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]
  • See Evidence submitted by expert panel for details.

Variant: NM_000314.6(PTEN):c.698G>A (p.Arg233Gln)

CA060404

376510 (ClinVar)

Gene: PTEN
Condition: PTEN hamartoma tumor syndrome
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 84ca1fb2-bf36-42c2-8262-5a470ed8dfa7
Approved on: 2019-03-05
Published on: 2019-07-23

HGVS expressions

NM_000314.6:c.698G>A
NM_000314.6(PTEN):c.698G>A (p.Arg233Gln)
NC_000010.11:g.87957916G>A
CM000672.2:g.87957916G>A
NC_000010.10:g.89717673G>A
CM000672.1:g.89717673G>A
NC_000010.9:g.89707653G>A
NG_007466.2:g.99478G>A
ENST00000700029.2:c.698G>A
ENST00000710265.1:c.698G>A
ENST00000472832.3:c.698G>A
ENST00000688158.2:n.1433G>A
ENST00000688922.2:c.*528G>A
ENST00000700021.1:c.653G>A
ENST00000700022.1:c.*37G>A
ENST00000700023.1:n.1856G>A
ENST00000700024.1:n.2090G>A
ENST00000700025.1:n.1467G>A
ENST00000700026.1:n.335G>A
ENST00000700029.1:c.532G>A
ENST00000706954.1:c.698G>A
ENST00000706955.1:c.*733G>A
ENST00000686459.1:c.*284G>A
ENST00000688158.1:c.*809G>A
ENST00000688308.1:c.698G>A
ENST00000688922.1:c.619G>A
ENST00000693560.1:c.1217G>A
ENST00000371953.8:c.698G>A
ENST00000371953.7:c.698G>A
ENST00000472832.2:c.125G>A
NM_000314.5:c.698G>A
NM_001304717.2:c.1217G>A
NM_001304718.1:c.107G>A
NM_000314.7:c.698G>A
NM_001304717.5:c.1217G>A
NM_001304718.2:c.107G>A
NM_000314.8:c.698G>A
More

Uncertain Significance

Met criteria codes 3
BS3_Supporting PP2 PM2
Not Met criteria codes 22
BS1 BS4 BS2 PS1 PS2 PS3 PS4 BP5 BP7 BP4 BP3 BP1 BP2 PVS1 BA1 PP1 PP3 PM6 PM1 PM3 PM5 PM4

Evidence Links 2

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
PTEN VCEP
PTEN c.698G>A (p.R233Q) 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). 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. BS3_P: In vitro or in vivo functional study or studies showing no damaging effect on protein function but BS3 not met. (PMID 29706350)
Met criteria codes
BS3_Supporting
Mighell WT-like phosphatase results.
Variant score 0.116 (WT-like range) on high throughput lipid phosphatase assay. PubMed:29706350
Variant inserted into HA1E (human epithelial kidney) cells - showed gene expression pattern similar to WT. No phosphatase/other assays done to which criteria can be applied. PubMed:27147599
PP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM2
1 allele gnomAD
Not Met criteria codes
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
BS2
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
PS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS4
CC score = 0
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
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
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
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
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
Curation History
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