Table 1.

Potentially Deleterious Nonsynonymous cSNPs Predicted by SIFT and Polyphen

Symbola
LocusLinkb
rs (dbSNP)c
AA Pos.d
Major allelee
Minor allelef
Freqg
Pfam domainsh
ARSA 410 6151411 82 P L 0.01 PF00884 Sulfatase
BRCA1 672 356 Q R 0.01
CASP2 835 4647338 424 R G 0.02 PF00655 ICE-like protease caspase p10 domain
CCNG2 901 28 E G 0.01 PF00134 cyclin
CDC6 990 4135016 378 R H 0.01 PF01078 Mg_chelatase PF00004 AAA
CDC6 990 4135013 299 T M 0.01 PF01078 Mg_chelatasePF00004 AAA
CDK7 1022 285 T M 0.02 PF00069 pkinase
CDKN1B 1027 2066828 15 R W 0.01
CYP2C9 1559 144 R C 0.06 PF00067 p450
CYP2C9 1559 251 H R 0.01 PF00067 p450PF03011 PFEMP
CYP2C9 1559 489 P S 0.01
E2F3 1871 4134973 344 G R 0.01 PF02319 E2F_TDP
ERBB2 2064 4252633 452 W C 0.01
ERCC1 2067 3212977 266 A T 0.01 PF00633 HHH
ERCC4 2072 1799802 379 P S 0.01
ERCC4 2072 1800124 875 E G 0.01
ERCC5 2073 1104 D H 0.38
ERCC5 2073 311 S C 0.01
EXO1 9156 93 R G 0.01
EXO1 9156 456 S Y 0.01
FGF11 2256 163 R C 0.01 PF00167 FGF
GCKR 2646 446 P L 0.33
GCKR 2646 256 G S 0.01 PF01380 SIS
GPI 2821 208 I T 0.02 PF00342 PGI
GSR 2936 110 R C 0.03 PF00070 pyr_redox
GSTZ1 2954 32 E K 0.3 PF02798 GST_N
GTF2H1 2965 234 R W 0.01
HGF 3082 5745688 330 D Y 0.01 PF00051 Kringle domain
HSPB2 3316 4252589 111 G S 0.01 PF00011 HSP20
IGF1R 3480 605 R H 0.01
IGF2R 3482 203 P L 0.02 PF00878 CIMR_repeat
IGF2R 3482 231 G D 0.01 PF00878 CIMR_repeat
LPO 4025 414 R Q 0.01 PF03098 Animal haem peroxidase
LPO 4025 514 R Q 0.01 PF03098 Animal haem peroxidase
LPO 4025 614 I T 0.01 PF03098 Animal haem peroxidase
MTHFR 4524 429 E A 0.27
MTHFR 4524 222 A V 0.22 PF02219 MTHFR
MTHFR 4524 422 G R 0.01
MUTYH 4595 3219494 500 G E 0.01
MYC 4609 4645959 11 N S 0.02 PF01056 Myc_N_term
NAT2 10 64 R Q 0.02 PF00797 Acetyltransf2
NEIL1 79661 5745906 83 G D 0.01 PF01149 Fapy_DNA_glyco
NFKB1 4790 4648099 711 H Q 0.02
PKMYT1 9088 140 R C 0.01 PF00069 pkinase
PMS1 5378 1145232 501 G R 0.01 PF02465 HATPase_c
PMS1 5378 1145234 793 Y H 0.01
PNKP 11284 3739206 478 V G 0.01
POLB 5423 3136797 242 P R 0.01 PF00966 DNA_polymeraseX
POLG 5428 2307441 1143 E G 0.03 PF00476 DNA_pol_A
POLG 5428 2307440 1146 R C 0.01 PF00476 DNA_pol_A
POLG 5428 2307442 1142 R W 0.01 PF00476 DNA_pol_A
POLI 11201 3218778 71 R G 0.01 PF00817 IMS
POLI 11201 3218787 535 C R 0.01
POLI 11201 3218786 507 F S 0.01
POLL 27343 3730477 438 R W 0.13 PF00966 DNA_polymeraseX
RFC2 5982 3135684 232 A V 0.01 PF00004 AAA
SOD2
 6648
5746129
156
R
W
0.01
PF02777 sodfe_C

a HUGO symbol.

b LocusLink identifier (http://www.ncbi.nlm.nih.gov/LocusLink).

c Reference SNP cluster identifier (http://www.ncbi.nlm.nih.gov/SNP).

d Amino acid position in coding sequence.

e Amino acid substitution of higher frequency allele in the PDR.

f Amino acid substitution of lower frequency allele in the PDR.

g Estimated frequency of minor allele in 180 chromosomes.

h Protein family (http://www.sanger.ac.uk/Software/Pfam).