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.1146del (p.Lys382fs)

CA497711354

1408583 (ClinVar)

Gene: TP53 (HGNC:7157)
Condition: Li-Fraumeni syndrome (MONDO:0018875)
Inheritance Mode: Autosomal dominant inheritance
UUID: cbf33d9d-4af0-4b9d-bc0d-163d4df14e20
Approved on: 2025-05-07
Published on: 2025-07-18

HGVS expressions

NM_000546.6:c.1146del
NM_000546.6(TP53):c.1146del (p.Lys382fs)
NC_000017.11:g.7669650del
CM000679.2:g.7669650del
NC_000017.10:g.7572968del
CM000679.1:g.7572968del
NC_000017.9:g.7513693del
NG_017013.2:g.22906del
ENST00000503591.2:c.1146del
ENST00000508793.6:c.1146del
ENST00000509690.6:c.750del
ENST00000514944.6:c.867del
ENST00000604348.6:c.1125del
ENST00000269305.9:c.1146del
ENST00000269305.8:c.1146del
ENST00000359597.8:c.994-3401del
ENST00000413465.6:c.782+4536del
ENST00000420246.6:c.*253del
ENST00000445888.6:c.1146del
ENST00000455263.6:c.*165del
ENST00000504290.5:c.*165del
ENST00000504937.5:c.750del
ENST00000510385.5:c.*253del
ENST00000576024.1:c.99del
ENST00000610292.4:c.1029del
ENST00000610538.4:c.*165del
ENST00000610623.4:c.*165del
ENST00000615910.4:c.1113del
ENST00000617185.4:c.*253del
ENST00000618944.4:c.*253del
ENST00000619186.4:c.669del
ENST00000619485.4:c.1029del
ENST00000620739.4:c.1029del
ENST00000622645.4:c.*253del
ENST00000635293.1:c.983+964del
NM_000546.5:c.1146del
NM_001126112.2:c.1146del
NM_001126113.2:c.*165del
NM_001126114.2:c.*253del
NM_001126115.1:c.750del
NM_001126116.1:c.*253del
NM_001126117.1:c.*165del
NM_001126118.1:c.1029del
NM_001276695.1:c.*165del
NM_001276696.1:c.*253del
NM_001276697.1:c.669del
NM_001276698.1:c.*253del
NM_001276699.1:c.*165del
NM_001276760.1:c.1029del
NM_001276761.1:c.1029del
NM_001276695.2:c.*165del
NM_001276696.2:c.*253del
NM_001276697.2:c.669del
NM_001276698.2:c.*253del
NM_001276699.2:c.*165del
NM_001276760.2:c.1029del
NM_001276761.2:c.1029del
NM_001126112.3:c.1146del
NM_001126113.3:c.*165del
NM_001126114.3:c.*253del
NM_001126115.2:c.750del
NM_001126116.2:c.*253del
NM_001126117.2:c.*165del
NM_001126118.2:c.1029del
NM_001276695.3:c.*165del
NM_001276696.3:c.*253del
NM_001276697.3:c.669del
NM_001276698.3:c.*253del
NM_001276699.3:c.*165del
NM_001276760.3:c.1029del
NM_001276761.3:c.1029del
More

Likely Pathogenic

Met criteria codes 4
PM2_Supporting PP1 PS4_Moderate PVS1_Moderate
Not Met criteria codes 6
BS3 BS1 PS3 PP4 PM1 BA1

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.1146del (p.Lys382AsnfsTer?) is a TP53 frameshift variant inducing a stop codon read-through. The variant is predicted to escape nonsense mediated decay, targeting a region of unknown function representing <10% of the protein and introducing a C-terminal extension of 28 residues in the protein (PVS1_Moderate). This variant has been reported in 3 unrelated families meeting Revised Chompret criteria and reported in 1 individual under the age of 40 diagnosed with a HER2+ breast cancer. Based on this evidence, this variant scores 2 total points meeting the TP53 VCEP phenotype scoring criteria of 2-3.5 points. (PS4_Moderate; Internal lab contributors). The variant has been reported to segregate with LFS-associated cancers in 3-4 meioses in 1 family (PP1; Internal lab contributors). This variant has an allele frequency of 6.196e-7 (1/1614052 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 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: PVS1_Moderate, PS4_Moderate, PP1, PM2_Supporting. (Bayesian Points: 6; VCEP specifications version 2.3)
Met criteria codes
PM2_Supporting
This variant has an allele frequency of 6.196e-7 (1/1614052 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).
PP1
The variant has been reported to segregate with LFS-associated cancers in 3-4 meioses in 1 family (PP1; Internal lab contributors).
PS4_Moderate
This variant has been reported in 3 unrelated families meeting Revised Chompret criteria and reported in 1 individual under the age of 40 diagnosed with a HER2+ breast cancer. Based on this evidence, this variant scores 2 total points meeting the TP53 VCEP phenotype scoring criteria of 2-3.5 points. (PS4_Moderate; Internal lab contributors).
PVS1_Moderate
The NM_000546.6 c.1146del (p.Lys382AsnfsTer?) is a TP53 frameshift variant inducing a stop codon read-through. The variant is predicted to escape nonsense mediated decay, targeting a region of unknown function representing <10% of the protein and introducing a C-terminal extension of 28 residues in the protein (PVS1_Moderate). It’s right at the end of the gene and predicted to cause a fs then a protein extension of 28 aa’s. Not predicted to be subject to NMD or NSD. Affects <10% of protein and not a functional domain although 3 of the aa’s affected are highly conserved but no pathogenic missense variants reported in this region.
Not Met criteria codes
BS3
Additional functional studies are needed for code application (PS3/BS3 not met).
BS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS3
Additional functional studies are needed for code application (PS3/BS3 not met).
PP4
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).
BA1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. If you have questions about the information contained on this website, please see a health care professional.
ClinGen Terms of Use.
¤ Powered by BCM's Genboree.