2.xlsx.txt.
• No qualifying variant-specific functional study showing no damaging effect on protein function is available for BS3 assessment.

Sources

Reasoning

No affected relatives, family-level segregation analysis, or non-segregation observation is documented for NM_000314.8:c.922_923insT. Therefore, the PTEN VCEP BS4 threshold for one versus two or more families cannot be evaluated.

Evidence considered

• The case materials contain no documented affected-family non-segregation result for NM_000314.8:c.922_923insT.
• The PTEN VCEP BS4 rule assigns supporting evidence for lack of segregation in one family and strong evidence for lack of segregation in affected members of two or more families.

Still missing

• Affected family members and their variant results
• Documented lack of segregation, if present
• Number of families with non-segregation
• Assessment of phenotype overlap or possible phenocopies

Sources

Reasoning

BP2 is applicable in the PTEN VCEP framework, but the available case evidence documents no affected-proband observation with this variant in trans with a pathogenic or likely pathogenic PTEN variant, and no three observations in cis or phase unknown with different pathogenic or likely pathogenic PTEN variants. Phase, parental/offspring testing, and qualifying allelic observations are therefore insufficient to determine whether BP2 is met.

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 CSPEC BP2 entry: the criterion 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/likely pathogenic PTEN variants.
• Case evidence contains no documented phase, parental/offspring testing, affected-proband allelic observation, or qualifying cis/trans/unknown-phase PTEN partner variant for NM_000314.8:c.922_923insT.

Still missing

• Phase-resolved case or family observations pairing NM_000314.8:c.922_923insT with a pathogenic or likely pathogenic PTEN variant are unavailable.
• No documented count of at least three cis or phase-unknown observations with different pathogenic or likely pathogenic PTEN variants is available.

Sources

Reasoning

The PTEN VCEP requires at least two cases with an alternate molecular basis, a highly penetrant other gene/disorder, and personal or family history demonstrating no overlap between that disorder and PTEN. The available case evidence does not document two qualifying cases, an alternate molecular diagnosis, or the required non-overlapping personal/family histories. Therefore BP5 cannot be assessed.

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. ... 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 specification v3.2 requires at least two qualifying cases and the specified alternate-disorder penetrance and history conditions; those case details are unavailable.

Still missing

• At least two cases with an alternate molecular basis are not documented.
• Highly penetrant alternate gene/disorder and non-overlapping personal/family histories are not documented.

Sources