PTEN c.585_586del, p.(Phe195LeufsTer6)

Reasoning

NM_000314.8:c.585_586del is a frameshift producing NP_000305.3:p.(Phe195LeufsTer6) / p.(F195Lfs*6). The premature stop is at amino acid 200, 175 residues 5' of the VCEP's p.D375 (c.1121) threshold, in the VCEP-designated biologically relevant transcript NM_000314.8. The PTEN VCEP PVS1 decision tree 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 and the exon is present in NM_000314.8; no named downgrade rule applies. The requested searches of PVS1_DecisionTree_PTEN.pdf.txt found no direct row for c.585_586del, p.Phe195LeufsTer6, or p.F195Lfs*6, so the call is based on the governing decision-tree path and case consequence facts rather than a pre-assigned variant-specific row.

VCEP rule

Use PTEN PVS1 decision tree. ... 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 consequence facts: NM_000314.8:c.585_586del is a frameshift with NP_000305.3:p.(Phe195LeufsTer6) / p.(F195Lfs*6).
• ClinGen PTEN VCEP PVS1 decision tree: the stop/disruption is at or 5' to p.D375 (c.1121), and the biologically relevant transcript is NM_000314.8; this is the full-strength PVS1 path.
• PVS1_DecisionTree_PTEN.pdf.txt was searched under c.585_586del, p.Phe195LeufsTer6, and p.F195Lfs*6; no pre-assigned variant-specific row was present.

Still missing

• PVS1_DecisionTree_PTEN.pdf.txt was searched for c.585_586del, p.Phe195LeufsTer6, and p.F195Lfs*6; no direct variant-specific entry was found.

Sources

Reasoning

The PTEN VCEP permits PM2 at supporting strength when a variant is present at <0.00001 (0.001%) allele frequency in gnomAD or another large sequenced population; if multiple alleles are present within a subpopulation, that subpopulation frequency must be <0.00002 (0.002%). NM_000314.8:c.585_586del is absent from the default all-comers gnomAD v2.1 and v4.1 datasets, satisfying the stated population-absence criterion.

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 instruction: criteria may be applied below 0.00001 (0.001%) allele frequency in gnomAD or another large sequenced population; if multiple alleles are present within a subpopulation, that subpopulation frequency must be below 0.00002 (0.002%).
• gnomAD v2.1 all-comers: NM_000314.8:c.585_586del absent.
• gnomAD v4.1 all-comers: NM_000314.8:c.585_586del absent.

Sources

Reasoning

The VCEP defines PM1 to include PTEN catalytic-motif residues 90-94, 123-130, and 166-168 in NP_000305.3. The variant alters residue 195, outside all three explicitly defined motifs, and the case evidence reports no statistically significant hotspot for PTEN F195. No PM1 qualifying location is therefore 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

• CSPEC PM1 rule defines the included catalytic motifs as residues 90-94, 123-130, and 166-168 of NP_000305.3; the variant is p.(Phe195LeufsTer6), affecting residue 195.
• The hotspot query for PTEN F195 reported no statistically significant hotspot.

Sources

Reasoning

The PTEN VCEP BA1 rule requires a gnomAD filtering allele frequency >0.00056 (0.056%). NM_000314.8:c.585_586del is absent from gnomAD v2.1 and gnomAD v4.1, so no qualifying population frequency is present and 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 all-comers: NM_000314.8:c.585_586del absent; no allele frequency or homozygote count reported.
• gnomAD v4.1 all-comers: NM_000314.8:c.585_586del absent; no allele frequency or homozygote count reported.

Sources

Reasoning

The PTEN VCEP BS1 thresholds require 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. NM_000314.8:c.585_586del is absent from gnomAD v2.1 and gnomAD v4.1, so neither 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 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 all-comers: NM_000314.8:c.585_586del absent; no allele frequency reported.
• gnomAD v4.1 all-comers: NM_000314.8:c.585_586del absent; no allele frequency reported.

Sources

Reasoning

The PTEN VCEP BS2 rule requires observation in the homozygous state in a healthy or PHTS-unaffected individual, with one confirmed observation or two if homozygous status is not confirmed; the supporting rule requires two homozygous observations without clinical data or BS2 with BS1. The variant is absent from gnomAD v2.1 and v4.1, with no homozygous observations, so 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. ... 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 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; supporting level applies if BS1 is also applied.
• ClinGen PTEN VCEP Version 3.2 BS2 supporting rule: two homozygous observations with no clinical data provided, or BS2 when BS1 is also applied.
• gnomAD v2.1 all-comers: NM_000314.8:c.585_586del absent; no homozygous observation reported.
• gnomAD v4.1 all-comers: NM_000314.8:c.585_586del absent; no homozygous observation reported.

Sources

Reasoning

The case evidence contains no documented affected proband observation with confirmed maternity and paternity, no family-history assessment, and no parental test results. Therefore the PTEN VCEP PS2 rule cannot be evaluated without substituting unsupported assumptions.

VCEP rule

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

Evidence considered

• No proband, parental-testing, or family-history evidence relevant to PS2 was documented in the available case evidence.
• The variant is NM_000314.8:c.585_586del, predicted as a frameshift, but variant consequence alone does not establish de novo occurrence.

Still missing

• Affected proband documentation
• Confirmed maternity and paternity
• Family-history assessment

Sources

Reasoning

The PTEN VCEP permits PS3 for validated functional evidence, including PS3_Moderate from Mighell et al. 2018 when the Table S2 phosphatase-assay result is high confidence and the cumulative score is ≤ -1.11, and PS3_Supporting for specified abnormal functional assays. The governing mmc2.xlsx file was searched for c.585_586del, p.Phe195LeufsTer6, and p.F195Lfs*6; no entry was found. The variant is a frameshift, whereas mmc2 Table S2 contains missense saturation-mutagenesis variants. The two functional-theme papers in the case evidence were also reviewed through their extracted findings: neither mentions this variant or provides a variant-specific damaging assay. Therefore, the available evidence does not permit a PS3 strength assignment.

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 rule: PS3_Moderate requires phosphatase activity ≤ -1.11 per Mighell et al. 2018, PMID: 29706350; PS3_Supporting covers phosphatase activity <50% of wild type or specified abnormal cellular/transgenic assays.
• Mighell et al. 2018 supplementary mmc2.xlsx, Table S2: searched for c.585_586del, p.Phe195LeufsTer6, and p.F195Lfs*6; no matching row was found. The table describes protein-level missense variants and high-confidence phosphatase-assay results.
• PTEN: life as a tumor suppressor (PMID:11237521): extracted paper finding states that c.585_586del and p.(F195Lfs*6) are not mentioned and no assay specific to this variant is described.
• Essential role for nuclear PTEN in maintaining chromosomal integrity (PMID:17218262): extracted paper finding states that c.585_586del and p.(F195Lfs*6) are not mentioned; reported experiments concern other PTEN truncations and PTEN-null models.

Still missing

• No c.585_586del, p.Phe195LeufsTer6, or p.F195Lfs*6 entry was found in mmc2.xlsx full text, including the Table S2 variant records.
• No variant-specific validated damaging functional assay result is available in the reviewed case evidence.

Sources

Reasoning

The PTEN VCEP permits PS4 from phenotype-specific proband scores or a sufficiently powered case-control study. The available evidence provides no Cleveland Clinic score, pediatric phenotype score, independent-proband specificity total, odds ratio, p-value, or confidence interval for this variant. Therefore, no VCEP PS4 strength can be assigned.

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 PTEN VCEP PS4 rule provides phenotype-specific proband-score ranges and a case-control alternative.
• No Cleveland Clinic score, pediatric phenotype score, independent-proband specificity total, odds ratio, p-value, or confidence interval for NM_000314.8:c.585_586del is present in the available case evidence.

Still missing

• A qualifying VCEP PS4 evaluation requires independent-proband phenotype scores or a sufficiently powered case-control study with odds ratio, p-value, and 95% confidence interval.

Sources

Reasoning

The case evidence contains no assumed or presumed de novo observation in a patient with disease and no family history, and no information about maternity or paternity confirmation. None of the VCEP PM6 observation-count thresholds can therefore 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; or assumed de novo, but without confirmation of paternity and maternity, in proband with the disease and no family history.

Evidence considered

• No proband-level de novo observations or parental-testing results relevant to PM6 were documented in the available case evidence.
• No evidence establishes whether the patient has disease or no family history, so presumed, assumed, and proven de novo categories cannot be assigned.

Still missing

• De novo observation count
• Affected-patient documentation
• Family-history assessment
• Maternity and paternity confirmation status

Sources

Reasoning

The case evidence contains no affected relatives, familial genotype-phenotype observations, segregation results, or countable meioses. The VCEP PP1 thresholds of 3 or more meioses cannot be assessed.

VCEP rule

Co-segregation with disease in multiple affected family members, with >=7 meioses observed across at least two families; 5 or 6 meioses observed; or 3 or 4 meioses observed.

Evidence considered

• No family segregation data or meiosis count relevant to PP1 was documented in the available case evidence.
• No published paper in the available literature extracts reports segregation of NM_000314.8:c.585_586del in affected family members.

Still missing

• Affected family-member observations
• Familial variant testing results
• Countable meioses

Sources

Reasoning

The PTEN VCEP permits BS3 for validated functional evidence showing no damaging effect, including BS3_Supporting from Mighell et al. 2018 when the Table S2 phosphatase-assay result is high confidence and the cumulative score is >0, and BS3_Strong for well-established functional studies showing no damaging effect. The governing mmc2.xlsx file was searched for c.585_586del, p.Phe195LeufsTer6, and p.F195Lfs*6; no entry was found. The variant is a frameshift, whereas mmc2 Table S2 contains missense saturation-mutagenesis variants. The two functional-theme papers in the case evidence were also reviewed through their extracted findings: neither mentions this variant or provides a variant-specific benign functional assay. Therefore, the available evidence does not permit a BS3 strength assignment.

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 rule: BS3_Supporting permits phosphatase activity >0 per Mighell et al. 2018, PMID: 29706350; BS3_Strong requires well-established functional studies showing no damaging effect on protein function.
• Mighell et al. 2018 supplementary mmc2.xlsx, Table S2: searched for c.585_586del, p.Phe195LeufsTer6, and p.F195Lfs*6; no matching row was found. The table describes protein-level missense variants and high-confidence phosphatase-assay results.
• PTEN: life as a tumor suppressor (PMID:11237521): extracted paper finding states that c.585_586del and p.(F195Lfs*6) are not mentioned and no assay specific to this variant is described.
• Essential role for nuclear PTEN in maintaining chromosomal integrity (PMID:17218262): extracted paper finding states that c.585_586del and p.(F195Lfs*6) are not mentioned; reported experiments concern other PTEN truncations and PTEN-null models.

Still missing

• No c.585_586del, p.Phe195LeufsTer6, or p.F195Lfs*6 entry was found in mmc2.xlsx full text, including the Table S2 variant records.
• No variant-specific validated functional assay showing no damaging effect is available in the reviewed case evidence.

Sources

Reasoning

The case evidence contains no affected family members in whom the variant fails to segregate and no family-level non-segregation observations. The VCEP BS4 one-family and two-or-more-family rules cannot be evaluated.

VCEP rule

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

Evidence considered

• No affected relatives with negative variant testing or other non-segregation evidence were documented in the available case evidence.
• No published paper in the available literature extracts reports non-segregation of NM_000314.8:c.585_586del in affected family members.

Still missing

• Affected-family variant observations
• Family-level non-segregation evidence
• Number of families evaluated

Sources

Reasoning

The PTEN VCEP 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 affected-proband, phase, cis/trans, or other allelic observations for NM_000314.8:c.585_586del, so BP2 cannot be evaluated.

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 Expert Panel Version 3.2 CSPEC rule for BP2 requires trans with a pathogenic or likely pathogenic PTEN variant, or at least three cis and/or phase-unknown observations with different pathogenic/likely pathogenic PTEN variants.
• The case evidence reports no phase, cis/trans, compound-heterozygous, or affected-proband observations for NM_000314.8:c.585_586del.

Still missing

• Affected-proband or other case-level observations with documented cis/trans or phase-unknown status and the accompanying pathogenic/likely pathogenic PTEN variants are unavailable.

Sources

Reasoning

The PTEN VCEP requires at least two cases with an alternate molecular basis, a highly penetrant other gene or disorder, and personal or family history demonstrating no overlap between that disorder and PTEN. No such qualifying cases or clinical-history evidence are available for this variant, so BP5 is not assessed.

VCEP rule

At least two such cases are required for criteria to apply. ... 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 a highly penetrant alternate gene or disorder with no overlap between the alternate disorder and PTEN personal or family history.
• The available case evidence contains no documented alternate molecular diagnosis or qualifying non-overlapping clinical histories for at least two cases.

Still missing

• At least two qualifying cases, evidence that the alternate gene or disorder is highly penetrant, and non-overlapping personal or family histories are required for BP5.

Sources