Mutagenetix > Incidental Mutation

Incidental Mutation 'R9647:Rora'

726814

Institutional Source

Beutler Lab

Gene Symbol

Rora

Ensembl Gene

ENSMUSG00000032238

Gene Name

RAR-related orphan receptor alpha

Synonyms

tmgc26, Nr1f1, 9530021D13Rik

MMRRC Submission

Accession Numbers

Essential gene?

Probably essential (E-score: 0.911) question?

Stock #

R9647 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

68561068-69295528 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 69255450 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glycine at position 78 (D78G)

Ref Sequence

ENSEMBL: ENSMUSP00000034766 (fasta)

Gene Model

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

AlphaFold

P51448

Predicted Effect

probably damaging
Transcript: ENSMUST00000034766
AA Change: D78G

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000034766
Gene: ENSMUSG00000032238
AA Change: D78G

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 damaging
Transcript: ENSMUST00000113624
AA Change: D22G

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000109254
Gene: ENSMUSG00000032238
AA Change: D22G

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

probably benign
Transcript: ENSMUST00000174296

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 99.1%

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: 78 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcc5	C	A	16: 20,195,310 (GRCm39)	R729L	probably benign	Het
Actr3b	T	C	5: 26,037,408 (GRCm39)	S295P	probably benign	Het
Alb	G	A	5: 90,620,544 (GRCm39)		probably null	Het
Ank2	T	A	3: 126,792,623 (GRCm39)	N756I	possibly damaging	Het
Ankar	A	G	1: 72,689,307 (GRCm39)	Y1275H	probably damaging	Het
Ankrd11	C	T	8: 123,617,682 (GRCm39)	A2057T	probably benign	Het
Birc6	G	A	17: 74,999,305 (GRCm39)	V4678M	probably damaging	Het
Bmpr1a	A	G	14: 34,136,694 (GRCm39)	V499A	probably benign	Het
Ccdc142	A	G	6: 83,079,259 (GRCm39)	N199D	probably benign	Het
Ccdc179	G	T	7: 51,663,311 (GRCm39)	Y38*	probably null	Het
Cdhr2	A	T	13: 54,867,394 (GRCm39)	M438L	probably benign	Het
Cfap74	A	T	4: 155,549,373 (GRCm39)	Q78L	unknown	Het
Crocc	A	T	4: 140,774,335 (GRCm39)	S155T	probably benign	Het
Depdc5	T	A	5: 33,081,567 (GRCm39)	H576Q	possibly damaging	Het
Dhx30	A	T	9: 109,922,214 (GRCm39)	L156Q	probably damaging	Het
Dido1	T	A	2: 180,315,068 (GRCm39)	T795S	probably benign	Het
Dlx1	T	C	2: 71,360,476 (GRCm39)	S47P	probably benign	Het
Dspp	G	A	5: 104,323,636 (GRCm39)	A260T	possibly damaging	Het
Ephx2	T	C	14: 66,326,957 (GRCm39)	T413A	probably benign	Het
Erp44	A	C	4: 48,205,166 (GRCm39)	L276V	probably benign	Het
Fastkd5	T	A	2: 130,457,729 (GRCm39)	Q287L	probably damaging	Het
Foxh1	T	A	15: 76,553,460 (GRCm39)	H114L	possibly damaging	Het
Fry	A	T	5: 150,292,984 (GRCm39)	L410F	probably damaging	Het
Gamt	T	A	10: 80,095,672 (GRCm39)	H86L	probably damaging	Het
Gdpd5	G	T	7: 99,104,241 (GRCm39)	R483L	probably benign	Het
Gm17067	A	C	7: 42,357,569 (GRCm39)	V311G	probably benign	Het
Gpatch2	C	T	1: 187,054,542 (GRCm39)	T422I	probably damaging	Het
Gpi1	A	G	7: 33,901,879 (GRCm39)	I546T	probably damaging	Het
Gyg1	A	C	3: 20,177,007 (GRCm39)	S328A	probably benign	Het
Heatr1	T	A	13: 12,441,679 (GRCm39)	V1491E	probably benign	Het
Hrob	A	T	11: 102,146,586 (GRCm39)	Q287H	possibly damaging	Het
Ildr2	T	C	1: 166,137,038 (GRCm39)	S626P	probably benign	Het
Insr	T	G	8: 3,205,874 (GRCm39)	E1305A	probably benign	Het
Iqca1	T	A	1: 89,998,258 (GRCm39)	T572S	probably benign	Het
Kdm4a	A	T	4: 118,003,790 (GRCm39)	M762K	probably benign	Het
Kdm4a	T	A	4: 118,017,399 (GRCm39)	T556S	probably benign	Het
Lama1	A	G	17: 68,024,170 (GRCm39)	I89M		Het
Larp7	T	C	3: 127,334,211 (GRCm39)	K539E	probably damaging	Het
Mmadhc	C	A	2: 50,186,482 (GRCm39)		probably benign	Het
Mmp2	A	G	8: 93,567,114 (GRCm39)	D478G	probably damaging	Het
Nat10	T	C	2: 103,578,538 (GRCm39)	Q222R	probably benign	Het
Nlgn1	A	T	3: 25,488,182 (GRCm39)	Y718N	probably damaging	Het
Nlrp5	A	T	7: 23,107,576 (GRCm39)	E83V	probably benign	Het
Odc1	T	C	12: 17,598,614 (GRCm39)	V218A	possibly damaging	Het
Or10al4	A	T	17: 38,037,796 (GRCm39)	I294F	probably damaging	Het
Or11g26	G	C	14: 50,753,552 (GRCm39)	R297T	probably damaging	Het
Or9r3	A	G	10: 129,948,029 (GRCm39)	I210T	probably damaging	Het
Oxsr1	G	A	9: 119,083,932 (GRCm39)	S324F	probably damaging	Het
Pclo	C	T	5: 14,731,788 (GRCm39)	T304M		Het
Pgghg	A	G	7: 140,526,743 (GRCm39)	R687G	possibly damaging	Het
Plxna4	A	G	6: 32,228,044 (GRCm39)	S521P	probably damaging	Het
Rasgrp4	A	G	7: 28,839,917 (GRCm39)	S172G	probably damaging	Het
Sec1	G	T	7: 45,328,556 (GRCm39)	R164S	probably benign	Het
Sesn3	A	G	9: 14,225,999 (GRCm39)	N245D	probably benign	Het
Slc44a5	T	A	3: 153,953,370 (GRCm39)	W251R	possibly damaging	Het
Ssr2	T	C	3: 88,487,206 (GRCm39)	V7A	possibly damaging	Het
Syne2	A	G	12: 76,151,875 (GRCm39)	D1912G	possibly damaging	Het
Tcea2	C	A	2: 181,322,984 (GRCm39)	T1N	probably benign	Het
Tmem131l	T	C	3: 83,836,018 (GRCm39)	Y697C	probably damaging	Het
Tmx4	T	C	2: 134,481,588 (GRCm39)	M112V	probably benign	Het
Tom1	G	T	8: 75,785,495 (GRCm39)	A330S	probably benign	Het
Trip4	A	T	9: 65,765,616 (GRCm39)	L361*	probably null	Het
Trmt9b	T	C	8: 36,979,210 (GRCm39)	I271T	probably benign	Het
Trp73	T	G	4: 154,165,788 (GRCm39)	T142P	probably damaging	Het
Trpm5	T	A	7: 142,634,498 (GRCm39)	D683V	possibly damaging	Het
Trpm7	T	C	2: 126,667,562 (GRCm39)	I810V	probably damaging	Het
Trps1	A	T	15: 50,524,944 (GRCm39)	S995R	probably benign	Het
Ttn	C	A	2: 76,608,269 (GRCm39)	E17885*	probably null	Het
Uggt2	A	T	14: 119,256,312 (GRCm39)	Y1120N	probably damaging	Het
Unc13a	A	T	8: 72,104,882 (GRCm39)	N793K	probably damaging	Het
Vcf1	T	C	11: 113,568,146 (GRCm39)	D103G	probably damaging	Het
Vmn2r94	T	C	17: 18,463,884 (GRCm39)	H802R	probably benign	Het
Vmn2r-ps158	T	C	7: 42,697,171 (GRCm39)	C743R	probably damaging	Het
Zdhhc5	A	T	2: 84,524,750 (GRCm39)	M190K	probably benign	Het
Zfp719	A	T	7: 43,233,602 (GRCm39)	N7I	possibly damaging	Het
Zfp735	A	G	11: 73,580,600 (GRCm39)	Y33C	probably damaging	Het
Zgrf1	C	T	3: 127,355,251 (GRCm39)	T159I	probably benign	Het
Zzef1	A	T	11: 72,760,651 (GRCm39)	T1325S	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
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
Z1176:Rora	UTSW	9	69,271,654 (GRCm39)	missense	probably damaging	0.99

Predicted Primers

PCR Primer
(F):5'- GAAAGCTATTATATAACGAGCAGCC -3'
(R):5'- ACCCTGCTGTCATCACTCAG -3'

Sequencing Primer
(F):5'- CCATAATTTAGTCCAGGGCTCTAGG -3'
(R):5'- TGCTGTCATCACTCAGAATCTCAAGG -3'

Posted On

2022-10-06