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This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with TP53-related conditions. This variant is also known as 163N. ClinVar contains an entry for this variant (Variation ID: 376679). Invitae Evidence Modeling incorporating data from in vitro experimental studies (PMID: 12826609, 29979965, 30224644) indicates that this missense variant is expected to disrupt TP53 function with a positive predictive value of 97.5%. Experimental studies have shown that this missense change affects TP53 function (PMID: 10229196, 12826609). 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."],"method":"clinical testing","submitter_name":"Labcorp Genetics (formerly Invitae), Labcorp","review_date":20251028,"diseases":[{"symbols":{"medgen":"C0085390"}}],"date_updated":20260307,"clinical_significance":["Uncertain significance"],"review_status":"criteria provided, single submitter","accession_id":"SCV000754569"}],"submission_description":[],"review_date":20251028,"diseases":[{"pub_med":[17392385,24493721,26389210,26389258],"normalized_disease":["Li-Fraumeni Syndrome"],"symbols":{"omim":"151623","medgen":"C0085390","mondo":"MONDO:0018875"},"names":["Li-Fraumeni Syndrome","Sarcoma Family Syndrome  Li  Fraumeni"]}],"date_created":20180528,"variation_id":376679,"clinical_significance":["Uncertain significance"],"variant_id":10190170075784430004,"review_description":"Uncertain significance","allele_id":363558,"title":"NM_000546.6(TP53):c.487T>A (p.Tyr163Asn) AND Li-Fraumeni syndrome","accession_id":"RCV000633347"},{"submissions":[{"submitter_date":20250617,"review_description":"Likely pathogenic","origin":"germline","submission_description":["The p.Y163N variant (also known as c.487T>A), located in coding exon 4 of the TP53 gene, results from a T to A substitution at nucleotide position 487. The tyrosine at codon 163 is replaced by asparagine, an amino acid with dissimilar properties. This variant is in the DNA binding domain of the TP53 protein and is reported to have non-functional transactivation in yeast based assays (Kato S et al. Proc. Natl. Acad. Sci. USA. 2003 Jul;100:8424-9). Studies conducted in human cell lines indicate this alteration is deficient at growth suppression and has a dominant negative effect (Kotler E et al. Mol.Cell. 2018 Jul;71:178-190.e8; Giacomelli AO et al. Nat. Genet. 2018 Oct;50:1381-1387). This amino acid position is well conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the majority of available evidence to date, this variant is likely to be pathogenic."],"method":"clinical testing","submitter_name":"Ambry Genetics","review_date":20250514,"diseases":[{"symbols":{"medgen":"C0027672"}}],"date_updated":20250713,"clinical_significance":["Likely pathogenic"],"review_status":"criteria provided, single submitter","accession_id":"SCV002638731"}],"submission_description":[],"review_date":20250514,"diseases":[{"pub_med":[25394175],"symbols":{"medgen":"C0027672","mesh":"D009386","mondo":"MONDO:0015356"},"names":["Hereditary Cancer-Predisposing Syndrome","Hereditary Neoplastic Syndrome","Tumor Predisposition","Hereditary Neoplastic Syndrome","Hereditary Neoplastic Syndrome"],"normalized_disease":["Hereditary Neoplastic Syndrome"],"keyword":"Hereditary cancer syndrome"}],"date_created":20221129,"variation_id":376679,"clinical_significance":["Likely pathogenic"],"variant_id":10190170075784430004,"review_description":"Likely pathogenic","allele_id":363558,"title":"NM_000546.6(TP53):c.487T>A (p.Tyr163Asn) AND Hereditary cancer-predisposing syndrome","accession_id":"RCV002338982"},{"submissions":[{"submitter_date":20240422,"review_description":"Likely pathogenic","origin":"unknown","submission_description":["This variant is considered likely pathogenic. Functional studies indicate this variant impacts protein function [PMID: 10229196, 29979965]. 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1"],"annotation_id":"VAR_044871"}]}}]}],"alpha_missense":[{"version":"03-Jul-2024","main_data":"Likely Pathogenic","alpha_missense_score":0.9957884456923124}],"acmg_annotation":{"version_name":"13.17.0","gene_symbol":"TP53","transcript":"NM_000546.6","transcript_reason":"MANE select","coding_impact":"missense","blosum_score":-5,"verdict":{"ACMG_rules":{"benign_score":0,"benign_subscore":"Uncertain Significance","clinical_score":4.256,"pathogenic_score":6,"pathogenic_subscore":"Likely Pathogenic","total_score":6,"verdict":"Likely Pathogenic"},"classifications":["PM1","PM5","PM2_Supporting","PP5"]},"classifications":[{"name":"PM1","met_criteria":true,"user_explain":["Hot-spot of length 17 amino-acids has 107 missense/in-frame variants (33 pathogenic variants, 73 uncertain variants, and 1 benign variant), which qualifies as strong pathogenic.","UniProt protein P53_HUMAN region of interest 'Required for interaction with FBXO42' has 690 missense/in-frame variants (225 pathogenic variants, 454 uncertain variants, and 11 benign variants), which qualifies as moderate pathogenic.","UniProt protein P53_HUMAN DNA-binding domain 'DNA-binding region_102-292' has 1 147 missense/in-frame variants (420 pathogenic variants, 711 uncertain variants, and 16 benign variants), which qualifies as moderate pathogenic.","UniProt protein P53_HUMAN region of interest 'Interaction with AXIN1' has 1 068 missense/in-frame variants (387 pathogenic variants, 667 uncertain variants, and 14 benign variants), which qualifies as moderate pathogenic.","UniProt protein P53_HUMAN region of interest 'Required for interaction with ZNF385A' has 1 183 missense/in-frame variants (421 pathogenic variants, 746 uncertain variants, and 16 benign variants), which qualifies as moderate pathogenic.","UniProt protein P53_HUMAN region of interest 'Interaction with CCAR2' has 1 555 missense/in-frame variants (427 pathogenic variants, 1 061 uncertain variants, and 67 benign variants), which qualifies as supporting pathogenic.","UniProt protein P53_HUMAN region of interest 'Interaction with HIPK1' has 1 462 missense/in-frame variants (446 pathogenic variants, 952 uncertain variants, and 64 benign variants), which qualifies as supporting pathogenic.","Limiting strength to Moderate due to co-occurrence with other predictive evidence."]},{"name":"PM5","met_criteria":true,"user_explain":["Alternative variant ##chr17:7578443 A⇒G## (Tyr163His) is classified Pathogenic, 3 stars, by ClinVar in article %%PUBMED:0%% (confirmed using the germline classifier).","Alternative variant ##chr17:7578442 T⇒C## (Tyr163Cys) is classified Pathogenic, 3 stars, by ClinVar in article %%PUBMED:0%% (confirmed using the germline classifier).","2 pathogenic alternative variants identified.","Limiting strength to Moderate due to co-occurrence with other predictive evidence."]},{"name":"PM2","met_criteria":true,"user_explain":["Variant not found in gnomAD genomes, good gnomAD genomes coverage = 31.9.","Variant not found in gnomAD exomes, good gnomAD exomes coverage = 88.3."],"strength":"Supporting"},{"name":"PP5","met_criteria":true,"user_explain":["Supporting: ClinVar classifies this variant as Uncertain Significance but a high confidence submitter has classified as Likely Pathogenic, 1 star (reviewed Mar '26, 3 submissions of which 1 is from high confidence submitter), citing %%PUBMED:10229196%%."]}],"gene_id":33956,"sample_findings":{"phenotypes":"No matching phenotype found for gene TP53 which is associated with Adrenocortical Carcinoma, Hereditary, Adult Hepatocellular Carcinoma, Alveolar Rhabdomyosarcoma, B-Cell Chronic Lymphocytic Leukemia, and 25 more, according to CGD, ClinGen Disease Validity, GenCC, Mondo, and gene2phenotype.","mode_of_inheritance":"AD, based on gene information from CGD, ClinGen Disease Validity, GenCC, Mondo, and gene2phenotype."}},"amp_annotation":{"version_name":"13.17.0","verdict":{"tier":"Tier I","approx_score":3.3249999999999997},"classifications":[{"name":"Crtd","tier":"Tier I","user_explain":{"Tier I":["AML with Myelodysplasia-Related Changes, Acute Myeloid Leukemia, Chronic Lymphocytic Leukemia/Small Lymphocytic Lymphoma, Essential Thrombocythemia, and 5 more, prognostic, curated, from OncoKB, citing %%PUBMED:29296692%%, %%PUBMED:28819011%%, %%PUBMED:26022239%%, %%PUBMED:25952993%%, and 20 more. No patient information was provided to match the cancer."],"Tier III":["Variant not found in CKB."]},"approx_score":9.0},{"name":"Drug","tier":"Tier II","user_explain":{"Tier II":["10 therapies (Azacitidine, Capecitabine + Cetuximab + Oxaliplatin, Carboplatin + Cisplatin, Cisplatin, and 6 more), Actionable, curated, from CIViC. Related to Esophageal/Stomach Cancer, Breast Cancer, Non-Small Cell Lung Cancer, Colorectal Cancer, and 2 more. No patient information was provided to match the cancer."],"Tier III":["6 therapies (Alemtuzumab, Cisplatin, Doxorubicin, Etoposide, and 2 more), Actionable, curated, from CIViC. Related to Stomach Adenocarcinoma, Breast Cancer, Chronic Lymphocytic Leukemia/Small Lymphocytic Lymphoma, and Sarcoma, NOS. No patient information was provided to match the cancer.","No additional relevant drugs or clinical trials found in AACT, CIViC genes, CKB Genes, DGI, or PharmGKB."]},"approx_score":8.0},{"name":"Germ","tier":"Tier II","user_explain":{"Tier II":["This missense variant is classified Likely Pathogenic by the germline classifier, using rules PM1, PM5, PM2_Supporting, and PP5."]},"approx_score":7.0},{"name":"Path","tier":"Tier I","user_explain":{"Tier I":["The Human Protein Atlas classifies TP53 as tumour-suppressing."]},"approx_score":6.0},{"name":"Pubs","tier":"Tier III","user_explain":{"Tier III":["No publications have been linked by VarSome users."]},"approx_score":5.0},{"name":"Soma","tier":"Tier I","user_explain":{"Tier I":["This variant is reported in 101 out of the 42 872 somatic samples for gene TP53, which has 5 872 reported somatic variants. It is not found in GnomAD. This is statistically rated Tier I."],"Tier III":["TP53 Somatic reports 25 samples, cancer_type = 8 x Breast Cancer, 4 x Cancer of Unknown Primary, 3 x Hepatobiliary Cancer, and 9 more, tissue_type = 8 x Breast, 4 x Other, 2 x Liver, and 11 more.","CBioPortal reports 64 samples, cancer type = 14 x Prostate Cancer, 9 x Hepatobiliary Cancer, 7 x Non-Small Cell Lung Cancer, and 14 more, sample type = 39 x Primary, 14 x Metastasis, and 1 x Metastatic, tissue = 14 x Prostate, 8 x Liver, 7 x Lung, and 14 more.","CancerHotspots reports 9 samples, bio-type = 1 x protein_coding, cancer type = 3 x Hepatobiliary Cancer, 1 x Esophagogastric Cancer, 1 x Glioma, and 3 more, tissue site = 3 x Liver, 1 x CNS/Brain, 1 x Esophagus/Stomach, and 3 more.","GDC reports 3 samples, drugs = 2 x Carboplatin, 2 x Taxol, 1 x Cisplatin, and 2 more, outcomes = 2 x Recurred, sex = 3 x Female, tissues = 1 x CNS/Brain, 1 x Malignant Peripheral Nerve Sheath Tumors (MPNST), and 1 x Ovary/Fallopian Tube.","Variant not found in ICGC or TP53 Germline."]},"total_samples":101,"approx_score":4.0},{"name":"Freq","tier":"Tier II","user_explain":{"Tier II":["Variant not found in gnomAD genomes, good gnomAD genomes coverage = 31.9.\nVariant not found in gnomAD exomes, good gnomAD exomes coverage = 88.3."]},"approx_score":3.0},{"name":"Type","tier":"Tier III","user_explain":{"Tier III":["No relevant information.","Variant is not predicted splicing: no prediction from MaxEntScan."]},"approx_score":2.0},{"name":"Pred","tier":"Tier III","user_explain":{"Tier III":["No relevant 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Expression of this mutation in osteosarcoma cell lines that lack wildtype TP53 is associated with decreased transcriptional activation of the p53 target gene p21. Additionally, cell lines expressing this mutation have decreased apoptosis and enhanced cell growth as compared to cell lines that express wildtype form of TP53 (PMID: 10229196) suggesting that this mutation confers loss of p53 function.","knowneffect":"Likely Loss-of-function"},"oncogenic":"Likely Oncogenic","other_significant_resistance_levels":null,"other_significant_sensitive_levels":null,"prognostic_implications":[{"abstracts":[],"alterations":["Oncogenic Mutations"],"description":"This assertion is supported by (PMID: 24220272, 21714648, 25092778).","level_of_evidence":"LEVEL_Px1","pmids":["21714648","25092778","24220272"],"tumor_type":{"children":{},"code":"MDS","color":"LightSalmon","id":505,"level":3,"main_type":{"id":null,"name":"Myelodysplastic Syndromes","tumor_form":"LIQUID"},"name":"Myelodysplastic Syndromes","parent":"MNM","tissue":"Myeloid","tumor_form":"LIQUID"}},{"abstracts":[],"alterations":["Oncogenic Mutations"],"description":"This assertion is supported by (PMID: 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24004666).","level_of_evidence":"LEVEL_Px1","pmids":["23243274","24004666","20697090","19188171","24652989"],"tumor_type":{"children":{},"code":"CLLSLL","color":"LimeGreen","id":887,"level":5,"main_type":{"id":null,"name":"Mature B-Cell Neoplasms","tumor_form":"LIQUID"},"name":"Chronic Lymphocytic Leukemia/Small Lymphocytic Lymphoma","parent":"MBN","tissue":"Lymphoid","tumor_form":"LIQUID"}},{"abstracts":[],"alterations":["Oncogenic Mutations"],"description":"This assertion is supported by (PMID: 22887079, 25516983, 22052707).","level_of_evidence":"LEVEL_Px1","pmids":["25516983","22052707","22887079"],"tumor_type":{"children":{},"code":"PMF","color":"LightSalmon","id":747,"level":4,"main_type":{"id":null,"name":"Myeloproliferative Neoplasms","tumor_form":"LIQUID"},"name":"Primary Myelofibrosis","parent":"MPN","tissue":"Myeloid","tumor_form":"LIQUID"}},{"abstracts":[],"alterations":["Oncogenic Mutations"],"description":"This assertion is supported by (PMID: 22186996, 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