Incidental Mutation 'R0609:Rora'
ID 54537
Institutional Source Beutler Lab
Gene Symbol Rora
Ensembl Gene ENSMUSG00000032238
Gene Name RAR-related orphan receptor alpha
Synonyms tmgc26, Nr1f1, 9530021D13Rik
MMRRC Submission 038798-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.854) question?
Stock # R0609 (G1)
Quality Score 190
Status Not validated
Chromosome 9
Chromosomal Location 68653786-69388246 bp(+) (GRCm38)
Type of Mutation missense
DNA Base Change (assembly) T to A at 69361869 bp (GRCm38)
Zygosity Heterozygous
Amino Acid Change Methionine to Lysine at position 82 (M82K)
Ref Sequence ENSEMBL: ENSMUSP00000109254 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000034766] [ENSMUST00000113624] [ENSMUST00000174296]
AlphaFold P51448
Predicted Effect probably damaging
Transcript: ENSMUST00000034766
AA Change: M138K

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000034766
Gene: ENSMUSG00000032238
AA Change: M138K

low complexity region 2 26 N/A INTRINSIC
ZnF_C4 70 141 4.71e-41 SMART
low complexity region 161 175 N/A INTRINSIC
HOLI 325 481 8.8e-32 SMART
Predicted Effect probably damaging
Transcript: ENSMUST00000113624
AA Change: M82K

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000109254
Gene: ENSMUSG00000032238
AA Change: M82K

ZnF_C4 14 85 4.71e-41 SMART
low complexity region 105 119 N/A INTRINSIC
HOLI 269 425 8.8e-32 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000152570
Predicted Effect probably benign
Transcript: ENSMUST00000174296
Coding Region Coverage
  • 1x: 99.4%
  • 3x: 98.9%
  • 10x: 97.6%
  • 20x: 95.6%
Validation Efficiency
MGI Phenotype FUNCTION: The protein encoded by this gene is a member of the NR1 subfamily of nuclear hormone receptors. It can bind as a monomer or as a homodimer to hormone response elements upstream of several genes to enhance the expression of those genes. The encoded protein has been shown to interact with NM23-2, a nucleoside diphosphate kinase involved in organogenesis and differentiation, as well as with NM23-1, the product of a tumor metastasis suppressor candidate gene. Also, it has been shown to aid in the transcriptional regulation of some genes involved in circadian rhythm. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2014]
PHENOTYPE: Homozygotes for null mutations exhibit ataxia, cerebellar dysgenesis, impaired Purkinje and granule cell development, olfactory defects, hypoalphalipoproteinemia, and death around 4 weeks. Heterozygotes show slow Purkinje cell dedritic atrophy and loss. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 103 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4930596D02Rik A T 14: 35,811,461 (GRCm38) probably null Het
Abcb4 T A 5: 8,947,376 (GRCm38) C952S probably damaging Het
Adamtsl2 A G 2: 27,089,635 (GRCm38) D272G probably benign Het
Aim2 G A 1: 173,461,964 (GRCm38) D158N probably damaging Het
Aldh3b1 C T 19: 3,914,024 (GRCm38) R426H probably damaging Het
Apoc2 A G 7: 19,673,353 (GRCm38) S28P probably benign Het
Arfgef3 G A 10: 18,597,431 (GRCm38) T1628I probably benign Het
Atp10a G A 7: 58,819,740 (GRCm38) probably null Het
Bcl2 G A 1: 106,712,562 (GRCm38) R107C probably damaging Het
Bmp8b T A 4: 123,121,899 (GRCm38) D226E probably benign Het
Brsk2 T C 7: 141,998,492 (GRCm38) Y618H probably damaging Het
Casp12 T A 9: 5,346,554 (GRCm38) F27Y probably damaging Het
Casp8 T A 1: 58,844,792 (GRCm38) N439K probably benign Het
Ccdc175 T A 12: 72,157,507 (GRCm38) K253N probably benign Het
Cdc42bpa A G 1: 180,040,179 (GRCm38) H193R probably damaging Het
Cdk17 T C 10: 93,216,472 (GRCm38) M105T probably benign Het
Cdon C A 9: 35,478,611 (GRCm38) P854T probably damaging Het
Cep44 A G 8: 56,544,152 (GRCm38) M117T possibly damaging Het
Cep89 A T 7: 35,435,530 (GRCm38) E674D probably damaging Het
Cit C T 5: 115,873,943 (GRCm38) A203V probably damaging Het
Clstn1 C A 4: 149,629,300 (GRCm38) probably null Het
Col7a1 T A 9: 108,958,147 (GRCm38) D565E unknown Het
Cpb1 T A 3: 20,262,474 (GRCm38) Y304F probably damaging Het
Cps1 T G 1: 67,172,802 (GRCm38) Y710D probably damaging Het
Creb3l1 T C 2: 91,987,053 (GRCm38) T372A possibly damaging Het
Dars A G 1: 128,405,381 (GRCm38) V102A probably benign Het
Dhx35 C T 2: 158,817,415 (GRCm38) T168I possibly damaging Het
Dnah5 T C 15: 28,327,779 (GRCm38) S2100P probably benign Het
Dst T C 1: 34,266,960 (GRCm38) probably null Het
Egflam A C 15: 7,253,523 (GRCm38) L351R possibly damaging Het
Elp2 T A 18: 24,626,156 (GRCm38) D523E probably benign Het
Exo5 C A 4: 120,921,684 (GRCm38) G328V probably damaging Het
Fam208a C T 14: 27,461,750 (GRCm38) T722I probably benign Het
Fut9 A G 4: 25,620,811 (GRCm38) M1T probably null Het
Galnt5 A G 2: 58,024,625 (GRCm38) N584S possibly damaging Het
Gbp3 T C 3: 142,567,772 (GRCm38) V360A probably damaging Het
Gdf6 G A 4: 9,859,977 (GRCm38) C353Y probably damaging Het
Gm13089 A T 4: 143,698,503 (GRCm38) D123E probably benign Het
Hace1 A G 10: 45,648,869 (GRCm38) T244A probably damaging Het
Hr T C 14: 70,559,657 (GRCm38) I500T probably benign Het
Ifnl2 A T 7: 28,509,282 (GRCm38) L115Q probably damaging Het
Iigp1 T C 18: 60,389,824 (GRCm38) F5L probably benign Het
Inhbb A G 1: 119,417,416 (GRCm38) L381P probably damaging Het
Irx3 A T 8: 91,801,093 (GRCm38) S50T probably benign Het
Ivns1abp C T 1: 151,360,145 (GRCm38) T363I probably benign Het
Izumo1 A T 7: 45,622,899 (GRCm38) T35S probably benign Het
Kank4 A G 4: 98,777,105 (GRCm38) S651P probably damaging Het
Kit T C 5: 75,610,879 (GRCm38) V232A probably benign Het
Klhl11 T C 11: 100,463,714 (GRCm38) Y427C probably damaging Het
Laptm4b T A 15: 34,258,689 (GRCm38) N36K probably damaging Het
Lrrk1 T C 7: 66,266,615 (GRCm38) probably null Het
Mamdc4 G T 2: 25,564,193 (GRCm38) Q1042K probably benign Het
Mical2 A G 7: 112,321,440 (GRCm38) probably null Het
Ms4a3 C A 19: 11,631,361 (GRCm38) V176F possibly damaging Het
Myo3a A C 2: 22,396,299 (GRCm38) E626D possibly damaging Het
Myo3a T C 2: 22,333,513 (GRCm38) V427A probably benign Het
Nckap5 A T 1: 126,027,288 (GRCm38) L509* probably null Het
Ndufa5 A T 6: 24,519,249 (GRCm38) D64E possibly damaging Het
Nedd4l T C 18: 65,208,461 (GRCm38) Y753H probably damaging Het
Nynrin T C 14: 55,872,761 (GRCm38) V1775A probably damaging Het
Olfr141 A G 2: 86,806,861 (GRCm38) L46S probably damaging Het
Olfr292 T C 7: 86,694,876 (GRCm38) V140A possibly damaging Het
Olfr694 A T 7: 106,688,998 (GRCm38) H244Q probably damaging Het
Olfr735 T C 14: 50,345,926 (GRCm38) Y141C probably damaging Het
Olfr823 G A 10: 130,112,580 (GRCm38) S70F probably damaging Het
Oplah A G 15: 76,302,992 (GRCm38) S570P probably benign Het
Osbpl11 C A 16: 33,234,444 (GRCm38) Y632* probably null Het
Osbpl5 A T 7: 143,694,821 (GRCm38) L644Q probably damaging Het
Pcdhb19 T C 18: 37,497,952 (GRCm38) W267R probably benign Het
Pkhd1l1 A C 15: 44,467,424 (GRCm38) S132R possibly damaging Het
Ptpn13 T A 5: 103,556,145 (GRCm38) S1348T probably benign Het
Rc3h1 T A 1: 160,930,135 (GRCm38) W8R probably damaging Het
Rgs3 T G 4: 62,625,936 (GRCm38) V315G probably damaging Het
Rph3al T C 11: 75,908,969 (GRCm38) I55V probably benign Het
Sag T C 1: 87,812,991 (GRCm38) V45A probably damaging Het
Scn3a T C 2: 65,536,510 (GRCm38) E56G probably damaging Het
Sec24c T G 14: 20,686,948 (GRCm38) V324G probably damaging Het
Sptbn1 A G 11: 30,138,979 (GRCm38) L748S probably damaging Het
Stard9 A T 2: 120,706,306 (GRCm38) D4186V probably damaging Het
Stk39 T C 2: 68,366,167 (GRCm38) E306G probably damaging Het
Sycp1 C A 3: 102,898,849 (GRCm38) probably null Het
Taf2 A C 15: 55,060,050 (GRCm38) L277R probably damaging Het
Tbc1d23 T A 16: 57,173,106 (GRCm38) I566F possibly damaging Het
Tekt5 T C 16: 10,361,304 (GRCm38) T400A possibly damaging Het
Tgfbrap1 T C 1: 43,060,141 (GRCm38) H401R probably benign Het
Tie1 T A 4: 118,476,147 (GRCm38) I841L possibly damaging Het
Tln1 T G 4: 43,544,645 (GRCm38) T1095P possibly damaging Het
Tmem147 A G 7: 30,728,102 (GRCm38) Y72H probably benign Het
Tnfaip2 A G 12: 111,453,507 (GRCm38) N691S probably benign Het
Trim24 G A 6: 37,957,783 (GRCm38) C811Y probably damaging Het
Trim30b T A 7: 104,357,976 (GRCm38) probably benign Het
Trpc4 T G 3: 54,194,768 (GRCm38) L29R probably damaging Het
Trpm6 A T 19: 18,825,862 (GRCm38) I890F probably damaging Het
Ttc23l C T 15: 10,504,536 (GRCm38) E442K probably benign Het
Uggt2 A G 14: 119,095,336 (GRCm38) V62A probably damaging Het
Ugt1a6a C A 1: 88,138,884 (GRCm38) S137R probably benign Het
Unc13a A G 8: 71,658,467 (GRCm38) Y367H probably damaging Het
Vmn2r49 A G 7: 9,976,306 (GRCm38) I833T probably benign Het
Vmn2r7 T C 3: 64,716,479 (GRCm38) D231G probably benign Het
Ythdc2 A T 18: 44,864,357 (GRCm38) M994L probably benign Het
Zcchc6 A T 13: 59,799,782 (GRCm38) C506* probably null Het
Zfp804a G A 2: 82,257,588 (GRCm38) S587N probably damaging Het
Zswim2 A G 2: 83,923,659 (GRCm38) I219T probably benign Het
Other mutations in Rora
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00811:Rora APN 9 69,371,290 (GRCm38) missense probably benign 0.31
IGL02355:Rora APN 9 69,374,092 (GRCm38) missense probably damaging 1.00
IGL02362:Rora APN 9 69,374,092 (GRCm38) missense probably damaging 1.00
PIT4696001:Rora UTSW 9 69,364,559 (GRCm38) missense possibly damaging 0.92
R0091:Rora UTSW 9 69,374,048 (GRCm38) missense probably damaging 1.00
R0555:Rora UTSW 9 69,361,746 (GRCm38) missense probably damaging 1.00
R1483:Rora UTSW 9 69,364,385 (GRCm38) missense probably benign 0.00
R1712:Rora UTSW 9 69,375,489 (GRCm38) missense probably benign 0.23
R1785:Rora UTSW 9 69,376,837 (GRCm38) missense probably benign 0.30
R2883:Rora UTSW 9 69,375,435 (GRCm38) missense probably damaging 1.00
R4173:Rora UTSW 9 68,653,910 (GRCm38) missense probably benign 0.41
R5226:Rora UTSW 9 69,364,141 (GRCm38) intron probably benign
R5660:Rora UTSW 9 68,653,921 (GRCm38) missense probably benign 0.27
R6029:Rora UTSW 9 69,364,452 (GRCm38) missense probably benign 0.04
R6054:Rora UTSW 9 69,378,802 (GRCm38) missense probably benign 0.04
R6114:Rora UTSW 9 69,371,323 (GRCm38) missense probably benign
R6329:Rora UTSW 9 69,373,186 (GRCm38) missense probably damaging 1.00
R7028:Rora UTSW 9 69,196,083 (GRCm38) missense possibly damaging 0.46
R7170:Rora UTSW 9 69,373,190 (GRCm38) nonsense probably null
R7233:Rora UTSW 9 69,197,522 (GRCm38) nonsense probably null
R7512:Rora UTSW 9 69,374,085 (GRCm38) missense probably benign 0.00
R9647:Rora UTSW 9 69,348,168 (GRCm38) missense probably damaging 1.00
Z1176:Rora UTSW 9 69,364,372 (GRCm38) missense probably damaging 0.99
Predicted Primers PCR Primer

Sequencing Primer
Posted On 2013-07-11