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]
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  • See Evidence submitted by expert panel for details.

Variant: NM_000314.6(PTEN):c.586delC (p.His196Thrfs)

CA000526

7823 (ClinVar)

Gene: PTEN
Condition: PTEN hamartoma tumor syndrome
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 47291ab6-b17d-4e14-9acd-faae6fe9ec1e
Approved on: 2018-04-06
Published on: 2018-12-10

HGVS expressions

NM_000314.6:c.586delC
NM_000314.6(PTEN):c.586delC (p.His196Thrfs)
NC_000010.11:g.87952211del
CM000672.2:g.87952211del
NC_000010.10:g.89711968del
CM000672.1:g.89711968del
NC_000010.9:g.89701948del
NG_007466.2:g.93773del
NM_000314.5:c.586del
NM_000314.6:c.586del
NM_001304717.2:c.1105del
NM_001304718.1:c.-6del
NM_000314.7:c.586del
NM_001304717.5:c.1105del
NM_001304718.2:c.-6del
ENST00000371953.7:c.586del
ENST00000472832.2:n.13del

Pathogenic

Met criteria codes 3
PM2 PS4_Supporting PVS1
Not Met criteria codes 20
PM6 PM5 PM4 PM1 BA1 BS2 BS1 BS3 BS4 PS1 PS3 PS2 BP4 BP2 BP7 BP5 PP3 PP2 PP1 PP4

Evidence Links 1

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
PTEN VCEP
PTEN c.586delC (p.H196Tfs) 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). PS4_P: Proband(s) with phenotype specificity score of 1-1.5. (PMID 9832032)
Met criteria codes
PM2
Absent gnomAD
PS4_Supporting
PMID 9832032
17 year old French male, mild MR, macrocephaly (OFC=64 CM), GI hamartomatous polyps, hemangioma, oral papillomas, 2 cafe au lait macules, and penile freckling. Peds score = 16. PubMed:9832032
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
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
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
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
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
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.
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