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Table 1 Genes (within the congenic loci) containing non-synonymous coding SNPs with potential relevance to the senescence-accelerated phenotype in OXYS rats.

From: Application of quantitative trait locus mapping and transcriptomics to studies of the senescence-accelerated phenotype in rats

Gene
symbol
Official gene name Allele CDS position Protein position AA change Codon
change
SIFT prediction (score) Co-located variation
Congenic locus in WAG/OXYS-1.1 strain
Hps5 Hermansky-Pudlak syndrome 5 C 667 223 R/G Aga/Gga tolerated (0.46) -
Hps5 Hermansky-Pudlak syndrome 5 T 188 63 R/K aGg/aAg tolerated (0.25) -
Cic capicua transcriptional repressor A 1517 506 C/Y tGc/tAc tolerated (0.08) -
Arhgap33 RhoGTPase activating protein 33 T 3466 1156 D/N Gat/Aat deleterious (0) -
Lin37 lin-37 homolog (Caenorhabditis elegans) A 547 183 P/S Cca/Tca tolerated (0.18) -
Cebpg CCAAT/enhancer binding protein (C/EBP), γ T 410 137 S/N aGc/aAc tolerated (0.45) -
Nudt19 nudix (nucleoside diphosphate linked moiety X)-type motif 19 C 1015 339 S/G Agc/Ggc tolerated (0.42) -
Congenic locus in WAG/OXYS-1.2 strain
Ccp110 centriolar coiled coil protein 110 kDa A 868 290 D/N Gat/Aat tolerated (0.17) rs197588212
Gtf3c1 general transcription factor IIIC, polypeptide 1, α A 6379 2127 R/C Cgt/Tgt - rs8156681
Gtf3c1 general transcription factor IIIC, polypeptide 1, α C 5692 1898 T/A Aca/Gca tolerated (0.75) rs198509438
Gtf3c1 general transcription factor IIIC, polypeptide 1, α C 5021 1674 N/S aAt/aGt tolerated (0.74) rs106585674
Rabep2 rabaptin, RAB GTPase binding effector protein 2 C 1007 336 I/T aTc/aCc tolerated (1) rs8153744
Aldoa aldolase A, fructose-bisphosphate C 493 165 M/V Atg/Gtg tolerated (0.58) rs8160964
Inpp5f inositol polyphosphate-5-phosphatase F C 3075 1025 L/F ttG/ttC tolerated (0.44) -
Psat1 phosphoserine aminotransferase 1 T 316 106 A/T Gct/Act tolerated (0.61) -
Tjp2 tight junction protein 2 T 767 256 R/H cGc/cAc tolerated (0.59) rs198995028
Ak3 adenylate kinase 3 T 368 123 L/Q cTa/cAa tolerated (0.66) rs197195051
Ric1 RAB6A GEF complex partner 1 G 229 77 N/D Aac/Gac tolerated (1) rs197794754
RGD1311595 similar to KIAA2026 protein C 2613 871 I/M atA/atG tolerated (1) rs198237726
Sfxn3 sideroflexin 3 A 927 309 N/K aaC/aaA tolerated (0.92) rs8163692
Nolc1 nucleolar and coiled-body phosphoprotein 1 A 421 141 E/K Gag/Aag tolerated (0.61) rs8165446
Pdcd11 programmed cell death 11 C 3005 1002 I/T aTc/aCc tolerated (1) -
  1. The SNP quality integral parameter threshold (in Samtools/Bcftools) was Qual> 180, and the consequence according to the Variant Effect Predictor tool, VEP [41] was "missense". Only 1 SNP, located in the Arhgap33 gene, was predicted to significantly affect protein structure (marked as "deleterious" by VEP). Position = position in base pairs (for CDS sequence) or in amino acid residues (for protein); AA = amino acid residue; colocated variation is presented according to the ENCODE data.