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.105G>A (p.Met35Ile)

CA377784465

536558 (ClinVar)

Gene: PTEN
Condition: PTEN hamartoma tumor syndrome
Inheritance Mode: Autosomal dominant inheritance
UUID: bedc52a0-7126-41cd-896a-0f53a8b5636b
Approved on: 2023-10-11
Published on: 2023-10-16

HGVS expressions

NM_000314.8:c.105G>A
NM_000314.8(PTEN):c.105G>A (p.Met35Ile)
NC_000010.11:g.87894050G>A
CM000672.2:g.87894050G>A
NC_000010.10:g.89653807G>A
CM000672.1:g.89653807G>A
NC_000010.9:g.89643787G>A
NG_007466.2:g.35612G>A
ENST00000686459.1:c.105G>A
ENST00000688158.1:c.*275+13612G>A
ENST00000688308.1:c.105G>A
ENST00000693560.1:c.624G>A
ENST00000371953.8:c.105G>A
ENST00000371953.7:c.105G>A
ENST00000462694.1:n.107G>A
ENST00000610634.1:c.3G>A
NM_000314.5:c.105G>A
NM_000314.6:c.105G>A
NM_001304717.2:c.624G>A
NM_001304718.1:c.-601G>A
NM_000314.7:c.105G>A
NM_001304717.5:c.624G>A
NM_001304718.2:c.-601G>A

Uncertain Significance

Met criteria codes 4
PP3 PP2 PM2_Supporting PM5

Evidence Links 0

Expert Panel

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.105G>A (p.Met35Ile) is currently classified as a variant of uncertain significance 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). PM5: Missense change at an amino acid residue where a different missense change determined to be pathogenic or likely pathogenic and with equal or lesser BLOSUM62 score has been seen before (ClinVar Variation ID: 231916). 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 =0.947). PM2_P: Absent in gnomAD.
Met criteria codes
PP3
REVEL score > 0.7 (score of this variant =0.947)
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.
PM2_Supporting
Absent in gnomAD.
PM5
Missense change at an amino acid residue where a different missense change determined to be pathogenic or likely pathogenic and with equal or lesser BLOSUM62 score has been seen before (ClinVar Variation ID: 231916).
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