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Table 1 Structural classification of TP53 mutations in primary central nervous system lymphoma. The structural classification includes an absolute number of 39 TP53 mutations divided on 32 patients, of which 24 combination chemotherapy treated patients harbored 28 mutations (IDs 1–24), and the remaining 8, who harbored 11 mutations, received other therapies (IDs 25–32)

From: TP53 hotspot mutations are predictive of survival in primary central nervous system lymphoma patients treated with combination chemotherapy

ID Exon TP53 Mutation Sequence change Protein change Basepair change Localization Hotspot mutation Direct DNA contact/Zn CpG Site Conserved region Siftclass Mutation type Transactivation class
1 5I CYS-135-TYR TGC > TAC p.C135Y C.404G > A LSH     2 Deleterious Missense Non-Active
2 5I THR-140-ILE ACC > ATC p.T140I C.419C > T β     2 Deleterious Missense Partially Active
3 5I PRO-142-SER CCT > TCT p.P142S C.424C > T β     2 Deleterious Missense Partially Active
4a 5I GLN-144-STOP CAG > CTG p.Q144 C.430C > T β     99 Deleterious Nonsense NA
5a 5I ASP-148-ASN GAT > AAT p.D148N C.442G > A L2     3 Neutral Missense Active
6 5II MET-169-ILE ATG > ATA p.M169I C.507G > A L2     3 Partially Deleterious Missense Partially Active
7 5II MET-169-ILE ATG > ATA p.M169I C.507G > A L2     3 Partially Deleterious Missense Partially Active
8 5II MET-169-ILE ATG > ATA p.M169I C.507G > A L2     3 Partially Deleterious Missense Partially Active
9 5II GLU-171-LYS GAG > AAG p.E171K C.511G > A L2     3 Deleterious Missense Active
10a 5II VAL-173-MET GTG > ATG p.V173M C.517G > A L2     3 Deleterious Missense Non-Active
10b 5II ARG-181-HIS CGC > CAC p.R181H c.542G > A L2    CpG 3 Deleterious Missense Partially Active
11 5II ARG-175-HIS CGC > CAC p.R175H C.524G > A L2 Hotspot Direct DNA Contact CpG 3 Deleterious Missense Non-Active
12 5II ARG-175-HIS CGC > CAC p.R175H C.524G > A L2 Hotspot Direct DNA Contact CpG 3 Deleterious Missense Non-Active
5b 5II Frameshift deletion NA C.528.del1 L2   Zn-binding Site CpG 3 Frameshift Deletion NA (Zn-binding Site)
13 5II HIS-179-ARG CAT > CGT p.H179R C.536A > G L2 Hotspot Zn-binding Site   3 Deleterious Missense Non-Active
14 5II ASP-184-GLY GAT > GGT p.D184G C.551A > G L2     3 Neutral Missense Active
15 6 ARG-202-CYS CGT > TGT p.R202C C.604C > T β    CpG 99 Deleterious Missense Active
16a 6 ASP-208-GLY GAC > GGC p.D208G C.623A > G β     99 Deleterious Missense Active
17 7 TYR-236-CYS TAC > TGC p.Y236C C.707A > G β     99 Deleterious Missense Non-Active
4b 7 MET-237-VAL ATG > GTG p.M237V C.709A > G L3     99 Deleterious Missense Non-Active
18 7 ASN-239-SER AAC > AGC p.N239S C.716A > G L3 Hotspot Direct DNA Contact   4 Deleterious Missense Non-Active
19 7 ARG-248-GLN CGG > CAG p.R248Q C.743G > A L3 Hotspot Direct DNA Contact CpG 4 Deleterious Missense Non-Active
20 7 ARG-249-LYS AGG > AAG p.R249K C.746G > A L3 Hotspot Direct DNA Contact   4 Deleterious Missense Non-Active
16b 7 THR-256-ILE ACA > ATA p.T256I C.767C > T L3     4 Deleterious Missense Partially Active
21 8 ARG-273-CYS CGT > TGT p.R273C C.817C > T LSH Hotspot Direct DNA Contact CpG 5 Deleterious Missense Non-Active
22 8 GLY-279-GLU GGG > GAG p.G279E C.836G > A LSH     5 Deleterious Missense Non-Active
23 8 ARG-280-LYS AGA > AAA p.R280K C.839G > A LSH Hotspot Direct DNA Contact   5 Deleterious Missense Non-Active
24 8 GLU-286-LYS GAA > AAA p.E286K C.856G > A LSH     5 Deleterious Missense Non-Active
25a 5I THR-140-ILE ACC > ATC p.T140I C.419C > T β     99 Deleterious Missense Partially Active
26a 5I PRO-151-SER CCC > CCT p.P151S C.451C > T β   Direct DNA Contact   99 Deleterious Missense Non-Active
27 5I ILE-162-MET ATC > ATG p.I162M C.486C > G β     99 Deleterious Missense Partially Active
28a 5II VAL-172-ALA GTG > GCG p.V172A C.515 T > C L2     3 Deleterious Missense Active
29 5II ARG-175-HIS CGC > CAC p.R175H C.524G > A L2 Hotspot Direct DNA Contact CpG 3 Deleterious Missense Non-Active
30 5II GLY-187-ASP GGT > GAT p.G187D C.560G > A L2     3 Neutral Missense Active
26b 5II GLY-187-ASP GGT > GAT p.G187D C.560G > A L2     3 Neutral Missense Active
31 7 MET-243-ILE ATG > ATA p.M243I C.729G > A L3   Direct DNA Contact   4 Deleterious Missense Non-Active
28b 8 VAL-272-MET GTG > ATG p.V272M C.814G > A LSH     5 Deleterious Missense Non-Active
32 8 ARG-290-CYS CGC > TGC p.R290C C.868C > T β    CpG 99 Deleterious Missense Active
25b 8 GLY-302-ARG GGG > AGG p.G302R C.904G > A C-Term     99 Neutral Missense Active