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_000314.6(PTEN):c.801+1delG

CA16613026

404140 (ClinVar)

Gene: PTEN
Condition: PTEN hamartoma tumor syndrome
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: d8470abc-cd84-4dd7-aa9d-def2c9c878aa
Approved on: 2020-03-23
Published on: 2020-03-25

HGVS expressions

NM_000314.6:c.801+1delG
NM_000314.6(PTEN):c.801+1delG
NC_000010.11:g.87958020del
CM000672.2:g.87958020del
NC_000010.10:g.89717777del
CM000672.1:g.89717777del
NC_000010.9:g.89707757del
NG_007466.2:g.99582del
ENST00000700029.2:c.801+1del
ENST00000710265.1:c.801+1del
ENST00000472832.3:c.801+1del
ENST00000688158.2:n.1536+1del
ENST00000688922.2:c.*631+1del
ENST00000700021.1:c.756+1del
ENST00000700022.1:c.*140+1del
ENST00000700023.1:n.1959+1del
ENST00000700024.1:n.2193+1del
ENST00000700025.1:n.1570+1del
ENST00000700026.1:n.438+1del
ENST00000700029.1:c.635+1del
ENST00000706954.1:c.801+1del
ENST00000706955.1:c.*836+1del
ENST00000686459.1:c.*387+1del
ENST00000688158.1:c.*912+1del
ENST00000688308.1:c.801+1del
ENST00000688922.1:c.722+1del
ENST00000693560.1:c.1320+1del
ENST00000371953.8:c.801+1del
ENST00000371953.7:c.801+1del
ENST00000472832.2:c.228+1del
NM_000314.5:c.801+1del
NM_000314.6:c.801+1del
NM_001304717.2:c.1320+1del
NM_001304718.1:c.210+1del
NM_000314.7:c.801+1del
NM_001304717.5:c.1320+1del
NM_001304718.2:c.210+1del
NM_000314.8:c.801+1del
More

Pathogenic

Met criteria codes 3
PS4_Supporting PM2 PVS1
Not Met criteria codes 23
BP5 BP7 BP4 BP3 BP1 BP2 BA1 PS1 PS2 PS3 PP1 PP2 PP3 PP4 PM6 PM1 PM3 PM5 PM4 BS2 BS1 BS4 BS3

Evidence Links 1

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
PTEN VCEP
PTEN c.801+1delG (IVS7+1delG) 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 23335809)
Met criteria codes
PS4_Supporting
Identified in patient #122, CC score = 34, 1 phenotype specificity point. Mucocutaneous lesions, facial papules, skin oral mucosal papillomatosis, acral keratoses, macrocephaly, GI polyps, lipomas/vascular lesions, GU lesions, benign thyroid disease, benign breast disease, malignant breast, melanoma. Personal communication from Dr. Longy: Cranial perimeter at 43 years measured 61 cm. Notion of glycogenic acanthosis of the esophagus, glandulocystic polyps of the stomach and hamartomatous polyps of the colon.
PubMed:23335809
PM2
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
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
BP4
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
BP2
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
PS1
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
PS3
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
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
PP4
See PS4
PM6
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
PM3
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
BS2
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
BS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
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