Submissions for variant NM_000546.6(TP53):c.743G>A (p.Arg248Gln) (rs11540652)

Total submissions: 49

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
ClinGen TP53 Variant Curation Expert Panel,ClinGen	RCV000197114	SCV001142549	pathogenic	Li-Fraumeni syndrome	2019-08-28	reviewed by expert panel	curation	This variant is within a codon that is an established hotspot in the TP53 gene (PM1; PMID: 2046748). This variant has a BayesDel score > 0.16 and Align GVGD (Zebrafish) is Class 15 or higher (PP3). Transactivation assays show a low functioning allele according to Kato, et al. and there is evidence of a dominant negative effect and loss of function according to Giacomelli, et al. (PS3; PMID: 12826609, 30224644). This variant has been reported in at least 3 probands meeting classic Li-Fraumeni syndrome and 2 probands meeting Chompret criteria (PS4; PMID: 1565143, 9242456, 15381368, 7887414). There is a de novo observation of a proband with adrenocortical carcinoma with parental confirmation (PS2; PMID: 15381368). In summary, TP53 c.743G>A; p.Arg248Gln meets criteria to be classified as pathogenic for Li-Fraumeni syndrome. ACMG/AMP criteria applied, as specified by the TP53 Variant Curation Expert Panel: PM1, PP3, PS3, PS4, PS2.
GeneDx	RCV000235221	SCV000149645	pathogenic	not provided	2018-10-05	criteria provided, single submitter	clinical testing	This pathogenic variant is denoted TP53 c.743G>A at the cDNA level, p.Arg248Gln (R248Q) at the protein level, and results in the change of an Arginine to a Glutamine (CGG>CAG). This variant has been observed in several Li-Fraumeni or Li-Fraumeni-like families and has also been reported as an apparently de novo heterozygous or mosaic finding in individuals meeting Chompret criteria (Toguchida 1992, Monti 2007, Prochazkova 2009, Masciari 2011, Villani 2011, Behjati 2014, Patrier-Sallebert 2015, Parsons 2016, Sherborne 2016). Functional studies have found that TP53 Arg248Gln impacts DNA binding, apoptosis, growth suppression, and transactivation activities and leads to a dominant-negative effect (Lomax 1998, Dearth 2007, Malcikova 2010, Monti 2011). This variant is also reported as having non-functional transactivation in the International Agency for Research on Cancer TP53 database based on functional studies by Kato et al. (2003). TP53 Arg248Gln was not observed at a significant allele frequency in large population cohorts (Lek 2016). This variant is located within the DNA binding domain (Bode 2004). In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function. Based on the current evidence, we consider this variant to be pathogenic.
Ambry Genetics	RCV000115736	SCV000185472	pathogenic	Hereditary cancer-predisposing syndrome	2018-09-07	criteria provided, single submitter	clinical testing	Confirmed de novo alteration in the setting of a new disease (appropriate phenotype) in the family;Well-characterized mutation at same position;Detected in individual satisfying established diagnostic critera for classic disease without a clear mutation;Deficient protein function in appropriate functional assay(s);Other strong data supporting pathogenic classification
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics	RCV000235221	SCV000232078	pathogenic	not provided	2014-06-09	criteria provided, single submitter	clinical testing
Invitae	RCV000197114	SCV000253851	pathogenic	Li-Fraumeni syndrome	2020-01-09	criteria provided, single submitter	clinical testing	This sequence change replaces arginine with glutamine at codon 248 of the TP53 protein (p.Arg248Gln). The arginine residue is highly conserved and there is a small physicochemical difference between arginine and glutamine. This variant is present in population databases (rs11540652, ExAC 0.02%). This variant was reported in multiple individuals and families affected with Li-Fraumeni and Li-Fraumeni-like syndromes (PMID: 1565143, 17606709, 21601526, 7887414, 21305319). ClinVar contains an entry for this variant (Variation ID: 12356). Experimental studies have shown that this missense change severely affects the functional activity of the p53 protein, abolishing its DNA-binding and transcriptional transactivation activities. This variant is classified as a severe deficiency allele with possible dominant-negative inhibitory effects (PMID: 21343334, 17606709, 20128691). For these reasons, this variant has been classified as Pathogenic.
University of Washington Department of Laboratory Medicine, University of Washington	RCV000115736	SCV000266133	likely pathogenic	Hereditary cancer-predisposing syndrome	2015-11-20	criteria provided, single submitter	clinical testing
Color	RCV000115736	SCV000686766	pathogenic	Hereditary cancer-predisposing syndrome	2015-04-14	criteria provided, single submitter	clinical testing
Counsyl	RCV000013150	SCV000785422	likely pathogenic	Li-Fraumeni syndrome 1	2017-07-27	criteria provided, single submitter	clinical testing
GeneKor MSA	RCV000115736	SCV000821785	pathogenic	Hereditary cancer-predisposing syndrome	2020-01-01	criteria provided, single submitter	clinical testing	This sequence change replaces Arginine with Glutamine at codon 248 of the TP53 protein. The arginine residue is highly conserved among species and is located in a functional domain of the protein. There is a small physiochemical difference between arginine and glutamine (Grantham Score 43).This variant is present in population databases at a very low frequency (rs11540652, ExAC 0.02%) and has been reported in multiple individuals and families affected with Li-Fraumeni and Li-Fraumeni-like syndromes (PMID: 1565143, 17606709, 21601526).Algorithms developed to predict the effect of missense changes on protein structure and function suggest that this variant is likely to be damaging to the protein. Moreover, experimental studies have shown that this missense change severely affects the functional activity of the p53 protein. This variant is classified as a severe deficiency allele with possible dominant-negative inhibitory effects (PMID: 21343334, 17606709, 20128691). The mutation database Clinvar contains entries for this variant (Variation ID:12356).
Mendelics	RCV000197114	SCV000839112	pathogenic	Li-Fraumeni syndrome	2018-07-02	criteria provided, single submitter	clinical testing
Fulgent Genetics,Fulgent Genetics	RCV000763417	SCV000894154	pathogenic	Adrenocortical carcinoma, hereditary; Familial cancer of breast; Glioma susceptibility 1; Osteosarcoma; Li-Fraumeni syndrome 1; Nasopharyngeal carcinoma; Carcinoma of pancreas; Choroid plexus papilloma; Carcinoma of colon; Basal cell carcinoma, susceptibility to, 7; Hepatocellular carcinoma	2018-10-31	criteria provided, single submitter	clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano	RCV000235221	SCV001134877	pathogenic	not provided	2018-11-21	criteria provided, single submitter	clinical testing	The best available variant frequency is uninformative because it is below the disease allele frequency. Statistically enriched in patients compared to ethnically matched controls. Found in at least one symptomatic patient. Predicted to have a damaging effect on the protein. Two other pathogenic or likely pathogenic variants affect the same amino acid. Assessment of experimental evidence suggests this variant results in abnormal protein function. One de novo case with parental identity confirmed.
Integrated Genetics/Laboratory Corporation of America	RCV000197114	SCV001363225	pathogenic	Li-Fraumeni syndrome	2019-09-20	criteria provided, single submitter	clinical testing	Variant summary: TP53 c.743G>A (p.Arg248Gln) results in a conservative amino acid change located in the p53, DNA-binding domain (IPR011615) of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 1.2e-05 in 251474 control chromosomes (gnomAD). c.743G>A has been reported in the literature in multiple individuals/families affected with Li-Fraumeni or Li-Fraumeni-like syndromes (e.g. Haque_2018, Rapakko_2001, Vahteristo_2001, Villani_2011) while, it was also reported in a LFS patient with a suggested de novo occurrence (Bendig_2004). These data indicate that the variant is very likely to be associated with disease. Functional studies demonstrate that the R248Q substitution impairs the DNA binding capability of TP53 essential for its tumor suppressor function (Merabet_2010), and the variant exhibited less than 25% of wild-type transcriptional transactivation activity. Additional studies have classified this variant as a severe deficiency allele with a dominant negative effect (Monti_2011, Zerdoumi_2017). Nine ClinVar submitters (evaluation after 2014) cite the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.
OMIM	RCV000013150	SCV000033397	pathogenic	Li-Fraumeni syndrome 1	2000-05-15	no assertion criteria provided	literature only
Pathway Genomics	RCV000013150	SCV000190000	pathogenic	Li-Fraumeni syndrome 1	2014-07-24	no assertion criteria provided	clinical testing
CSER _CC_NCGL, University of Washington	RCV000148913	SCV000190659	pathogenic	Sarcoma	2014-06-01	no assertion criteria provided	research
Database of Curated Mutations (DoCM)	RCV000445244	SCV000504693	likely pathogenic	Glioblastoma	2016-05-31	no assertion criteria provided	literature only
Database of Curated Mutations (DoCM)	RCV000426606	SCV000504694	likely pathogenic	Neoplasm	2015-07-14	no assertion criteria provided	literature only
Database of Curated Mutations (DoCM)	RCV000437291	SCV000504695	likely pathogenic	Carcinoma of esophagus	2016-05-31	no assertion criteria provided	literature only
Database of Curated Mutations (DoCM)	RCV000419135	SCV000504696	likely pathogenic	Neoplasm of the breast	2016-05-31	no assertion criteria provided	literature only
Database of Curated Mutations (DoCM)	RCV000426359	SCV000504697	likely pathogenic	Neoplasm of brain	2016-05-31	no assertion criteria provided	literature only
Database of Curated Mutations (DoCM)	RCV000437935	SCV000504698	likely pathogenic	Myelodysplastic syndrome	2016-05-31	no assertion criteria provided	literature only
Database of Curated Mutations (DoCM)	RCV000420727	SCV000504699	likely pathogenic	Malignant melanoma of skin	2016-05-31	no assertion criteria provided	literature only
Database of Curated Mutations (DoCM)	RCV000430513	SCV000504700	likely pathogenic	Squamous cell carcinoma of the skin	2016-05-31	no assertion criteria provided	literature only
Database of Curated Mutations (DoCM)	RCV000441226	SCV000504701	likely pathogenic	Squamous cell lung carcinoma	2016-05-31	no assertion criteria provided	literature only
Database of Curated Mutations (DoCM)	RCV000417916	SCV000504702	likely pathogenic	Acute myeloid leukemia	2016-05-31	no assertion criteria provided	literature only
Database of Curated Mutations (DoCM)	RCV000428591	SCV000504703	likely pathogenic	Adenocarcinoma of stomach	2016-05-31	no assertion criteria provided	literature only
Database of Curated Mutations (DoCM)	RCV000438410	SCV000504704	likely pathogenic	Hepatocellular carcinoma	2016-05-31	no assertion criteria provided	literature only
Database of Curated Mutations (DoCM)	RCV000421194	SCV000504705	likely pathogenic	Ovarian Serous Cystadenocarcinoma	2016-05-31	no assertion criteria provided	literature only
Database of Curated Mutations (DoCM)	RCV000432778	SCV000504706	likely pathogenic	Transitional cell carcinoma of the bladder	2016-05-31	no assertion criteria provided	literature only
Database of Curated Mutations (DoCM)	RCV000439963	SCV000504707	likely pathogenic	Pancreatic adenocarcinoma	2016-05-31	no assertion criteria provided	literature only
Database of Curated Mutations (DoCM)	RCV000421893	SCV000504708	likely pathogenic	Neoplasm of the large intestine	2016-05-31	no assertion criteria provided	literature only
Database of Curated Mutations (DoCM)	RCV000432587	SCV000504709	likely pathogenic	Uterine Carcinosarcoma	2016-05-31	no assertion criteria provided	literature only
Database of Curated Mutations (DoCM)	RCV000445235	SCV000504710	likely pathogenic	Lung adenocarcinoma	2016-05-31	no assertion criteria provided	literature only
Database of Curated Mutations (DoCM)	RCV000426233	SCV000504711	likely pathogenic	Adenocarcinoma of prostate	2016-05-31	no assertion criteria provided	literature only
Database of Curated Mutations (DoCM)	RCV000433424	SCV000504712	likely pathogenic	Brainstem glioma	2016-05-31	no assertion criteria provided	literature only
Database of Curated Mutations (DoCM)	RCV000444656	SCV000504713	likely pathogenic	Squamous cell carcinoma of the head and neck	2016-05-31	no assertion criteria provided	literature only
Database of Curated Mutations (DoCM)	RCV000427709	SCV000504714	likely pathogenic	Medulloblastoma	2016-05-31	no assertion criteria provided	literature only
Database of Curated Mutations (DoCM)	RCV000437518	SCV000504715	likely pathogenic	Malignant neoplasm of body of uterus	2016-05-31	no assertion criteria provided	literature only
Database of Curated Mutations (DoCM)	RCV000420303	SCV000504716	likely pathogenic	Small cell lung cancer	2016-05-31	no assertion criteria provided	literature only
Database of Curated Mutations (DoCM)	RCV000424869	SCV000504717	likely pathogenic	Multiple myeloma	2016-05-31	no assertion criteria provided	literature only
Database of Curated Mutations (DoCM)	RCV000435533	SCV000504718	likely pathogenic	Chronic lymphocytic leukemia	2016-05-31	no assertion criteria provided	literature only
Donald Williams Parsons Laboratory,Baylor College of Medicine	RCV000013150	SCV000599966	pathogenic	Li-Fraumeni syndrome 1	2012-12-27	no assertion criteria provided	research	This variant has been previously reported as disease-causing and was found once in our study maternally inherited in a 2-year-old female with neuroblastoma, in a family meeting criteria for Li-Fraumeni (history of early breast, brain tumors, rhabdomyosarcoma).
Mayo Clinic Genetic Testing Laboratories,Mayo Clinic	RCV000235221	SCV000692073	pathogenic	not provided		no assertion criteria provided	clinical testing
Genome Sciences Centre,British Columbia Cancer Agency	RCV000589336	SCV000693734	pathogenic	Malignant Colorectal Neoplasm	2016-04-12	no assertion criteria provided	research
German Consortium for Hereditary Breast and Ovarian Cancer Center Cologne,University Hospital Cologne	RCV000785344	SCV000923912	likely pathogenic	Ovarian Neoplasms	2018-12-01	no assertion criteria provided	research
Xiao lab, Department of Pathology, Memorial Sloan Kettering Cancer Center	RCV000790860	SCV000930032	likely pathogenic	Lymphoma	2019-07-25	no assertion criteria provided	clinical testing
Xiao lab, Department of Pathology, Memorial Sloan Kettering Cancer Center	RCV000424869	SCV001132099	likely pathogenic	Multiple myeloma	2019-08-31	no assertion criteria provided	clinical testing
Institute of Medical Sciences, Banaras Hindu University	RCV001255671	SCV001432236	pathogenic	Lip and oral cavity carcinoma	2019-04-30	no assertion criteria provided	research