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.328C>G (p.Arg110Gly)

CA397844579

823452 (ClinVar)

Gene: TP53
Condition: Li-Fraumeni syndrome
Inheritance Mode: Autosomal dominant inheritance
UUID: 25368fd9-d67d-4cc1-a726-ed149aced67e
Approved on: 2025-06-05
Published on: 2025-07-18

HGVS expressions

NM_000546.6:c.328C>G
NM_000546.6(TP53):c.328C>G (p.Arg110Gly)
NC_000017.11:g.7676041G>C
CM000679.2:g.7676041G>C
NC_000017.10:g.7579359G>C
CM000679.1:g.7579359G>C
NC_000017.9:g.7520084G>C
NG_017013.2:g.16510C>G
ENST00000503591.2:c.328C>G
ENST00000508793.6:c.328C>G
ENST00000509690.6:c.-21-805C>G
ENST00000514944.6:c.96+341C>G
ENST00000604348.6:c.328C>G
ENST00000269305.9:c.328C>G
ENST00000269305.8:c.328C>G
ENST00000359597.8:c.328C>G
ENST00000413465.6:c.328C>G
ENST00000420246.6:c.328C>G
ENST00000445888.6:c.328C>G
ENST00000455263.6:c.328C>G
ENST00000503591.1:c.328C>G
ENST00000505014.5:n.584C>G
ENST00000508793.5:c.328C>G
ENST00000509690.5:c.-21-805C>G
ENST00000514944.5:c.96+341C>G
ENST00000604348.5:c.328C>G
ENST00000610292.4:c.211C>G
ENST00000610538.4:c.211C>G
ENST00000615910.4:c.328C>G
ENST00000617185.4:c.328C>G
ENST00000619485.4:c.211C>G
ENST00000620739.4:c.211C>G
ENST00000622645.4:c.211C>G
ENST00000635293.1:c.211C>G
NM_000546.5:c.328C>G
NM_001126112.2:c.328C>G
NM_001126113.2:c.328C>G
NM_001126114.2:c.328C>G
NM_001126118.1:c.211C>G
NM_001276695.1:c.211C>G
NM_001276696.1:c.211C>G
NM_001276760.1:c.211C>G
NM_001276761.1:c.211C>G
NM_001276695.2:c.211C>G
NM_001276696.2:c.211C>G
NM_001276760.2:c.211C>G
NM_001276761.2:c.211C>G
NM_001126112.3:c.328C>G
NM_001126113.3:c.328C>G
NM_001126114.3:c.328C>G
NM_001126118.2:c.211C>G
NM_001276695.3:c.211C>G
NM_001276696.3:c.211C>G
NM_001276760.3:c.211C>G
NM_001276761.3:c.211C>G
More

Likely Pathogenic

Met criteria codes 4
PM2 PM5_Strong BP4 PS3
Not Met criteria codes 9
PM1 BS1 BS2 BP2 PS4 BA1 PP4 PP1 PP3

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.328C>G variant in TP53 is a missense variant predicted to cause substitution of arginine by glycine at amino acid 110 (p.Arg110Gly). This variant is absent from gnomAD v4.1.0 (PM2_Supporting). 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; Internal lab contributors). 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). 2 different missense variants (p.Arg110Leu, p.Arg110Pro) (ClinVar Variation IDs: 406597, 233627), in the same codon have been classified as pathogenic for Li-Fraumeni syndrome by the ClinGen TP53 VCEP’s specifications. (PM5_Strong). Computational predictor scores (BayesDel = 0.056; Align GVGD Class C15) are below the recommended thresholds (BayesDel < 0.16 and > -0.008 and an Align GVGD Class ≤ 55), evidence that does not predict a damaging effect on TP53 via protein change. SpliceAI predicts that the variant has no impact on splicing (BP4). 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: PM2_Supporting, PS3, PM5_Strong, BP4. (Bayesian Points: 8; VCEP specifications version 2.3)
Met criteria codes
PM2
This variant is absent from gnomAD v4.1.0 (PM2_Supporting).
PM5_Strong
2 different missense variants (p.Arg110Leu, p.Arg110Pro) (ClinVar Variation IDs: 406597, 233627), in the same codon have been classified as pathogenic for Li-Fraumeni syndrome by the ClinGen TP53 VCEP’s specifications. (PM5_Strong).
BP4
Computational predictor scores (BayesDel = 0.056; Align GVGD Class C15) are below the recommended thresholds (BayesDel < 0.16 and > -0.008 and an Align GVGD Class ≤ 55), evidence that does not predict a damaging effect on TP53 via protein change. SpliceAI predicts that the variant has no impact on splicing (BP4).
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
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).
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
BP2
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
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
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
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