Submissions for variant NM_000546.6(TP53):c.1003C>T (p.Arg335Cys)

dbSNP: rs375444154

Total submissions: 9

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
ClinGen TP53 Variant Curation Expert Panel, ClinGen	RCV000538993	SCV001432165	likely benign	Li-Fraumeni syndrome	2025-02-06	reviewed by expert panel	curation	The NM_000546.6: c.1003C>T variant in TP53 is a missense variant predicted to cause substitution of arginine by cysteine at amino acid 335 (p.Arg335Cys). 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). This variant has been observed in 2-3 heterozygous unrelated females from the same data source with no personal history of cancer prior to age 60 years and no personal history of sarcoma at any age (BS2_Supporting; ClinVar SCV: SCV000629764.4). This variant has an allele frequency of 0.000001859 (3/1613806 alleles) across gnomAD v4.1.0 which is lower than the Clingen TP53 VCEP threshold (<0.00003) for PM2_Supporting and has a subpopulation allele frequency of <0.00004 in all non-bottleneck populations with 2 or more alleles present (PM2_Supporting). In vitro assays performed in yeast and/or human cell lines showed functional transactivation and retained growth suppression activity indicating that this variant does not impact protein function(BS3; PMIDs: 12826609, 29979965, 30224644). Computational predictor scores (BayesDel = 0.275; Align GVGD = Class C25) are above recommended thresholds (BayesDel > 0.16 and an Align GVGD Class of > 15), evidence that correlates with impact to TP53 via protein change (PP3). In summary, this variant meets the criteria to be classified as Likely Benign for Li Fraumeni syndrome based on the ACMG/AMP criteria applied, as specified by the ClinGen TP53 VCEP: BS2_Supporting, PM2_Supporting, BS3, PP3. (Bayesian Points: -3; VCEP specifications version 2.2; 2/6/2025).
Ambry Genetics	RCV000129547	SCV000184327	uncertain significance	Hereditary cancer-predisposing syndrome	2023-11-21	criteria provided, single submitter	clinical testing	The p.R335C variant (also known as c.1003C>T), located in coding exon 9 of the TP53 gene, results from a C to T substitution at nucleotide position 1003. The arginine at codon 335 is replaced by cysteine, an amino acid with highly dissimilar properties. This variant is in the tetramerization domain of the TP53 protein and is reported to have transactivation similar to wild type in yeast based assays, and maintain the ability to form tetrames (IARC TP53 database: Kato S et al. Proc. Natl. Acad. Sci. USA 2003 Jul;100:8424-9; Kawaguchi T et al. Oncogene. 2005 Oct 20;24(46):6976-81). However, another study indicated that this alteration showed a decrease from wild type in DNA binding, transactivation activity, apoptosis induction and binding to the PAb421 regulatory protein, but did not affect TP53 gene repressor activity or oligomerization (Atz J et al. J. Cell. Biochem., 2000 Jan;76:572-84). Additional studies conducted in human cell lines indicate this alteration has no dominant negative effect and remains proficient at growth suppression (Giacomelli AO et al. Nat. Genet. 2018 Oct;50:1381-1387). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
GeneDx	RCV000213066	SCV000211765	uncertain significance	not provided	2021-05-05	criteria provided, single submitter	clinical testing	Not observed in large population cohorts (Lek 2016); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Published functional studies are conflicting: functional transactivation activity, normal temperature sensitivity, no impact on growth suppression, decreased DNA binding, decreased apoptosis, and decreased gene repressor activity (Atz 2000, Kato 2003, Shiraishi 2004, Giacomelli 2018); This variant is associated with the following publications: (PMID: 14559903, 30224644, 16007150, 19011621, 10653977, 23515929, 24665023)
Labcorp Genetics (formerly Invitae), Labcorp	RCV000538993	SCV000629764	uncertain significance	Li-Fraumeni syndrome	2025-02-02	criteria provided, single submitter	clinical testing	This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 335 of the TP53 protein (p.Arg335Cys). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with pancreatic cancer (PMID: 35047863). ClinVar contains an entry for this variant (Variation ID: 141159). Invitae Evidence Modeling incorporating data from in vitro experimental studies (PMID: 12826609, 29979965, 30224644) indicates that this missense variant is not expected to disrupt TP53 function with a negative predictive value of 97.5%. Experimental studies have shown that this missense change does not substantially affect TP53 function (PMID: 12826609, 30224644). RNA analysis performed to evaluate the impact of this missense change on mRNA splicing indicates it does not significantly alter splicing (internal data). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Color Diagnostics, LLC DBA Color Health	RCV000129547	SCV000691569	uncertain significance	Hereditary cancer-predisposing syndrome	2023-10-12	criteria provided, single submitter	clinical testing	This missense variant replaces arginine with cysteine at codon 335 of the TP53 protein. Computational prediction suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). Experimental functional studies of this variant have indicated that the transactivation activity (PMID: 12826609) and oligomerization of the protein (PMID 16007150) are not impaired. The variant also display no dominant-negative behavior or loss-of-function in human cell growth suppression assays (PMID: 30224644). However another study showed partial effects on transactivation activity, repression activity, DNA binding, and induction of apoptosis (PMID: 10653977). To our knowledge, this variant has not been reported in individuals affected with hereditary cancer in the literature. This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.
Sema4, Sema4	RCV000129547	SCV002530416	uncertain significance	Hereditary cancer-predisposing syndrome	2022-03-17	criteria provided, single submitter	curation
All of Us Research Program, National Institutes of Health	RCV000538993	SCV004823733	uncertain significance	Li-Fraumeni syndrome	2024-09-23	criteria provided, single submitter	clinical testing	This missense variant replaces arginine with cysteine at codon 335 of the TP53 protein. Computational prediction suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). Experimental functional studies of this variant have indicated that the transactivation activity (PMID: 12826609) and oligomerization of the protein (PMID 16007150) are not impaired. The variant also display no dominant-negative behavior or loss-of-function in human cell growth suppression assays (PMID: 30224644). However another study showed partial effects on transactivation activity, repression activity, DNA binding, and induction of apoptosis (PMID: 10653977). To our knowledge, this variant has not been reported in individuals affected with hereditary cancer in the literature. This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.
Baylor Genetics	RCV004567087	SCV005054355	uncertain significance	Adrenocortical carcinoma, hereditary	2023-11-14	criteria provided, single submitter	clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	RCV000213066	SCV005878018	uncertain significance	not provided	2024-04-03	criteria provided, single submitter	clinical testing	The TP53 c.1003C>T; p.Arg335Cys variant (rs375444154, ClinVar variation ID: 141159) is reported in the literature in one individual affected with pancreatic cancer (Yu 2021). This variant is absent from the Genome Aggregation Database (v2.1.1), indicating it is not a common polymorphism. Functional analyses of the variant protein show minimal effects on protein function (Giacomelli 2018) and in vitro functional analyses in yeast demonstrate transactivation similar to WT (Kato 2003). However, computational analyses predict that this variant is deleterious (REVEL: 0.819). Due to conflicting information, the clinical significance of this variant is uncertain at this time. References: Giacomelli et al. Mutational processes shape the landscape of TP53 mutations in human cancer. Nat Genet. 2018 Oct;50(10):1381-1387. PMID: 30224644. Kato S et al. Understanding the function-structure and function-mutation relationships of p53 tumor suppressor protein by high-resolution missense mutation analysis. Proc Natl Acad Sci U S A. 2003 Jul 8;100(14):8424-9. PMID: 12826609. Yu Y et al. A whole-exome case-control association study to characterize the contribution of rare coding variation to pancreatic cancer risk. HGG Adv. 2021 Dec 10;3(1):100078. PMID: 35047863.