PTEN c.105G>T, p.Met35Ile

Reasoning

The VCEP PM1 rule allows a variant located in a mutational hotspot or a critical, well-established functional domain. The case evidence reports that PTEN M35 lies in a statistically significant hotspot. The authoritative PTEN domain_tables entry is empty, and residue 35 is outside the VCEP-listed catalytic-motif residues 90-94, 123-130, and 166-168; the hotspot path independently satisfies PM1 at Moderate strength.

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

• Cancer Hotspots result for PTEN M35: the variant lies in a statistically significant hotspot; the extracted record is flagged for partial parsing.
• vcep_materials.json domain_tables is empty for PTEN in this case, so no additional authoritative domain-table interval applies.
• The VCEP CSPEC lists catalytic-motif residues 90-94, 123-130, and 166-168; the variant is at residue 35.

Still missing

• The hotspot extraction is flagged as partially parsed and should be confirmed against the hotspot-source record or screenshot.

Sources

Reasoning

The PTEN VCEP PM2 rule applies at supporting strength when the variant is absent in population databases and 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%). The variant is absent from gnomAD v2.1 and has AF=0.0 (0/1,612,312 alleles) in gnomAD v4.1, with AF=0.0 in every reported subpopulation, so PM2 Supporting is met.

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 specification v3.2, PM2 supporting: 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, that subpopulation allele frequency must be <0.00002 (0.002%).
• gnomAD v2.1: variant absent.
• gnomAD v4.1: total AC=0, total AN=1,612,312, total AF=0.0, homozygotes=0; highest reported subpopulation AF is 0.0 in African/African American individuals (0/74,964 alleles).

Sources

Reasoning

The PTEN VCEP rule applies a missense-specific computational path using REVEL. This variant is a missense change, NM_000314.8:c.105G>T (p.Met35Ile), and the recorded REVEL score is 0.947, which is greater than the VCEP threshold of 0.7. PP3 is met at supporting strength. SpliceAI and other predictors were not used for PP3 because the VCEP names REVEL for the missense situation.

VCEP rule

Multiple lines of computational evidence support a deleterious effect on the gene or gene product. * Splicing variants: Concordance of SpliceAl and VarSeak * Missense variants: REVEL score > 0.7

Evidence considered

• ClinGen PTEN VCEP Version 3.2 specifies the missense PP3 path as REVEL score > 0.7.
• NM_000314.8:c.105G>T is annotated as missense, p.(Met35Ile), with REVEL score 0.947; 0.947 > 0.7.

Sources

Reasoning

PTEN missense variant p.M35I is present in Mighell et al. 2018 supplementary Table S2 with High_conf=True and Cum_score=-0.876619465. The governing PTEN VCEP rule requires phosphatase activity ≤ -1.11 for PS3_Moderate; -0.876619465 is above that threshold. No separate variant-specific assay result meeting the VCEP PS3 Strong or PS3 Supporting rule was identified in the consulted evidence.

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

• Mighell et al. 2018 supplementary Table S2, row M35I / Met35Ile: missense variant, Cum_score=-0.876619465, Cum_SE=0.200469132, High_conf=True, High_conf_nature=Pass SE Filter.
• The M35I row is high confidence, but its Cum_score=-0.876619465 does not satisfy the VCEP PS3_Moderate cutoff of ≤ -1.11.
• The VCEP PS3 Strong and PS3 Supporting paths require splicing evidence or other qualifying functional studies; the consulted variant-specific evidence does not provide such a qualifying result for M35I.

Sources

Reasoning

The PTEN VCEP BA1 rule requires a gnomAD Filtering allele frequency greater than 0.00056 (0.056%). This variant has total allele frequency 0.0 in gnomAD v4.1 (0/1,612,312 alleles), with 0.0 in every reported subpopulation, and is absent from gnomAD v2.1; therefore the BA1 threshold is not met.

VCEP rule

gnomAD Filtering allele frequency >0.00056 (0.056%)

Evidence considered

• ClinGen PTEN VCEP specification v3.2, BA1: gnomAD Filtering allele frequency >0.00056 (0.056%).
• gnomAD v4.1: total AC=0, total AN=1,612,312, total AF=0.0, homozygotes=0; all reported subpopulation allele counts are 0.
• gnomAD v2.1: variant absent.

Sources

Reasoning

The PTEN VCEP BS1 rules require a gnomAD Filtering allele frequency from 0.000043 (0.0043%) up to 0.00056 (0.056%) for strong strength, or from 0.0000043 (0.00043%) up to 0.000043 (0.0043%) for supporting strength. The variant has AF=0.0 in gnomAD v4.1 and is absent from gnomAD v2.1, so neither BS1 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 specification v3.2, BS1 strong: gnomAD Filtering allele frequency from 0.000043 (0.0043%) up to 0.00056 (0.056%).
• ClinGen PTEN VCEP specification v3.2, BS1 supporting: Allele frequency from 0.0000043 (0.00043%) up to 0.000043 (0.0043%).
• gnomAD v4.1: total AC=0, total AN=1,612,312, total AF=0.0, homozygotes=0.
• gnomAD v2.1: variant absent.

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 unconfirmed observations; its supporting rule also requires two homozygous observations without clinical data or application of the BS2 rule when BS1 is applied. gnomAD v4.1 reports 0 homozygotes and no homozygous observations are otherwise available, 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 specification v3.2, BS2 strong: observed in the homozygous state in a healthy or PHTS-unaffected individual; one observation if confirmed and two if not confirmed; supporting level if BS1 is also applied.
• ClinGen PTEN VCEP specification v3.2, BS2 supporting: two homozygous observations with no clinical data provided, or meets criteria for BS2 but BS1 is also applied.
• gnomAD v4.1: homozygotes=0; all reported subpopulations also have homozygote count 0.

Sources

Reasoning

PTEN missense variant p.M35I is present in Mighell et al. 2018 supplementary Table S2 with High_conf=True and Cum_score=-0.876619465. The governing PTEN VCEP rule requires phosphatase activity >0 for BS3_Supporting; the reported score is negative. The result therefore does not support a benign functional effect under BS3, and no separate variant-specific assay result meeting the VCEP BS3 Strong rule was identified in the consulted evidence.

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

• Mighell et al. 2018 supplementary Table S2, row M35I / Met35Ile: missense variant, Cum_score=-0.876619465, Cum_SE=0.200469132, High_conf=True, High_conf_nature=Pass SE Filter.
• The M35I row is high confidence, but its Cum_score=-0.876619465 does not satisfy the VCEP BS3_Supporting requirement of phosphatase activity >0.
• The VCEP BS3 Strong path requires well-established functional studies showing no damaging effect; the consulted variant-specific evidence does not provide such a result for M35I.

Sources

Reasoning

The PTEN VCEP rule applies a missense-specific computational path using REVEL. This variant is a missense change, NM_000314.8:c.105G>T (p.Met35Ile), and the recorded REVEL score is 0.947, which does not satisfy the VCEP benign threshold of less than 0.5. SpliceAI was not used for BP4 because the VCEP names REVEL for the missense situation.

VCEP rule

Multiple lines of computational evidence suggest no impact on gene or gene product. * Splicing variants: Concordance of SpliceAl and VarSeak * Missense variants: REVEL scores < 0.5

Evidence considered

• ClinGen PTEN VCEP Version 3.2 specifies the missense BP4 path as REVEL score < 0.5.
• NM_000314.8:c.105G>T is annotated as missense, p.(Met35Ile), with REVEL score 0.947; 0.947 is not < 0.5.

Sources

Reasoning

The variant is NP_000305.3:p.(Met35Ile). The PTEN VCEP PS1 rule requires the same amino-acid change as a previously established pathogenic variant, not merely a different missense change at the same residue. Table S3 records Met35Arg as Pathogenic and Met35Thr as Likely pathogenic, but neither produces Met35Ile; the exact variant is only single-submitter Likely pathogenic in ClinVar. The alternative splicing path is not applicable to this missense variant.

VCEP rule

Same amino acid change as a previously established pathogenic variant regardless of nucleotide change OR different variant at same nucleotide position as a pathogenic splicing variant, where in silico models predict impact equal to or greater than the known pathogenic variant.

Evidence considered

• Mighell et al. 2018 supplementary file mmc2, Table S3, row NM_000314.6(PTEN):c.104T>G (p.Met35Arg): Pathogenic; this is an alternate substitution at residue 35, not p.Met35Ile.
• Mighell et al. 2018 supplementary file mmc2, Table S3, row NM_000314.6(PTEN):c.104T>C (p.Met35Thr): Likely pathogenic; this is also not p.Met35Ile.
• ClinVar variation 3663585, exact variant NM_000314.8:c.105G>T (p.Met35Ile): Likely pathogenic, criteria provided, single submitter.

Still missing

• A previously established pathogenic variant producing the identical p.Met35Ile amino-acid change is not documented.

Sources

Reasoning

The PTEN VCEP PS2 rule requires a de novo observation in a patient with the disease and no family history, with both maternity and paternity confirmed. The available case evidence contains no proband-level de novo finding, parental testing, disease phenotype documentation, or family-history information, so PS2 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

• The available case evidence provides no proband-level de novo observation, parental testing results, disease phenotype documentation, or family-history information.
• No reviewed paper extraction provides variant-specific de novo or parental-testing evidence for NM_000314.8:c.105G>T (p.Met35Ile).

Still missing

• Proband disease phenotype and clinical diagnosis
• Maternal and paternal testing confirming biological parentage and absence of the variant
• Family-history information

Sources

Reasoning

The PTEN VCEP permits PS4 for 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; it also permits specificity-score paths of >=16 for very strong, 4-15.5 for strong, 2-3.5 for moderate, or 1-1.5 for supporting evidence, and prohibits applying PS4 with PP4 or when BS1 applies. No case-control counts, odds ratio, p value, confidence interval, Cleveland Clinic score, pediatric phenotype score, or qualifying proband-level phenotype data for NM_000314.8:c.105G>T (p.Met35Ile) are available. The literature packet has no ai_classified_papers, and the four available full-text extracts do not mention this exact variant; therefore PS4 cannot be evaluated rather than being treated as absent evidence.

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: Adults:  * 1 point per proband with Cleveland Clinic (CC) score ≥ 30 (Tan 2011) * 0.5 points per proband with CC score of 25-29. Children: * 1 point per proband with pediatric phenotype score ≥ 5 (please see supplementary information in manuscript for scoring rubric). * 0.5 points per proband with pediatric phenotype score of 4, but autism/developmental delay/intellectual disability may not contribute to the score. 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 specification v3.2, PS4 commentary: sufficiently powered case-control study with odds ratio >2 for a PHTS component phenotype, p<0.05, and 95% confidence-interval lower limit >1.5; PS4 may not be applied in combination with PP4 or when BS1 applies.
• ClinGen PTEN VCEP specification v3.2, PS4 specificity-score paths: adults receive 1 point for Cleveland Clinic score >=30 or 0.5 points for 25-29; children receive 1 point for pediatric phenotype score >=5 or 0.5 points for score 4, with stated exclusions; strength thresholds are >=16, 4-15.5, 2-3.5, and 1-1.5.
• No case-control counts, OR, p value, 95% CI, Cleveland Clinic score, pediatric phenotype score, or qualifying proband phenotype record for NM_000314.8:c.105G>T was present in the reviewed case evidence.
• The literature_pass packet contains no ai_classified_papers. Available full-text extracts for PMID:21828076, PMID:23788249, PMID:25645574, and PMID:25875300 do not mention c.105G>T or p.Met35Ile and do not provide variant-specific PS4 evidence.

Still missing

• Variant-specific affected-case and control counts or matched-ancestry control frequency sufficient to calculate OR and 95% CI.
• Variant-specific proband Cleveland Clinic scores or pediatric phenotype scores, with independent-proband details.

Sources

Reasoning

A same-residue comparator is available: Table S3 lists Met35Arg as Pathogenic and Met35Thr as Likely pathogenic. However, the VCEP PM5 rule also requires the assessed Met35Ile substitution to have a BLOSUM62 score equal to or less than the known comparator. The available case evidence does not provide the applicable BLOSUM62 scores, so PM5 cannot be adjudicated without importing an unprovided value.

VCEP rule

Missense change at an amino acid residue where a different missense change determined to be pathogenic or likely pathogenic has been seen before. In addition, variant being interrogated must have BLOSUM62 score equal to or less than the known variant.

Evidence considered

• Mighell et al. 2018 supplementary file mmc2, Table S3, row p.Met35Arg: Pathogenic; row p.Met35Thr: Likely pathogenic.
• Rodríguez-Escudero et al. 2011 (PMID:21828076) reports functional testing of M35R in a PTEN yeast PIP3-phosphatase assay; the paper does not report M35I.
• Gil et al. 2015 (PMID:25875300) reports functional effects of M35R and M35A; the paper does not report M35I.
• The VCEP PM5 rule requires the assessed variant's BLOSUM62 score to be equal to or less than the known comparator's score; no applicable scores are supplied in the case evidence.

Still missing

• BLOSUM62 scores for Met35Ile and the selected pathogenic or likely pathogenic Met35 comparator are required.

Sources

Reasoning

The PTEN VCEP PM6 rule requires assumed de novo occurrence without confirmed maternity and paternity in a proband with the disease and no family history, or the specified stronger counts of presumed de novo observations. The available case evidence contains none of these observations or required clinical context, so PM6 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

• The available case evidence contains no documented presumed or assumed de novo observations for NM_000314.8:c.105G>T.
• The available case evidence provides no proband disease status, family-history information, or parentage and parental-testing details.

Still missing

• One or more documented presumed de novo observations
• Proband disease phenotype and clinical diagnosis
• Family-history information
• Parentage and parental-variant testing details for each observation

Sources

Reasoning

The PTEN VCEP PP1 rule requires co-segregation with disease in multiple affected family members, with strength determined by 3 or 4, 5 or 6, or at least 7 observed meioses across the specified family structure. The available case evidence contains no affected relatives, genotype-phenotype segregation data, or meioses, so PP1 cannot be evaluated.

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

• The available case evidence contains no family pedigree, affected-relative testing, co-segregation results, or meiosis count for NM_000314.8:c.105G>T.
• No reviewed paper extraction provides variant-specific segregation evidence.

Still missing

• Genotypes and disease phenotypes for affected family members
• Pedigree structure and number of informative meioses
• Evidence spanning the required number of families where applicable

Sources

Reasoning

The VCEP PP2 rule requires both a low rate of benign missense variation in the gene and missense variants being a common mechanism of disease. The available case evidence does not establish both required PP2 conditions under the VCEP rule; generic gene-level context and predictor scores cannot substitute for this VCEP-specific evidence.

VCEP rule

Missense variant in a gene that has a low rate of benign missense variation and where missense variants are a common mechanism of disease.

Evidence considered

• No PTEN-specific evidence satisfying both PP2 conditions is provided in the available VCEP materials.

Still missing

• VCEP-compliant evidence establishing PTEN's low benign missense variation rate and common missense disease mechanism is required.

Sources

Reasoning

The PTEN VCEP BS4 rule requires lack of segregation in affected members of one family for supporting strength or two or more families for strong strength. The available case evidence contains no affected-family-member testing or non-segregation observations, so BS4 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

• The available case evidence contains no affected-relative genotypes, pedigree information, or documented lack-of-segregation observations.
• No reviewed paper extraction provides variant-specific non-segregation evidence.

Still missing

• Testing results for affected family members
• Disease status and pedigree information for each tested relative
• Family count establishing lack of segregation

Sources

Reasoning

The PTEN VCEP allows 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 available case evidence does not document a second PTEN variant with confirmed trans phase, nor three qualifying cis or phase-unknown observations, so the rule 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

• The case evidence documents PTEN c.105G>T (p.Met35Ile) but contains no qualifying observation of this variant in trans with another pathogenic or likely pathogenic PTEN variant.
• The case evidence contains no set of at least three observations of this variant in cis or phase unknown with different pathogenic or likely pathogenic PTEN variants.

Still missing

• Documented allelic observations pairing PTEN c.105G>T with a different pathogenic or likely pathogenic PTEN variant, including confirmed trans phase or at least three cis/phase-unknown observations.
• For each observation, affected-proband status and the pathogenic or likely pathogenic classification of the other PTEN variant.

Sources

Reasoning

The PTEN VCEP BP5 supporting rule requires a variant found in a case with an alternate molecular basis for disease, a highly penetrant other gene or disorder, and a personal or family history demonstrating no overlap between that disorder and PTEN; the VCEP additionally requires at least two such cases. No qualifying alternate molecular diagnosis, penetrance assessment, non-overlapping history, or two-case series is available for this variant, so BP5 is not assessed.

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

• ClinGen PTEN VCEP specification v3.2, BP5 instructions: at least two such cases are required; the other gene/disorder must be highly penetrant and the patient's personal/family history must demonstrate no overlap between the other gene and PTEN.
• No qualifying alternate molecular basis, highly penetrant alternate disorder, non-overlapping personal/family history, or two-case series for NM_000314.8:c.105G>T is available in the reviewed evidence.

Still missing

• At least two variant-positive cases with an alternate highly penetrant molecular diagnosis and documented absence of phenotype overlap with PTEN.

Sources