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Variant: NM_000314.8(PTEN):c.16A>G (p.Lys6Glu)

CA377781810

644390 (ClinVar)

Gene: PTEN
Condition: PTEN hamartoma tumor syndrome
Inheritance Mode: Autosomal dominant inheritance
UUID: 42dd26e4-54dd-4c3b-abdc-5f9f3dac0795
Approved on: 2021-06-04
Published on: 2022-09-30

HGVS expressions

NM_000314.8:c.16A>G
NM_000314.8(PTEN):c.16A>G (p.Lys6Glu)
NC_000010.11:g.87864485A>G
CM000672.2:g.87864485A>G
NC_000010.10:g.89624242A>G
CM000672.1:g.89624242A>G
NC_000010.9:g.89614222A>G
NG_007466.2:g.6047A>G
NG_033079.1:g.3953T>C
ENST00000686459.1:c.16A>G
ENST00000688158.1:c.16A>G
ENST00000688308.1:c.16A>G
ENST00000693560.1:c.535A>G
ENST00000371953.8:c.16A>G
ENST00000371953.7:c.16A>G
ENST00000462694.1:n.18A>G
ENST00000487939.1:n.37A>G
ENST00000610634.1:c.-87A>G
NM_000314.5:c.16A>G
NM_000314.6:c.16A>G
NM_001304717.2:c.535A>G
NM_001304718.1:c.-690A>G
NM_000314.7:c.16A>G
NM_001304717.5:c.535A>G
NM_001304718.2:c.-690A>G
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Pathogenic

Met criteria codes 5
PS2_Very Strong PS3_Supporting PP2 PM2 PS4_Moderate

Evidence Links 4

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.16A>G (p.Lys6Glu) meets criteria to be classified as 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). PS2_VS: One proven plus two assumed de novo observations in a patient with the disease and no family history. (internal laboratory contributor(s) SCV001369131.2, SCV001819316.1) PS4_M: Probands with phenotype specificity score of 2-3.5. (internal laboratory contributor(s) SCV001819316.1) 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. PS3_P: Abnormal in vitro cellular assay or transgenic model with phenotype different from wild type that does not meet PS3. (PMID 32366478, PMID 32350270, PMID 29706350)
Met criteria codes
PS2_Very Strong
Internal lab cases SCV001369131.2, SCV001819316.1
PS3_Supporting
VCEP approved criteria based on combined published evidence suggesting some functional impact, but not strong enough for full PS3

PP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM2
absent
PS4_Moderate
Internal lab cases, 3 total phenotype specificity points (SCV001819316.1 )
Curation History
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