Table 2

Amino acid substitution variants identified in DNA repair and repair-related genes

The common nucleotide followed by the variant nucleotide is enclosed in parentheses, and the codon for the amino acid residue is underlined and bold. The nine amino acid substitutions reported previously (25) are indicated with an asterisk.

Gene name	Exon	Codon	Common residue	Variant residue	Allele frequency	Mouse residue	cDNA sequence 5′→3′
BER
ADPRT	4	188	Ala	Thr	0.006	Ser	TCCTT(G/A)CTACA
ADPRT	7	334	Val	Ile	0.011	Val	AGTGG(G/A)TAACC
ADPRT	8	383	Ser	Tyr	0.014	Ser	CTCCT(C/A)TGCTT
ADPRT	17	761	Val	Ala	0.18	Val	CAAGG(T/C)GGAAA
ADPRT	21	940	Lys	Arg	0.011	Lys	CAGCA(A/G)GTTAC
APE1	3	51	Gln	His	0.03	Gln	GATCA(G/C)AAAAC
APE1	3	64	Ile	Val	0.01	Ile	TCAAG(A/G)TCTGC
APE1	5	148	Asp	Glu	0.33	Glu	GGCGA(T/G)GAGGA
APE1	5	241	Gly	Arg	0.01	Gly	GCTTC(G/A)GGGAA
FEN1		No variants
LIG1	3	24	Ala	Val	0.01	Thr	GGAGG(C/T)ATCCA
LIG1	4	62	Arg	Trp	0.01	Gln	CGGCC(C/T)GGGTC
LIG1	9	249	Gly	Glu	0.01	Gly	GCCAG(G/A)GGCTC
LIG1	10	267	Asn	Ser	0.02	Asn	TTACA(A/G)TCCTG
LIG1	13	369	Val	Ile	0.01	Ile	AGTCC(G/A)TCCGG
LIG1	13	409	Arg	His	0.01	Cys	GTTCC(G/A)CGACA
LIG1	16	480	Met	Val	0.01	Val	CAGCC(A/G)TGGTG
LIG1	20	614	Thr	Ile	0.01	Thr	GGTCA(C/T)ATCCT
LIG1	22	673	Glu	Asp	0.01	Gln	CGTGA(G/T)CCCCT
LIG1	22	677	Arg	Leu	0.01	Arg	TTCCC(G/T)GCGCC
LIG3	18	780	Arg	His	0.03	Cys	GTCCC(G/A)CAAGG
LIG3	19	811	Lys	Thr	0.01	Lys	TGCAA(A/C)GCCTT
LIG3	21	899	Pro	Ser	0.01	Thr	AGAAC(C/T)CTGCG
NTHL1	1	21	Arg	Trp	0.006	Arg	GGAGC(C/T)GGAGC
NTHL1	1	31	Gly	Val	0.006	Gly	GCGGG(G/T)GTGTA
NTHL1	1	33	Arg	Lys	0.006	Arg	GTGTA(G/A)GGAGG
NTHL1	3	176	Ile	Thr	0.005	Ile	GCTCA(T/C)CTACC
NTHL1	4	234	Ser	Leu	0.006	Ser	TGTGT(C/T)AGGCA
NUDT1	3	83	Val	Met	0.006	Val	TGGAC(G/A)TGCAT
NUDT1	4	135	Gly	Trp	0.006	Gly	TCCAC(G/T)GGTAC
PCNA		No variants
POLB	1	8	Gln	Arg	0.01	Gln	GCCGC(A/G)GGAGA
POLB	7	137	Arg	Gln	0.006	Arg	TCAGC(G/A)AATTG
POLB	12	242	Pro	Arg	0.005	Pro	GCTTC(C/G)CAGTA
POLD1	1	19	Arg	His	0.12	Arg	GGCCC(G/A)TGGGG
POLD1	1	30	Arg	Trp	0.006	Ser	CACCT(C/T)GGCCA
POLD1	3	119	Arg	His	0.15	Arg	ATCCC(G/A)CGGCT
POLD1	4	173	Ser	Asn	0.05	Ser	CATCA(G/A)CCGGG
POLD1	4	177	Arg	His	0.003	Arg	CAGTC(G/A)CGGGG
POLD1	19	849	Arg	His	0.011	Arg	ACTGC(G/A)CCGCC
POLD1	26	1086	Arg	Gln	0.01	Arg	GGTGC(G/A)GAAGG
POLD2	8	303	Asn	Ser	0.005	Asn	CACCA(A/G)TTACA
XRCC1	3	72	Val	Ala	0.03	Val	GCTGG(T/C)GGGCA
XRCC1	5	161	Pro	Leu	0.005	Thr	GGCCC(C/T)GTCCC
XRCC1	5	173	Phe	Leu	0.005	Phe	CAGTT(C/G)CGTGT
XRCC1	6	194*	Arg	Trp	0.13	Arg	TCAGC(C/T)GGATC
XRCC1	9	280*	Arg	His	0.03	Arg	AACTC(G/A)TACCC
XRCC1	9	309	Pro	Ser	0.01	Ala	GACGA(C/T)CCCGA
XRCC1	10	399*	Arg	Gln	0.24	Arg	CTCCC(G/A)GAGGT
XRCC1	15	560	Arg	Trp	0.01	Arg	AGCGG(C/T)GGAAA
XRCC1	16	576	Tyr	Ser	0.01	Tyr	GGACT(A/C)TATGA

NER
ERCC1		No variants
ERCC2	8	199*	Ile	Met	0.01	Ile	TCAAT(C/G)CTGCA
ERCC2	8	201*	His	Tyr	0.01	His	TCCTG(C/T)ATGCC
ERCC2	10	312*	Asp	Asn	0.40	Asp	TGCCC(G/A)ACGAA
ERCC2	20	616	Arg	Pro	0.01	Arg	CGGGC(G/C)GGCCG
ERCC2	23	751*	Lys	Gln	0.32	Gln	CGCTG(A/C)AGAGG
ERCC3		No variants
ERCC4	7	379*	Pro	Ser	0.03	Pro	GCAAC(C/T)CAAAG
ERCC4	8	415	Arg	Gln	0.06	Arg	TGACC(G/A)AACAT
ERCC5	4	141	Asn	Asp	0.02	Asp	GAGAA(A/G)ACGAC
ERCC5	7	254	Met	Val	0.012	Met	AGGAA(A/G)TGAAT
ERCC5	8	529	Cys	Ser	0.03	Arg	AACTT(G/C)TACAA
ERCC5	8	597	Val	Leu	0.011	Met	AGGCA(G/C)TAGAT
ERCC5	10	761	Ala	Thr	0.011	Ala	GGATC(G/A)CTGCT
ERCC5	15	1090	Glu	Asp	0.011	Asp	GGGGA(G/C)ACCTG
ERCC5	15	1104	Asp	His	0.18	Asp	GTGAA(G/C)ATGCT
LIG1		See above
PCNA		See above
POLD1		See above
POLD2		See above
RAD23A	5	200	Thr	Met	0.03	Thr	GCTCA(C/T)GGGAA
RAD23B	7	249	Ala	Val	0.10	Ala	TGGGG(C/T)TCCTC
XPA	6	256	Met	Ile	0.01	Met	GACAT(G/C)TACCG
XPC	1	16	Leu	Val	0.04	none	GCGAA(C/G)TGCGC
XPC	2	48	Leu	Phe	0.04	Ser	GCCTT(C/T)TCTCC
XPC	8	492	Arg	His	0.04	Arg	CCATC(G/A)TAAGG
XPC	8	499	Ala	Val	0.24	Ala	GCCAG(C/T)GGCAT
XPC	15	939	Lys	Gln	0.38	Lys	TTGAG(A/C)AGCTG

DSB/RR
LIG3		See above
NBS1	4	142	Asn	Ser	0.006	Asn	AAACA(A/G)TTGGA
NBS1	5	185	Gln	Glu	0.34	Glu	CAGTT(G/C)AGTCC
NBS1	6	196	Phe	Val	0.005	Phe	AAAGT(T/G)TTTAC
NBS1	6	216	Gln	Lys	0.005	His	GACGG(C/A)AGGAA
NBS1	14	716	Asn	Asp	0.013	Asn	GAAAG(A/G)ATACA
RAD50	5	191	Thr	Ile	0.01	Thr	AGAAA(C/T)ACTTC
RAD50	16	884	Arg	His	0.024	Arg	ACGTC(G/A)TCAGC
RAD50	24	1239	Arg	Gln	0.01	Arg	TGACC(G/A)AGAAA
RAD51		No variants
XRCC2	2	16	Ala	Ser	0.01	Ala	TCCTT(G/T)CCCGA
XRCC2	3	188	Arg	His	0.05	Arg	CTATC(G/A)CCTGG
XRCC3	7	241*	Thr	Met	0.43	Thr	GGCCA(C/T)GCTGC
XRCC4	1	12	Ser	Cys	0.01	Ser	TGTTT(C/G)TGAAC
XRCC4	2	75	Leu	Ser	0.006	Val	ATTGT(T/C)GTCAG
XRCC4	3	134	Ile	Thr	0.016	Ile	CACCA(T/C)TGCAG
XRCC4	3	137	Asn	Cys	0.005	Lys	GAAAA(T/G)CAAGC
XRCC4	5	247	Ala	Ser	0.08	Ala	GGTTG(G/T)CTTCA

Damage recognition and cell cycle checkpoints
CDK4	2	20	Val	Leu	0.03	Val	GGACA(G/T)TGTAC
CDKN2A	2	148	Ala	Thr	0.05	Leu	ATGCC(G/A)CGGAA
FANCG	7	297	Thr	Ile	0.01	Ala	CACAA(C/T)AGCAG
FANCG	8	330	Pro	Ser	0.01	Pro	TACTG(C/T)CACCA
FANCG	9	378	Ser	Leu	0.02	Ser	TAGCT(C/T)GGAGC
FANCG	10	464	Val	Phe	0.01	Ser	CCTGG(G/T)TTCAA
RAD52	4	70	Arg	Trp	0.005	Arg	GTCAT(C/T)GGGTA
RAD52	7	221	Gln	Glu	0.011	Glu	TGCAG(C/G)AGGTG
RAD52	8	287	Ser	Asn	0.05	His	GAAGA(G/A)TGAGG
RAD54L	4	74	Ile	Met	0.006	Ile	TTTAT(T/G)CGAAG
RAD54L	7	202	Arg	Cys	0.006	Arg	TTTTA(C/T)GCCAG
RAD54L	10	380	Arg	Gln	0.011	Arg	GGAGC(G/A)GCTGC
RAD54L	16	583	Ile	Thr	0.01	Ile	TCTCA(T/C)TGGGG
MLH1	8	213	Val	Met	0.04	Val	CAACC(G/A)TGGGAC
MLH1	8	219	Ile	Val	0.12	Ile	GCTCC(A/G)TCTTT
MLH1	11	325	Arg	Gln	0.01	Arg	GGAGC(G/A)GGTGC
MLH1	11	326	Val	Ala	0.01	Val	GCGGG(T/C)GCAGC
MLH1	12	452	Thr	Ser	0.01	Leu	ATACA(A/T)CAAAG
MLH1	16	618	Lys	Ala	0.01	Lys	AGAAG(A/G)&(A/C)GGCTG
MLH1	16	618	Lys	Thr or Glu	0.01	Lys	AGAAG(A/G)or(A/C)GGCTG
MLH1	19	718	His	Tyr	0.01	His	TGGAA(C/T)ACATTG
MSH2	3	127	Asn	Ser	0.006	Asn	TGGCA(A/G)TCTCT
MSH2	3	170	Gln	Glu	0.006	Gln	CCATA(C/G)AGAGG
MSH2	6	319	Asp	Val	0.009	Asp	TGAAG(A/T)TACCA
MSH2	6	322	Gly	Asp	0.011	Gly	CACTG(G/A)CTCTC
MSH2	7	390	Leu	Phe	0.005	Leu	ACCGA(C/T)TTGCC

MMR
MSH2	13	735	Ile	Val	0.006	Ile	CTTCT(A/G)TCCTC
MSH3	8	429	Ala	Val	0.04	Met	AGAGG(C/T)GCTCA
MSH3	9	456	Tyr	Cys	0.006	Tyr	TGAAT(A/G)CAGCC
MSH3	10	514	Glu	Lys	0.05	Glu	AACCT(G/A)AGAAT
MSH3	13	597	Ser	Asn	0.014	Ser	ATCTA(G/A)TGTGT
MSH3	15	700	Phe	Leu	0.005	Phe	CTGAC(T/C)TCCCT
MSH3	21	931	Gly	Cys	0.006	Gly	GGATG(G/T)GTGCT
MSH3	21	940	Arg	Gln	0.10	Arg	AGGAC(G/A)GAGTA
MSH3	23	1036	Thr	Ala	0.30	Asp	CAGGC(A/G)CAGCA
MSH6	1	25	Ala	Val	0.003	Ala	CTCGG(C/T)CAGGG
MSH6	1	39	Gly	Glu	0.24	Gly	CCCCG(G/A)GGCCT
MSH6	4	396	Leu	Val	0.009	Leu	CTACA(C/G)TCTAT
MSH6	4	878	Val	Ala	0.016	Val	AGAAG(T/C)TGCTG
MSH6	6	1152	Val	Ile	0.009	Val	TAGCT(G/A)TAATG