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]
Link to SEPIO compliant JSON-LD document
  • See Evidence submitted by expert panel for details.

Variant: NM_000314.6(PTEN):c.766G>T (p.Glu256Ter)

CA000569

7828 (ClinVar)

Gene: PTEN
Condition: PTEN hamartoma tumor syndrome
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 4284ff17-816f-4321-a0b3-e3baeb0afc95

HGVS expressions

NM_000314.6:c.766G>T
NM_000314.6(PTEN):c.766G>T (p.Glu256Ter)
NM_000314.5:c.766G>T
NM_001304717.2:c.1285G>T
NM_001304718.1:c.175G>T
NM_000314.7:c.766G>T
NM_001304717.5:c.1285G>T
NM_001304718.2:c.175G>T
ENST00000371953.7:c.766G>T
ENST00000472832.2:n.193G>T
NC_000010.11:g.87957984G>T
CM000672.2:g.87957984G>T
NC_000010.10:g.89717741G>T
CM000672.1:g.89717741G>T
NC_000010.9:g.89707721G>T
NG_007466.2:g.99546G>T

Pathogenic

Met criteria codes 4
PVS1 PS4_Supporting PM2 PM6
Not Met criteria codes 19
PS1 PS3 PS2 PP3 PP2 PP1 PP4 BA1 BS2 BS1 BS3 BS4 PM5 PM4 PM1 BP4 BP2 BP7 BP5

Evidence Links 1

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
PTEN VCEP
PTEN c.766G>T (p.E256X) 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). PVS1: Null variant predicted to result in nonsense-mediated decay or causing truncation/frameshift at or 5’ to c.1121 (NM_000314.4). 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. (PMID 9832032) PS4_P: Proband(s) with phenotype specificity score of 1-1.5. (PMID 9832032)
Met criteria codes
PVS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS4_Supporting
PMID: 9832032
Variant in a 2yo male with macrocephaly (+4.5SD), 2 lipomas, psychomotor retardation. Peds score = 6, 1 PP4 point. PubMed:9832032
PM2
Absent gnomAD
PM6
PMID 9832032
Not Met criteria codes
PS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS3
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
PP3
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
PP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP4
Wrapped into PS4.
BA1
Absent gnomAD
BS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS1
Absent gnomAD
BS3
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
PM5
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
PM1
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
BP2
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
BP5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Approved on: 2018-04-06
Published on: 2018-12-10
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