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