Mutagenetix > Incidental Mutation

Incidental Mutation 'R6029:Rora'

480268

Institutional Source

Beutler Lab

Gene Symbol

Rora

Ensembl Gene

ENSMUSG00000032238

Gene Name

RAR-related orphan receptor alpha

Synonyms

tmgc26, Nr1f1, 9530021D13Rik

MMRRC Submission

044201-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.915) question?

Stock #

R6029 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

68561068-69295528 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 69271734 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Lysine at position 181 (N181K)

Ref Sequence

ENSEMBL: ENSMUSP00000109254 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000034766] [ENSMUST00000113624] [ENSMUST00000174296]

AlphaFold

P51448

Predicted Effect

probably benign
Transcript: ENSMUST00000034766
AA Change: N237K

PolyPhen 2 Score 0.011 (Sensitivity: 0.96; Specificity: 0.78)

SMART Domains

Protein: ENSMUSP00000034766
Gene: ENSMUSG00000032238
AA Change: N237K

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: N181K

PolyPhen 2 Score 0.035 (Sensitivity: 0.94; Specificity: 0.82)

SMART Domains

Protein: ENSMUSP00000109254
Gene: ENSMUSG00000032238
AA Change: N181K

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000152570

Predicted Effect

probably benign
Transcript: ENSMUST00000174296

Meta Mutation Damage Score

0.0591

Coding Region Coverage

1x: 99.9%
3x: 99.5%
10x: 97.7%
20x: 92.7%

Validation Efficiency

97% (87/90)

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: 90 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4932414N04Rik	G	A	2: 68,524,370 (GRCm39)		probably null	Het
Adi1	G	A	12: 28,729,318 (GRCm39)		probably benign	Het
Afg3l2	G	T	18: 67,554,329 (GRCm39)	L458M	probably damaging	Het
Apob	A	G	12: 8,066,243 (GRCm39)	E4371G	probably damaging	Het
Ash1l	T	C	3: 88,892,326 (GRCm39)	Y1402H	probably damaging	Het
Aspm	T	G	1: 139,408,728 (GRCm39)	C2538W	possibly damaging	Het
Brd10	A	G	19: 29,732,367 (GRCm39)		probably benign	Het
Btbd16	T	C	7: 130,420,802 (GRCm39)	V353A	probably benign	Het
Cad	C	T	5: 31,212,327 (GRCm39)	S10L	possibly damaging	Het
Cdc42bpa	T	C	1: 179,939,352 (GRCm39)	S877P	probably damaging	Het
Cep152	A	T	2: 125,405,552 (GRCm39)	V1660D	probably benign	Het
Clrn2	G	T	5: 45,617,528 (GRCm39)	G133V	probably damaging	Het
Clstn2	T	C	9: 97,338,634 (GRCm39)	I842V	probably benign	Het
Cpt1c	C	T	7: 44,614,548 (GRCm39)	A434T	probably benign	Het
D130052B06Rik	G	T	11: 33,573,477 (GRCm39)	V70L	possibly damaging	Het
Dlg1	T	A	16: 31,612,388 (GRCm39)	V317E	probably damaging	Het
Dock10	T	C	1: 80,514,663 (GRCm39)	E1084G	possibly damaging	Het
Dync2h1	A	G	9: 7,157,646 (GRCm39)	V827A	probably benign	Het
E030030I06Rik	A	G	10: 22,024,832 (GRCm39)	L27P	unknown	Het
Ero1b	T	A	13: 12,589,714 (GRCm39)	L39Q	probably damaging	Het
Erp27	T	C	6: 136,888,609 (GRCm39)	D123G	probably damaging	Het
Fasn	G	T	11: 120,711,735 (GRCm39)	F148L	probably damaging	Het
Fbxl5	T	C	5: 43,922,746 (GRCm39)	E218G	probably damaging	Het
Fbxw28	A	T	9: 109,158,493 (GRCm39)	D210E	probably damaging	Het
Gm10653	T	A	9: 62,748,796 (GRCm39)		probably benign	Het
Gm17067	A	G	7: 42,357,554 (GRCm39)	L316S	probably benign	Het
Gm29106	T	C	1: 118,127,990 (GRCm39)	S561P	probably damaging	Het
Hmcn1	C	A	1: 150,508,188 (GRCm39)	K3699N	probably benign	Het
Itch	T	A	2: 155,021,009 (GRCm39)		probably null	Het
Itpr3	C	T	17: 27,317,145 (GRCm39)	A800V	probably damaging	Het
Kdm2b	A	T	5: 123,017,650 (GRCm39)	M1052K	probably damaging	Het
Kdm4b	T	C	17: 56,703,576 (GRCm39)	M712T	probably damaging	Het
Kmt5b	A	G	19: 3,852,104 (GRCm39)	E137G	probably damaging	Het
Krt33a	G	A	11: 99,903,289 (GRCm39)	T251I	probably benign	Het
Lrrc4b	G	T	7: 44,111,754 (GRCm39)	R542L	probably benign	Het
Macf1	C	A	4: 123,401,126 (GRCm39)	S653I	probably damaging	Het
Macrod2	G	A	2: 142,160,367 (GRCm39)	V408M	probably damaging	Het
Macroh2a2	T	C	10: 61,583,541 (GRCm39)	T200A	possibly damaging	Het
Mapkapk3	G	T	9: 107,166,425 (GRCm39)	A40E	possibly damaging	Het
Mmp20	G	A	9: 7,639,302 (GRCm39)	V157I	probably benign	Het
Mrps28	T	C	3: 8,988,805 (GRCm39)	R18G	possibly damaging	Het
Msrb2	T	A	2: 19,399,122 (GRCm39)	C162S	probably damaging	Het
Naa80	A	G	9: 107,460,753 (GRCm39)	Y216C	probably damaging	Het
Nckap5	T	G	1: 125,953,523 (GRCm39)	T1078P	possibly damaging	Het
Nectin3	T	C	16: 46,256,763 (GRCm39)	Y91C	probably benign	Het
Nf2	G	T	11: 4,734,566 (GRCm39)		probably null	Het
Or10d1b	G	A	9: 39,613,696 (GRCm39)	A123V	probably damaging	Het
Or13a23-ps1	A	T	7: 140,118,789 (GRCm39)	M120L	unknown	Het
Or1e16	AGCGGTCGTAGGC	AGC	11: 73,286,480 (GRCm39)		probably null	Het
Or2y10	A	T	11: 49,455,428 (GRCm39)	I227F	possibly damaging	Het
Or4c29	T	C	2: 88,740,380 (GRCm39)	D119G	probably damaging	Het
Or4g7	T	A	2: 111,309,310 (GRCm39)	Y60*	probably null	Het
Or8b36	ATTGCTGTTT	ATTGCTGTTTGCTGTTT	9: 37,937,836 (GRCm39)		probably null	Het
Oxr1	T	G	15: 41,689,297 (GRCm39)	L507W	probably damaging	Het
Plxna2	A	T	1: 194,481,883 (GRCm39)	K1451M	probably damaging	Het
Plxna2	A	G	1: 194,476,735 (GRCm39)	M1184V	probably benign	Het
Pofut1	G	A	2: 153,101,713 (GRCm39)		probably null	Het
Ppp1r16b	T	C	2: 158,597,137 (GRCm39)	V257A	possibly damaging	Het
Prss56	G	A	1: 87,115,279 (GRCm39)	W498*	probably null	Het
Ptpru	A	G	4: 131,498,604 (GRCm39)	F1329S	probably damaging	Het
Pusl1	A	G	4: 155,973,920 (GRCm39)	F278S	probably damaging	Het
Qars1	A	T	9: 108,390,889 (GRCm39)	L470F	probably damaging	Het
Rbm8a2	T	C	1: 175,806,312 (GRCm39)	D55G	probably benign	Het
Rufy3	A	G	5: 88,775,114 (GRCm39)	D262G	probably damaging	Het
Sh3gl2	G	A	4: 85,299,651 (GRCm39)	V212M	probably damaging	Het
Sis	G	A	3: 72,835,641 (GRCm39)	T907I	probably benign	Het
Slc38a3	A	T	9: 107,529,374 (GRCm39)	I456N	probably damaging	Het
Slc4a8	T	A	15: 100,705,220 (GRCm39)	C809S	probably benign	Het
Snap91	A	T	9: 86,707,133 (GRCm39)		probably null	Het
Spaca6	A	G	17: 18,051,458 (GRCm39)	T45A	probably benign	Het
Speer1m	A	T	5: 11,970,680 (GRCm39)	L84F	probably damaging	Het
Spry1	T	C	3: 37,696,997 (GRCm39)	I80T	possibly damaging	Het
St8sia2	A	G	7: 73,610,458 (GRCm39)	L275P	possibly damaging	Het
Supt7l	C	A	5: 31,684,331 (GRCm39)		probably null	Het
Tdo2	T	A	3: 81,868,747 (GRCm39)	K304N	probably damaging	Het
Tdrd12	A	T	7: 35,184,655 (GRCm39)	Y753N	probably damaging	Het
Topbp1	A	T	9: 103,222,152 (GRCm39)	Q1341L	probably benign	Het
Trim14	G	T	4: 46,506,998 (GRCm39)	A406E	probably benign	Het
Trp63	C	T	16: 25,686,964 (GRCm39)	R393W	probably damaging	Het
Trrap	T	C	5: 144,754,489 (GRCm39)	V1932A	possibly damaging	Het
Trrap	T	C	5: 144,762,724 (GRCm39)	M2399T	possibly damaging	Het
Unc45b	A	G	11: 82,804,153 (GRCm39)	N110S	probably damaging	Het
Usp32	G	T	11: 84,916,408 (GRCm39)	H845Q	probably damaging	Het
Usp44	G	A	10: 93,682,494 (GRCm39)	D268N	probably damaging	Het
Vmn1r18	T	G	6: 57,367,451 (GRCm39)	R34S	possibly damaging	Het
Vmn2r103	T	A	17: 20,014,478 (GRCm39)	Y423*	probably null	Het
Wapl	A	T	14: 34,461,204 (GRCm39)	E1054V	possibly damaging	Het
Zbtb8b	A	G	4: 129,322,286 (GRCm39)	Y392H	probably damaging	Het
Zdhhc2	A	T	8: 40,925,968 (GRCm39)	Q321L	probably null	Het
Zfp983	A	G	17: 21,881,401 (GRCm39)	D443G	probably benign	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
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'- AGAGAGACAGCTTGTACGCC -3'
(R):5'- CTTTCACTTCACAGGGAATGCC -3'

Sequencing Primer
(F):5'- TTGTACGCCGAGGTGCAG -3'
(R):5'- CCCAGAGCAAACCAGGAGG -3'

Posted On

2017-06-26