Mutagenetix > Incidental Mutation

Incidental Mutation 'R6913:Rxra'

539140

Institutional Source

Beutler Lab

Gene Symbol

Rxra

Ensembl Gene

ENSMUSG00000015846

Gene Name

retinoid X receptor alpha

Synonyms

RXRalpha1, 9530071D11Rik, RXR alpha 1

MMRRC Submission

045034-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R6913 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

27566452-27652969 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 27631186 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Asparagine at position 139 (I139N)

Ref Sequence

ENSEMBL: ENSMUSP00000133044 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000077257] [ENSMUST00000100251] [ENSMUST00000113934] [ENSMUST00000129514] [ENSMUST00000166775]

AlphaFold

P28700

PDB Structure

CRYSTAL STRUCTURE OF A HETERODIMERIC COMPLEX OF RAR AND RXR LIGAND-BINDING DOMAINS [X-RAY DIFFRACTION]
Crystal Structure of the RARbeta/RXRalpha Ligand Binding Domain Heterodimer in Complex with 9-cis Retinoic Acid and a Fragment of the TRAP220 Coactivator [X-RAY DIFFRACTION]
Crystal structure of a mixed agonist-bound RAR-alpha and antagonist-bound RXR-alpha heterodimer ligand binding domains [X-RAY DIFFRACTION]

Predicted Effect

probably damaging
Transcript: ENSMUST00000077257
AA Change: I139N

PolyPhen 2 Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000076491
Gene: ENSMUSG00000015846
AA Change: I139N

Domain	Start	End	E-Value	Type
Pfam:Nuc_recep-AF1	18	132	4.2e-42	PFAM
ZnF_C4	137	208	1.76e-40	SMART
Blast:HOLI	233	265	1e-8	BLAST
HOLI	275	434	1.62e-53	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000100251
AA Change: I111N

PolyPhen 2 Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000097822
Gene: ENSMUSG00000015846
AA Change: I111N

Domain	Start	End	E-Value	Type
Pfam:Nuc_recep-AF1	1	104	1.8e-38	PFAM
ZnF_C4	109	180	1.76e-40	SMART
Blast:HOLI	205	237	1e-8	BLAST
HOLI	247	406	1.62e-53	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000113934
AA Change: I111N

PolyPhen 2 Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000109567
Gene: ENSMUSG00000015846
AA Change: I111N

Domain	Start	End	E-Value	Type
Pfam:Nuc_recep-AF1	1	104	1.8e-38	PFAM
ZnF_C4	109	180	1.76e-40	SMART
Blast:HOLI	205	237	1e-8	BLAST
HOLI	247	406	1.62e-53	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000129514
AA Change: I111N

PolyPhen 2 Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000115165
Gene: ENSMUSG00000015846
AA Change: I111N

Domain	Start	End	E-Value	Type
Pfam:Nuc_recep-AF1	1	104	2e-39	PFAM
ZnF_C4	109	165	1.17e-18	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000166775
AA Change: I139N

PolyPhen 2 Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000133044
Gene: ENSMUSG00000015846
AA Change: I139N

Domain	Start	End	E-Value	Type
Pfam:Nuc_recep-AF1	17	132	6.5e-41	PFAM
ZnF_C4	137	208	1.76e-40	SMART
Blast:HOLI	233	265	1e-8	BLAST
HOLI	275	434	1.62e-53	SMART

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.1%
20x: 96.9%

Validation Efficiency

97% (74/76)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] Retinoid X receptors (RXRs) and retinoic acid receptors (RARs) are nuclear receptors that mediate the biological effects of retinoids by their involvement in retinoic acid-mediated gene activation. These receptors function as transcription factors by binding as homodimers or heterodimers to specific sequences in the promoters of target genes. The protein encoded by this gene is a member of the steroid and thyroid hormone receptor superfamily of transcriptional regulators. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, May 2014]
PHENOTYPE: Null embryos have multiple organ defects and die of cardiac failure by E14.5. Gene ablation in liver, prostate, fat or epidermis tissue-specifically affects development, function and/or neoplasia. Hypomorphic mutants develop alopecia, progressively severe dermal cysts and late corneal opacity. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 76 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcc5	A	T	16: 20,197,494 (GRCm39)	I619N	possibly damaging	Het
Accsl	T	C	2: 93,696,488 (GRCm39)	K41E	possibly damaging	Het
Actr6	T	C	10: 89,562,558 (GRCm39)	E107G	probably damaging	Het
Adam7	T	A	14: 68,771,100 (GRCm39)	M9L	probably benign	Het
Adamts12	T	A	15: 11,215,778 (GRCm39)	H266Q	probably damaging	Het
Adamts16	A	G	13: 70,877,017 (GRCm39)	F1208S	possibly damaging	Het
Ankrd11	T	C	8: 123,621,650 (GRCm39)	D734G	probably benign	Het
Ap1b1	T	C	11: 4,962,972 (GRCm39)	V43A	possibly damaging	Het
Asnsd1	A	G	1: 53,387,390 (GRCm39)	V79A	probably damaging	Het
Aste1	T	A	9: 105,274,607 (GRCm39)	S221R	probably benign	Het
Ccndbp1	G	A	2: 120,840,347 (GRCm39)	E94K	probably benign	Het
Cdc34	G	A	10: 79,520,937 (GRCm39)		probably null	Het
Cdh16	T	C	8: 105,348,896 (GRCm39)	D67G	probably benign	Het
Chd8	T	C	14: 52,451,951 (GRCm39)	E1348G	probably damaging	Het
Chl1	C	T	6: 103,642,909 (GRCm39)	Q216*	probably null	Het
Cse1l	G	A	2: 166,771,797 (GRCm39)	V353I	possibly damaging	Het
Ctbp2	G	A	7: 132,616,455 (GRCm39)	S160F	possibly damaging	Het
Cyp1a1	C	A	9: 57,607,576 (GRCm39)	T68K	probably damaging	Het
Dennd11	T	C	6: 40,383,851 (GRCm39)	N397S	possibly damaging	Het
Dlgap2	T	A	8: 14,828,374 (GRCm39)	M594K	probably benign	Het
Dnah6	C	T	6: 73,189,505 (GRCm39)	E48K	probably benign	Het
Dock2	A	G	11: 34,647,049 (GRCm39)	V35A	probably damaging	Het
Edem2	A	T	2: 155,568,594 (GRCm39)	S73R	probably damaging	Het
Eps15	T	C	4: 109,218,427 (GRCm39)	V430A	probably benign	Het
Frem2	T	C	3: 53,424,242 (GRCm39)	N3065S	probably damaging	Het
Gal3st4	A	T	5: 138,269,090 (GRCm39)	S123R	possibly damaging	Het
Garnl3	T	A	2: 32,876,841 (GRCm39)	I937F	possibly damaging	Het
Gfod2	C	T	8: 106,443,995 (GRCm39)	V183M	possibly damaging	Het
Glipr1l1	T	C	10: 111,898,339 (GRCm39)		probably null	Het
Gm7145	T	G	1: 117,913,711 (GRCm39)	C198G	probably damaging	Het
Gvin2	G	A	7: 105,551,187 (GRCm39)	Q622*	probably null	Het
H2-Eb2	G	A	17: 34,552,523 (GRCm39)	A123T	possibly damaging	Het
Ighv1-55	T	C	12: 115,172,129 (GRCm39)	I7V	probably benign	Het
Itpripl2	G	T	7: 118,090,332 (GRCm39)	P76T	possibly damaging	Het
Kat6a	C	A	8: 23,393,215 (GRCm39)	A231E	possibly damaging	Het
Lipo3	C	T	19: 33,757,705 (GRCm39)	V255I	probably benign	Het
Mamstr	A	T	7: 45,292,662 (GRCm39)	M141L	probably benign	Het
Med13	A	G	11: 86,210,702 (GRCm39)	V480A	probably benign	Het
Mei1	A	G	15: 81,973,810 (GRCm39)	N523S	probably benign	Het
Mill2	A	G	7: 18,590,351 (GRCm39)	T144A	probably null	Het
Muc16	C	A	9: 18,553,959 (GRCm39)	L4111F	unknown	Het
Mylk2	G	A	2: 152,755,610 (GRCm39)	G258E	possibly damaging	Het
Myom2	T	G	8: 15,115,710 (GRCm39)	S42A	probably benign	Het
Nab1	C	A	1: 52,503,995 (GRCm39)	G401C	possibly damaging	Het
Nifk	T	C	1: 118,260,592 (GRCm39)	V244A	possibly damaging	Het
Nipsnap2	C	A	5: 129,830,357 (GRCm39)	Q224K	probably benign	Het
Nop16	T	G	13: 54,737,553 (GRCm39)	K47Q	probably damaging	Het
Nup153	A	T	13: 46,853,192 (GRCm39)	S548R	probably damaging	Het
Or2at1	A	C	7: 99,416,924 (GRCm39)	D185A	probably damaging	Het
Or4g17	A	G	2: 111,209,347 (GRCm39)	M1V	probably null	Het
Or5b111	A	G	19: 13,290,998 (GRCm39)	I217T	probably benign	Het
Pard6g	G	A	18: 80,160,534 (GRCm39)	V216I	possibly damaging	Het
Pcdh20	C	T	14: 88,706,038 (GRCm39)	V421I	probably benign	Het
Pcif1	G	A	2: 164,726,224 (GRCm39)		probably null	Het
Pde11a	C	A	2: 76,168,084 (GRCm39)	V290F	probably damaging	Het
Pisd	T	C	5: 32,894,773 (GRCm39)	Y511C	probably damaging	Het
Polg	A	T	7: 79,110,405 (GRCm39)	D276E	probably damaging	Het
Polr3b	T	C	10: 84,549,496 (GRCm39)	V906A	probably damaging	Het
Prkcg	C	T	7: 3,362,335 (GRCm39)	P270S	probably benign	Het
Rapgef2	T	A	3: 78,993,281 (GRCm39)	I884F	probably damaging	Het
Rpl13	C	A	8: 123,830,014 (GRCm39)	N113K	possibly damaging	Het
Sf3b5	T	A	10: 12,884,487 (GRCm39)	C41S	probably benign	Het
Spata31e3	G	T	13: 50,399,293 (GRCm39)	P1011H	probably damaging	Het
Stk24	C	T	14: 121,540,221 (GRCm39)	R126Q	probably damaging	Het
Taar8b	T	C	10: 23,967,963 (GRCm39)	D77G	possibly damaging	Het
Tbc1d1	T	A	5: 64,468,452 (GRCm39)	C566S	probably benign	Het
Tenm3	A	T	8: 48,751,972 (GRCm39)	M948K	probably damaging	Het
Thbs4	T	A	13: 92,894,444 (GRCm39)	Q693L	possibly damaging	Het
Tnfrsf26	A	T	7: 143,172,126 (GRCm39)	C61*	probably null	Het
Trp63	A	G	16: 25,707,918 (GRCm39)	E636G	probably damaging	Het
Try5	T	C	6: 41,288,266 (GRCm39)	Y121C	probably damaging	Het
Ttn	G	T	2: 76,660,755 (GRCm39)		probably benign	Het
Vamp1	T	A	6: 125,195,908 (GRCm39)	V55D	probably damaging	Het
Vmn2r117	T	C	17: 23,698,537 (GRCm39)	N12S	probably damaging	Het
Vmn2r90	G	A	17: 17,924,323 (GRCm39)	G41S	probably damaging	Het
Zfp462	T	A	4: 55,007,775 (GRCm39)	D71E	probably benign	Het

Other mutations in Rxra

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01941:Rxra	APN	2	27,644,253 (GRCm39)	missense	probably damaging	1.00
IGL03006:Rxra	APN	2	27,649,657 (GRCm39)	missense	probably damaging	1.00
pinkie	UTSW	2	27,642,346 (GRCm39)	missense	probably damaging	0.98
R0265:Rxra	UTSW	2	27,642,442 (GRCm39)	missense	probably damaging	1.00
R0578:Rxra	UTSW	2	27,649,582 (GRCm39)	missense	probably damaging	1.00
R1555:Rxra	UTSW	2	27,638,690 (GRCm39)	missense	probably benign	0.00
R1775:Rxra	UTSW	2	27,646,256 (GRCm39)	missense	probably damaging	1.00
R3725:Rxra	UTSW	2	27,644,289 (GRCm39)	missense	probably damaging	1.00
R3756:Rxra	UTSW	2	27,631,923 (GRCm39)	missense	probably damaging	1.00
R3804:Rxra	UTSW	2	27,646,272 (GRCm39)	missense	probably damaging	1.00
R3965:Rxra	UTSW	2	27,642,318 (GRCm39)	splice site	probably benign
R4490:Rxra	UTSW	2	27,631,207 (GRCm39)	missense	probably damaging	0.99
R4898:Rxra	UTSW	2	27,631,195 (GRCm39)	missense	probably damaging	1.00
R5154:Rxra	UTSW	2	27,647,880 (GRCm39)	critical splice donor site	probably null
R5651:Rxra	UTSW	2	27,627,353 (GRCm39)	missense	probably benign	0.25
R6880:Rxra	UTSW	2	27,638,668 (GRCm39)	missense	possibly damaging	0.64
R7404:Rxra	UTSW	2	27,631,866 (GRCm39)	missense	probably damaging	0.99
R8324:Rxra	UTSW	2	27,631,195 (GRCm39)	missense	probably damaging	1.00
R9098:Rxra	UTSW	2	27,638,756 (GRCm39)	missense	possibly damaging	0.50
R9200:Rxra	UTSW	2	27,627,496 (GRCm39)	missense	possibly damaging	0.64
R9356:Rxra	UTSW	2	27,649,675 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- TCATTAGTGCCCATCCCCAG -3'
(R):5'- CTTGGCATACCTCTAGACCAC -3'

Sequencing Primer
(F):5'- ATCCCCAGCCTGCCAGG -3'
(R):5'- AATGAGACCCCTGGAGCTC -3'

Posted On

2018-11-06