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_000546.6(TP53):c.523C>G (p.Arg175Gly)

CA16603066

376649 (ClinVar)

Gene: TP53
Condition: Li-Fraumeni syndrome
Inheritance Mode: Autosomal dominant inheritance
UUID: fd72fc13-1dd7-4c83-938d-845d8cfb8668
Approved on: 2024-09-06
Published on: 2024-09-06

HGVS expressions

NM_000546.6:c.523C>G
NM_000546.6(TP53):c.523C>G (p.Arg175Gly)
NC_000017.11:g.7675089G>C
CM000679.2:g.7675089G>C
NC_000017.10:g.7578407G>C
CM000679.1:g.7578407G>C
NC_000017.9:g.7519132G>C
NG_017013.2:g.17462C>G
ENST00000503591.2:c.523C>G
ENST00000508793.6:c.523C>G
ENST00000509690.6:c.127C>G
ENST00000514944.6:c.244C>G
ENST00000604348.6:c.502C>G
ENST00000269305.9:c.523C>G
ENST00000269305.8:c.523C>G
ENST00000359597.8:c.523C>G
ENST00000413465.6:c.523C>G
ENST00000420246.6:c.523C>G
ENST00000445888.6:c.523C>G
ENST00000455263.6:c.523C>G
ENST00000504290.5:c.127C>G
ENST00000504937.5:c.127C>G
ENST00000505014.5:n.779C>G
ENST00000509690.5:c.127C>G
ENST00000510385.5:c.127C>G
ENST00000514944.5:c.244C>G
ENST00000574684.1:n.31C>G
ENST00000610292.4:c.406C>G
ENST00000610538.4:c.406C>G
ENST00000610623.4:c.46C>G
ENST00000615910.4:c.490C>G
ENST00000617185.4:c.523C>G
ENST00000618944.4:c.46C>G
ENST00000619186.4:c.46C>G
ENST00000619485.4:c.406C>G
ENST00000620739.4:c.406C>G
ENST00000622645.4:c.406C>G
ENST00000635293.1:c.406C>G
NM_000546.5:c.523C>G
NM_001126112.2:c.523C>G
NM_001126113.2:c.523C>G
NM_001126114.2:c.523C>G
NM_001126115.1:c.127C>G
NM_001126116.1:c.127C>G
NM_001126117.1:c.127C>G
NM_001126118.1:c.406C>G
NM_001276695.1:c.406C>G
NM_001276696.1:c.406C>G
NM_001276697.1:c.46C>G
NM_001276698.1:c.46C>G
NM_001276699.1:c.46C>G
NM_001276760.1:c.406C>G
NM_001276761.1:c.406C>G
NM_001276695.2:c.406C>G
NM_001276696.2:c.406C>G
NM_001276697.2:c.46C>G
NM_001276698.2:c.46C>G
NM_001276699.2:c.46C>G
NM_001276760.2:c.406C>G
NM_001276761.2:c.406C>G
NM_001126112.3:c.523C>G
NM_001126113.3:c.523C>G
NM_001126114.3:c.523C>G
NM_001126115.2:c.127C>G
NM_001126116.2:c.127C>G
NM_001126117.2:c.127C>G
NM_001126118.2:c.406C>G
NM_001276695.3:c.406C>G
NM_001276696.3:c.406C>G
NM_001276697.3:c.46C>G
NM_001276698.3:c.46C>G
NM_001276699.3:c.46C>G
NM_001276760.3:c.406C>G
NM_001276761.3:c.406C>G
More

Pathogenic

Met criteria codes 6
PP3_Moderate PS3 PM5 PM1 PM2_Supporting PS4_Supporting
Not Met criteria codes 5
BA1 BS1 BS2 BP4 PP4

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen TP53 Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for TP53 Version 2.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
TP53 VCEP
The NM_000546.6: c.523C>G variant in TP53 is a missense variant predicted to cause substitution of arginine by glycine at amino acid 175 (p.Arg175Gly). This variant has been reported in 2 unrelated probands meeting Revised Chompret criteria. Based on this evidence, this variant scores 1 total point meeting the TP53 VCEP phenotype scoring criteria of 1-1.5 points. (PS4_Supporting; PMIDs: 11370630, 25927356). This variant has an allele frequency of 0.000002542 (3/1180042 alleles) in the European (non-Finnish) population in gnomAD v4.1.0 which is lower than the Clingen TP53 VCEP threshold (<0.00004) for PM2_Supporting, and therefore meets this criterion (PM2_Supporting). Another missense variant(c.524G>A, p.Arg175His) (ClinVar Variation ID: 12374), in the same codon has been classified as pathogenic for Li-Fraumeni syndrome by the ClinGen TP53 VCEP’s specifications. (PM5). This variant resides within a codon (NM_00546.4: 175, 245, 248, 249, 273, 282) of TP53 that is defined as a mutational hotspot by the ClinGen TP53 VCEP (PM1; PMID: 8023157). Computational predictor scores (BayesDel = 0.554513; Align GVGD = Class C65) are above recommended thresholds (BayesDel > 0.16 and an Align GVGD Class of 65), evidence that correlates with impact to TP53 via protein change (PP3_Moderate). In vitro assays performed in yeast and/or human cell lines showed non-functional transactivation and loss of growth suppression activity indicating that this variant impacts protein function (PS3; PMIDs: 12826609, 30224644, 29979965). In summary, this variant meets the criteria to be classified as Pathogenic for Li Fraumeni syndrome based on the ACMG/AMP criteria applied, as specified by the ClinGen TP53 VCEP: PS4_Supporting, PM2_Supporting, PM5, PM1, PP3_Moderate, PS3. (Bayesian Points: 12; VCEP specifications version 2.0; 9/6/2024)
Met criteria codes
PP3_Moderate
Computational predictor scores (BayesDel = 0.554513; Align GVGD = Class C65) are above recommended thresholds (BayesDel > 0.16 and an Align GVGD Class of 65), evidence that correlates with impact to TP53 via protein change (PP3_Moderate).
PS3
In vitro assays performed in yeast and/or human cell lines showed non-functional transactivation and loss of growth suppression activity indicating that this variant impacts protein function (PS3; PMIDs: 12826609, 30224644, 29979965).
PM5
Another missense variant(c.524G>A, p.Arg175His) (ClinVar Variation ID: 12374), in the same codon has been classified as pathogenic for Li-Fraumeni syndrome by the ClinGen TP53 VCEP’s specifications. (PM5).
PM1
This variant resides within a codon (NM_00546.4: 175, 245, 248, 249, 273, 282) of TP53 that is defined as a mutational hotspot by the ClinGen TP53 VCEP (PM1; PMID: 8023157).
PM2_Supporting
This variant has an allele frequency of 0.000002542 (3/1180042 alleles) in the European (non-Finnish) population in gnomAD v4.1.0 which is lower than the Clingen TP53 VCEP threshold (<0.00004) for PM2_Supporting, and therefore meets this criterion (PM2_Supporting).
PS4_Supporting
This variant has been reported in 2 unrelated probands meeting Revised Chompret criteria. Based on this evidence, this variant scores 1 total point meeting the TP53 VCEP phenotype scoring criteria of 1-1.5 points. (PS4_Supporting; PMIDs: 11370630, 25927356).
Not Met criteria codes
BA1
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
BP4
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
Curation History
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