Evidence Repository - Clinical Genome Resources

The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]

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Variant: NM_000314.8(PTEN):c.107G>A (p.Gly36Glu)

CA377784477

486972 (ClinVar)

Gene: PTEN

Condition: PTEN hamartoma tumor syndrome

Inheritance Mode: Autosomal dominant inheritance

Link to MONDO

UUID: 03ccb7a8-afaa-4bf5-8165-93fc607ae327

Approved on: 2023-10-11

Published on: 2023-10-18

HGVS expressions

NM_000314.8:c.107G>A

NM_000314.8(PTEN):c.107G>A (p.Gly36Glu)

NC_000010.11:g.87894052G>A

CM000672.2:g.87894052G>A

NC_000010.10:g.89653809G>A

CM000672.1:g.89653809G>A

NC_000010.9:g.89643789G>A

NG_007466.2:g.35614G>A

ENST00000686459.1:c.107G>A

ENST00000688158.1:c.*275+13614G>A

ENST00000688308.1:c.107G>A

ENST00000693560.1:c.626G>A

ENST00000371953.8:c.107G>A

ENST00000371953.7:c.107G>A

ENST00000462694.1:n.109G>A

ENST00000610634.1:c.5G>A

NM_000314.5:c.107G>A

NM_000314.6:c.107G>A

NM_001304717.2:c.626G>A

NM_001304718.1:c.-599G>A

NM_000314.7:c.107G>A

NM_001304717.5:c.626G>A

NM_001304718.2:c.-599G>A

Pathogenic

PS3_Moderate PS2 PP3 PP2 PM2_Supporting PS4_Supporting

Evidence Links 0

Expert Panel

PTEN VCEP

Criteria Specification Information

Criteria Specification: ClinGen PTEN Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for PTEN Version 3.0.0

Criteria Specification Approval History

Criteria Specifications for this VCEP

Evidence submitted by expert panel

PTEN VCEP

NM_000314.8(PTEN):c.107G>A (p.Gly36Glu) meets criteria to be classified as pathogenic for PTEN Hamartoma Tumor syndrome in an autosomal dominant manner using modified ACMG criteria (ACMG Classification Rules Specified for PTEN Variant Curation version 3.0.0). Please see a summary of the rules and criteria codes in the “PTEN ACMG Specifications Summary” document (assertion method column). PS2: De novo (both maternity and paternity confirmed) observation in a patient with the disease and no family history. (internal laboratory contributor: SCV001781083.1) PS3_M: Functional studies supportive of a damaging effect on the gene or gene product. Score of this variant = -1.797438259 (≤ -1.11) on a high throughput phosphatase assay (PMID:29706350). PS4_P: Proband(s) with phenotype specificity score of 1-1.5. (internal laboratory contributor: SCV001781083.1) PM2_P: Absent in gnomAD. PP2: PTEN is defined by the PTEN Expert Panel as a gene that has a low rate of benign missense variation and where missense variants are a common mechanism of disease. PP3: REVEL score > 0.7 (score of this variant = 0.98).

PS3_Moderate

Functional studies supportive of a damaging effect on the gene or gene product. Score of this variant = -1.797438259 (≤ -1.11) on a high throughput phosphatase assay (PMID:29706350). Mighell et al. 2018 PMID: 29706350: Lipid phosphatase activity score, -1.797438259 (TRUE).

PS2

De novo (both maternity and paternity confirmed) observation in a patient with the disease and no family history. (internal laboratory contributor: SCV001781083.1)

PP3

REVEL score of 0.98 (>0.7)

PP2

missense constraint

PM2_Supporting

Absent in gnomAD.

PS4_Supporting

Proband(s) with phenotype specificity score of 1-1.5. (internal laboratory contributor: SCV001781083.1)

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