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.80A>G (p.Tyr27Cys)

CA16613238

404160 (ClinVar)

Gene: PTEN
Condition: PTEN hamartoma tumor syndrome
Inheritance Mode: Autosomal dominant inheritance
UUID: d78c91f0-0265-4f61-9c40-6a7bc3309acb
Approved on: 2023-10-11
Published on: 2023-10-18

HGVS expressions

NM_000314.8:c.80A>G
NM_000314.8(PTEN):c.80A>G (p.Tyr27Cys)
NC_000010.11:g.87894025A>G
CM000672.2:g.87894025A>G
NC_000010.10:g.89653782A>G
CM000672.1:g.89653782A>G
NC_000010.9:g.89643762A>G
NG_007466.2:g.35587A>G
ENST00000686459.1:c.80A>G
ENST00000688158.1:c.*275+13587A>G
ENST00000688308.1:c.80A>G
ENST00000693560.1:c.599A>G
ENST00000371953.8:c.80A>G
ENST00000371953.7:c.80A>G
ENST00000462694.1:n.82A>G
ENST00000610634.1:c.-23A>G
NM_000314.5:c.80A>G
NM_000314.6:c.80A>G
NM_001304717.2:c.599A>G
NM_001304718.1:c.-626A>G
NM_000314.7:c.80A>G
NM_001304717.5:c.599A>G
NM_001304718.2:c.-626A>G
More

Likely Pathogenic

Met criteria codes 5
PS3_Moderate PP3 PP2 PM6_Strong PM2_Supporting
Not Met criteria codes 20
PVS1 BA1 BS4 BS3 BS1 BS2 BP5 BP7 BP2 BP3 BP4 BP1 PS2 PS1 PP1 PP4 PM3 PM1 PM4 PM5

Evidence Links 3

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.80A>G (p.Tyr27Cys) 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). PM6_S: Assumed de novo, but without confirmation of paternity and maternity in a patient with the disease and no family history in a proband(s) with phenotype specificity score of 1-1.5 (PMID: 24375884). PS3_M: Functional studies supportive of a damaging effect on the gene or gene product. Score of this variant = -1.648 (≤ -1.11) on a high throughput phosphatase assay (PMID:29706350). 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 = 0.991)
Met criteria codes
PS3_Moderate
Functional studies supportive of a damaging effect on the gene or gene product. Score of this variant = -1.648 (≤ -1.11) on a high throughput phosphatase assay (PMID:29706350). Note: discussed with team, decided to not apply criteria to Mingo given lack of positive control. Mighell et al (2018): High confidence variant, cum_score = -1.648

PP3
REVEL score > 0.7 (score of this variant = 0.991)
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.
PM6_Strong
One proband with presumed de novo occurrence (maternity/paternity not confirmed) for a patient with highly specific phenotype. (PMID: 24375884) Vanderver 2014 (PMID: 24375884): Per v3 guidelines (released 3/27/23), can bump PM6 to PM6_S for de novo occurrence with highly specific phenotype (meets criteria to count towards PS4).
PM2_Supporting
Absent in gnomAD
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
BP5
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
BP2
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
BP4
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
PS2
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
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP4
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
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
PM5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
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