Table 1.

TP53 variants targeting specifically exon 9β and exon 9γ sequences and their splice sites.

Sample ID/SNP_IDaOriginbChromosomal reference NC_000017.10cMain TP53 transcript NM_000546.5dExon 9β transcript NM_001126114.2eExon 9γ transcript NM_001126113.2fExon 9β protein NP_001119586.1gExon 9γ protein NP_001119585.1h
V6Skin SCCg.7576659A>Gc.993+194A>Gc.994-2A>Gc.994-73A>Gp.(?)
rs750031971dbSNPg.7576655C>Tc.993+198C>Tc.996C>Tc.994-69C>Tp.(D332=)
rs764851816dbSNPg.7576654C>Gc.993+199C>Gc.997C>Gc.994-68C>Gp.Q333E
rs761303879dbSNPg.7576637A>Cc.993+216A>Cc.1014A>Cc.994-51A>Cp.K338N
12aHead and neck SCCg.7576636G>Cc.993+217G>Cc.1015G>Cc.994-50G>Cp.E339Q
SA500637HCCg.7576633A>Gc.993+220A>Gc.1018A>Gc.994-47A>Gp.N340D
JEN9 (rs3021068)dbSNPg.7576630T>Gc.993+223T>Gc.1021T>Gc.994-44T>Gp.C341G
rs3021068dbSNPg.7576630T>Gc.993+223T>Gc.1021T>Gc.994-44T>Gp.C341G
rs3021068dbSNPg.7576630T>Ac.993+223T>Ac.1021T>Ac.994-44T>Gp.C341S
SLN2522Burkitt lymphomag.7576626A>Cc.993+227A>Cc.1025A>Cc.994-40>Cp.*342Sext17
Au3Melanomag.7576626A>Gc.993+227A>Gc.1025A>Gc.994-40A>Gp.(*=)
rs764562217dbSNPg.7576626A>Cc.993+227A>Cc.1025A>Cc.994-40A>Gp.*342Sext17
rs761121529dbSNPg.7576625A>Gc.993+228A>Gc.1026A>Gc.994-39A>Gp.(*=)
rs17883348dbSNPg.7576619G>Ac.993+234G>Ac.*6G>Ac.994-33G>A
rs576532147dbSNPg.7576609G>Tc.993+244G>Tc.*16G>Tc.994-23G>T
HPB-ALLiT-ALLg.7576607T>Ac.993+246T>Ac.*18T>Ac.994-21T>A
RPMIiT-ALLg.7576607T>Ac.993+246T>Ac.*18T>Ac.994-21T>A
XHDG17Gallbladder ca.g.7576601G>Ac.993+252G>Ac.*24G>Ac.994-15G>A
SA6251-BRCA-UKBreast carcinomag.7576591G>Ac.993+262G>Ac.*34G>Ac.994-5G>A
BRCA_UK_1Breast carcinomag.7576591G>Ac.993+262G>Ac.*34G>Ac.994-5G>A
117B-Chronic lymphocytic leukemiag.7576572T>Gc.993+281T>Gc.*53T>Gc.1006T>Gp.L336V
19Uterine carcinosarcomag.7576572_7576568delc.993+281_993+285del5c.*53_*57del5c.1006_1010el5p.L336Mfs*12
3129EsophagealAdcg.7576570A>Cc.993+283A>Cc.*55A>Cc.1008A>Cp.L336F
SA529425-LINC-JPHepatocellular carcinomag.7576570A>Cc.993+283A>Cc.*55A>Cc.1008A>Cp.L336F
SA529505-LINC-JPHepatocellular carcinomag.7576570A>Cc.993+283A>Cc.*55A>Cc.1008A>Cp.L336F
COSM1610827dbSNPg.7576570A>Cc.993+283A>Cc.*55A>Cc.1008A>Cp.L336F
rs554738122dbSNPg.7576569C>Tc.993+284C>Tc.*56C>Tc.1009C>Tp.R337*
DS-54750Colorectal carcinomag.7576568G>Ac.993+285G>Ac.*57G>Ac.1010G>Ap.R337Q
15Bladder carcinomag.7576568G>Cc.993+285G>Cc.*57G>Cc.1010G>Cp.R337P
rs771319678dbSNPg.7576568G>Ac.993+285G>Ac.*57G>Ac.1010G>Ap.R337Q
rs749361930dbSNPg.7576566T>Cc.993+287T>Cc.*59T>Cc.1012T>Cp.W338R
rs1642789dbSNPg.7576563T>Cc.993+290T>Cc.*62T>Cc.1015T>Cp.C339R
rs1642789dbSNPg.7576563T>Ac.993+290T>Ac.*62T>Ac.1015T>Ap.C339S
DS-53453Colorectal carcinomag.7576558C>Tc.993+295C>Tc.*67C>Tc.1020C>Tp.(Y340=)
rs770028766dbSNPg.7576554C>Tc.993+299C>Tc.*71C>Tc.1024C>Tp.(Y340=)
rs200274944dbSNPg.7576546C>Tc.993+307C>Tc.*79C>Tc.1032C>Tp.(Y340=)
rs200274944dbSNPg.7576546C>Gc.993+307C>Gc.*79C>Gc.1032C>Gp.N344K
YUMULMelanomag.7576544C>Tc.993+309C>Tc.*81C>Tc.1034C>Tp.S345L
SJNBL197jNeuroblastomag.7576544C>Tc.993+309C>Tc.*81C>Tc.1034C>Tp.S345L
5-VS065-T1Skin basal cell carcinomag.7576544C>Tc.993+309C>Tc.*81C>Tc.1034C>Tp.S345L
rs758194998dbSNPg.7576544C>Tc.993+309C>Tc.*81C>Tc.1034C>Tp.S345L
WD_06Skin squamous cell carcinomag.7576543G>Ac.993+310G>Ac.*82G>Ac.1035G>Ap.(S345=)
rs201293647dbSNPg.7576543G>Tc.993+310G>Tc.*82G>Tc.1035G>Tp.(S345=)
rs201293647dbSNPg.7576543G>Ac.993+310G>Ac.*82G>Ac.1035G>Ap.(S345=)
12-RSRichter syndromeg.7576542T>Gc.993+311T>Gc.*83T>Gc.1036T>Gp.S346A
DS-53382Colorectal carcinomag.7576542T>Cc.993+311T>Cc.*83T>Cc.1036T>Cp.S346P
COSM1731910dbSNPg.7576542T>Gc.993+311T>Gc.*83T>Gc.1036T>Gp.S346A
TCGA-HT-A616Glioma (low grade)g.7576541C>Gc.993+312C>Gc.*84C>Gc.1037C>Gp.S346W
rs756952434dbSNPg.7576541C>Tc.993+312C>Tc.*84C>Tc.1037C>Tp.S346L
rs372821099dbSNPg.7576540G>Ac.993+313G>Ac.*85G>Ac.1038G>Ap.(S346=)
SC_9007-TumorProstate carcinomag.7576539T>Cc.993+314T>Cc.*86T>Cc.1039T>Cp.*347Qext67
CCRF-CEMT-Acute lymphoblastic leukemiag.7576533G>Ac.993+320G>Ac.*92G>Ac.*4G>A
rs730882013dbSNPg.7576527_7576512delc.993+326_993+341del16c.*98_*100+13del16C*10_12+13del16
MEL-Ma-Mel-94Melanomag.7576525T>Gc.993+328T>Gc.*100T>Gc.*12T>G
83kBreast carcinomag.7576525T>Gc.993+328T>Gc.*100T>Gc.*12T>G
SA505836-OV-AUOvarian carcinomag.7576525T>Gc.993+328T>Gc.*100T>Gc.*12T>G
ATH-2Splenic marginal zone lymphomag.7576522insTCTc.993+331_993+332insTCTc.*100+2_*100+3*3insTCTc.*12+2_*12+3*3insTCT
  • Abbreviations: BCC, basal cell carcinoma; HCC, hepatocellular carcinoma; SCC, squamous cell carcinoma; T-ALL, T-cell acute lymphoblastic leukemia.

  • aSample identifier used in the original publication or in dbSNP.

  • bOrigin: somatic data were extracted from tumors included in the latest version of the TP53 mutation database (http://p53.fr). For several studies, matched normal DNA was not available. dbSNP were extracted from version NCBI dbSNP Build 148 (http://www.ncbi.nlm.nih.gov/snp). For most variants described in dbSNP, the minor allele frequency is less than 0.001.

  • cTP53 genomic variant descriptions according to chromosomal reference sequence NC_000017.10 of the GRCh37 (hg19) genome assembly.

  • dRef-Seq transcript NM_000546.5 encodes the TP53 full-length protein (NP_000537.3).

  • eTP53 coding DNA variant descriptions according to Ref-Seq transcripts encoding TP53β (NM_001126114.2).

  • fTP53 coding DNA variant descriptions according to Ref-Seq transcripts encoding TP53γ (NM_001126113.2).

  • gTP53 protein variant descriptions according to Ref-Seq proteins TP53β (NP_001119586.1).

  • hTP53 protein variant descriptions according to Ref-Seq proteins TP53γ (NP_001119585.1).

  • iBoth T-ALL cell lines carry the same rare variant, suggesting cross-contamination.

  • jThis variant was described as germline in a patient with a pediatric neuroblastoma.

  • kThe variant in this patient was shown to modify TP53 splicing.