Table 1 Functional analysis and classification of 21 TP53 variants found in the human populationa.

From: Identification and functional characterization of new missense SNPs in the coding region of the TP53 gene

TP53_variant

Functional analysisb

Growth suppression (Kotler et al.)

DNE/LOF (Giacomelli et al.)

LOF (Giacomelli et al.)

Population classification (ACMG)

Population classification (ACMG)c

ClinVar datad

c.31G>C_E11Q

Functional

No data

Functional

Functional

BA1 (Japan; Korea); BS1(EAS)

Benign (BA1; BS3; BP4)

LB (2) VUS (4)

c.91G>A_V31I

Functional

No data

Functional

Functional

BA1 (China; Japan; Korea; Taiwan; gnomAD_EAS)

Benign (BA1; BS3; BP4)

B (1) LB (4) LP (1) VUS (3) Star (1)

c.139C>T_P47S

Functional

No data

Functional

Functional

BA1 (Brazil; Flossies; GnomAD; Kaviar; EVS; gnomAD_AFR)

Benign (BA1; BS3; BP4)

B (10) VUS (1) Star (1)

c.145G>C_D49H

Functional

No data

Functional

Functional

BA1 (Japan)

Benign (BA1; BS3; BP4)

VUS

c.173C>G_P58R

Functional

No data

Functional

Functional

BS1 (gnomAD_AFR; Flossies; EVS)

Benign (BA1; BS3; BP4)

LB (6) VUS (1)

c.215C>G_P72R

Functional

No data

Functional

Functional

BA1 (all datasets)

Benign (BA1; BS3; BP4)

B Star (3)

c.319T>C_Y107H

Functional

Functional

Functional

Functional

BA1 (gnomAD_AFR); BS1 (Flossies)

Benign (BA1; BS3; BP4)

LB (3) VUS (4)

c.329G>A_R110H

Functional

Functional

Functional

Functional

–

Likely benign (BS3; BP4)

VUS

c.466C>T_R156C

Functional

Functional

Functional

Functional

–

Likely benign (BS3; BP4)

VUS

c.554G>A_S185N

Functional

Functional

Functional

Functional

–

Likely benign (BS3; BP4)

VUS

c.566C>T_A189V

Functional

Functional

Functional

Functional

BA1 (China)

Benign (BA1; BS3; BP4)

VUS

c.665C>T_P222L

Functional

Functional

Functional

Functional

–

VUS (BS3)

VUS

c.704A>G_N235S

Functional

Functional

Functional

Functional

BA1 (Australia); BS1 (FIN; Finland; NFE)

Benign (BA1;BS1;BP4)

B (1)LB (5) VUS (3) Star (1)

c.760A>G_I254V

Functional

Functional

Functional

Functional

–

VUS (PP3; BS3)

VUS

c.787A>G_N263D

Functional

Functional

Functional

Functional

SAS

Benign (BS1; BS3)

LB (1) VUS (4)

c.847C>T_R283C

Functional

Functional

Functional

Functional

EVS

Benign (BS1; BS3)

LB (1) LP (1) VUS (12)

c.869G>A_R290H

Functional

Functional

Functional

Functional

BS1 (Finland; Flossies; FIN)

Benign (BS1; BS3)

B (1) LB (1) VUS (10) Star (1)

c.935C>G_T312S

Functional

No data

Functional

Functional

BS1 (gnomAD_AFR)

Benign (BS1; BS3)

B (1)LB (1) VUS (4) Star (1)

c.1015G>A_E339K

Functional

No data

Functional

Functional

BS1 (gnomAD_EAS)

Benign (BS1; BS3)

LB (2) VUS (3)

c.1073A>T_E358V

Functional

No data

Functional

Functional

BA1 (China)

Benign (BA1; BS3; BP4)

LB (1) VUS (2) Star (2)

c.1079G>C_G360A

Functional

No data

Functional

Functional

BS1 (gnomAD_LAT; gnomAD_AFR)

Benign (BS1; BS3)

B LB

c.524G>A_R175H

Defective

Defective

Defective

Defective

–

Pathogenic (PS3; PS4; PM1; PP3)

P

c.761T>C_I254T

Defective

Defective

Defective

Defective

–

Pathogenic (PS3; PS4; PM1; PP3)

No data

c.1025G>C_R342P

Defective

Functional

Functional

Defective

–

Pathogenic (PS3; PS4; PM1; PP3)

LP P

c.428T>C_V143A

Defective

Defective

Defective

Defective

–

Pathogenic (PS3; PS4; PM1; PP3)

No data

  1. DNE dominant negative effect, LOF loss of function.
  2. aA complete version of this table with detailed description of all data is available in Table S5.
  3. bFunctional analysis includes transcriptional activity, apoptosis, and cell proliferation assays performed both in human cells or in yeast in the present study.
  4. cFor each classification, identity of the dataset is indicated in brackets. gnomAD data were split into eight geographical datasets (EAS, AFR, SAS, FIN, LAT, EAS, ASJ, and OTH) leading to a total of 22 datasets.
  5. dAssessed June 2020.
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