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Table 2

Allelotypic analysis of novel nsSNPs in 410 controls and 390 centenarians.

Gene Transcript Nucleotide changea Amino acid change Minor allele count (%)b p-valuec Controls Centenarians GABRR3 NM_001105580 c.1394T>C p.V465A 10 (1.26) 1 (0.13) 0.01* EPHB2 NM_017449 c.1106G>A p.R369Q 26 (3.23) 38 (4.97) 0.10 PMS2 NM_000535 c.953A>G p.Y318C 4 (0.50) 10 (1.32) 0.11 ZMIZ1 NM_020338 c.1172C>T p.P391L 0 (0.00) 3 (0.41) 0.11 GRM1 NM_001114329 c.2581G>A p.G861S 14 (1.76) 22 (2.96) 0.13 RAD52 NM_134424 c.1186C>T p.R396C 14 (1.76) 20 (2.70) 0.23 PLCD4 NM_032726 c.118C>T p.L40F 0 (0.00) 2 (0.26) 0.23 CDC25A NM_001789 c.391A>G p.I131V 10 (1.25) 16 (2.12) 0.24 AFTPH NM_203437 c.1796G>A p.R599Q 12 (1.48) 6 (0.79) 0.24 RELN NM_173054 c.9340A>G p.I3114V 9 (1.13) 4 (0.54) 0.27 PCDH11X NM_032968 c.3140G>A p.G1047E 5 (0.62) 9 (1.19) 0.29 FOXO3 NM_001455 c.1021G>A p.A341T 44 (5.54) 32 (4.29) 0.29 UBE3C NM_014671 c.1406G>A p.R469Q 1 (0.13) 3 (0.41) 0.36 SENP6 NM_001100409 c.1447G>C p.D483H 1 (0.13) 3 (0.40) 0.36 OPRM1 NM_001008505 c.1256A>G p.Y419C 13 (1.61) 18 (2.37) 0.36 ATM NM_000051 c.4388T>G p.F1463C 21 (2.63) 26 (3.45) 0.38 ANAPC5 NM_016237 c.2027C>T p.A676V 9 (1.13) 13 (1.75) 0.39 MLH3 NM_014381 c.713A>C p.Y238S 11 (1.39) 14 (1.94) 0.43 PPIL2 NM_148175 c.655G>A p.E219K 12 (1.51) 16 (2.15) 0.45 FANCI NM_018193 c.1963G>A p.G655R 10 (1.26) 6 (0.80) 0.46 PCDH10 NM_032961 c.1469G>T p.R490L 0 (0.00) 1 (0.16) 0.47 DNAH1 NM_015512 c.10501A>G p.I3501V 0 (0.00) 1 (0.14) 0.48 SHC1 NM_003029 c.768G>A p.M256I 0 (0.00) 1 (0.13) 0.48 GRIA3 NM_000828 c.484G>A p.V162M 0 (0.00) 1 (0.13) 0.48 CHRNG NM_005199 c.1343T>C p.I448T 0 (0.00) 1 (0.13) 0.48 IL1A NM_000575 c.41G>C p.C14S 0 (0.00) 1 (0.13) 0.48 OPRK1 NM_000912 c.991G>A p.A331T 0 (0.00) 1 (0.13) 0.49 PCDH12 NM_016580 c.1453C>T p.H485Y 0 (0.00) 1 (0.13) 0.49 USP24 NM_015306 c.1024A>G p.I342V 0 (0.00) 1 (0.13) 0.49 CHEK2 NM_001005735 c.634T>G p.F212V 0 (0.00) 1 (0.13) 0.49 GRIK2 NM_175768 c.109A>G p.R37G 0 (0.00) 1 (0.13) 0.49 LTF NM_002343 c.1841C>T p.P614L 16 (2.00) 19 (2.60) 0.49 FARP1 NM_005766 c.692C>T p.P231L 17 (2.09) 20 (2.64) 0.51 THBS1 NM_003246 c.583G>A p.A195T 14 (1.86) 16 (2.30) 0.58 POLD1 NM_002691 c.2275G>A p.V759I 14 (1.77) 17 (2.28) 0.59 HERC1 NM_003922 c.1130G>T p.W377L 1 (0.13) 2 (0.27) 0.61 PCDH15 NM_001142769 c.4669A>G p.K1557E 3 (0.38) 1 (0.13) 0.63 POLI NM_007195 c.1169C>G p.P390R 10 (1.26) 7 (0.94) 0.63 MAPK8IP3 NM_015133 c.1772G>A p.R591H 29 (3.64) 23 (3.14) 0.67 NF1 NM_001042492 c.7595C>T p.A2532V 8 (0.99) 6 (0.80) 0.79 HIF1A NM_181054 c.2080G>A p.A694T 13 (1.63) 11 (1.48) 0.84 SIRT2 NM_012237 c.347G>A p.R116H 29 (3.58) 26 (3.46) 1.00 ANAPC7 NM_001137664 c.96G>C p.Q32H 25 (3.09) 23 (3.04) 1.00 ABCA1 NM_005502 c.3053A>G p.D1018G 8 (0.99) 8 (1.06) 1.00 GOLM1 NM_177937 c.179G>A p.R60K 7 (0.88) 6 (0.81) 1.00 MNAT1 NM_001177963 c.521T>C p.I174T 4 (0.50) 4 (0.53) 1.00 MLH3 NM_014381 c.3145G>A p.D1049N 1 (0.13) 1 (0.13) 1.00 POLE NM_006231 c.2131T>C p.S711P 2 (0.25) 1 (0.13) 1.00 RAD23A NM_005053 c.434G>A p.G145D 1 (0.13) 1 (0.14) 1.00 F13A1 NM_000129 c.1861G>T p.A621S 2 (0.26) 2 (0.28) 1.00 FARP1 NM_005766 c.2200A>G p.M734V 10 (1.25) 9 (1.23) 1.00

a cDNA change. b % minor allele frequency. c Fisher’s exact test. * p<0.05.

in human aging and longevity. GABRR3 amino acid change (p.V465A) was predicted to be benign according to the SIFT and PolyPhen2. However, the variation occurs at residue 465 of a 467 amino acid integral membrane protein. Transmembrane-predict- ingprogramssuggest that thisresidue will be rightat the endof the last transmembrane helix. It is conceivable that V to A substitution might introduce minor flexibility in this region by leaving a hydrophobic pocket to fill. If the C-terminus interacts with a factor like a PDZ domain, which recognizes C-terminal sequence motifs, it could have an impact on GABBR3 function. Further functional analysis will be needed to uncover molecular mechanisms by which these variants lead to changes in protein function and contribute to longevity.

Interestingly, none of the reported mutations from HNPCC patients is near this region, suggesting that the centenarian specific nsSNP may have a gain of function property beneficial to long lifespan.

may have a gain of function property beneficial to long lifespan. GABRR3 encodes the rho3 subunit of GABA -rho A receptor which is composed of 5 subunits. The 5 subunits can made up with any 3 kinds of subunit (rho 1, 2, 3) as a homo hetero pentamer complex. GABA -rho receptor is a kind A ionotropic GABA receptor which responds to the neurotransmitter, gamma-aminobutyric acid (GABA). About of neurons in the hippocampus are inhibitory and most of them GABAergic. It was reported that there was an aging related in GABA receptor composition and that the GABA receptor could relevant to AD pathogenesis (Rissman and Mobley, 2011). discovery on significant depletion of GABRR3 (p.V465A) in centenarians as compared to controls suggests its potential

We also identified 13 novel nsSNPs that were detected only in centenarians but not in controls (Table 2), although none of them

Please cite this article in press as: Han, J., et al., Discovery of novel non-synonymous SNP variants in 988 candidate genes from 6 centenarians by target capture and next-generation sequencing. Mech. Ageing Dev. (2013), http://dx.doi.org/10.1016/

J. Han et al./Mechanisms of Ageing and Development xxx (2013) xxx–xxx

Table 3

Genotypic analysis of novel nsSNPs in 410 controls and 390 centenarians.