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_000314.7(PTEN):c.579G>A (p.Leu193=)

CA000523

135911 (ClinVar)

Gene: PTEN
Condition: PTEN hamartoma tumor syndrome
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 28570ef1-4ba1-41b7-826e-bc8dda6b7fd3
Approved on: 2019-11-22
Published on: 2019-12-04

HGVS expressions

NM_000314.7:c.579G>A
NM_000314.7(PTEN):c.579G>A (p.Leu193=)
NC_000010.11:g.87952204G>A
CM000672.2:g.87952204G>A
NC_000010.10:g.89711961G>A
CM000672.1:g.89711961G>A
NC_000010.9:g.89701941G>A
NG_007466.2:g.93766G>A
NM_000314.5:c.579G>A
NM_000314.6:c.579G>A
NM_001304717.2:c.1098G>A
NM_001304718.1:c.-13G>A
NM_001304717.5:c.1098G>A
NM_001304718.2:c.-13G>A
ENST00000371953.7:c.579G>A
ENST00000472832.2:n.6G>A

Likely Benign

Met criteria codes 2
BP4 BS1
Not Met criteria codes 20
BP2 BP7 BP5 PVS1 PS3 PS2 PS4 PS1 PP2 PP3 PP1 PM4 PM1 PM5 PM2 PM6 BA1 BS2 BS3 BS4

Evidence Links 2

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
PTEN VCEP
PTEN c.579G>A (p.Leu193=) meets criteria to be classified as likely benign 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). BS1: Allele frequency of 0.00125 (0.125%, 13/10,360 alleles) in the Ashkenazi Jewish subpopulation of the gnomAD cohort. (PMID 27535533) BP4: Synonymous variant where at least 2 out of 3 in silico models predict no splicing impact.
Met criteria codes
BP4
The in silico tools of MaxEnt, NNS, and HSF show no difference between wildtype and variant (values = 0%).
BS1
Per BS1 criteria, gnomAD ASJ population has allele frequency of > 0.1% with ≥2,000 alleles tested and variant present in ≥5 alleles.
Not Met criteria codes
BP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP7
Not met because our variant is highly conserved across species in UCSC.
BP5
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
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
PS4
Please also see comment for criteria PP4 below.
PubMed:25669429
PubMed:16773562
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
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
PM2
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
BA1
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
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
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