Table 2.
Results from filtering analysis for SPAID-associated genotypes
| CFA | Position | Base change | Amino acid change | Consequence | Genotype (5 reference dogs) | Genotype (2 affected Shar-Pei) | Gene (transcript) | SIFT | PolyPhen-2 |
|---|---|---|---|---|---|---|---|---|---|
| 1 | 8186638 | A > G | K > R | missense variant | 0/0 | 1/1 | RTTN (ENSCAFT00000000055) | tolerated (0.3) | benign (0.036) |
| 1 | 112413056 | T > C | K > E/K > E | missense variant | 0/0 | 1/1 | CD79A (ENSCAFT00000037106/ENSCAFT00000008000) | tolerated low confidence | benign (0.227) |
| 1 | 112413114 | C > CGTGATG | I67_T68dup/I67_T68dup | disruptive inframe insertion | 0/0 | 1/1 | CD79A (ENSCAFT00000037106/ENSCAFT00000008000) | NA | NA |
| 3 | 14027517 | A > C | L > R | missense variant | 0/0 | 1/1 | ARSK (ENSCAFT00000012646) | deleterious low confidence | probably damaging (0.993) |
| 4 | 6374801 | G > A | C > Y | missense variant | 0/0 | 1/1 | PCNXL2 (ENSCAFT00000018397) | deleterious low confidence | NA |
| 4 | 19114717 | GT | D > E/D > E | missense variant | 0/0 | 1/1 | DNAJC12 (ENSCAFT00000021116/ENSCAFT00000049485) | tolerated (0.1/0.28) | benign/possibly damaging (0.023/0.579) |
| 4 | 75351270 | A > G | V > A | missense variant | 0/0 | 1/1 | PDZD2 (ENSCAFT00000047348) | tolerated (0.33) | benign (0.000) |
| 5 | 21123033 | C > T | R > Q/R > Q/R > Q | missense variant | 0/0 | 1/1 | DIXDC1 (ENSCAFT00000022334/ENSCAFT00000022333/ENSCAFT00000035298) | tolerated (1/1/1) | benign (0.000/0.003/0.001) |
| 5 | 48648175 | G > C | - | non coding transcript exon variant, non coding transcript variant | 0/0 | 1/1 | ENSCAFG00000018860 (novel gene; ENSCAFT00000029943) | NA | NA |
| 5 | 60223074 | G > T | P > Q | missense variant | 0/0 | 1/1 | ACOT7 (ENSCAFT00000049704) | deleterious low confidence | possibly damaging (0.694) |
| 6 | 36821482 | G > T | S > Y | missense variant | 0/0 | 1/1 | C16orf96 (ENSCAFT00000048346) | deleterious (0) | probably damaging (0.995) |
| 6 | 38937765 | C > T | A > V | missense variant | 0/0 | 1/1 | ZNF598 (ENSCAFT00000030940) | tolerated (0.62) | benign (0.017) |
| 6 | 40648375 | C > T | P > S/P > S/P > S | missense variant | 0/0 | 1/1 | ENSCAFG00000024344 (novel gene; ENSCAFT00000037586/ENSCAFT00000037216/ENSCAFT00000037580) | deleterious (0/0/0) | probably damaging (1.00/1.00/1.00) |
| 6 | 56637047 | TACAA > T | F76fs | frameshift variant | 0/0 | 1/1 | RPAP2 (novel gene; ENSCAFT00000032095) | NA | NA |
| 6 | 56760354 | T > C | K > E | missense variant | 0/0 | 1/1 | KIAA1107 (ENSCAFT00000032101) | tolerated (0.26) | benign (0.053) |
| 6 | 56786359 | G > C | D > E | missense variant | 0/0 | 1/1 | KIAA1107 (ENSCAFT00000032101) | tolerated (1) | benign (0.000) |
| 6 | 57204844 | A > G | Y > C | missense variant | 0/0 | 1/1 | TGFBR3 (ENSCAFT00000032134) | deleterious (0) | probably damaging (0.998) |
| 9 | 3074837 | G > C | H > Q/H > Q/H > Q | missense variant | 0/0 | 1/1 | TNRC6C (ENSCAFT00000048770/ENSCAFT00000050041/ENSCAFT00000008443) | tolerated (0.12/0.8/0.72) | probably damaging (0.999/0.988/0.999) |
| 11 | 62457942 | G > A | A > T | missense variant | 0/0 | 1/1 | ZNF462 (ENSCAFT00000004432) | NA | benign (0.000) |
| 13 | 19383758 | G > A | E > K | missense variant | 0/0 | 1/1 | MTBP (ENSCAFT00000001477) | deleterious (0.01) | probably damaging (0.979) |
| 13 | 58949521 | C > G | L > V/L > V | missense variant | 0/0 | 1/1 | UGT2B31 (ENSCAFT00000022724/ENSCAFT00000004520) | tolerated (1/1) | benign (0.000/0.000) |
| 13 | 58949524 | G > A | V > I/V > I | missense variant | 0/0 | 1/1 | UGT2B31 (ENSCAFT00000022724/ENSCAFT00000004520) | tolerated (0.49/0.48) | benign (0.005/0.001) |
| 13 | 58949536 | A > G | T > A/T > A | missense variant | 0/0 | 1/1 | UGT2B31 (ENSCAFT00000022724/ENSCAFT00000004520) | tolerated (0.66/0.65) | benign (0.000/0.000) |
| 15 | 42583230 | A > C | N > H/N > H | missense variant | 0/0 | 1/1 | HCFC2 (ENSCAFT00000011975/ENSCAFT00000011972) | tolerated (0.09)/deleterious (0.04) | possibly damaging (0.583/0.616 |
| 17 | 58777715 | G > A | S > L | missense variant | 0/0 | 1/1 | TXNIP (ENSCAFT00000018124) | tolerated (0.2) | benign (0.126) |
| 18 | 40794747 | C > T | R > H | missense variant | 0/0 | 1/1 | OR10H12 (ENSCAFT00000037956) | tolerated (0.37) | benign (0.000) |
| 20 | 54717650 | G > A | T > M | missense variant | 0/0 | 1/1 | KDM4B (ENSCAFT00000030040) | tolerated (0.05) | possibly damaging (0.934) |
| 20 | 54729635 | A > G | - | splice acceptor variant | 0/0 | 1/1 | KDM4B (ENSCAFT00000030040) | NA | NA |
| 22 | 30574626 | C > T | T > M | missense variant | 0/0 | 1/1 | CLN5 (ENSCAFT00000008156) | deleterious (0.01) | probably damaging (1.000) |
| 24 | 46507770 | C > T | R > W | missense variant | 0/0 | 1/1 | ENSCAFG00000030917 (novel gene; ENSCAFT00000046966) | NA | NA |
| 27 | 31792218 | T > C | I > V | missense variant | 0/0 | 1/1 | C12orf60 (ENSCAFT00000020587) | tolerated (0.39) | benign (0.009) |
| 28 | 34998871 | G > A | V > I | missense variant | 0/0 | 1/1 | BCCIP (ENSCAFT00000020430) | tolerated (0.24) | possibly damaging (0.992) |
| 30 | 29440908 | C > T | E > K | missense variant | 0/0 | 1/1 | RASL12 (ENSCAFT00000027120) | tolerated (0.08) | benign (0.034) |
| 30 | 29986720 | G > A | E > K | missense variant | 0/0 | 1/1 | SLC24A1 (ENSCAFT00000027314) | tolerated (0.09) | benign (0.223) |
| 32 | 22124585 | GTCTTT > G | K64fs | frameshift variant (microsatellite) | 0/0 | 1/1 | ENSCAFG00000031054 (novel gene; ENSCAFT00000047190) | NA | NA |
| 37 | 502225 | CCTTGTGCAA > C | L4_K6del | inframe deletion | 0/0 | 1/1 | OSGEPL1 (ENSCAFT00000014928) | NA | NA |
| 38 | 20346455 | T > A | V > D | missense variant | 0/0 | 1/1 | C1orf111 (ENSCAFT00000036623) | tolerated (0.94) | benign (0.000) |
In total 37 variants with predicted high or moderate effects (SNPEff) could be exclusively found homozygous for the mutant allele in SPAID-affected Shar-Pei. SIFT and PolyPhen-2 variant effect estimations are shown for each position