PTEN c.562T>G, p.Tyr188Asp

Reasoning

The PTEN VCEP permits PS3_Moderate for the Mighell et al. 2018 massively parallel phosphatase assay when the Table S2 variant is high confidence and its cumulative score is <= -1.11. The variant is listed in Table S2 as Y188D / Tyr188Asp, missense, with Cum_score -2.31723372 and High_conf True (Pass SE Filter), satisfying the VCEP-specific PS3_Moderate rule. The exact HGVS strings c.562T>G, p.Tyr188Asp, and p.Y188D were not literal row keys in the converted text; the governing table match is the one-letter and three-letter protein notation Y188D / Tyr188Asp.

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 Y188D / Tyr188Asp: missense; Cum_score = -2.31723372; High_conf = True; filter = Pass SE Filter.
• The converted mmc2.xlsx full text was searched for c.562T>G, p.Tyr188Asp, and p.Y188D; the matching record is keyed as Y188D / Tyr188Asp.
• ClinGen PTEN VCEP v3.2 PS3 rule: the Table S2 row must be high confidence, and Cum_score <= -1.11 qualifies for PS3_Moderate.

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 are present within a subpopulation, that subpopulation frequency must be less than 0.00002 (0.002%). The variant was absent from the default all-comers gnomAD v2.1 and v4.1 datasets, and also absent from the available non-cancer subset queries, providing no observed allele and satisfying the VCEP's ultra-rare population 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 specification v3.2, PM2 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 within a subpopulation if multiple alleles are present.
• gnomAD v2.1 result for NM_000314.8:c.562T>G: absent; no allele frequency reported.
• gnomAD v4.1 result for NM_000314.8:c.562T>G: absent; no allele frequency reported.
• gnomAD v2.1 non-cancer and gnomAD v3.1 non-cancer results: absent; the VCEP does not specify these subsets as required for PM2.

Sources

Reasoning

The variant is a missense variant, so the PTEN VCEP's missense path applies. The VCEP permits PP3 at Supporting strength when the missense REVEL score is greater than 0.7. The case-specific REVEL score is 0.896, which exceeds that cutoff. SpliceAI is not used for this PP3 decision because the governing missense path names REVEL, and the same prediction is not double-counted across PP3, BP4, and BP7.

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

• PTEN VCEP PP3 instructions: missense variants may receive PP3 when REVEL score >0.7.
• Local REVEL predictor lookup for NM_000314.8:c.562T>G / p.Tyr188Asp: REVEL = 0.896.
• The variant consequence is missense; SpliceAI is not used because the VCEP's missense path names REVEL rather than a splice predictor.

Sources

Reasoning

The PTEN VCEP defines PM1 for a mutational hotspot and/or critical functional domain and specifically includes residues 90-94, 123-130, and 166-168 of NP_000305.3. The variant is p.Tyr188Asp at residue 188, outside every listed catalytic motif; vcep_materials.json has no PTEN domain_tables entry adding further approved domains, and the hotspot result reports no statistically significant hotspot at Y188.

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 specification v3.2, PM1 defines critical catalytic motifs at residues 90-94, 123-130, and 166-168 in NP_000305.3.
• The normalized variant is NP_000305.3:p.(Tyr188Asp), placing the altered residue at 188, outside all three VCEP-listed motifs.
• The Cancer Hotspots result for PTEN Y188 reports that the variant does not lie in a statistically significant hotspot.
• vcep_materials.json domain_tables is empty for PTEN, so no additional authoritative domain-table entry applies.

Sources

Reasoning

The PTEN VCEP defines BA1 as 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 qualifying allele frequency above the BA1 threshold was observed. The non-cancer subset queries were also absent, but the VCEP does not require a non-cancer-specific source for BA1.

VCEP rule

gnomAD Filtering allele frequency >0.00056 (0.056%)

Evidence considered

• ClinGen PTEN VCEP specification v3.2, BA1 rule: gnomAD Filtering allele frequency >0.00056 (0.056%).
• gnomAD v2.1 result for NM_000314.8:c.562T>G: absent; no allele frequency or homozygote count reported.
• gnomAD v4.1 result for NM_000314.8:c.562T>G: absent; no allele frequency or homozygote count reported.
• gnomAD v2.1 non-cancer and gnomAD v3.1 non-cancer results: absent.

Sources

Reasoning

The PTEN VCEP assigns BS1 Strong to a gnomAD filtering allele frequency from 0.000043 (0.0043%) up to 0.00056 (0.056%), and BS1 Supporting to an allele frequency from 0.0000043 (0.00043%) up to 0.000043 (0.0043%). The variant was absent from gnomAD v2.1 and gnomAD v4.1, with no reported allele frequency in either interval; therefore BS1 is not met at either strength.

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 rule: gnomAD Filtering allele frequency from 0.000043 (0.0043%) up to 0.00056 (0.056%).
• ClinGen PTEN VCEP specification v3.2, 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.562T>G: absent; no allele frequency reported.
• gnomAD v4.1 result for NM_000314.8:c.562T>G: absent; no allele frequency reported.

Sources

Reasoning

The PTEN VCEP permits BS3_Supporting for the Mighell et al. 2018 Table S2 phosphatase assay only when the high-confidence variant has phosphatase activity >0. The Y188D / Tyr188Asp row is high confidence but has Cum_score -2.31723372, which is not greater than 0; therefore this functional result does not meet BS3 and instead supports damaging function.

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 Y188D / Tyr188Asp: Cum_score = -2.31723372 and High_conf = True; this is below, rather than above, the BS3 cutoff of >0.
• The converted mmc2.xlsx full text was searched for c.562T>G, p.Tyr188Asp, and p.Y188D; the matching record is keyed as Y188D / Tyr188Asp.
• ClinGen PTEN VCEP v3.2 BS3 rule specifies BS3_Supporting for high-confidence Mighell Table S2 variants with phosphatase activity >0.

Sources

Reasoning

The variant is a missense variant, so the PTEN VCEP's missense path applies. The VCEP permits BP4 at Supporting strength when the missense REVEL score is less than 0.5. The case-specific REVEL score is 0.896, which does not satisfy the benign cutoff; therefore BP4 is not met. SpliceAI is not used for this BP4 decision because the governing missense path names REVEL, and the same prediction is not double-counted across PP3, BP4, and BP7.

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

• PTEN VCEP BP4 instructions: missense variants may receive BP4 when REVEL score <0.5.
• Local REVEL predictor lookup for NM_000314.8:c.562T>G / p.Tyr188Asp: REVEL = 0.896.
• The variant consequence is missense; SpliceAI is not used because the VCEP's missense path names REVEL rather than a splice predictor.

Sources

Reasoning

The PTEN VCEP requires the same amino acid change as a previously established pathogenic variant, but the available evidence does not identify an independent established pathogenic PTEN variant at Tyr188 producing the same amino acid change. The queried variant's own conflicting single-submitter ClinVar classifications cannot serve as the required comparator evidence.

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

• ClinGen PTEN VCEP specification v3.2, PS1 rule: same amino acid change as a previously established pathogenic variant is required.
• ClinVar variation 1401407 concerns the queried NM_000314.8:c.562T>G (p.Tyr188Asp) and has conflicting single-submitter classifications; it does not provide an independent comparator variant.

Still missing

• An independently established pathogenic PTEN variant causing p.Tyr188Asp at Tyr188 is needed to evaluate PS1.

Sources

Reasoning

The PTEN VCEP requires a confirmed de novo observation in an affected patient with no family history for PS2 Strong, or specified numbers of proven or assumed de novo observations for PS2 Very Strong. The available case evidence does not document a de novo observation for NM_000314.8:c.562T>G, parental maternity or paternity testing, or family history. The reviewed literature extracts do not mention this variant or provide de novo evidence.

VCEP rule

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

Evidence considered

• The case evidence identifies NM_000314.8:c.562T>G (p.Tyr188Asp) but contains no variant-specific de novo, parental-testing, or family-history result.
• PMID:23519317, PMID:25190698, PMID:27854360, and PMID:28492532 were reviewed through their extracted findings; none mentions c.562T>G or p.(Y188D), and none supplies de novo evidence for this variant.
• The governing PTEN VCEP PS2 rule is the only rule applied.

Still missing

• A variant-specific affected proband report is needed.
• Maternity and paternity confirmation are needed to assess PS2 Strong.
• Family-history information is needed.
• Additional proven or assumed de novo observations would be needed for PS2 Very Strong.

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 summed Cleveland Clinic or pediatric phenotype specificity scores. No case-control odds ratio, p value, confidence interval, Cleveland Clinic score, pediatric phenotype score, or independent-proband tally for NM_000314.8:c.562T>G is available. The reviewed papers describe PTEN/PHTS phenotype associations but do not mention this variant, so they cannot establish PS4 for it. The VCEP also states that PS4 may not be applied with PP4, and this variant has no applicable PP4 path because PP4 is not applicable under this VCEP.

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. * Use 2: Patient’s phenotype or family history is highly specific for a disease with a single genetic etiology. **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

• The case evidence identifies NM_000314.8:c.562T>G as a PTEN missense variant, p.(Tyr188Asp).
• No case-control enrichment statistics or variant-specific phenotype specificity scores were provided.
• PMID:23519317 reports 15 of 318 individuals with autism spectrum disorders had pathogenic PTEN mutations and macrocephaly was present in all positive cases, but the paper does not mention c.562T>G or p.(Y188D); this is gene/disease-level context, not variant-specific PS4 evidence.
• PMID:25190698 describes PTEN hamartoma tumor syndrome and approximately 80% penetrance, but does not mention c.562T>G or p.(Y188D); this is not variant-specific PS4 evidence.
• PMID:27854360 lists PTEN hamartoma tumor syndrome among secondary-finding conditions, but does not mention c.562T>G or p.(Y188D); this is not variant-specific PS4 evidence.
• PMID:28492532 does not mention PTEN or c.562T>G and provides no variant-specific case or phenotype evidence.

Still missing

• Variant-specific case-control odds ratio, p value, and 95% confidence interval are unavailable.
• Cleveland Clinic scores or pediatric phenotype scores for independent probands carrying this variant are unavailable.

Sources

Reasoning

The PTEN VCEP requires a different missense change at the same amino acid residue that is pathogenic or likely pathogenic, plus a BLOSUM62 score for the queried variant equal to or less than that of the known variant. The available same-residue search found no usable Tyr188 comparator candidates, and therefore supplies neither the required pathogenic or likely pathogenic comparator nor the comparator BLOSUM62 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

• ClinGen PTEN VCEP specification v3.2, PM5 requires a different pathogenic or likely pathogenic missense change at the same residue and a queried-variant BLOSUM62 score equal to or less than the known variant.
• The PM5 comparator collection recorded six candidates but zero same-residue candidates, zero expert-panel pathogenic/likely pathogenic candidates, and zero non-expert majority pathogenic/likely pathogenic candidates; no BLOSUM62 comparator value was available.

Still missing

• A pathogenic or likely pathogenic missense variant at Tyr188 and its BLOSUM62 score are needed for PM5.

Sources

Reasoning

The PTEN VCEP requires assumed or presumed de novo observations in an affected patient with no family history, with strength determined by the number of observations and whether maternity and paternity are confirmed. The available case evidence documents no assumed or presumed de novo occurrence, parental testing, or family history for NM_000314.8:c.562T>G. The reviewed literature extracts do not mention this variant or provide qualifying de novo observations.

VCEP rule

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

Evidence considered

• The case evidence identifies NM_000314.8:c.562T>G (p.Tyr188Asp) but contains no variant-specific presumed or assumed de novo report, parental-testing result, or family-history result.
• PMID:23519317, PMID:25190698, PMID:27854360, and PMID:28492532 were reviewed through their extracted findings; none mentions c.562T>G or p.(Y188D), and none supplies qualifying de novo evidence for this variant.
• The governing PTEN VCEP PM6 rule is the only rule applied.

Still missing

• A variant-specific affected proband report is needed.
• The number of qualifying presumed or assumed de novo observations is unknown.
• Maternity and paternity confirmation status is unknown.
• Family-history information is needed.

Sources

Reasoning

The PTEN VCEP requires co-segregation with disease in multiple affected family members and assigns Supporting for 3 or 4 observed meioses, Moderate for 5 or 6, and Strong for at least 7 across at least two families. The available case evidence provides no affected relatives, segregation results, family count, or meiosis count for NM_000314.8:c.562T>G. The reviewed literature extracts do not mention this variant or provide segregation data.

VCEP rule

Co-segregation with disease in multiple affected family members, with ≥7 meioses observed across at least two families.

Evidence considered

• The case evidence identifies NM_000314.8:c.562T>G (p.Tyr188Asp) but contains no variant-specific affected-relative testing, segregation result, family count, or meiosis count.
• PMID:23519317, PMID:25190698, PMID:27854360, and PMID:28492532 were reviewed through their extracted findings; none mentions c.562T>G or p.(Y188D), and none supplies segregation evidence for this variant.
• The governing PTEN VCEP PP1 rule is the only rule applied.

Still missing

• Variant-specific family segregation data are needed.
• The number of affected relatives and informative meioses is unknown.
• The number of families represented is unknown.

Sources

Reasoning

The VCEP makes PP2 applicable at supporting strength, but evaluation requires evidence that PTEN has a low rate of benign missense variation and that missense variants are a common disease mechanism. The available case evidence establishes that this variant is missense but does not provide VCEP-grounded evidence for both required gene-level conditions.

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

• ClinGen PTEN VCEP specification v3.2 lists PP2 as applicable at supporting strength but provides no case-specific determination of the two required gene-level conditions.
• The variant is a missense substitution, NM_000314.8:c.562T>G (NP_000305.3:p.Tyr188Asp), but missense consequence alone does not establish PP2.

Still missing

• VCEP-grounded evidence for PTEN's low rate of benign missense variation and common missense disease mechanism is needed.

Sources

Reasoning

The PTEN VCEP requires observation of the variant in the homozygous state in a healthy or PHTS-unaffected individual. The available gnomAD results report the variant as absent and provide no homozygous observations, so the BS2 requirement cannot be evaluated.

Evidence considered

• ClinGen PTEN VCEP specification v3.2, BS2 requirement: observed in the homozygous state in a healthy or PHTS-unaffected individual; one observation if homozygous status is confirmed and two if not confirmed.
• gnomAD v2.1 and gnomAD v4.1 reported the variant absent and did not report homozygote counts or individual-level homozygous observations.

Still missing

• A confirmed homozygous observation in a healthy or PHTS-unaffected individual, or two unconfirmed homozygous observations, is unavailable.

Sources

Reasoning

The PTEN VCEP requires lack of segregation in affected members of one family for BS4 Supporting or two or more families for BS4 Strong. The available case evidence contains no affected-family-member testing, non-segregation result, or family count for NM_000314.8:c.562T>G. The reviewed literature extracts do not mention this variant or provide non-segregation evidence.

VCEP rule

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

Evidence considered

• The case evidence identifies NM_000314.8:c.562T>G (p.Tyr188Asp) but contains no variant-specific affected-family-member testing, non-segregation result, or family count.
• PMID:23519317, PMID:25190698, PMID:27854360, and PMID:28492532 were reviewed through their extracted findings; none mentions c.562T>G or p.(Y188D), and none supplies non-segregation evidence for this variant.
• The governing PTEN VCEP BS4 rule is the only rule applied.

Still missing

• Variant-specific testing of affected family members is needed.
• A documented lack of segregation is needed.
• The number of families with non-segregation evidence is unknown.

Sources

Reasoning

The PTEN VCEP BP2 rule requires the variant to be observed in trans with a pathogenic or likely pathogenic PTEN variant, or in 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 genotype, paired PTEN variant, phase assignment, or qualifying observation count for NM_000314.8:c.562T>G (p.Tyr188Asp), so 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 Expert Panel Specifications, criterion BP2: "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."
• The case evidence reports only a ClinVar classification for c.562T>G (p.Tyr188Asp) and does not provide a paired PTEN variant, phase, or qualifying observation count.
• The reviewed variant-specific literature extracts do not report c.562T>G (p.Tyr188Asp), phase, trans/cis observations, or affected-proband genotype data.

Still missing

• Affected-proband or case-level genotype data identifying another pathogenic or likely pathogenic PTEN variant.
• Phase evidence establishing trans, or at least three qualifying cis/phase-unknown observations with different pathogenic or likely pathogenic PTEN variants.

Sources

Reasoning

The PTEN VCEP requires at least two cases in which the variant is found with an alternate molecular basis for disease; the other gene/disorder must be highly penetrant, and each patient's personal or family history must show no overlap between that disorder and PTEN. The available evidence contains no such cases, alternate gene/disorder, penetrance assessment, or non-overlapping phenotype histories.

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_.

Evidence considered

• No alternate molecular diagnosis or qualifying personal/family history was provided for this variant.

Still missing

• At least two variant-positive cases with an alternate molecular basis are required.
• The alternate disorder's high penetrance and each patient's non-overlapping personal/family history are undocumented.

Sources