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_000546.5(TP53):c.641A>G (p.His214Arg)

CA16040595

376615 (ClinVar)

Gene: TP53
Condition: Li-Fraumeni syndrome
Inheritance Mode: Autosomal dominant inheritance
UUID: b36419d2-274a-4464-b4c9-c0ff2471c0d9
Approved on: 2024-08-05
Published on: 2024-08-05

HGVS expressions

NM_000546.5:c.641A>G
NM_000546.5(TP53):c.641A>G (p.His214Arg)
NC_000017.11:g.7674890T>C
CM000679.2:g.7674890T>C
NC_000017.10:g.7578208T>C
CM000679.1:g.7578208T>C
NC_000017.9:g.7518933T>C
NG_017013.2:g.17661A>G
ENST00000503591.2:c.641A>G
ENST00000508793.6:c.641A>G
ENST00000509690.6:c.245A>G
ENST00000514944.6:c.362A>G
ENST00000604348.6:c.620A>G
ENST00000269305.9:c.641A>G
ENST00000269305.8:c.641A>G
ENST00000359597.8:c.641A>G
ENST00000413465.6:c.641A>G
ENST00000420246.6:c.641A>G
ENST00000445888.6:c.641A>G
ENST00000455263.6:c.641A>G
ENST00000504290.5:c.245A>G
ENST00000504937.5:c.245A>G
ENST00000505014.5:n.897A>G
ENST00000509690.5:c.245A>G
ENST00000510385.5:c.245A>G
ENST00000514944.5:c.362A>G
ENST00000574684.1:n.67+163A>G
ENST00000610292.4:c.524A>G
ENST00000610538.4:c.524A>G
ENST00000610623.4:c.164A>G
ENST00000615910.4:c.608A>G
ENST00000617185.4:c.641A>G
ENST00000618944.4:c.164A>G
ENST00000619186.4:c.164A>G
ENST00000619485.4:c.524A>G
ENST00000620739.4:c.524A>G
ENST00000622645.4:c.524A>G
ENST00000635293.1:c.524A>G
NM_001126112.2:c.641A>G
NM_001126113.2:c.641A>G
NM_001126114.2:c.641A>G
NM_001126115.1:c.245A>G
NM_001126116.1:c.245A>G
NM_001126117.1:c.245A>G
NM_001126118.1:c.524A>G
NM_001276695.1:c.524A>G
NM_001276696.1:c.524A>G
NM_001276697.1:c.164A>G
NM_001276698.1:c.164A>G
NM_001276699.1:c.164A>G
NM_001276760.1:c.524A>G
NM_001276761.1:c.524A>G
NM_001276695.2:c.524A>G
NM_001276696.2:c.524A>G
NM_001276697.2:c.164A>G
NM_001276698.2:c.164A>G
NM_001276699.2:c.164A>G
NM_001276760.2:c.524A>G
NM_001276761.2:c.524A>G
NM_000546.6:c.641A>G
NM_001126112.3:c.641A>G
NM_001126113.3:c.641A>G
NM_001126114.3:c.641A>G
NM_001126115.2:c.245A>G
NM_001126116.2:c.245A>G
NM_001126117.2:c.245A>G
NM_001126118.2:c.524A>G
NM_001276695.3:c.524A>G
NM_001276696.3:c.524A>G
NM_001276697.3:c.164A>G
NM_001276698.3:c.164A>G
NM_001276699.3:c.164A>G
NM_001276760.3:c.524A>G
NM_001276761.3:c.524A>G
More

Pathogenic

Met criteria codes 5
PP4_Moderate PS4_Supporting PM2_Supporting PM1 PS3
Not Met criteria codes 12
BA1 PM5 BS2 BS4 BS3 BS1 PVS1 BP4 PS1 PS2 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 2.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
TP53 VCEP
The NM_000546.6: c.641A>G variant in TP53 is a missense variant predicted to cause substitution of histidine by arginine at amino acid 214 (p.His214Arg). This variant has been reported in 2 unrelated families 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; PMID: 20522432; Internal lab contributor: SCV000581129.5). 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 contributor: SCV000581129.5). This variant is absent from gnomAD v4.1.0 (PM2_Supporting). In vitro assays performed in yeast and human cell lines showed non-functional transactivation and loss of growth suppression activity indicating that this variant impacts protein function (PMIDs: 12826609, 30224644, 29979965) (PS3). This variant has 35 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 (≥ 10 somatic occurrences, PMID: 30311369) (PM1). 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, PP4_Moderate, PM2_Supporting, PS3, PM1. (Bayesian Points: 10; VCEP specifications version 2.0; 7/24/2024)
Met criteria codes
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 contributor: SCV000581129.5).
PS4_Supporting
This variant has been reported in 2 unrelated families 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; PMID: 20522432; Internal lab contributor: SCV000581129.5).
PM2_Supporting
This variant is absent from gnomAD v4.1.0 (PM2_Supporting).
PM1
This variant has 35 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 (≥ 10 somatic occurrences, PMID: 30311369) (PM1).
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 (PMIDs: 12826609, 30224644, 29979965) (PS3).
Not Met criteria codes
BA1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM5
5 different missense variants (p.His214Gln; p.His214Pro; p.His214Leu; p.His214Tyr; p.His214Asn) in the same codon have been reported (ClinVar Variation IDs: 140943, 643078, 376616, 1053808, 230254). However, these variants have not yet met the criteria to be classified as pathogenic or likely pathogenic by the ClinGen TP53 VCEP’s specifications (PM5 not met).
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
PVS1
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
PP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP3
The results from the computational predictors BayesDel and AlignGVGD do not agree, providing no evidence that correlates with a damaging or benign impact on TP53 function via protein change. Additionally, the computational splicing predictor SpliceAI gives a score of 0.06, predicting that the variant has no impact on splicing (score threshold ≤ 0.10) (PP3 and BP4 not met).
Curation History
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