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_000314.6(PTEN):c.103A>G (p.Met35Val)

CA10578906

231916 (ClinVar)

Gene: PTEN
Condition: PTEN hamartoma tumor syndrome
Inheritance Mode: Autosomal dominant inheritance
UUID: 4f6345e3-25b1-48cd-9697-1a5624715071
Approved on: 2024-02-09
Published on: 2024-03-04

HGVS expressions

NM_000314.6:c.103A>G
NM_000314.6(PTEN):c.103A>G (p.Met35Val)
NC_000010.11:g.87894048A>G
CM000672.2:g.87894048A>G
NC_000010.10:g.89653805A>G
CM000672.1:g.89653805A>G
NC_000010.9:g.89643785A>G
NG_007466.2:g.35610A>G
ENST00000700029.2:c.103A>G
ENST00000710265.1:c.103A>G
ENST00000472832.3:c.103A>G
ENST00000688158.2:n.899+13610A>G
ENST00000688922.2:c.103A>G
ENST00000700021.1:c.103A>G
ENST00000700022.1:c.103A>G
ENST00000706954.1:c.103A>G
ENST00000706955.1:c.*138A>G
ENST00000686459.1:c.103A>G
ENST00000688158.1:c.*275+13610A>G
ENST00000688308.1:c.103A>G
ENST00000693560.1:c.622A>G
ENST00000371953.8:c.103A>G
ENST00000371953.7:c.103A>G
ENST00000462694.1:n.105A>G
ENST00000610634.1:c.1A>G
NM_000314.5:c.103A>G
NM_001304717.2:c.622A>G
NM_001304718.1:c.-603A>G
NM_000314.7:c.103A>G
NM_001304717.5:c.622A>G
NM_001304718.2:c.-603A>G
NM_000314.8:c.103A>G
NM_000314.8(PTEN):c.103A>G (p.Met35Val)
More

Pathogenic

Met criteria codes 6
PS3_Supporting PS2_Very Strong PP2 PP3 PM2_Supporting PS4_Supporting
Not Met criteria codes 20
PVS1 BA1 BS4 BS3 BS1 BS2 BP7 BP5 BP3 BP2 BP1 BP4 PS1 PP1 PP4 PM5 PM1 PM4 PM3 PM6

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.103A>G (p.Met35Val) 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_VS: At least two proven de novo observations in a patient with the disease and no family history. (internal laboratory contributors: SCV000275912.7, SCV000565444.8). PS3_P: Abnormal in vitro cellular assay or transgenic model with phenotype different from wild type that does not meet PS3 (Post et al. 2020 PMID: 32350270: pAKT levels similar to C124S). PS4_P: Proband(s) with phenotype specificity score of 1-1.5. (PMID: 27531073, internal laboratory contributor: SCV000275912.7). PM2_P: Absent in large sequenced populations (PMID 27535533). 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 =0.953)
Met criteria codes
PS3_Supporting
Abnormal in vitro cellular assay or transgenic model with phenotype different from wild type that does not meet PS3 (Post et al. 2020 PMID: 32350270: pAKT levels similar to C124S).
PS2_Very Strong
At least two proven de novo observations in a patient with the disease and no family history. (internal laboratory contributors: SCV000275912.7, SCV000565444.8)
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 =0.953)
PM2_Supporting
Absent in gnomAD.
PS4_Supporting
Proband(s) with phenotype specificity score of 1-1.5. (PMID: 27531073, internal laboratory contributor: SCV000275912.7)
Not Met criteria codes
PVS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BA1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP7
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP1
2 meioses in internal lab cases per March 2020 meeting - check for more in future cases.
PP4
Wrapped into PS4
PM5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM6
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
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