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.368A>G (p.His123Arg)

CA000418

7816 (ClinVar)

Gene: PTEN
Condition: PTEN hamartoma tumor syndrome
Inheritance Mode: Autosomal dominant inheritance
UUID: 4ed5aa0a-d183-4c08-b6f6-23ffb9904a78
Approved on: 2021-04-29
Published on: 2021-04-29

HGVS expressions

NM_000314.6:c.368A>G
NM_000314.6(PTEN):c.368A>G (p.His123Arg)
NC_000010.11:g.87933127A>G
CM000672.2:g.87933127A>G
NC_000010.10:g.89692884A>G
CM000672.1:g.89692884A>G
NC_000010.9:g.89682864A>G
NG_007466.2:g.74689A>G
ENST00000371953.8:c.368A>G
ENST00000371953.7:c.368A>G
ENST00000610634.1:c.266A>G
NM_000314.5:c.368A>G
NM_001304717.2:c.887A>G
NM_001304718.1:c.-383A>G
NM_000314.7:c.368A>G
NM_001304717.5:c.887A>G
NM_001304718.2:c.-383A>G
NM_000314.8:c.368A>G
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Pathogenic

Met criteria codes 5
PM1 PM6 PM2 PS3 PP2

Evidence Links 1

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
PTEN VCEP
PTEN c.368A>G (p.His123Arg) 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). PS3: Phosphatase activity <50% of wild type (PMID 29706350) PM1: Located at a residue within a catalytic motif as defined by the ClinGen PTEN Expert Panel. PM2: Absent in large sequenced populations PM6: Assumed de novo, but without confirmation of paternity and maternity in a patient with the disease and no family history. (PMID 10234502) 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
PM1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM6
Nelen 1999 PMID 10234502
PM2
Absent in gnomAD
PS3
Matreyek: Low abundance class (score = 0.407828388) [score is greater than 0.25, so cannot apply PS3_Supporting to Matreyek results]; Mighell: truncation-like range (score = -3.834466422)

PP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
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