Impaired 8-Hydroxyguanine Repair Activity of MUTYH Variant p.Arg109Trp Found in a Japanese Patient with Early-Onset Colorectal Cancer

Table 3

Characteristics of the MUTYH and OGG1 nucleotide variations found in 34 Japanese patients with early-onset colorectal carcinoma.

Gene	Variant	Position^a	dbSNP ID^b	PolyPhen-2; prediction (score)^d	SIFT prediction; (score)^d	PROVEAN prediction (score)^d	Allele frequency in a Japanese SNP database^e
MUTYH	c.36+11C>T	45805880	rs2275602	—	—	—	0.048
MUTYH	c.55C>T; (p.Arg19*)	45800165	NA^c	—	—	—	0.002
MUTYH	c.325C>T; (p.Arg109Trp)	45799108	NA	Probably damaging (1)	Damaging (0)	Deleterious; (−7.22)	NS^f
MUTYH	c.504+35A>G	45798555	rs3219487	—	—	—	0.12
MUTYH	c.934−2A>G	45797760	rs77542170	—	—	—	0.026
MUTYH	c.1014G>C; (p.Gln338His)	45797505	rs3219489	Benign (0.343)	Tolerated (0.136)	Neutral (−1.03)	0.434
MUTYH	c.1118C>T; (p.Ala373Val)	45797401	rs35352891	Possibly damaging (0.506)	Tolerated (0.128)	Neutral (−2.324)	0.01
MUTYH	c.1431G>C; (p.Thr477Thr)	45796899	rs74318065	—	—	—	0.051
MUTYH	c.1477−40C>G	45796269	rs3219493	—	—	—	0.885
OGG1	c.−23A>G	9791948	rs1801129	—	—	—	0.039
OGG1	c.−18G>T	9791953	rs1801126	—	—	—	0.033
OGG1	c.294G>A; (p.Lys98Lys)	9792785	rs1801127	—	—	—	0.015
OGG1	c.748−15C>G	9798140	rs2072668	—	—	—	0.452
OGG1	c.949−89G>T	9798656	NA	—	—	—	NS
OGG1	c.966C>T; (p.Asp322Asp)	9798762	NA	—	—	—	NS
OGG1	c.977C>G; (p.Ser326Cys)	9798773	rs1052133	Benign (0.121)	Tolerated (0.176)	Neutral (−0.647)	0.446

aGenome positions of MUTYH and OGG1 variants are shown according to the reference sequences (GRCh37) of chromosome 1 and chromosome 3, respectively. ^bIdentification number of variants according to the database of single nucleotide polymorphisms (dbSNP) located on the homepage of the National Center for Biotechnology Information web site (http://www.ncbi.nlm.nih.gov/SNP/). ^cNA, not assigned. ^dThe accession numbers for the reference proteins of MUTYH and OGG1 are E5KP25 and O15527, respectively. ^eVariant allele frequency in a reference database of genetic variations in the Japanese population (http://www.genome.med.kyoto-u.ac.jp/SnpDB/). ^fNS, not shown.