×

Please note this is a beta version of the ClinGen Evidence Repository. This resource is intended to provide access to variant level evidence used and applied by ClinGen Variant Curation Expert Panels in the classification of variants. In this beta version, the evidence is limited to curation notes and referenced literature (PMIDs).

For general information about ClinGen Expert Panels and Variant Curation please visit: Clinical Domain Working Groups. For specific inquiries regarding a variant classification or evidence curation (e.g. population database queried, segregation counts or other evidence used) or to submit general comments about the evidence repo, please email us.

The resource is undergoing updates and tesing. Should you encounter any issues regarding the data displayed, lack of functionality or other problems, please let us know so we can rectify these accordingly. Your help in this regard is greatly appreciated.

ACMG-PTEN Variant Curation Guideline

Benign
Pathogenic
Stand Alone
Strong
Supporting
Supporting
Moderate
Strong
Very Strong
Population Data

Allele frequency is above 5% in Exome Sequencing Project, 1000 Genomes, or ExAC.
PTEN EP Specification: To be applied for variants with allele frequency >0.01 (>1%) in a studied population with >2,000 alleles tested and variant present in >5 alleles. Please see supplementary information in manuscript for data supporting this lowered allele frequency threshold. BA1

Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder with full penetrance expected at an early age.
PTEN EP Specification: Variant must be observed in the homozygous state in a healthy or PHTS-unaffected individual. Two independent observations are required if the homozygous status is not confirmed via parental testing. If BS1 is also applied, this criteria will be applied at the supporting evidence level to avoid a variant reaching benign status solely based on homozygous occurrences due to high population frequency (BS1+BS2). BS2

Allele frequency is greater than expected for disorder.
PTEN EP Specification: To be applied for variants with allele frequency of 0.001 up to 0.01 (0.1% up to 1%) in a studied population with >2,000 alleles tested and variant present in >5 alleles. Please see supplementary information in manuscript for data supporting this lowered allele frequency threshold. BS1

Two homozygous observations with no clinical data provided, or meets criteria for BS2 but BS1 is also applied. BS2-Supporting

Allele frequency from 0.000043 (0.0043%) up to 0.001 (0.1%) in a studied population with >2,000 alleles BS1-Supporting

Proband(s) with specificity score of 1-1.5. PS4-Supporting

Probands with specificity score of 2-3.5. PS4-Moderate

Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes or ExAC.
PTEN EP Specification:Criteria may be applied if 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, allele frequency in that subpopulation must be <0.00002 (0.002%). Please see supplementary information in manuscript supporting application of PM2 for ultra-rare alleles. PM2

Use 1: The prevalence of the variant in affected individuals is significantly increased compared with the prevalence in controls.
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

Probands with specificity score >= 16. PS4-Very Strong

Computational And Predictive Data

A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved.
PTEN EP Specification: Intronic variants must be positioned at or beyond +7/-21. Nucleotide may be defined as 'not conserved' with PhastCons score <1 and PhyloP score <0.1. BP7

Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.).
PTEN EP Specification: To be applied only to synonymous or intronic variants where at least 2 out of 3 in silico models predict no splicing impact. Not to be applied for variants which may impact the intron 1 splice donor or acceptor sites, and to be used cautiously for variants which may impact the intron 6 splice acceptor.

PTEN EP Commentary: Given the lack of known benign or likely benign PTEN missense variants, the Expert Panel was unable to test the accuracy of in silico predictors to be used as evidence to apply BP4 or PP3 for PTEN missense variants. While investigating potential in silico tools, the Expert Panel also came to find that some algorithm predictions were highly sensitive to sequence alignment, further limiting confidence in these tools. Should the Expert Panel classify several missense variants as benign or likely benign, another attempt will be made to validate in silico tools to apply PP3/BP4 for missense variants. Please see supplementary information in manuscript detailing validation of splicing in silico tools and challenges presented by the specified donor/acceptor sites.

BP4

Multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc).
PTEN EP Specification: To be applied only to synonymous or intronic variants where at least 2 out of 3 in silico models predict a splicing impact. Not to be applied for variants which may impact the intron 1 splice donor or acceptor sites, and to be used cautiously for variants which may impact the intron 6 splice acceptor.

PTEN EP Commentary: Given the lack of known benign or likely benign PTEN missense variants, the Expert Panel was unable to test the accuracy of in silico predictors to be used as evidence to apply BP4 or PP3 for PTEN missense variants. While investigating potential in silico tools, the Expert Panel also came to find that some algorithm predictions were highly sensitive to sequence alignment, further limiting confidence in these tools. Should the Expert Panel classify several missense variants as benign or likely benign, another attempt will be made to validate in silico tools to apply PP3/BP4 for missense variants. Please see supplementary information in manuscript detailing validation of splicing in silico tools and challenges presented by the specified donor/acceptor sites.

PP3

Novel missense change at an amino acid residue where a different missense change determined to be pathogenic has been seen before.
PTEN EP Specification:

This rule may be applied when the known variant is likely pathogenic unless applying would lead to a higher (pathogenic) classification for the variant being assessed

The variant in question need not be novel but must have a BLOSUM62 (Henikoff 1992) score equal to or less than the known variant.

PM5

Protein length changes due to in-frame deletions/insertions in a non-repeat region or stop-loss variants.
PTEN EP Specification: For in-frame insertions or deletions, criteria may apply only if the variant impacts at least one residue in one of the catalytic motifs specified in the PM1 criteria. Criteria will also apply for variants resulting in truncation 3' to c.1121 (NM_000314.6) or variants resulting in protein extension. PM4

Same amino acid change as a previously established pathogenic variant regardless of nucleotide change.
PTEN EP Specification: PS1 will be applied as described and expanded to include a different nucleotide substitution for an intronic splice site variant if the predicted impact is equal to or greater than the known pathogenic variant per in silico splicing tools. Caution should be used when applying this criteria to exonic variants causing aberrant splicing. PS1

Null variant (nonsense, frameshift, canonical +/-1 or 2 splice sites, initiation codon, single or multi-exon deletion) in a gene where loss of function (LOF) is a known mechanism of disease.
PTEN EP Specification: For nonsense or frameshift variants at the 3' end of the gene NOT predicted to result in nonsense-mediated decay, PVS1 may still be applied if the protein is disrupted at or 5' to c.1121 (NM_000314.6). Please see supplementary information in manuscript for evidence supporting this cutoff. PVS1

Functional Data

Well-established in vitro or in vivo functional studies show no damaging effect on protein function or splicing.
PTEN EP Specification: BS3 may be applied to the following assays:

For missense variants: Lipid phosphatase activity comparable to wild type in addition to a second assay appropriate to the protein domain demonstrating no statistically significant difference from wild type. Phosphatase assays for which criteria may be applied must include a catalytic dead control, such as p.C124S (NP_ 000305.3), as well as at least three biological replicates (Myers 1998, Stambolic 1998, Han 2000, Rodriguez-Escudero 2011, Costa 2015, Malek 2017). Examples of second assays may include:
Decreased PTEN or increased pAKT expression (Tan 2011, Spinelli 2015).
Disruption of protein cellular localization (Lobo 2009, He 2012, Gil 2015).
Aberrant cellular phenotypes, including defective cell migration, proliferation, and invasion (Costa 2015, Malek 2017).

For intronic or synonymous variants: RNA, mini-gene, or other assay demonstrate no impact on splicing.

BS3

In vitro or in vivo functional study or studies showing no damaging effect on protein function but BS3 not met. BS3-Supporting

Missense variant in a gene that has a low rate of benign missense variation and where missense variants are a common mechanism of disease. PP2

Abnormal in vitro cellular assay or transgenic model with phenotype different from wild-type that does not meet PS3. Examples of in vitro cellular assays to be considered for PS3_supporting evidence may include:
Decreased PTEN or increased pAKT expression (Tan 2011, Spinelli 2015).
Disruption of protein cellular localization (Lobo 2009, He 2012, Gil 2015).
Aberrant cellular phenotypes, including defective cell migration, proliferation, and invasion (Costa 2015, Malek 2017). PS3-Supporting

Located in a mutational hot spot and/or critical and well-established functional domain (e.g. active site of an enzyme) without benign variation.
PTEN EP Specification: Defined to include residues in one of PTEN’s catalytic motifs, which include the WPD loop (residues 90-94), P-loop (also described as phosphatase core, residues 123-130), and the TI-loop (residues 166-168) (NP_ 000305.3) (Lee 1999). PM1

Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product.
PTEN EP Specification: PS3 may be applied to the following assays:
In vitro or in vivo assay demonstrating >50% reduction in phosphatase activity compared to wild type control. Phosphatase assays for which criteria may be applied must include a catalytic dead control, such as p.C124S, as well as at least three biological replicates (Myers 1998, Stambolic 1998, Han 2000, Rodriguez-Escudero 2011, Costa 2015, Malek 2017).
RNA, mini-gene, or other assay demonstrating an impact on splicing. PS3

Segregation Data

Lack of segregation in affected members of a family.
PTEN EP Specification: Two or more families are require for strong evidence level. BS4

Lack of segregation in one family. BS4-Supporting

Co-segregation with disease in multiple affected family members in a gene definitively known to cause the disease.
PTEN EP Specification: Requires 3 or 4 meioses in order to apply. PP1

Requires 5 or 6 meioses in order to apply. PP1-Moderate

At least 7 meioses required across at least two families. PP1-Strong

De novo Data

Assumed de novo, but without confirmation of paternity and maternity in a patient with the disease and no family history. PM6

Two occurrences of PM6. PM6-Strong

De novo (both maternity and paternity confirmed) in a patient with the disease and no family history. Note: Confirmation of paternity only is insufficient. Egg donation, surrogate motherhood, errors in embryo transfer, etc. can contribute to non-maternity. PS2

Four or more occurrences of PM6 OR two occurrences of PM6 AND one occurrence of PS2. PM6-Very Strong

Two or more occurrences of PS2 OR two or more occurrences of PM6 AND one occurrence of PS2. PS2-Very Strong

Allelic Data

Observed in trans with a pathogenic variant for a fully penetrant dominant gene/disorder; or observed in cis with a pathogenic variant in any inheritance pattern.
PTEN EP Specification: The other variant may be either pathogenic or likely pathogenic. This rule may also be applied for at least three observations of the variant in cis or unknown phase with different pathogenic or likely pathogenic PTEN variants. BP2

Other Data

Variant found in a case with an alternate molecular basis for disease.
PTEN EP Specification: 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 BP5

The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. If you have questions about the information contained on this website, please see a health care professional.
¤ Powered by BCM's Genboree.