Incidental Mutation 'PIT4696001:Rora'
ID 556801
Institutional Source Beutler Lab
Gene Symbol Rora
Ensembl Gene ENSMUSG00000032238
Gene Name RAR-related orphan receptor alpha
Synonyms tmgc26, Nr1f1, 9530021D13Rik
Accession Numbers
Essential gene? Probably essential (E-score: 0.915) question?
Stock # PIT4696001 (G1)
Quality Score 225.009
Status Validated
Chromosome 9
Chromosomal Location 68561068-69295528 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 69271841 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Leucine to Proline at position 273 (L273P)
Ref Sequence ENSEMBL: ENSMUSP00000034766 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000034766] [ENSMUST00000113624] [ENSMUST00000174296]
AlphaFold P51448
Predicted Effect possibly damaging
Transcript: ENSMUST00000034766
AA Change: L273P

PolyPhen 2 Score 0.917 (Sensitivity: 0.81; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000034766
Gene: ENSMUSG00000032238
AA Change: L273P

DomainStartEndE-ValueType
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 possibly damaging
Transcript: ENSMUST00000113624
AA Change: L217P

PolyPhen 2 Score 0.769 (Sensitivity: 0.85; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000109254
Gene: ENSMUSG00000032238
AA Change: L217P

DomainStartEndE-ValueType
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 probably benign
Transcript: ENSMUST00000174296
Coding Region Coverage
  • 1x: 93.5%
  • 3x: 91.0%
  • 10x: 86.2%
  • 20x: 75.9%
Validation Efficiency 100% (57/57)
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: 58 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Acsm3 G A 7: 119,384,209 (GRCm39) probably null Het
Adam20 T A 8: 41,247,985 (GRCm39) Y32N probably benign Het
Adm T C 7: 110,227,496 (GRCm39) V4A probably benign Het
Anpep G A 7: 79,489,212 (GRCm39) T320I possibly damaging Het
Atp8b1 T C 18: 64,672,341 (GRCm39) S1008G possibly damaging Het
B9d1 T A 11: 61,396,069 (GRCm39) M12K possibly damaging Het
Cad T C 5: 31,229,438 (GRCm39) L1435P probably damaging Het
Cat T C 2: 103,302,157 (GRCm39) D180G probably damaging Het
Cntln C T 4: 84,892,237 (GRCm39) T374M probably damaging Het
Cyp2a5 G A 7: 26,540,404 (GRCm39) R339Q probably benign Het
Defa22 T C 8: 21,652,352 (GRCm39) L6P probably damaging Het
Dr1 T A 5: 108,417,604 (GRCm39) I50K probably damaging Het
Eln C T 5: 134,766,032 (GRCm39) G57E unknown Het
Fat4 T C 3: 38,943,153 (GRCm39) I682T probably benign Het
Fat4 C A 3: 39,036,506 (GRCm39) A3386E probably damaging Het
Fcgr3 T A 1: 170,885,319 (GRCm39) Y102F probably damaging Het
Gm5930 A T 14: 44,573,993 (GRCm39) L115M probably damaging Het
Herc1 T A 9: 66,386,291 (GRCm39) V3748D probably damaging Het
Ino80d A G 1: 63,125,145 (GRCm39) S106P probably benign Het
Kcns3 C T 12: 11,142,749 (GRCm39) probably benign Het
Kndc1 T A 7: 139,512,830 (GRCm39) L1527Q probably damaging Het
Lepr T G 4: 101,637,180 (GRCm39) S690A probably benign Het
Lrfn5 T C 12: 61,890,343 (GRCm39) F544S probably damaging Het
Mapkap1 C A 2: 34,509,861 (GRCm39) H450Q probably damaging Het
Mdm1 A G 10: 117,994,445 (GRCm39) T485A probably benign Het
Megf10 T C 18: 57,410,760 (GRCm39) C690R probably damaging Het
Myo7a A G 7: 97,712,806 (GRCm39) M1723T probably benign Het
Nrip3 A T 7: 109,364,714 (GRCm39) C137* probably null Het
Or5w22 T A 2: 87,363,124 (GRCm39) I249N probably damaging Het
Pde4a T A 9: 21,122,297 (GRCm39) M731K probably benign Het
Pebp1 A G 5: 117,421,527 (GRCm39) L117P probably damaging Het
Phc2 T C 4: 128,598,995 (GRCm39) Y51H probably damaging Het
Ppp2r5b A G 19: 6,284,713 (GRCm39) F50S probably benign Het
Prpf4b A G 13: 35,083,825 (GRCm39) S865G probably benign Het
Ptpn5 C T 7: 46,738,354 (GRCm39) V243M probably benign Het
Rtp4 T A 16: 23,432,204 (GRCm39) S245R probably benign Het
Scgb2b20 C T 7: 33,063,985 (GRCm39) G95D probably benign Het
Sec24b A G 3: 129,788,040 (GRCm39) V820A probably benign Het
Sim2 A G 16: 93,895,168 (GRCm39) D62G possibly damaging Het
Slc17a4 A T 13: 24,084,497 (GRCm39) V429D probably benign Het
Sp2 T C 11: 96,852,799 (GRCm39) T42A probably damaging Het
Spata3 G A 1: 85,952,169 (GRCm39) R141Q unknown Het
Sptbn2 A T 19: 4,795,605 (GRCm39) E1658D probably benign Het
Tcaf1 T C 6: 42,655,473 (GRCm39) H501R probably benign Het
Tec G A 5: 72,931,178 (GRCm39) T262M possibly damaging Het
Timm9 A T 12: 71,172,305 (GRCm39) N22K possibly damaging Het
Tln1 C T 4: 43,542,701 (GRCm39) probably null Het
Tmbim4 A G 10: 120,053,529 (GRCm39) I109M probably benign Het
Tmc7 T C 7: 118,163,566 (GRCm39) K110E probably benign Het
Tmem107 C T 11: 68,963,399 (GRCm39) P136L probably benign Het
Ttc21b T C 2: 66,061,563 (GRCm39) probably null Het
Ubd A C 17: 37,506,335 (GRCm39) T74P probably damaging Het
Vps11 A G 9: 44,269,486 (GRCm39) V255A possibly damaging Het
Vsnl1 T C 12: 11,376,448 (GRCm39) T146A probably benign Het
Wdr38 G T 2: 38,889,984 (GRCm39) probably null Het
Yes1 T A 5: 32,841,969 (GRCm39) S498T possibly damaging Het
Zc3h13 G A 14: 75,569,323 (GRCm39) R1390H probably damaging Het
Zscan4b A G 7: 10,635,949 (GRCm39) V126A possibly damaging Het
Other mutations in Rora
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00811:Rora APN 9 69,278,572 (GRCm39) missense probably benign 0.31
IGL02355:Rora APN 9 69,281,374 (GRCm39) missense probably damaging 1.00
IGL02362:Rora APN 9 69,281,374 (GRCm39) missense probably damaging 1.00
R0091:Rora UTSW 9 69,281,330 (GRCm39) missense probably damaging 1.00
R0555:Rora UTSW 9 69,269,028 (GRCm39) missense probably damaging 1.00
R0609:Rora UTSW 9 69,269,151 (GRCm39) missense probably damaging 1.00
R1483:Rora UTSW 9 69,271,667 (GRCm39) missense probably benign 0.00
R1712:Rora UTSW 9 69,282,771 (GRCm39) missense probably benign 0.23
R1785:Rora UTSW 9 69,284,119 (GRCm39) missense probably benign 0.30
R2883:Rora UTSW 9 69,282,717 (GRCm39) missense probably damaging 1.00
R4173:Rora UTSW 9 68,561,192 (GRCm39) missense probably benign 0.41
R5226:Rora UTSW 9 69,271,423 (GRCm39) intron probably benign
R5660:Rora UTSW 9 68,561,203 (GRCm39) missense probably benign 0.27
R6029:Rora UTSW 9 69,271,734 (GRCm39) missense probably benign 0.04
R6054:Rora UTSW 9 69,286,084 (GRCm39) missense probably benign 0.04
R6114:Rora UTSW 9 69,278,605 (GRCm39) missense probably benign
R6329:Rora UTSW 9 69,280,468 (GRCm39) missense probably damaging 1.00
R7028:Rora UTSW 9 69,103,365 (GRCm39) missense possibly damaging 0.46
R7170:Rora UTSW 9 69,280,472 (GRCm39) nonsense probably null
R7233:Rora UTSW 9 69,104,804 (GRCm39) nonsense probably null
R7512:Rora UTSW 9 69,281,367 (GRCm39) missense probably benign 0.00
R9647:Rora UTSW 9 69,255,450 (GRCm39) missense probably damaging 1.00
Z1176:Rora UTSW 9 69,271,654 (GRCm39) missense probably damaging 0.99
Predicted Primers PCR Primer
(F):5'- CTGCATGATGACCTCAGCAC -3'
(R):5'- TTTGCAGTGGACACCCATG -3'

Sequencing Primer
(F):5'- TGACCTCAGCACCTATATGGATGG -3'
(R):5'- GCAGTGGACACCCATGAGAAAC -3'
Posted On 2019-06-07