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.314G>A (p.Gly105Asp)

CA000102

141114 (ClinVar)

Gene: TP53 (HGNC:7157)
Condition: Li-Fraumeni syndrome (MONDO:0018875)
Inheritance Mode: Autosomal dominant inheritance
UUID: 829ee774-9dfe-4254-b974-aca431ea5d1d
Approved on: 2026-06-04
Published on: 2026-09-22

HGVS expressions

NM_000546.6(TP53):c.314G>A (p.Gly105Asp)
NM_000546.6:c.314G>A
NC_000017.11:g.7676055C>T
CM000679.2:g.7676055C>T
NC_000017.10:g.7579373C>T
CM000679.1:g.7579373C>T
NC_000017.9:g.7520098C>T
NG_017013.2:g.16496G>A
ENST00000503591.2:c.314G>A
ENST00000508793.6:c.314G>A
ENST00000509690.6:c.-21-819G>A
ENST00000514944.6:c.96+327G>A
ENST00000604348.6:c.314G>A
ENST00000269305.9:c.314G>A
ENST00000269305.8:c.314G>A
ENST00000359597.8:c.314G>A
ENST00000413465.6:c.314G>A
ENST00000420246.6:c.314G>A
ENST00000445888.6:c.314G>A
ENST00000455263.6:c.314G>A
ENST00000503591.1:c.314G>A
ENST00000505014.5:n.570G>A
ENST00000508793.5:c.314G>A
ENST00000509690.5:c.-21-819G>A
ENST00000514944.5:c.96+327G>A
ENST00000604348.5:c.314G>A
ENST00000610292.4:c.197G>A
ENST00000610538.4:c.197G>A
ENST00000615910.4:c.314G>A
ENST00000617185.4:c.314G>A
ENST00000619485.4:c.197G>A
ENST00000620739.4:c.197G>A
ENST00000622645.4:c.197G>A
ENST00000635293.1:c.197G>A
NM_000546.5:c.314G>A
NM_001126112.2:c.314G>A
NM_001126113.2:c.314G>A
NM_001126114.2:c.314G>A
NM_001126118.1:c.197G>A
NM_001276695.1:c.197G>A
NM_001276696.1:c.197G>A
NM_001276760.1:c.197G>A
NM_001276761.1:c.197G>A
NM_001276695.2:c.197G>A
NM_001276696.2:c.197G>A
NM_001276760.2:c.197G>A
NM_001276761.2:c.197G>A
NM_001126112.3:c.314G>A
NM_001126113.3:c.314G>A
NM_001126114.3:c.314G>A
NM_001126118.2:c.197G>A
NM_001276695.3:c.197G>A
NM_001276696.3:c.197G>A
NM_001276760.3:c.197G>A
NM_001276761.3:c.197G>A
More

Likely Pathogenic

Met criteria codes 5
PM1_Supporting PM2_Supporting PP4_Moderate PP3_Moderate PS4_Supporting
Not Met criteria codes 13
PS2 PS3 PS1 PM5 BA1 PP1 PVS1 BS2 BS4 BS3 BS1 BP4 BP7

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 2.4

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
TP53 VCEP
The NM_000546.6: c.314G>A variant in TP53 is a missense variant predicted to cause substitution of glycine by aspartic acid at amino acid 105 (p.Gly105Asp). At least two individuals with this variant were found to have a variant allele fraction of 5-25%, which is a significant predictor of variant pathogenicity (PP4_Moderate, PMID: 34906512, Internal lab contributors). This variant has been reported in 3 unrelated probands meeting Revised Chompret criteria. Based on this evidence, this variant scores 1.5 total point meeting the TP53 VCEP phenotype scoring criteria of 1-1.5 points. (PS4_Supporting; PMID:38714106, Internal lab contributor). This variant has an allele frequency of 6.201e-7 (1/1612526 alleles) across gnomAD v4.1.0 which is lower than the Clingen TP53 VCEP threshold (<0.00003) for PM2_Supporting and has no more than one allele per non-bottleneck subpopulation (PM2_Supporting). In vitro assays performed in yeast and/or human cell lines showed conflicting results with respect to transactivation, growth suppression activity, and/or tetramer formation (PS3/BS3 not met; PMIDs: 12826609, 39774325, 29979965, 30224644). Computational predictor scores (BayesDel = 0.568262; 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). This variant has 4 somatic occurrences for the same amino acid change in cancerhotspots.org (v2) sufficient to be defined as a mutational hotspot by the Clingen TP53 VCEP (2-9 somatic occurrences, PMID: 30311369) (PM1_Supporting). 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: PS4_Supporting, PP4_Moderate, PM2_Supporting, PP3_Moderate, PM1_Supporting. (Bayesian Points: 7; VCEP specifications version 2.4)
Met criteria codes
PM1_Supporting
This variant has 4 somatic occurrences for the same amino acid change in cancerhotspots.org (v2) sufficient to be defined as a mutational hotspot by the Clingen TP53 VCEP (2-9 somatic occurrences, PMID: 30311369) (PM1_Supporting).
PM2_Supporting
This variant has an allele frequency of 6.201e-7 (1/1612526 alleles) across gnomAD v4.1.0 which is lower than the Clingen TP53 VCEP threshold (<0.00003) for PM2_Supporting and has no more than one allele per non-bottleneck subpopulation (PM2_Supporting).
PP4_Moderate
At least two individuals with this variant were found to have a variant allele fraction of 5-25%, which is a significant predictor of variant pathogenicity (PP4_Moderate, PMID: 34906512, Internal lab contributors).
PP3_Moderate
Computational predictor scores (BayesDel = 0.568262; 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).
PS4_Supporting
This variant has been reported in 3 unrelated probands meeting Revised Chompret criteria. Based on this evidence, this variant scores 1.5 total point meeting the TP53 VCEP phenotype scoring criteria of 1-1.5 points. (PS4_Supporting; PMID:38714106, Internal lab contributor).
Not Met criteria codes
PS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS3
In vitro assays performed in yeast and/or human cell lines showed conflicting results with respect to transactivation, growth suppression activity, and/or tetramer formation (PS3/BS3 not met; PMIDs: 12826609, 39774325, 29979965, 30224644).
PS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM5
Another missense variant(c., 313G>A, p.Gly105Ser) with Grantham score equal to or less than the current variant in the same codon has been reported. However, this variant does not meet criteria for PM5 code application as it is currently classified as VUS (PM5 not met).
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
PVS1
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
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
BP4
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
Curation History
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