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]
  • See Evidence submitted by expert panel for details.

Variant: NM_000314.7(PTEN):c.165-1G>C

CA377784976

427613 (ClinVar)

Gene: PTEN
Condition: PTEN hamartoma tumor syndrome
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 1baf0f96-4866-4e7c-aa93-f3055ef6a2d5
Approved on: 2020-03-23
Published on: 2020-03-25

HGVS expressions

NM_000314.7:c.165-1G>C
NM_000314.7(PTEN):c.165-1G>C
NM_000314.5:c.165-1G>C
NM_000314.6:c.165-1G>C
NM_001304717.2:c.684-1G>C
NM_001304718.1:c.-541-5534G>C
NM_001304717.5:c.684-1G>C
NM_001304718.2:c.-541-5534G>C
NM_000314.8:c.165-1G>C
ENST00000371953.7:c.165-1G>C
ENST00000610634.1:c.63-1G>C
NC_000010.11:g.87925512G>C
CM000672.2:g.87925512G>C
NC_000010.10:g.89685269G>C
CM000672.1:g.89685269G>C
NC_000010.9:g.89675249G>C
NG_007466.2:g.67074G>C
More

Pathogenic

Met criteria codes 3
PS4_Supporting PM2 PVS1
Not Met criteria codes 19
PM1 PM4 PM5 BA1 PM6 BS3 BS1 BS4 BS2 BP7 BP5 BP4 BP2 PS3 PS2 PS1 PP2 PP3 PP1

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
PTEN VCEP
PTEN c.165-1G>C (IVS2-1G>C) 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 PS4_P: Proband(s) with phenotype specificity score of 1-1.5. (PMID 28677221)
Met criteria codes
PS4_Supporting
Susswein LR et al reported on a single patient with this variant. This paper reported pathogenetic and likely pathogenic variants found in 10,000 patients referred for NGS. Tan et al reported patient 230 as meeting relaxed CS criteria. Chen 2017 Eng Lab: 2 cases: (1) M, child age 12 (consented age 6), OFC, 57cm, penile macules, thyroid nodule = CC score of 16? per Eng notes (peds score = 7 per MP) either way 1 point; (2) M, age 44 (consented age 39), OFC: 59cm, lipoma = CC score of 7
PM2
Variant not found in gnomAD.
PVS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Not Met criteria codes
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
PM6
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
BS4
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
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
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
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
PS1
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
PP3
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
Curation History
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