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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  • See Evidence submitted by expert panel for details.

Variant: NM_000314.6(PTEN):c.78C>T (p.Thr26=)

CA000203

184104 (ClinVar)

Gene: PTEN
Condition: PTEN hamartoma tumor syndrome
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 5ae8d67a-b184-476c-878e-aef6ec246a56
Approved on: 2020-03-23
Published on: 2020-03-30

HGVS expressions

NM_000314.6:c.78C>T
NM_000314.6(PTEN):c.78C>T (p.Thr26=)
NC_000010.11:g.87864547C>T
CM000672.2:g.87864547C>T
NC_000010.10:g.89624304C>T
CM000672.1:g.89624304C>T
NC_000010.9:g.89614284C>T
NG_007466.2:g.6109C>T
NG_033079.1:g.3891G>A
ENST00000686459.1:c.78C>T
ENST00000688158.1:c.78C>T
ENST00000688308.1:c.78C>T
ENST00000693560.1:c.597C>T
ENST00000371953.8:c.78C>T
ENST00000371953.7:c.78C>T
ENST00000462694.1:n.80C>T
ENST00000487939.1:n.99C>T
ENST00000610634.1:c.-25C>T
ENST00000618586.1:n.47C>T
NM_000314.5:c.78C>T
NM_001304717.2:c.597C>T
NM_001304718.1:c.-628C>T
NM_000314.7:c.78C>T
NM_001304717.5:c.597C>T
NM_001304718.2:c.-628C>T
NM_000314.8:c.78C>T
NM_000314.8(PTEN):c.78C>T (p.Thr26=)
More

Uncertain Significance

Met criteria codes 2
PM2 BP7
Not Met criteria codes 24
PS1 PS2 PS3 PS4 PP1 PP2 PP3 PP4 PVS1 PM1 PM6 PM3 PM5 PM4 BA1 BS2 BS1 BS4 BS3 BP4 BP3 BP1 BP2 BP5

Evidence Links 1

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
PTEN VCEP
PTEN c.78C>T (p.T26=) is currently classified as a variant of uncertain significance 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). PM2: Present at extremely low (<0.00001, 0.001%) allele frequency in the gnomAD cohort. (PMID 27535533). BP7: Variant is synonymous (silent), nucleotide is not conserved, and no splicing impact is predicted.
Met criteria codes
PM2
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
Not Met criteria codes
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
PS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS4
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
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
PP4
PubMed:30287823
PVS1
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
PM6
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
PM5
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
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
BS1
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
BS3
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
BP3
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
BP2
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
Curation History
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