Table 2 Missense variants predicted to be highly deleterious (PROVEAN score < − 5.0) and their phenotypic consequences in null mutant mice based on the MGI database
From: A survey of functional genomic variation in domesticated chickens
Chr. | Position | Ref. | Alt. | Heterozygotes | Line | Symbol | AA position | AA change | SIFT score | Provean score | MGI phenotype |
|---|---|---|---|---|---|---|---|---|---|---|---|
1 | 49464407 | C | T | 7 | W1 | NAGA | 271 | R/C | 0 | − 6.42 | Homeostasis |
1 | 51524116 | A | G | 3 | WA | TMPRSS6 | 688 | E/G | 0 | − 5.771 | Reproductive, growth/size/body, endocrine/exocrine, liver/biliary, immune, homeostasis, mortality/aging, integument, hematopoietic, digestive/alimentary |
1 | 118357796 | A | C | 7 | W1 | PRDX4 | 81 | F/V | 0.02 | − 5.65 | Reproductive, cellular, endocrine/exocrine |
1 | 122963712 | T | C | 18 | W1 | OFD1 | 19 | Y/C | 0 | − 7.42 | Embryo, nervous, system, skeleton, craniofacial, limbs/digits/tail, renal/urinary, respiratory, cellular, mortality/aging, cardiovascular, growth/size/body, digestive/alimentary |
2 | 66538263 | T | A | 9 | WA | BPHL | 70 | D/V | 0 | − 8.815 | Hearing/vestibular/ear, homeostasis |
3 | 108278046 | C | T | 3 | WD | PKHD1 | 3397 | R/W | 0.03 | − 5.066 | Respiratory, growth/size/body, endocrine/exocrine, liver/biliary, renal/urinary, cellular, mortality/aging, cardiovascular, nervous system, hematopoietic, digestive/alimentary |
4 | 51931175 | G | T | 4 | W1 | CENPC | 729 | P/Q | 0 | − 7.783 | Embryo, mortality/aging, growth/size/body, cellular |
4 | 62191743 | T | C | 3 | WD | FAT1 | 796 | Y/C | 0.01 | − 7.534 | Nervous system, craniofacial, renal/urinary, vision/eye, mortality/aging, pigmentation, growth/size/body, homeostasis |
4 | 70191405 | G | A | 15 | WD | TBC1D1 | 182 | R/C | 0 | − 6.635 | Growth/size/body, adipose, cellular, no abnormal phenotype observed, muscle, homeostasis |
5 | 58052925 | G | A | 7 | W1 | NIN | 1206 | R/C | 0.02 | − 6.045 | Hearing/vestibular/ear, nervous system, behaviour, cardiovascular |
5 | 58235842 | C | T | 8 | W1 | NID2 | 944 | G/S | 0 | − 5.151 | Immune, skeleton |
9 | 17236801 | C | A | 3 | WA | CCDC39 | 857 | P/H | 0 | − 5.599 | Respiratory, skeleton, craniofacial, liver/biliary, immune, renal/urinary, homeostasis, cellular, mortality/aging, digestive/alimentary, growth/size/body, hematopoietic, cardiovascular |
9 | 17571682 | C | A | 3 | WD | MFN1 | 439 | G/W | 0 | − 7.551 | Embryo, mortality/aging, growth/size/body, cellular |
19 | 4443604 | A | T | 11 | WD | UNC45B | 225 | I/N | 0 | − 5.4 | Mortality/aging |
19 | 6266804 | C | T | 9 | WD | CPD | 994 | P/L | 0.01 | − 6.728 | Respiratory, behaviour, reproductive, craniofacial, endocrine/exocrine, liver/biliary, immune, digestive/alimentary, homeostasis, cellular, vision/eye, integument, nervous system, skeleton, growth/size/body, hematopoietic, cardiovascular |
24 | 4359027 | G | A | 3 | WA | KMT2A | 1941 | P/L | 0 | − 9.253 | Embryo, liver/biliary, muscle, cellular, reproductive, immune, craniofacial, limbs/digits/tail, hearing/vestibular/ear, renal/urinary, neoplasm, homeostasis, behaviour, cardiovascular, mortality/aging, integument, nervous system, growth/size/body, hematopoietic, skeleton |
27 | 3474503 | C | A | 4 | WA | MPP3 | 206 | S/Y | 0 | − 5.649 | Nervous system, vision/eye, cellular |