Variant classification summary

NM_000314.8:c.544T>G

PTEN · NP_000305.3:p.(Leu182Val) · NM_000314.8

GRCh37: chr10:89711926 T>G · GRCh38: chr10:87952169 T>G

Gene: PTEN Transcript: NM_000314.8

Final call

VUS

PS3 moderate PM2 supporting PP2 supporting

Variant details

Gene

PTEN

Transcript

NM_000314.8

Protein

NP_000305.3:p.(Leu182Val)

gnomAD AF

0.0 (v4.1)

ClinVar

OncoKB

Unknown Oncogenic Effect

Classification rationale

Interpretation summary

Generated evidence synthesis

1

NM_000314.8:c.544T>G (p.Leu182Val) is a missense variant in exon 6 of PTEN. It is absent from gnomAD v2.1 and v4.1 (0/1,612,242 alleles), meeting PM2_Supporting per the PTEN VCEP threshold of <0.001%.

2

In the Mighell et al. 2018 (PMID:29706350) saturation mutagenesis functional assay, L182V has a cumulative fitness score of -1.24 (High_conf=True), meeting the PTEN VCEP PS3_Moderate threshold of Cum_score <= -1.11, indicating a damaging effect on PTEN phosphatase activity.

3

PTEN is a gene with a low rate of benign missense variation where missense variants are a common mechanism of disease (PHTS, autosomal dominant). PP2 is applied at Supporting level per the PTEN VCEP specification.

4

L182V REVEL score is 0.682, below the PTEN VCEP PP3 threshold of >0.7, and above the BP4 missense threshold of <0.5. Computational evidence is indeterminate and does not contribute to either pathogenic or benign criteria.

5

The variant lies outside PTEN catalytic motifs (WPD loop 90-94, P-loop 123-130, TI-loop 166-168). PM1 is not met.

6

L182S (c.545T>C) is a pathogenic ClinVar missense at the same residue, but PM5 is not met because the BLOSUM62 score for Leu->Val (+1) is greater than Leu->Ser (-2), failing the VCEP BLOSUM62 requirement.

7

No proband, segregation, de novo, or case-control data are available. PS2, PS4, PM6, PP1, BS4, BP2, and BP5 are not met. Criteria not applicable per the PTEN VCEP include PVS1 (missense, not null), PP4, PP5, BP1, BP6, and BP7.

8

Overall, met criteria: PS3_Moderate (1 moderate), PM2_Supporting (1 supporting), PP2 (1 supporting). This yields 1 moderate + 2 supporting pathogenic criteria with no benign criteria. Under the PTEN VCEP/ACMG 2015 combination rules, Likely Pathogenic requires at least 3 moderate, or 2 moderate + >=2 supporting, or 1 strong + >=2 supporting, or 1 strong + 1 moderate. With only 1 moderate + 2 supporting, none of the Pathogenic or Likely Pathogenic rules are satisfied. The variant is classified as a Variant of Uncertain Significance (VUS).

Final determination: No criteria-combination rule matched the adjudicated criteria in the Richards et.al., 2015 - Combining rules v3.2.0 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	PVS1 applies only to null variants (nonsense, frameshift, canonical splice site, initiation codon, exon deletion). NM_000314.8:c.544T>G is a missense substitution (p.Leu182Val) and does not fall into any PVS1 null-variant bucket per the PTEN VCEP PVS1 decision tree.
PS1	Not met	PS1 requires the same amino acid change (L182V) to have been previously established as pathogenic via a different nucleotide change. No alternative nucleotide substitution producing L182V has been identified as pathogenic in ClinVar; the variant is absent from ClinVar entirely. No evidence of a prior established pathogenic L182V from a different codon change is available.	clinvar
PS2	Not met	PS2 requires a proven de novo observation (both maternity and paternity confirmed) in a patient with PHTS and no family history. No de novo data are available; the variant is absent from ClinVar and no publications were identified.
PS3	Met	L182V has a cumulative fitness score of -1.24 (Cum_SE=0.49, High_conf=True) in the Mighell et al. 2018 (PMID:29706350) massively parallel phosphatase activity saturation mutagenesis assay. This meets the PTEN VCEP PS3_Moderate threshold of Cum_score <= -1.11, indicating well-established in vitro functional evidence supportive of a damaging effect on protein function.	vcep_mmc2
PS4	Not met	PS4 requires proband counts with phenotype specificity scores. No proband data are available; the variant is absent from ClinVar and no case reports were identified in the literature.
PS5	N/A	PS5 is not a criterion in the ACMG/AMP 2015 guidelines nor in the ClinGen PTEN Expert Panel specifications v3.2.0. This criterion is not defined for PTEN variant interpretation.
PM1	Not met	PM1 requires the variant to be located in a PTEN catalytic motif. The PTEN VCEP defines catalytic motifs as the WPD loop (residues 90-94), P-loop (residues 123-130), and TI-loop (residues 166-168) per NP_000305.3. Position 182 lies outside all three catalytic motifs. Additionally, the variant is not in a statistically significant hotspot.	cspec
PM2	Met	NM_000314.8:c.544T>G is absent from gnomAD v2.1 and gnomAD v4.1 (0/1,612,242 alleles, AF=0.00000%). Per the PTEN VCEP specification, PM2 is applied at Supporting level for variants with allele frequency <0.00001 (0.001%) in gnomAD.	gnomad_v2 gnomad_v4
PM5	Not met	PM5 requires a different missense change at the same residue (Leu182) to be pathogenic or likely pathogenic, AND the interrogated variant must have a BLOSUM62 score equal to or less than the known variant. L182S (c.545T>C, p.Leu182Ser) is classified as Pathogenic in ClinVar for macrocephaly/autism syndrome. However, the BLOSUM62 score for Leu->Ser is -2, while Leu->Val (L182V) is +1. Since L182V's BLOSUM62 score (+1) is greater than L182S's score (-2), the BLOSUM62 criterion is not satisfied.	vcep_mmc2 clinvar
PM6	Not met	PM6 requires assumed de novo occurrence in a proband with PHTS and no family history. No de novo data are available; the variant is absent from ClinVar and no publications were identified.
PP1	Not met	PP1 requires co-segregation data with at least 3 meioses across affected family members. No segregation data are available for this variant.
PP2	Met	PTEN is a gene with a low rate of benign missense variation where missense variants are a common mechanism of disease (PTEN hamartoma tumor syndrome, autosomal dominant). PP2 is applicable per the PTEN VCEP specification for missense variants in PTEN.	cspec
PP3	Not met	PP3 for missense variants requires REVEL score >0.7 per the PTEN VCEP specification. The REVEL score for L182V is 0.682, which falls below the >0.7 threshold. BayesDel score (0.206) also does not strongly support a deleterious prediction. SpliceAI max delta is 0.00 (no predicted splicing impact). Multiple lines of computational evidence do not support a deleterious effect at the VCEP-defined threshold.	revel bayesdel spliceai
PP4	N/A	PP4 is marked Not Applicable by the ClinGen PTEN Expert Panel v3.2.0. Phenotype specificity has been incorporated into PS4 Use 2 rule specifications.	cspec
PP5	N/A	PP5 is marked Not Applicable for this VCEP by the ClinGen PTEN Expert Panel v3.2.0. This criterion is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee.	cspec
BA1	Not met	BA1 requires gnomAD filtering allele frequency >0.00056 (0.056%) per the PTEN VCEP specification. The variant is absent from gnomAD v2.1 and v4.1 (0/1,612,242 alleles, AF=0.00000%). Frequency does not meet the BA1 threshold.	gnomad_v2 gnomad_v4
BS1	Not met	BS1 requires gnomAD filtering allele frequency from 0.000043 (0.0043%) to 0.00056 (0.056%) per the PTEN VCEP specification. The variant is absent from gnomAD (AF=0.00000%). Frequency does not meet the BS1 threshold.	gnomad_v2 gnomad_v4
BS2	Not met	BS2 requires observation in the homozygous state in a healthy or PHTS-unaffected individual. No homozygous observations are reported; the variant is absent from gnomAD (0 homozygotes).	gnomad_v4
BS3	Not met	BS3_Supporting requires phosphatase activity >0 per Mighell et al. 2018. L182V Cum_score is -1.24, indicating reduced (not normal) phosphatase activity. BS3 is not met. BS3_Strong applies only to intronic/synonymous variants with splicing assays showing no impact and is not applicable to this missense variant.	vcep_mmc2
BS4	Not met	BS4 requires lack of segregation in affected family members. No segregation data are available for this variant.
BP1	N/A	BP1 is marked Not Applicable by the ClinGen PTEN Expert Panel v3.2.0. This rule is not applicable to PTEN.	cspec
BP2	Not met	BP2 requires observation in trans with a pathogenic or likely pathogenic PTEN variant, or at least three observations in cis/unknown phase with different P/LP PTEN variants. No such phase data are available.
BP4	Not met	BP4 for missense variants requires REVEL score <0.5 per the PTEN VCEP specification. L182V REVEL score is 0.682, which exceeds this threshold. BP4 is not met.	revel
BP5	Not met	BP5 requires the variant to be found in a case with an alternate molecular basis for disease, with at least two such cases required per the PTEN VCEP specification. No such cases are available.
BP6	N/A	BP6 is marked Not Applicable for this VCEP by the ClinGen PTEN Expert Panel v3.2.0. This criterion is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee.	cspec
BP7	N/A	BP7 applies to synonymous or intronic variants (at or beyond +7/-21) for which splicing prediction algorithms predict no impact. NM_000314.8:c.544T>G is a missense variant (p.Leu182Val) and does not meet the variant type requirement for BP7.

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