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 computed assertion could be determined for this classification!


Variant: NM_000546.6(TP53):c.829T>G (p.Cys277Gly)

CA397836909

2757236 (ClinVar)

Gene: TP53 (HGNC:7157)
Condition: Li-Fraumeni syndrome (MONDO:0018875)
Inheritance Mode: Autosomal dominant inheritance
UUID: f72a812d-c9ff-4033-97b4-17c0e53dd427
Approved on: 2025-12-05
Published on: 2025-12-05

HGVS expressions

NM_000546.6(TP53):c.829T>G (p.Cys277Gly)
NM_000546.6:c.829T>G
NC_000017.11:g.7673791A>C
CM000679.2:g.7673791A>C
NC_000017.10:g.7577109A>C
CM000679.1:g.7577109A>C
NC_000017.9:g.7517834A>C
NG_017013.2:g.18760T>G
ENST00000503591.2:c.829T>G
ENST00000508793.6:c.829T>G
ENST00000509690.6:c.433T>G
ENST00000514944.6:c.550T>G
ENST00000604348.6:c.808T>G
ENST00000269305.9:c.829T>G
ENST00000269305.8:c.829T>G
ENST00000359597.8:c.829T>G
ENST00000413465.6:c.782+390T>G
ENST00000420246.6:c.829T>G
ENST00000445888.6:c.829T>G
ENST00000455263.6:c.829T>G
ENST00000504290.5:c.433T>G
ENST00000504937.5:c.433T>G
ENST00000509690.5:c.433T>G
ENST00000510385.5:c.433T>G
ENST00000610292.4:c.712T>G
ENST00000610538.4:c.712T>G
ENST00000610623.4:c.352T>G
ENST00000615910.4:c.796T>G
ENST00000617185.4:c.829T>G
ENST00000618944.4:c.352T>G
ENST00000619186.4:c.352T>G
ENST00000619485.4:c.712T>G
ENST00000620739.4:c.712T>G
ENST00000622645.4:c.712T>G
ENST00000635293.1:c.712T>G
NM_000546.5:c.829T>G
NM_001126112.2:c.829T>G
NM_001126113.2:c.829T>G
NM_001126114.2:c.829T>G
NM_001126115.1:c.433T>G
NM_001126116.1:c.433T>G
NM_001126117.1:c.433T>G
NM_001126118.1:c.712T>G
NM_001276695.1:c.712T>G
NM_001276696.1:c.712T>G
NM_001276697.1:c.352T>G
NM_001276698.1:c.352T>G
NM_001276699.1:c.352T>G
NM_001276760.1:c.712T>G
NM_001276761.1:c.712T>G
NM_001276695.2:c.712T>G
NM_001276696.2:c.712T>G
NM_001276697.2:c.352T>G
NM_001276698.2:c.352T>G
NM_001276699.2:c.352T>G
NM_001276760.2:c.712T>G
NM_001276761.2:c.712T>G
NM_001126112.3:c.829T>G
NM_001126113.3:c.829T>G
NM_001126114.3:c.829T>G
NM_001126115.2:c.433T>G
NM_001126116.2:c.433T>G
NM_001126117.2:c.433T>G
NM_001126118.2:c.712T>G
NM_001276695.3:c.712T>G
NM_001276696.3:c.712T>G
NM_001276697.3:c.352T>G
NM_001276698.3:c.352T>G
NM_001276699.3:c.352T>G
NM_001276760.3:c.712T>G
NM_001276761.3:c.712T>G
More

Likely Pathogenic

Met criteria codes 4
PP3_Moderate PM2_Supporting PP4 PS3
Not Met criteria codes 12
BA1 BP4 BS4 BS3 BS1 BS2 PP1 PM1 PM5 PS2 PS4 PS1

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 2.3.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
TP53 VCEP
The NM_000546.6: c.829T>G variant in TP53 is a missense variant predicted to cause substitution of cysteine by glycine at amino acid 277 (p.Cys277Gly). Although this variant has been observed in germline cases, to our knowledge, this variant has not been reported in individuals meeting classical LFS or Chompret criteria (PS4 not met; PMIDs, ClinVar SCVs: SCV004323141.2, SCV004359981.2). At least one individual with this variant was found to have a variant allele fraction of 5-35%, which is a significant predictor of variant pathogenicity (PP4, PMID: 34906512, Internal lab contributor). This variant is absent from gnomAD v4.1.0 (PM2_Supporting). 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). Computational predictor scores (BayesDel = 0.388624; 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 summary, this variant meets the criteria to be classified as Likely Pathogenic for Li Fraumeni syndrome based on the ACMG/AMP criteria applied, as specified by the ClinGen TP53 VCEP: PP4, PM2_Supporting, PS3, PP3_Moderate. (Bayesian Points: 8; VCEP specifications version 2.3).
Met criteria codes
PP3_Moderate
Computational predictor scores (BayesDel = 0.388624; 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).
PM2_Supporting
This variant is absent from gnomAD v4.1.0 (PM2_Supporting).
PP4
At least one individual with this variant was found to have a variant allele fraction of 5-35%, which is a significant predictor of variant pathogenicity (PP4, PMID: 34906512, ClinVar GTRs, Internal lab contributors).
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).
Not Met criteria codes
BA1
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
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
PP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM1
This variant does not reside within a region of TP53 that is defined as a mutational hotspot by the ClinGen TP53 VCEP (PM1 not met).
PM5
Five missense variants in the same codon have been reported. However, these variants do not meet criteria for PM5 code application as most have higher Grantham scores and the final variant does not reach P/LP at this time (PM5 not met).
PS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS4
Although this variant has been observed in germline cases, to our knowledge, this variant has not been reported in individuals meeting classical LFS or Chompret criteria (PS4 not met; PMIDs, ClinVar SCVs: SCV004323141.2, SCV004359981.2).
PS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
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