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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Variant: NM_000314.7(PTEN):c.422A>C (p.His141Pro)

CA337448

216422 (ClinVar)

Gene: PTEN
Condition: PTEN hamartoma tumor syndrome
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: c9d4dbc9-56ea-4ae3-a6b9-27fc09d9501c
Approved on: 2020-06-18
Published on: 2022-09-23

HGVS expressions

NM_000314.7:c.422A>C
NM_000314.7(PTEN):c.422A>C (p.His141Pro)
NC_000010.11:g.87933181A>C
CM000672.2:g.87933181A>C
NC_000010.10:g.89692938A>C
CM000672.1:g.89692938A>C
NC_000010.9:g.89682918A>C
NG_007466.2:g.74743A>C
ENST00000686459.1:c.422A>C
ENST00000688158.1:c.*533A>C
ENST00000688308.1:c.422A>C
ENST00000688922.1:n.343A>C
ENST00000693560.1:c.941A>C
ENST00000371953.8:c.422A>C
ENST00000371953.7:c.422A>C
ENST00000498703.1:n.248A>C
ENST00000610634.1:c.320A>C
NM_000314.5:c.422A>C
NM_000314.6:c.422A>C
NM_001304717.2:c.941A>C
NM_001304718.1:c.-329A>C
NM_001304717.5:c.941A>C
NM_001304718.2:c.-329A>C
NM_000314.8:c.422A>C
NM_000314.8(PTEN):c.422A>C (p.His141Pro)
More

Likely Pathogenic

Met criteria codes 3
PS3 PP2 PM2
Not Met criteria codes 23
PVS1 BA1 PS1 PS2 PS4 PP4 PP1 PP3 PM6 PM1 PM5 PM3 PM4 BS2 BS3 BS4 BS1 BP2 BP4 BP1 BP3 BP5 BP7

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
PTEN VCEP
PTEN c.422A>C (p.His141Pro) meets criteria to be classified as likely 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). PS3: Phosphatase activity <50% of wild type (PMID 29706350) PM2: Absent in large sequenced populations (PMID 27535533) PP2: PTEN is defined by the PTEN Expert Panel as a gene that has a low rate of benign missense variation and where missense variants are a common mechanism of disease.
Met criteria codes
PS3
Matreyek: low abundance class (score = 0.133314163298692); Mighell: truncation-like range (score = -4.001333421)
PP2
This is a missense variant.
PM2
Absent in population databases.
Not Met criteria codes
PVS1
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
PS4
* Internal case data for Patient 1: female with adult-onset Lhermitte-Duclos disease, macrocephaly, multiple large fibroids at 40s (our variant identified through testing); mother with thyroid cancer, multiple large uterine fibroids at 40s (no genetic testing) * Internal case data for Patient 2: female with breast cancer at 30s, macrocephaly, polyposis, suspected neurofibroma(s); son with macrocephaly (64 cm), anteriovenous spinal epidural fistula at 20s (our variant identified through testing)
PP4
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
PP3
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
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
PM3
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
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
BS1
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
BP4
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
BP3
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
Curation History
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