Variant: NM_000314.6(PTEN):c.801+1delG

CA16613026

404140 (ClinVar)

Gene: PTEN

Condition: PTEN hamartoma tumor syndrome

Inheritance Mode: Autosomal dominant inheritance

UUID: d8470abc-cd84-4dd7-aa9d-def2c9c878aa

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
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
ENST00000371953.7:c.801+1del
ENST00000472832.2:n.228+1del

Pathogenic

• Met criteria codes: PM2 PS4_Supporting PVS1

• Not Met criteria codes: PM6 PM4 PM1 PM5 BS2 BS1 BS3 BS4 BP4 BP2 BP5 BP7 PS3 PS1 PS2 BA1 PP2 PP3 PP1

Expert Panel

PTEN VCEP

Criteria Specification Information

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

• PM2: No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
• 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.
• PVS1: No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline

Not Met criteria codes

• PM6: 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
• PM5: 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
• 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
• 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
• 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
• PS3: 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
• BA1: 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

Approved on: 2020-03-23

Published on: 2020-03-25