Mutagenetix > Incidental Mutation

Incidental Mutation 'R6114:Rora'

485026

Institutional Source

Beutler Lab

Gene Symbol

Rora

Ensembl Gene

ENSMUSG00000032238

Gene Name

RAR-related orphan receptor alpha

Synonyms

tmgc26, Nr1f1, 9530021D13Rik

MMRRC Submission

044263-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.915) question?

Stock #

R6114 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

68561068-69295528 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 69278605 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Serine at position 254 (N254S)

Ref Sequence

ENSEMBL: ENSMUSP00000109254 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000034766] [ENSMUST00000113624]

AlphaFold

P51448

Predicted Effect

probably benign
Transcript: ENSMUST00000034766
AA Change: N310S

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000034766
Gene: ENSMUSG00000032238
AA Change: N310S

Domain	Start	End	E-Value	Type
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 benign
Transcript: ENSMUST00000113624
AA Change: N254S

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000109254
Gene: ENSMUSG00000032238
AA Change: N254S

Domain	Start	End	E-Value	Type
ZnF_C4	14	85	4.71e-41	SMART
low complexity region	105	119	N/A	INTRINSIC
HOLI	269	425	8.8e-32	SMART

Coding Region Coverage

1x: 99.9%
3x: 99.6%
10x: 98.0%
20x: 94.0%

Validation Efficiency

94% (60/64)

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: 63 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adamdec1	C	A	14: 68,809,252 (GRCm39)	V237L	probably benign	Het
Aff1	T	C	5: 103,990,163 (GRCm39)	S878P	probably damaging	Het
Ahcy	A	C	2: 154,904,079 (GRCm39)	L386R	probably damaging	Het
Ank2	T	C	3: 126,804,700 (GRCm39)	N607D	probably damaging	Het
Arid5b	T	C	10: 67,933,574 (GRCm39)	D776G	possibly damaging	Het
Art4	T	A	6: 136,834,211 (GRCm39)	T11S	unknown	Het
Blm	T	C	7: 80,163,235 (GRCm39)	T39A	probably damaging	Het
Cabin1	T	A	10: 75,583,805 (GRCm39)	M221L	probably benign	Het
Cacna1c	T	C	6: 118,573,101 (GRCm39)	T1675A	probably benign	Het
Cacnb2	A	T	2: 14,980,012 (GRCm39)	H285L	possibly damaging	Het
Cchcr1	A	G	17: 35,836,227 (GRCm39)	E339G	probably damaging	Het
Cd14	A	G	18: 36,859,006 (GRCm39)	W150R	probably damaging	Het
Cep162	A	G	9: 87,085,763 (GRCm39)	I1187T	probably benign	Het
Cntnap4	A	G	8: 113,568,385 (GRCm39)	H807R	probably damaging	Het
Copb1	T	A	7: 113,846,036 (GRCm39)	H178L	probably benign	Het
Cpxm2	A	G	7: 131,756,035 (GRCm39)	V103A	probably benign	Het
Egfr	A	G	11: 16,854,374 (GRCm39)	T849A	possibly damaging	Het
Endou	T	A	15: 97,611,757 (GRCm39)	K294*	probably null	Het
Hoxd9	A	G	2: 74,529,709 (GRCm39)	N322D	probably damaging	Het
Hsph1	C	A	5: 149,550,852 (GRCm39)	V416L	possibly damaging	Het
Igkv4-78	T	A	6: 69,036,743 (GRCm39)	T97S	possibly damaging	Het
Itga10	G	T	3: 96,556,351 (GRCm39)	C162F	probably damaging	Het
Lmod2	A	G	6: 24,603,691 (GRCm39)	E222G	probably damaging	Het
Lpar5	A	G	6: 125,058,639 (GRCm39)	N120S	probably damaging	Het
Lrrc37	T	A	11: 103,508,617 (GRCm39)		probably benign	Het
Lrrk2	A	G	15: 91,632,029 (GRCm39)	I1318V	probably benign	Het
Lst1	T	C	17: 35,407,336 (GRCm39)	T11A	possibly damaging	Het
Mfn1	C	A	3: 32,617,985 (GRCm39)	A106D	probably damaging	Het
Ms4a12	G	T	19: 11,192,654 (GRCm39)	N227K	probably benign	Het
Nr1h4	T	A	10: 89,314,678 (GRCm39)	N273Y	possibly damaging	Het
Nrdc	A	T	4: 108,901,782 (GRCm39)	K617M	probably damaging	Het
Or10a3b	A	T	7: 108,444,593 (GRCm39)	M208K	possibly damaging	Het
Or1l8	A	T	2: 36,817,701 (GRCm39)	C142S	possibly damaging	Het
Or6c202	T	A	10: 128,996,202 (GRCm39)	H217L	probably benign	Het
Pcdhgc3	C	G	18: 37,940,925 (GRCm39)	T442R	probably benign	Het
Pcnx2	T	C	8: 126,500,686 (GRCm39)	N1468S	probably damaging	Het
Pde2a	A	T	7: 101,160,319 (GRCm39)		probably null	Het
Pitx2	C	G	3: 128,998,062 (GRCm39)		probably null	Het
Reck	T	A	4: 43,922,895 (GRCm39)	I390N	probably damaging	Het
Samd4b	A	G	7: 28,222,217 (GRCm39)		probably null	Het
Scn8a	A	G	15: 100,938,477 (GRCm39)	T1949A	probably damaging	Het
Slc22a15	A	T	3: 101,768,168 (GRCm39)	Y346*	probably null	Het
Slc24a5	A	G	2: 124,925,012 (GRCm39)	T218A	probably benign	Het
Slc38a10	G	A	11: 120,020,138 (GRCm39)	Q305*	probably null	Het
Slc45a4	G	A	15: 73,477,453 (GRCm39)	P28S	probably damaging	Het
Smyd5	A	T	6: 85,417,244 (GRCm39)		probably benign	Het
Sox8	T	C	17: 25,786,494 (GRCm39)	D403G	probably damaging	Het
Stx7	A	G	10: 24,060,883 (GRCm39)		probably null	Het
Svil	T	C	18: 5,108,639 (GRCm39)	S1522P	probably damaging	Het
Sycp2	G	C	2: 177,990,038 (GRCm39)	R1403G	probably benign	Het
Tasor2	G	A	13: 3,640,081 (GRCm39)	T352M	probably damaging	Het
Tcf25	A	T	8: 124,111,114 (GRCm39)	K192M	probably damaging	Het
Tecpr1	C	T	5: 144,141,458 (GRCm39)	G804S	possibly damaging	Het
Teddm1a	C	G	1: 153,767,614 (GRCm39)	S26C	probably damaging	Het
Usp13	C	T	3: 32,908,818 (GRCm39)	P155S	probably damaging	Het
Usp17lb	T	A	7: 104,489,571 (GRCm39)	D451V	possibly damaging	Het
Vmn1r173	A	G	7: 23,402,254 (GRCm39)	N163S	possibly damaging	Het
Vmn2r103	G	T	17: 20,032,587 (GRCm39)	C787F	probably damaging	Het
Vmn2r106	G	A	17: 20,488,638 (GRCm39)	P587L	probably benign	Het
Wdr24	C	T	17: 26,043,579 (GRCm39)	H134Y	probably benign	Het
Zbtb40	T	A	4: 136,716,002 (GRCm39)	I988F	probably damaging	Het
Zbtb47	T	A	9: 121,594,661 (GRCm39)	F540Y	probably damaging	Het
Zfp536	A	T	7: 37,179,161 (GRCm39)	I84N	probably damaging	Het

Other mutations in Rora

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH 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
PIT4696001:Rora	UTSW	9	69,271,841 (GRCm39)	missense	possibly damaging	0.92
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
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'- GCACATTGCTTTAAGTGAGTTGC -3'
(R):5'- ACACGCTAGCATCTCAGGAAG -3'

Sequencing Primer
(F):5'- CCGGCAGAAGAGTATTATTGGCTC -3'
(R):5'- TCTCAGGAAGACAACAAAGCTCTGG -3'

Posted On

2017-08-16