Evidence Repository
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_000314.7(PTEN):c.947T>C (p.Leu316Pro)

CA16619068

418653 (ClinVar)

Gene: PTEN
Condition: PTEN hamartoma tumor syndrome
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 255886f5-38f4-41db-b167-02609497e697
Approved on: 2024-02-09
Published on: 2024-03-04

HGVS expressions

NM_000314.7:c.947T>C
NM_000314.7(PTEN):c.947T>C (p.Leu316Pro)
NC_000010.11:g.87961039T>C
CM000672.2:g.87961039T>C
NC_000010.10:g.89720796T>C
CM000672.1:g.89720796T>C
NC_000010.9:g.89710776T>C
NG_007466.2:g.102601T>C
ENST00000700029.2:c.1040T>C
ENST00000710265.1:c.947T>C
ENST00000472832.3:c.947T>C
ENST00000688158.2:n.1682T>C
ENST00000688922.2:c.*777T>C
ENST00000700021.1:c.902T>C
ENST00000700022.1:c.*286T>C
ENST00000700023.1:n.2105T>C
ENST00000700024.1:n.2339T>C
ENST00000700025.1:n.1716T>C
ENST00000700026.1:n.584T>C
ENST00000706954.1:c.947T>C
ENST00000706955.1:c.*982T>C
ENST00000686459.1:c.*533T>C
ENST00000688158.1:c.*1058T>C
ENST00000688308.1:c.947T>C
ENST00000688922.1:c.868T>C
ENST00000693560.1:c.1466T>C
ENST00000371953.8:c.947T>C
ENST00000371953.7:c.947T>C
ENST00000472832.2:c.374T>C
NM_000314.5:c.947T>C
NM_000314.6:c.947T>C
NM_001304717.2:c.1466T>C
NM_001304718.1:c.356T>C
NM_001304717.5:c.1466T>C
NM_001304718.2:c.356T>C
NM_000314.8:c.947T>C
NM_000314.8(PTEN):c.947T>C (p.Leu316Pro)
More

Likely Pathogenic

Met criteria codes 6
PP3 PP2 PS4_Supporting PM2_Supporting PM6 PS3_Moderate
Not Met criteria codes 20
PS2 PS1 PP4 PP1 PVS1 PM3 PM1 PM4 PM5 BA1 BS4 BS3 BS1 BS2 BP5 BP7 BP2 BP3 BP4 BP1

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.947T>C (p.Leu316Pro) 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: Assumed de novo, but without confirmation of paternity and maternity in a patient with the disease and no family history. ( internal laboratory contributor: SCV000565874.4) PS3_M: Functional studies showing a damaging effect on protein function. Phosphatase activity ≤ -1.11 per Mighell et al. 2018 (PMID: 29706350). This variant: score of -1.74442367. PM2: 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 =0.77) PS4_P: Proband with phenotype specificity score of 2-3.5. (PMID:30311381, internal laboratory contributor: SCV000565874.4)
Met criteria codes
PP3
in silico REVEL score of 0.77 (>0.7)
PP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS4_Supporting
Proband with phenotype specificity score of 2-3.5. (PMID:30311381, internal laboratory contributor: SCV000565874.4)
PM2_Supporting
absent gnomAD
PM6
Assumed de novo, but without confirmation of paternity and maternity in a patient with the disease and no family history. ( internal laboratory contributor: SCV000565874.4)
PS3_Moderate
Mighell et al. 2018 PMID: 29706350: Lipid phosphatase activity score, -1.74442367 (TRUE).
Not Met criteria codes
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
PP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP1
2 meioses.
PVS1
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
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
Curation History
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