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_000314.6(PTEN):c.209T>C (p.Leu70Pro)

CA000350

7826 (ClinVar)

Gene: PTEN
Condition: PTEN hamartoma tumor syndrome
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 12985d15-e1e7-45ab-b3e5-48e082086d4d
Approved on: 2021-06-04
Published on: 2022-09-30

HGVS expressions

NM_000314.6:c.209T>C
NM_000314.6(PTEN):c.209T>C (p.Leu70Pro)
NC_000010.11:g.87925557T>C
CM000672.2:g.87925557T>C
NC_000010.10:g.89685314T>C
CM000672.1:g.89685314T>C
NC_000010.9:g.89675294T>C
NG_007466.2:g.67119T>C
ENST00000686459.1:c.209T>C
ENST00000688158.1:c.*320T>C
ENST00000688308.1:c.209T>C
ENST00000688922.1:n.78T>C
ENST00000693560.1:c.728T>C
ENST00000371953.8:c.209T>C
ENST00000371953.7:c.209T>C
ENST00000498703.1:n.35T>C
ENST00000610634.1:c.107T>C
NM_000314.5:c.209T>C
NM_001304717.2:c.728T>C
NM_001304718.1:c.-541-5489T>C
NM_000314.7:c.209T>C
NM_001304717.5:c.728T>C
NM_001304718.2:c.-541-5489T>C
NM_000314.8:c.209T>C
NM_000314.8(PTEN):c.209T>C (p.Leu70Pro)
More

Likely Pathogenic

Met criteria codes 4
PM2 PS3 PP2 PS4_Supporting
Not Met criteria codes 22
BP5 BP7 BP2 BP3 BP1 BP4 PM3 PM1 PM4 PM5 PM6 PVS1 PS2 PS1 BA1 PP1 PP4 PP3 BS4 BS3 BS1 BS2

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen PTEN Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines Version 2

PDF
Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
PTEN VCEP
PTEN c.209T>C (p.Leu70Pro) meets criteria to be classified as likely pathogenic for PTEN Hamartoma Tumor syndrome in an autosomal dominant manner using modified ACMG criteria (PMID 30311380). Please see a summary of the rules and criteria codes in the “PTEN ACMG Specifications Summary” document (assertion method column). PS3: Phosphatase activity <50% of wild type (PMID 29706350) 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. PS4_P: Proband(s) with phenotype specificity score of 1-1.5. (internal laboratory contributor(s) ClinVar Organization ID: 26957)
Met criteria codes
PM2
Absent gnomAD
PS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS4_Supporting
Internal lab case ClinVar Organization ID: 26957 1 phenotype specificity point. Pt also published in PMID
Not Met criteria codes
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
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
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
PM6
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
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
BA1
Absent gnomAD
PP1
1 meiosis internal lab case ClinVar Organization ID: 26957; proband infant F with macrocephaly, variant also present in brother with macro, lipoma, dev delay
PP4
Moved to PS4. 3 internal lab cases: #1 Young adult F, eth unk, Macrocephaly, FTC dx late teens, goiter, lipoma dx 3. Min CC score = 21. #2: 40s Asian F, BrCA dx 40s, goiter dx late 20s. OFC not provided. CC score = 5. #3: Pediatric M, eth unk, Macrocephaly, lipoma, dev delay. Peds score = 5, 1 PP4 point. His baby sister with macrocephaly also positive: 1 meiosis
PP3
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
Absent gnomAD
BS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
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