Mutagenetix > Incidental Mutation

Incidental Mutation 'R3804:Rxra'

274470

Institutional Source

Beutler Lab

Gene Symbol

Rxra

Ensembl Gene

ENSMUSG00000015846

Gene Name

retinoid X receptor alpha

Synonyms

RXRalpha1, 9530071D11Rik, RXR alpha 1

MMRRC Submission

040879-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R3804 (G1)

Quality Score

211

Status

Validated

Chromosome

Chromosomal Location

27566452-27652969 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 27646272 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Cysteine to Arginine at position 374 (C374R)

Ref Sequence

ENSEMBL: ENSMUSP00000133044 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000077257] [ENSMUST00000100251] [ENSMUST00000113934] [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: C374R

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

SMART Domains

Protein: ENSMUSP00000076491
Gene: ENSMUSG00000015846
AA Change: C374R

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: C346R

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

SMART Domains

Protein: ENSMUSP00000097822
Gene: ENSMUSG00000015846
AA Change: C346R

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: C346R

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

SMART Domains

Protein: ENSMUSP00000109567
Gene: ENSMUSG00000015846
AA Change: C346R

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: ENSMUST00000166775
AA Change: C374R

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

SMART Domains

Protein: ENSMUSP00000133044
Gene: ENSMUSG00000015846
AA Change: C374R

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

Meta Mutation Damage Score

0.9751

Coding Region Coverage

1x: 99.2%
3x: 98.7%
10x: 97.5%
20x: 95.8%

Validation Efficiency

100% (67/67)

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: 66 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700011L22Rik	C	T	8: 79,974,922 (GRCm39)	E54K	probably benign	Het
Adgra1	A	G	7: 139,425,510 (GRCm39)	T8A	probably benign	Het
Alms1	A	G	6: 85,596,629 (GRCm39)	Y954C	probably damaging	Het
AU021092	A	C	16: 5,034,626 (GRCm39)	F199V	possibly damaging	Het
Bahcc1	C	T	11: 120,174,184 (GRCm39)	P1648L	probably benign	Het
Cacna1s	T	A	1: 136,034,756 (GRCm39)	C1319S	possibly damaging	Het
Capn13	G	A	17: 73,646,396 (GRCm39)	P339L	probably benign	Het
Ccdc39	A	T	3: 33,874,044 (GRCm39)	M596K	probably damaging	Het
Cfap418	A	G	4: 10,898,014 (GRCm39)	T199A	probably benign	Het
Cntn5	A	G	9: 9,781,668 (GRCm39)		probably benign	Het
Cyth4	A	G	15: 78,494,002 (GRCm39)	K159E	probably damaging	Het
Dgkz	C	A	2: 91,769,975 (GRCm39)	R563L	probably benign	Het
Dnah8	A	G	17: 30,889,621 (GRCm39)	E718G	probably benign	Het
Dop1a	T	C	9: 86,403,048 (GRCm39)	L1416P	probably damaging	Het
Dstyk	G	A	1: 132,377,464 (GRCm39)	A110T	probably damaging	Het
Eif1	A	G	11: 100,211,650 (GRCm39)	K95E	probably damaging	Het
Espnl	A	G	1: 91,249,943 (GRCm39)	D30G	probably benign	Het
Gast	T	C	11: 100,227,636 (GRCm39)	S73P	probably damaging	Het
Gmppb	T	C	9: 107,927,773 (GRCm39)	Y176H	probably damaging	Het
Grap2	A	G	15: 80,507,947 (GRCm39)	T4A	possibly damaging	Het
Grm8	T	G	6: 28,125,635 (GRCm39)	N164H	possibly damaging	Het
Gstm3	G	A	3: 107,871,551 (GRCm39)	T210I	probably benign	Het
Gtf3c3	A	G	1: 54,463,166 (GRCm39)		probably null	Het
Hmcn2	A	G	2: 31,242,897 (GRCm39)		probably null	Het
Icam2	A	G	11: 106,271,648 (GRCm39)	L94P	probably damaging	Het
Iqcm	C	A	8: 76,396,021 (GRCm39)	T188K	possibly damaging	Het
Jarid2	T	A	13: 45,056,307 (GRCm39)	N365K	probably benign	Het
Kank4	A	G	4: 98,668,370 (GRCm39)	S26P	probably damaging	Het
Lgr4	A	G	2: 109,838,542 (GRCm39)	K498E	probably benign	Het
Meltf	A	G	16: 31,703,816 (GRCm39)	H181R	probably benign	Het
Mslnl	G	A	17: 25,961,908 (GRCm39)	V128M	probably damaging	Het
Nf1	A	G	11: 79,450,347 (GRCm39)	D511G	probably null	Het
Nhlrc3	A	G	3: 53,366,052 (GRCm39)	V147A	possibly damaging	Het
Nrap	C	T	19: 56,310,211 (GRCm39)	D1595N	probably damaging	Het
Or1e16	T	C	11: 73,286,776 (GRCm39)	Q24R	probably benign	Het
Or5p4	A	T	7: 107,680,378 (GRCm39)	I126F	probably damaging	Het
Or6c212	T	A	10: 129,558,918 (GRCm39)	D165V	possibly damaging	Het
Or6n2	T	A	1: 173,897,474 (GRCm39)	N203K	probably damaging	Het
Pak3	G	A	X: 142,492,727 (GRCm39)	V87I	probably damaging	Het
Pgm2l1	T	C	7: 99,901,474 (GRCm39)	V121A	probably benign	Het
Phf19	A	G	2: 34,789,670 (GRCm39)	L350P	probably damaging	Het
Phf8	T	C	X: 150,355,572 (GRCm39)	S512P	possibly damaging	Het
Phkb	G	T	8: 86,648,858 (GRCm39)	E225*	probably null	Het
Pif1	T	A	9: 65,495,588 (GRCm39)	V166E	probably damaging	Het
Plaa	T	C	4: 94,458,125 (GRCm39)	D615G	probably damaging	Het
Prpf4b	T	C	13: 35,067,665 (GRCm39)		probably benign	Het
Septin3	T	C	15: 82,170,630 (GRCm39)		probably benign	Het
Skint4	G	T	4: 111,975,378 (GRCm39)	V113L	probably damaging	Het
Slc16a10	G	C	10: 39,932,620 (GRCm39)	H314D	possibly damaging	Het
Slc22a15	C	T	3: 101,804,590 (GRCm39)	G145D	probably damaging	Het
Slc28a1	A	T	7: 80,775,969 (GRCm39)	I222F	probably damaging	Het
Slc43a2	T	C	11: 75,454,424 (GRCm39)	L323P	probably benign	Het
Sorbs3	A	G	14: 70,436,800 (GRCm39)		probably benign	Het
Spink10	C	T	18: 62,786,485 (GRCm39)		probably benign	Het
Suclg2	A	T	6: 95,474,649 (GRCm39)	I372N	probably damaging	Het
Sun1	C	A	5: 139,211,117 (GRCm39)	C164*	probably null	Het
Tax1bp1	T	C	6: 52,719,770 (GRCm39)	F453L	probably benign	Het
Tmem54	A	G	4: 129,002,013 (GRCm39)	N9S	probably benign	Het
Tmx4	A	G	2: 134,462,497 (GRCm39)	W145R	probably damaging	Het
Top1	A	G	2: 160,544,688 (GRCm39)	H268R	probably damaging	Het
Ttn	A	G	2: 76,641,075 (GRCm39)	L13598P	probably damaging	Het
Vmn1r40	A	G	6: 89,691,991 (GRCm39)	I269M	probably benign	Het
Wdr7	G	T	18: 63,853,907 (GRCm39)	R80L	probably benign	Het
Zap70	A	T	1: 36,810,223 (GRCm39)	Q111L	possibly damaging	Het
Zfp808	T	A	13: 62,319,897 (GRCm39)	H375Q	probably damaging	Het
Zkscan2	A	T	7: 123,094,365 (GRCm39)		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
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
R6913:Rxra	UTSW	2	27,631,186 (GRCm39)	missense	probably damaging	1.00
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'- AGAGCTTTCAGTCATTCTCGG -3'
(R):5'- CTAATGTCAAGTGCCTACTCTGG -3'

Sequencing Primer
(F):5'- ATTCTCGGTCCGTCCTGGG -3'
(R):5'- ATAGAGTGCCACTTGAGCCTC -3'

Posted On

2015-04-02