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.532C>G (p.His178Asp)

CA397841387

482223 (ClinVar)

Gene: TP53
Condition: Li-Fraumeni syndrome
Inheritance Mode: Autosomal dominant inheritance
UUID: a1e9d7d7-42fc-4628-a8f2-f372d4d051d1
Approved on: 2024-08-05
Published on: 2024-08-05

HGVS expressions

NM_000546.5:c.532C>G
NM_000546.5(TP53):c.532C>G (p.His178Asp)
NC_000017.11:g.7675080G>C
CM000679.2:g.7675080G>C
NC_000017.10:g.7578398G>C
CM000679.1:g.7578398G>C
NC_000017.9:g.7519123G>C
NG_017013.2:g.17471C>G
ENST00000503591.2:c.532C>G
ENST00000508793.6:c.532C>G
ENST00000509690.6:c.136C>G
ENST00000514944.6:c.253C>G
ENST00000604348.6:c.511C>G
ENST00000269305.9:c.532C>G
ENST00000269305.8:c.532C>G
ENST00000359597.8:c.532C>G
ENST00000413465.6:c.532C>G
ENST00000420246.6:c.532C>G
ENST00000445888.6:c.532C>G
ENST00000455263.6:c.532C>G
ENST00000504290.5:c.136C>G
ENST00000504937.5:c.136C>G
ENST00000505014.5:n.788C>G
ENST00000509690.5:c.136C>G
ENST00000510385.5:c.136C>G
ENST00000514944.5:c.253C>G
ENST00000574684.1:n.40C>G
ENST00000610292.4:c.415C>G
ENST00000610538.4:c.415C>G
ENST00000610623.4:c.55C>G
ENST00000615910.4:c.499C>G
ENST00000617185.4:c.532C>G
ENST00000618944.4:c.55C>G
ENST00000619186.4:c.55C>G
ENST00000619485.4:c.415C>G
ENST00000620739.4:c.415C>G
ENST00000622645.4:c.415C>G
ENST00000635293.1:c.415C>G
NM_001126112.2:c.532C>G
NM_001126113.2:c.532C>G
NM_001126114.2:c.532C>G
NM_001126115.1:c.136C>G
NM_001126116.1:c.136C>G
NM_001126117.1:c.136C>G
NM_001126118.1:c.415C>G
NM_001276695.1:c.415C>G
NM_001276696.1:c.415C>G
NM_001276697.1:c.55C>G
NM_001276698.1:c.55C>G
NM_001276699.1:c.55C>G
NM_001276760.1:c.415C>G
NM_001276761.1:c.415C>G
NM_001276695.2:c.415C>G
NM_001276696.2:c.415C>G
NM_001276697.2:c.55C>G
NM_001276698.2:c.55C>G
NM_001276699.2:c.55C>G
NM_001276760.2:c.415C>G
NM_001276761.2:c.415C>G
NM_000546.6:c.532C>G
NM_001126112.3:c.532C>G
NM_001126113.3:c.532C>G
NM_001126114.3:c.532C>G
NM_001126115.2:c.136C>G
NM_001126116.2:c.136C>G
NM_001126117.2:c.136C>G
NM_001126118.2:c.415C>G
NM_001276695.3:c.415C>G
NM_001276696.3:c.415C>G
NM_001276697.3:c.55C>G
NM_001276698.3:c.55C>G
NM_001276699.3:c.55C>G
NM_001276760.3:c.415C>G
NM_001276761.3:c.415C>G
More

Pathogenic

Met criteria codes 6
PS3 PS2_Moderate PM1_Supporting PM2_Supporting PP3_Moderate PS4_Supporting
Not Met criteria codes 12
PS1 BP4 BP7 BA1 PP1 PP4 PVS1 PM5 BS2 BS4 BS3 BS1

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.532C>G variant in TP53 is a missense variant predicted to cause substitution of histidine by aspartic acid at amino acid 178 (p.His178Asp). This variant has been identified as a de novo occurrence with unconfirmed parental relationships in 1 individual with a strongly-associated LFS-associated cancers totaling 2 phenotype points (PS2_Moderate; PMID 21345075). This variant has been reported in 2 additional 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; SCV000754561.6, SCV000667198.3). This variant has an allele frequency of 6.195e-7 (1/1614230 alleles) across gnomAD v4.1.0 which is lower than the Clingen TP53 VCEP threshold (<0.00003) for PM2_Supporting, and therefore meets this criterion (PM2_Supporting). In vitro assays performed in yeast and human cells showed non-functional transactivation and loss of growth suppression activity indicating that this variant impacts protein function (PS3; PMIDs: 12826609, 30224644). This variant has five 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). Computational predictor scores (BayesDel =0.4249); 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 pathogenic for Li Fraumeni Syndrome based on the ACMG/AMP criteria applied, as specified by the ClinGen TP53 VCEP: PS2_Moderate, PS4_Supporting, PM2_Supporting, PS3, PM1_Supporting, PP3_Moderate. (Bayesian Points: 11; VCEP specifications version 2.0; 7/24/2024)
Met criteria codes
PS3
In vitro assays performed in yeast and/or human cells lines showed non-functional transactivation and loss of growth suppression activity indicating that this variant impacts protein function (PS3; PMIDs: 12826609, 30224644).
PS2_Moderate
This variant has been identified as a de novo occurrence with unconfirmed parental relationships in 1 individual with a strongly-associated LFS-associated cancers totaling 2 phenotype points (PS2_Moderate; PMID 21345075).
PM1_Supporting
This variant has five 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 6.195e-7 (1/1614230 alleles) across gnomAD v4.1.0 which is lower than the Clingen TP53 VCEP threshold (<0.00003) for PM2_Supporting, and therefore meets this criterion (PM2_Supporting).
PP3_Moderate
Computational predictor scores (BayesDel =0.4249); 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 2 additional 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; SCV000754561.6, SCV000667198.3).
Not Met criteria codes
PS1
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
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
PP4
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
PM5
Four different missense variants (c.534C>G, p.His178Gln; c.534C>A, p.His178Gln; c.533A>C, p.His178Pro; c.532C>A, (p.His178Asn) in the same codon have been reported (ClinVar Variation IDs: 947223, 575702, 485030, 421546). However, the variants have not yet been curated to determine if they would be classified as pathogenic or likely pathogenic by the ClinGen TP53 VCEP's specifications (PM5 not evaluated).
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
Curation History
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