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.1061C>T (p.Pro354Leu)

CA000277

142212 (ClinVar)

Gene: PTEN
Condition: PTEN hamartoma tumor syndrome
Inheritance Mode: Autosomal dominant inheritance
UUID: 88bdf077-351e-40ca-bbdf-1299b17f80e5
Approved on: 2023-10-11
Published on: 2023-10-16

HGVS expressions

NM_000314.8:c.1061C>T
NM_000314.8(PTEN):c.1061C>T (p.Pro354Leu)
NC_000010.11:g.87965321C>T
CM000672.2:g.87965321C>T
NC_000010.10:g.89725078C>T
CM000672.1:g.89725078C>T
NC_000010.9:g.89715058C>T
NG_007466.2:g.106883C>T
ENST00000686459.1:c.*647C>T
ENST00000688158.1:c.*1172C>T
ENST00000688308.1:c.1061C>T
ENST00000688922.1:c.982C>T
ENST00000693560.1:c.1580C>T
ENST00000371953.8:c.1061C>T
ENST00000371953.7:c.1061C>T
NM_000314.5:c.1061C>T
NM_000314.6:c.1061C>T
NM_001304717.2:c.1580C>T
NM_001304718.1:c.470C>T
NM_000314.7:c.1061C>T
NM_001304717.5:c.1580C>T
NM_001304718.2:c.470C>T
More

Uncertain Significance

Met criteria codes 4
PM2_Supporting BP4 BS3_Supporting PP2
Not Met criteria codes 22
PM3 PM1 PM5 PM4 PM6 BA1 BS2 PVS1 BS4 BS1 BP2 BP1 BP3 BP5 BP7 PS2 PS4 PS3 PS1 PP4 PP1 PP3

Evidence Links 1

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
PTEN c.1061C>T (p.Pro354Leu) 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). PM2_P: Present at extremely low (<0.00001, 0.001%) allele frequency in the gnomAD cohort. (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. BS3_P: Well-established functional studies show no deleterious effect: Phosphatase activity >0 (score = 0.1615) per Mighell et al. 2018 (PMID: 29706350). BP4: REVEL score < 0.5 (score=0.402) Using the Bayesian point system (PMID: 29300386) for this variant with conflicting evidence: 2 benign supporting and 2 pathogenic supporting codes get -1*2 + 1*2 points, total is 0 (VUS).
Met criteria codes
PM2_Supporting
Present at extremely low (<0.00001, 0.001%) allele frequency in the gnomAD cohort.
BP4
REVEL score < 0.5 (score=0.402)
BS3_Supporting
Well-established functional studies show no deleterious effect: Phosphatase activity >0 (score = 0.1615) per Mighell et al. 2018 (PMID: 29706350).
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.
Not Met criteria codes
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
PM5
KS: Our VCEP curated P354Q as VOUS. This criteria is not met at this time.
PM4
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
BA1
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
PVS1
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
BS1
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
BP3
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
PS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS4
GeneDx internal data: 1 SSA dx 30s. Fam hx colon, ov, panc cancers. CC score = 0.

PS3
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
PP4
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
PP3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
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