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.314G>A (p.Cys105Tyr)

CA000393

142261 (ClinVar)

Gene: PTEN
Condition: PTEN hamartoma tumor syndrome
Inheritance Mode: Autosomal dominant inheritance
UUID: dce7b398-e447-420b-8da1-a51cbf6a8e69

HGVS expressions

NM_000314.6:c.314G>A
NM_000314.6(PTEN):c.314G>A (p.Cys105Tyr)
NC_000010.11:g.87933073G>A
CM000672.2:g.87933073G>A
NC_000010.10:g.89692830G>A
CM000672.1:g.89692830G>A
NC_000010.9:g.89682810G>A
NG_007466.2:g.74635G>A
ENST00000686459.1:c.314G>A
ENST00000688158.1:c.*425G>A
ENST00000688308.1:c.314G>A
ENST00000688922.1:n.235G>A
ENST00000693560.1:c.833G>A
ENST00000371953.8:c.314G>A
ENST00000371953.7:c.314G>A
ENST00000498703.1:n.140G>A
ENST00000610634.1:c.212G>A
NM_000314.5:c.314G>A
NM_001304717.2:c.833G>A
NM_001304718.1:c.-437G>A
NM_000314.7:c.314G>A
NM_001304717.5:c.833G>A
NM_001304718.2:c.-437G>A
NM_000314.8:c.314G>A
NM_000314.8(PTEN):c.314G>A (p.Cys105Tyr)

Likely Pathogenic

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

Evidence Links 3

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.314G>A (p.Cys105Tyr) 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). PM2: Absent in large sequenced populations (PMID 27535533). PM6: Assumed de novo, but without confirmation of paternity and maternity in a patient with the disease and no family history. (internal laboratory contributor ClinVar Organization ID 26957) 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 ClinVar Organization ID 26957)
Met criteria codes
PP2
I agree (FH)
PM6
Internal case. I agree (FH)
PM2
Absent in gnomAD I agree (FH)
PS4_Supporting
GDx internal case with peds score = 8.
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
I agree (FH)
BP4
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
BS4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS3
BS1
Absent in gnomAD I agree (FH)
PP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP4
GDx internal case with peds score = 8. I agree (FH) Criteria moved to PS4 section.

PP3
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
Could curate C105F if needed to help this get to PATH.
PS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS3
PS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BA1
Absent in gnomAD I agree (FH)
PVS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Approved on: 2021-06-04
Published on: 2022-09-30
The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. If you have questions about the information contained on this website, please see a health care professional.
¤ Powered by BCM's Genboree.