Mutagenetix > Incidental Mutation

Incidental Mutation 'R5226:Rora'

402619

Institutional Source

Beutler Lab

Gene Symbol

Rora

Ensembl Gene

ENSMUSG00000032238

Gene Name

RAR-related orphan receptor alpha

Synonyms

tmgc26, Nr1f1, 9530021D13Rik

MMRRC Submission

042799-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.911) question?

Stock #

R5226 (G1)

Quality Score

187

Status

Validated

Chromosome

Chromosomal Location

68561068-69295528 bp(+) (GRCm39)

Type of Mutation

intron

DNA Base Change (assembly)

T to A at 69271423 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000134291 (fasta)

Gene Model

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

AlphaFold

P51448

Predicted Effect

probably benign
Transcript: ENSMUST00000034766

SMART Domains

Protein: ENSMUSP00000034766
Gene: ENSMUSG00000032238

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

SMART Domains

Protein: ENSMUSP00000109254
Gene: ENSMUSG00000032238

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

Coding Region Coverage

1x: 99.3%
3x: 98.6%
10x: 97.3%
20x: 95.2%

Validation Efficiency

100% (66/66)

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: 56 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2010315B03Rik	T	C	9: 124,056,706 (GRCm39)	K98E	possibly damaging	Het
4933414I15Rik	A	T	11: 50,833,416 (GRCm39)	M62K	unknown	Het
Akr1d1	T	A	6: 37,512,949 (GRCm39)		probably null	Het
Ankrd63	T	C	2: 118,533,736 (GRCm39)		probably benign	Het
Atad5	T	C	11: 79,985,888 (GRCm39)	V325A	probably damaging	Het
Atp13a5	G	T	16: 29,067,031 (GRCm39)	N1025K	probably damaging	Het
Atrnl1	G	T	19: 57,638,767 (GRCm39)	V302L	probably benign	Het
Bend7	C	A	2: 4,757,789 (GRCm39)	S277*	probably null	Het
Btnl7-ps	A	T	17: 34,752,261 (GRCm39)		noncoding transcript	Het
Cbx4	T	C	11: 118,972,754 (GRCm39)	Y207C	probably damaging	Het
Ctla2b	C	T	13: 61,044,146 (GRCm39)	W63*	probably null	Het
Cux1	T	C	5: 136,399,027 (GRCm39)	T170A	probably benign	Het
Cyp3a57	T	C	5: 145,302,507 (GRCm39)	V101A	probably benign	Het
Dao	A	T	5: 114,159,094 (GRCm39)	T267S	probably benign	Het
Dsp	A	G	13: 38,370,746 (GRCm39)	D883G	probably damaging	Het
Dynlt4	A	G	4: 116,985,290 (GRCm39)	T38A	possibly damaging	Het
Eif4g3	C	A	4: 137,824,105 (GRCm39)	P36T	possibly damaging	Het
Elf3	G	A	1: 135,184,977 (GRCm39)	L70F	probably benign	Het
Epb41l4a	C	T	18: 33,943,366 (GRCm39)	D510N	probably damaging	Het
Gcn1	T	C	5: 115,726,126 (GRCm39)	S594P	probably benign	Het
Gm10722	T	C	9: 3,000,937 (GRCm39)	C6R	probably benign	Het
Gpr132	T	C	12: 112,815,768 (GRCm39)	T353A	probably benign	Het
Kntc1	A	G	5: 123,932,235 (GRCm39)	D1343G	probably benign	Het
L3mbtl4	T	A	17: 69,071,717 (GRCm39)		probably null	Het
Lrit2	A	G	14: 36,794,310 (GRCm39)	E458G	probably damaging	Het
Man1c1	A	T	4: 134,305,680 (GRCm39)	I348N	probably damaging	Het
Map4k2	A	G	19: 6,396,534 (GRCm39)		probably benign	Het
Nt5c2	A	C	19: 46,887,068 (GRCm39)	Y203D	probably damaging	Het
Oxgr1	A	G	14: 120,259,665 (GRCm39)	S181P	probably damaging	Het
Parn	A	G	16: 13,443,416 (GRCm39)	C400R	probably benign	Het
Pcdhgb7	T	C	18: 37,885,577 (GRCm39)	V249A	probably benign	Het
Pdzrn3	C	T	6: 101,130,272 (GRCm39)	D515N	probably damaging	Het
Plcg2	A	T	8: 118,304,613 (GRCm39)	I273F	possibly damaging	Het
Plin1	A	G	7: 79,372,447 (GRCm39)	V64A	probably damaging	Het
Ppfia4	C	A	1: 134,232,024 (GRCm39)		probably null	Het
Prkg2	A	C	5: 99,124,321 (GRCm39)	D376E	possibly damaging	Het
Ptgir	T	A	7: 16,642,645 (GRCm39)	I82N	probably damaging	Het
Pum2	C	T	12: 8,763,458 (GRCm39)	P205L	possibly damaging	Het
Rab26	T	A	17: 24,753,107 (GRCm39)		probably benign	Het
Recql4	T	C	15: 76,594,329 (GRCm39)	E63G	probably benign	Het
Rp1	A	C	1: 4,418,256 (GRCm39)	M952R	probably benign	Het
Rpap3	T	A	15: 97,601,104 (GRCm39)	R44S	possibly damaging	Het
Rufy4	T	C	1: 74,186,822 (GRCm39)	C537R	probably damaging	Het
Slc12a2	C	A	18: 58,012,092 (GRCm39)	P72T	probably damaging	Het
Slc1a3	C	T	15: 8,671,709 (GRCm39)	V416M	probably damaging	Het
Slfn4	A	T	11: 83,078,375 (GRCm39)	M388L	possibly damaging	Het
Snrnp48	G	A	13: 38,389,093 (GRCm39)	A49T	probably benign	Het
Tlx2	C	T	6: 83,045,911 (GRCm39)	G228D	possibly damaging	Het
Tmem132a	A	G	19: 10,844,508 (GRCm39)	V30A	possibly damaging	Het
Tnfrsf23	C	A	7: 143,239,522 (GRCm39)	L24F	possibly damaging	Het
Ubr2	A	T	17: 47,294,196 (GRCm39)	N312K	probably benign	Het
Vmn1r115	C	T	7: 20,578,169 (GRCm39)	V248I	probably damaging	Het
Vmn2r80	A	G	10: 79,029,874 (GRCm39)	T567A	probably benign	Het
Vps13c	A	G	9: 67,852,835 (GRCm39)	T2372A	probably benign	Het
Wnt10b	G	T	15: 98,674,495 (GRCm39)	H81N	probably damaging	Het
Zfp948	A	G	17: 21,808,505 (GRCm39)	T566A	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
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'- TGACCAGATTATGACACCACAGAG -3'
(R):5'- ATCATGCAGTTCCGTCAGCC -3'

Sequencing Primer
(F):5'- TTATGACACCACAGAGCTAGGTGC -3'
(R):5'- AGTTCCGTCAGCCCATTGG -3'

Posted On

2016-07-22