Evidence Repository - Clinical Genome Resources

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.633C>G (p.Cys211Trp)

CA10603125

279878 (ClinVar)

Gene: PTEN

Condition: PTEN hamartoma tumor syndrome

Inheritance Mode: Autosomal dominant inheritance

Link to MONDO

UUID: d2e370c6-311c-4c89-a383-c956681b1dfc

Approved on: 2020-06-18

Published on: 2022-09-23

HGVS expressions

NM_000314.7:c.633C>G

NM_000314.7(PTEN):c.633C>G (p.Cys211Trp)

NC_000010.11:g.87952258C>G

CM000672.2:g.87952258C>G

NC_000010.10:g.89712015C>G

CM000672.1:g.89712015C>G

NC_000010.9:g.89701995C>G

NG_007466.2:g.93820C>G

ENST00000686459.1:c.*219C>G

ENST00000688158.1:c.*744C>G

ENST00000688308.1:c.633C>G

ENST00000688922.1:n.554C>G

ENST00000693560.1:c.1152C>G

ENST00000371953.8:c.633C>G

ENST00000371953.7:c.633C>G

ENST00000472832.2:n.60C>G

NM_000314.5:c.633C>G

NM_000314.6:c.633C>G

NM_001304717.2:c.1152C>G

NM_001304718.1:c.42C>G

NM_001304717.5:c.1152C>G

NM_001304718.2:c.42C>G

NM_000314.8:c.633C>G

NM_000314.8(PTEN):c.633C>G (p.Cys211Trp)

Pathogenic

PS2_Very Strong PM2 PS4_Moderate PP2

Evidence Links 0

Expert Panel

PTEN VCEP

Criteria Specification Information

Criteria Specifications for this VCEP

Evidence submitted by expert panel

PTEN VCEP

PTEN c.633C>G (p.Cys211Trp) 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). PS2_VS: At least two proven OR one proven plus two assumed de novo observations in a patient with the disease and no family history. (internal laboratory contributor(s) SCV000329477.6) PS4_M: Probands with phenotype specificity score of 2-3.5. (PMID 24375884, internal laboratory contributor(s) SCV000329477.6) 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.

PS2_Very Strong

GeneDx reports 3 patients with confirmed de novo by WES trio

PM2

Absent from gnomAD

PS4_Moderate

Vanderver et al (PMID 24375884) patient #21 with macrocephaly, dev delay, and enlarged periventricular spaces; GeneDx 1 patient reported with extreme macrocephaly (+4-5SD), dev delay, hemihypertrophy, hypopigmented spot, and macrosomia

PP2

Missense is a known disease mechanism

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