Variant classification summary

NM_000314.8:c.203A>G

PTEN · NP_000305.3:p.(Tyr68Cys) · NM_000314.8

GRCh37: chr10:89685308 A>G · GRCh38: chr10:87925551 A>G

Gene: PTEN Transcript: NM_000314.8

Final call

VUS

PS3 moderate PM2 supporting PP2 supporting PP3 supporting

Variant details

Gene

PTEN

Transcript

NM_000314.8

Protein

NP_000305.3:p.(Tyr68Cys)

gnomAD AF

ClinVar

Pathogenic

OncoKB

Likely Oncogenic

Classification rationale

Interpretation summary

Generated evidence synthesis

1

PS3_Moderate is met: Y68C has a cumulative fitness score of -2.73 in the Mighell et al. 2018 PTEN saturation mutagenesis phosphatase activity assay (Table S2 of PMID 29706350), meeting the PTEN VCEP threshold of ≤ -1.11 for PS3_Moderate.

2

PM2_Supporting is met: NM_000314.8:c.203A>G is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0, meeting the PTEN VCEP threshold of < 0.00001 (0.001%) allele frequency.

3

PP2_Supporting is met: PTEN has a low rate of benign missense variation and missense variants are a well-established common mechanism of disease in PTEN hamartoma tumor syndrome.

4

PP3_Supporting is met: REVEL score of 0.985 exceeds the PTEN VCEP threshold of > 0.7 for missense variants.

5

No benign criteria are met. The variant is absent from population databases, functional data demonstrates a damaging effect, and computational predictions support pathogenicity.

6

Classification: VUS (Variant of Uncertain Significance). The variant has 1 moderate criterion (PS3_Moderate) and 3 supporting criteria (PM2_Supporting, PP2_Supporting, PP3_Supporting). This combination (1M + 3Spt) does not meet any PTEN VCEP Likely Pathogenic rule (Rule13 requires ≥3M; Rule14 requires 2M + ≥2Spt; others require ≥1 Strong). Under both the PTEN VCEP and generic ACMG/AMP 2015 classification frameworks, this combination falls into the VUS category.

Final determination: No criteria-combination rule matched the adjudicated criteria in the ClinGen PTEN Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for PTEN Version 3.2 v3.2 framework, so the variant remains a Variant of Uncertain Significance pending human review.

Criteria assessment

ACMG/AMP criteria review

Criteria shown when status is available

All criteria require review: For research and educational purposes only.

Criterion	Status	Rationale	Evidence used
PVS1	N/A	NM_000314.8:c.203A>G is a missense variant (p.Tyr68Cys). The PTEN VCEP PVS1 decision tree applies only to null variants (nonsense, frameshift, canonical ±1,2 splice site disruptions, and exon-level CNVs). Missense substitutions are outside the scope of PVS1.
PS1	Not met	PS1 requires a different nucleotide change resulting in the same amino acid as a previously established pathogenic variant, or a variant at the same nucleotide position as a known pathogenic splicing variant. c.203A>G is the only nucleotide change that produces p.Tyr68Cys (TAC→TGC), and the variant is a missense, not a splicing variant.
PS2	Not met	No de novo observation identified in the reviewed literature. The only case report with detailed pedigree (PMID: 26246517) describes an inherited variant — the proband's father also carries c.203A>G and has macrocephaly. No confirmed or assumed de novo evidence exists for this variant.
PS3	Met	Y68C has a cumulative fitness score (Cum_score) of -2.73 in the Mighell et al. 2018 (PMID: 29706350) PTEN saturation mutagenesis phosphatase activity assay (Table S2), meeting the VCEP PS3_Moderate threshold of ≤ -1.11. The measurement is high-confidence (High_conf=True, Pass SE Filter). This represents systematic functional characterization of all possible missense variants at position 68 via massively parallel assay.	vcep_mmc2
PS4	Not assessed	Insufficient proband-level data with specificity scores to apply PS4 per PTEN VCEP rules. The variant is reported in ClinVar as Pathogenic by 6 clinical laboratories and Likely Pathogenic by 1, and has been observed in CS patients (PMID: 19457929, PMID: 26246517), but individual proband specificity scores required by the VCEP PS4 framework (≥16 for Very Strong, 4-15.5 for Strong, 2-3.5 for Moderate, 1-1.5 for Supporting) could not be computed from available data.
PS5	N/A	PS5 is not defined in the PTEN VCEP criteria set (ClinGen PTEN Expert Panel Specifications Version 3.2).
PM1	Not met	The PTEN VCEP defines PM1 as applicable to residues in the catalytic motifs: 90-94, 123-130, and 166-168 (NP_000305.3). p.Tyr68Cys is at position 68, which lies within the ATP-binding motif (residues 60-73) but outside the VCEP-specified catalytic motif ranges. Although residue 68 is in a statistically significant cancer hotspot per cancerhotspots.org, the VCEP definition explicitly limits PM1 to the named catalytic residues.	cspec
PM2	Met	NM_000314.8:c.203A>G is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0. This meets the PTEN VCEP PM2_Supporting threshold of allele frequency < 0.00001 (0.001%).	gnomad_v2 gnomad_v4 gnomad_canada
PM5	Not met	PM5 requires a different missense change at the same amino acid residue previously determined to be pathogenic or likely pathogenic. At codon 68, p.Tyr68Asp (Y68D, PMID: 16704655) and p.Tyr68His (Y68H, PMID: 9600246) have been reported, but neither has been confirmed with P/LP classification in ClinVar through the available data. Additionally, BLOSUM62 comparison could not be performed. Without verified P/LP comparator at the same residue, PM5 cannot be applied.
PM6	Not met	No de novo observation identified. The one case with parental data (PMID: 26246517) shows inheritance from the father.
PP1	Not met	Insufficient segregation data. PMID 26246517 reports one affected parent-child pair (father with macrocephaly), providing at most 1 meiosis. The PTEN VCEP requires ≥3 meioses for PP1_Supporting, ≥5 for Moderate, and ≥7 across ≥2 families for Strong.
PP2	Met	PTEN is a gene with a low rate of benign missense variation (high missense constraint) and missense variants are a well-established common mechanism of disease in Cowden syndrome and related PTEN hamartoma tumor syndromes. NM_000314.8:c.203A>G is a missense variant meeting the PTEN VCEP PP2_Supporting criteria.	cspec
PP3	Met	REVEL score of 0.985 exceeds the PTEN VCEP PP3_Supporting threshold of >0.7 for missense variants. BayesDel score of 0.594 provides additional supporting computational evidence, though the VCEP rule specifies REVEL for missense variants.	revel bayesdel
PP4	N/A	PP4 is designated as Not Applicable by the PTEN VCEP. Phenotype specificity has been incorporated into the PS4 rule specifications instead.
PP5	N/A	PP5 is designated as Not Applicable by the PTEN VCEP. ClinVar review status is 'criteria provided, single submitter' (not 3-star expert panel), so even the PP5 override policy would not apply.
BA1	Not met	The variant is absent from all gnomAD populations. The PTEN VCEP BA1 threshold is filtering allele frequency > 0.00056 (0.056%). Zero allele count does not meet this threshold.	gnomad_v2 gnomad_v4
BS1	Not met	The variant is absent from gnomAD. The PTEN VCEP BS1 threshold is allele frequency ≥ 0.000043 (0.0043%) for strong and ≥ 0.0000043 (0.00043%) for supporting. Zero allele count does not meet either threshold.	gnomad_v2 gnomad_v4
BS2	Not met	No homozygous observations of c.203A>G in any population database or published report. The PTEN VCEP BS2 requires observation in the homozygous state in a healthy or PHTS-unaffected individual.
BS3	Not met	Functional data from Mighell et al. 2018 saturation mutagenesis (mmc2.xlsx) shows Y68C has a damaging effect on phosphatase activity (Cum_score = -2.73). The PTEN VCEP BS3 requires functional studies showing no damaging effect. The available evidence demonstrates the opposite — a deleterious functional consequence.	vcep_mmc2
BS4	Not met	No segregation data demonstrating lack of segregation in affected family members. PMID 26246517 shows co-occurrence of variant and phenotype (macrocephaly) in both proband and father, which is consistent with segregation, not lack thereof.
BP1	N/A	BP1 is designated as Not Applicable by the PTEN VCEP.
BP2	Not met	No evidence of the variant observed in trans with a pathogenic or likely pathogenic PTEN variant, nor ≥3 observations in cis/phase unknown with different P/LP PTEN variants.
BP4	Not met	The PTEN VCEP BP4 rule for missense variants requires REVEL score < 0.5. The REVEL score for c.203A>G is 0.985, strongly predicting a deleterious effect rather than no impact. SpliceAI shows no splicing impact (max delta = 0.01), but the REVEL criterion for missense variants is not met.	revel spliceai
BP5	Not met	No evidence that this variant has been found in a case with an alternate molecular basis for disease meeting the PTEN VCEP BP5 criteria (other gene/disorder must be highly penetrant, and the patient's personal/family history must show no overlap between the other gene disorder and PTEN).
BP6	N/A	BP6 is designated as Not Applicable by the PTEN VCEP.
BP7	N/A	BP7 applies to synonymous (silent) or intronic variants at or beyond +7/-21 with no predicted splice impact. NM_000314.8:c.203A>G is a missense variant (p.Tyr68Cys) and does not meet the variant type criteria for BP7.
BP3	N/A	BP3 applies to in-frame deletions/insertions in repetitive regions without a known function. NM_000314.8:c.203A>G is a missense substitution, not an in-frame indel.
PM3	N/A	PM3 applies to recessive disorders where the variant is detected in trans with a pathogenic variant. PTEN-associated disorders are autosomal dominant, and PM3 is designated Not Applicable by the PTEN VCEP.
PM4	N/A	PM4 applies to in-frame deletions/insertions in non-repeat regions or stop-loss variants. NM_000314.8:c.203A>G is a single-nucleotide missense substitution, not an in-frame indel or stop-loss variant.

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