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]

Variant: NM_000314.8(PTEN):c.106G>C (p.Gly36Arg)

CA000283

189400 (ClinVar)

Gene: PTEN (HGNC:5728)

Condition: PTEN hamartoma tumor syndrome (MONDO:0017623)

Inheritance Mode: Autosomal dominant inheritance

UUID: 6978957a-8d30-4cb6-8f2a-f14e69a78254

Approved on: 2023-10-11

Published on: 2023-10-18

HGVS expressions

NM_000314.8(PTEN):c.106G>C (p.Gly36Arg)

NM_000314.8:c.106G>C

NC_000010.11:g.87894051G>C

CM000672.2:g.87894051G>C

NC_000010.10:g.89653808G>C

CM000672.1:g.89653808G>C

NC_000010.9:g.89643788G>C

NG_007466.2:g.35613G>C

ENST00000686459.1:c.106G>C

ENST00000688158.1:c.*275+13613G>C

ENST00000688308.1:c.106G>C

ENST00000693560.1:c.625G>C

ENST00000371953.8:c.106G>C

ENST00000371953.7:c.106G>C

ENST00000462694.1:n.108G>C

ENST00000610634.1:c.4G>C

NM_000314.5:c.106G>C

NM_000314.6:c.106G>C

NM_001304717.2:c.625G>C

NM_001304718.1:c.-600G>C

NM_000314.7:c.106G>C

NM_001304717.5:c.625G>C

NM_001304718.2:c.-600G>C

Likely Pathogenic

PS3_Moderate PS1_Moderate PM2_Supporting PP3 PP2

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.106G>C (p.Gly36Arg) meets criteria to be classified as likely 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). PS1_M: Same amino acid change as a previously established likely pathogenic variant regardless of nucleotide change (ClinVar Variation ID: 1334551) PS3_M: Functional studies supportive of a damaging effect on the gene or gene product. Score of this variant = -2.69 (≤ -1.11) on a high throughput phosphatase assay (PMID:29706350). 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 = 0.995)

PS3_Moderate

Functional studies supportive of a damaging effect on the gene or gene product. Score of this variant = -2.69 (≤ -1.11) on a high throughput phosphatase assay (PMID:29706350).

PS1_Moderate

Same amino acid change as a previously established likely pathogenic variant regardless of nucleotide change (ClinVar Variation ID: 1334551)

PM2_Supporting

Absent in gnomAD

PP3

REVEL score > 0.7 (score of this variant = 0.995) [ In addition, SpliceAI shows weak SAS loss score 0.18 and some SAS gain score 0.27]

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.

Curation History

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