The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC computer assertion could be determined for this classification!


Variant: NM_000314.6(PTEN):c.44G>A (p.Arg15Lys)

CA16613142

404147 (ClinVar)

Gene: PTEN
Condition: PTEN hamartoma tumor syndrome
Inheritance Mode: Autosomal dominant inheritance
UUID: 9b8faad8-e78a-4d2f-8805-210367466752
Approved on: 2024-04-05
Published on: 2024-04-10

HGVS expressions

NM_000314.6:c.44G>A
NM_000314.6(PTEN):c.44G>A (p.Arg15Lys)
NC_000010.11:g.87864513G>A
CM000672.2:g.87864513G>A
NC_000010.10:g.89624270G>A
CM000672.1:g.89624270G>A
NC_000010.9:g.89614250G>A
NG_007466.2:g.6075G>A
NG_033079.1:g.3925C>T
ENST00000700029.2:c.44G>A
ENST00000710265.1:c.44G>A
ENST00000472832.3:c.44G>A
ENST00000688922.2:c.44G>A
ENST00000700021.1:c.44G>A
ENST00000700022.1:c.44G>A
ENST00000706954.1:c.44G>A
ENST00000706955.1:c.44G>A
ENST00000686459.1:c.44G>A
ENST00000688158.1:c.44G>A
ENST00000688308.1:c.44G>A
ENST00000693560.1:c.563G>A
ENST00000371953.8:c.44G>A
ENST00000371953.7:c.44G>A
ENST00000462694.1:n.46G>A
ENST00000487939.1:n.65G>A
ENST00000610634.1:c.-59G>A
ENST00000618586.1:n.13G>A
NM_000314.5:c.44G>A
NM_001304717.2:c.563G>A
NM_001304718.1:c.-662G>A
NM_000314.7:c.44G>A
NM_001304717.5:c.563G>A
NM_001304718.2:c.-662G>A
NM_000314.8:c.44G>A
More

Likely Pathogenic

Met criteria codes 4
PM6_Strong PM2_Supporting PS3_Moderate PP2
Not Met criteria codes 22
PM5 PM1 PM4 PM3 BS4 BS3 BS1 BS2 PVS1 BP7 BP5 BP3 BP2 BP1 BP4 PS1 PS2 PS4 BA1 PP4 PP1 PP3

Evidence Links 2

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen PTEN Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for PTEN Version 3.1.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
PTEN VCEP
NM_000314.8(PTEN):c.44G>A (p.Arg15Lys) 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 3.1.0). Please see a summary of the rules and criteria codes in the “PTEN ACMG Specifications Summary” document (assertion method column). PM2_P: Absent in large sequenced populations (PMID 27535533). PM6_S: One proband with presumed de novo occurrence (maternity/paternity not confirmed) for a patient with highly specific phenotype. (internal laboratory contributor: SCV000573362.4) 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. PS3_M: Functional studies supportive of a damaging effect on the gene or gene product. Score of this variant = -1.65 (≤ -1.11) on a high throughput phosphatase assay (PMID:29706350).
Met criteria codes
PM6_Strong
One proband with presumed de novo occurrence (maternity/paternity not confirmed) for a patient with highly specific phenotype. (internal laboratory contributor: SCV000573362.4)
PM2_Supporting
Absent in large sequenced populations in the gnomAD cohort. (PMID 27535533).
PS3_Moderate
Functional studies supportive of a damaging effect on the gene or gene product. Score of this variant = -1.65 (≤ -1.11) on a high throughput phosphatase assay (PMID:29706350).

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.
Not Met criteria codes
PM5
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
PM4
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
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
BS1
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
PVS1
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
BP5
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
BP2
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
BP4
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
PS4
This data is used toward PM6_S.
BA1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP4
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
REVEL score of 0.7 (needs to be >0.7)
Curation History
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