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_000314.8(PTEN):c.400A>G (p.Met134Val)

CA377482334

2033861 (ClinVar)

Gene: PTEN (HGNC:5728)
Condition: PTEN hamartoma tumor syndrome (MONDO:0017623)
Inheritance Mode: Autosomal dominant inheritance
UUID: c8832939-b814-49d6-8fd9-c35f3d40adbc
Approved on: 2026-06-17
Published on: 2026-06-26

HGVS expressions

NM_000314.8:c.400A>G
NM_000314.8(PTEN):c.400A>G (p.Met134Val)
NC_000010.11:g.87933159A>G
CM000672.2:g.87933159A>G
NC_000010.10:g.89692916A>G
CM000672.1:g.89692916A>G
NC_000010.9:g.89682896A>G
NG_007466.2:g.74721A>G
ENST00000700029.2:c.400A>G
ENST00000710265.1:c.400A>G
ENST00000472832.3:c.400A>G
ENST00000688158.2:n.1135A>G
ENST00000688922.2:c.*230A>G
ENST00000700021.1:c.355A>G
ENST00000700022.1:c.400A>G
ENST00000700029.1:c.234A>G
ENST00000706954.1:c.400A>G
ENST00000706955.1:c.*435A>G
ENST00000686459.1:c.400A>G
ENST00000688158.1:c.*511A>G
ENST00000688308.1:c.400A>G
ENST00000688922.1:c.321A>G
ENST00000693560.1:c.919A>G
ENST00000371953.8:c.400A>G
ENST00000371953.7:c.400A>G
ENST00000498703.1:n.226A>G
ENST00000610634.1:c.298A>G
NM_000314.5:c.400A>G
NM_000314.6:c.400A>G
NM_001304717.2:c.919A>G
NM_001304718.1:c.-351A>G
NM_000314.7:c.400A>G
NM_001304717.5:c.919A>G
NM_001304718.2:c.-351A>G
More

Pathogenic

Met criteria codes 6
PS2 PP3 PP2 PS3_Moderate PM6 PM2_Supporting
Not Met criteria codes 2
PM1 BP1

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen PTEN Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for PTEN Version 3.2.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
PTEN VCEP
PTEN c.400A>G (p.Met134Val) meets criteria to be classified as Likely Pathogenic for PTEN Hamartoma Tumor syndrome in an autosomal dominant manner using modified ACMG criteria (ACMG Classification Rules Specified for PTEN Variant Curation version 3.2.0). Please see a summary of the rules and criteria codes in the “PTEN ACMG Specifications Summary” document (assertion method column). PS2: De novo (both maternity and paternity confirmed) observation in a patient with the disease and no family history. PM6: Assumed de novo, but without confirmation of paternity and maternity in a patient with the disease and no family history. PS4: Proband(s) with phenotype specificity score of 2-3.5. (PMID 40564777). 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. PP3: REVEL score 0.75(score of this variant =0.86). PM2_P: Absent in large sequenced populations OR present at extremely low (<0.00001, 0.001%) allele frequency in the gnomAD cohort. (PMID 27535533).
Met criteria codes
PS2
Confirmed de novo patient with macrocephaly and motor delay
PP3
REVEL score 0.86 >0.75
PP2
missense variant
PS3_Moderate
Mighell et al = -1.608 < -1.1
PM6
assumed de novo patient with Macrocephaly and developmental delay
PM2_Supporting
Absent from gnomAD
Not Met criteria codes
PM1
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
Curation History
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