Mutagenetix > Incidental Mutation

Incidental Mutation 'R7404:Rxra'

574396

Institutional Source

Beutler Lab

Gene Symbol

Rxra

Ensembl Gene

ENSMUSG00000015846

Gene Name

retinoid X receptor alpha

Synonyms

RXRalpha1, 9530071D11Rik, RXR alpha 1

MMRRC Submission

045486-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R7404 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

27566452-27652969 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 27631866 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Isoleucine at position 179 (N179I)

Ref Sequence

ENSEMBL: ENSMUSP00000076491 (fasta)

Gene Model

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

AlphaFold

P28700

Predicted Effect

probably damaging
Transcript: ENSMUST00000077257
AA Change: N179I

PolyPhen 2 Score 0.986 (Sensitivity: 0.74; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000076491
Gene: ENSMUSG00000015846
AA Change: N179I

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: N151I

PolyPhen 2 Score 0.986 (Sensitivity: 0.74; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000097822
Gene: ENSMUSG00000015846
AA Change: N151I

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: N151I

PolyPhen 2 Score 0.986 (Sensitivity: 0.74; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000109567
Gene: ENSMUSG00000015846
AA Change: N151I

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: N151I

PolyPhen 2 Score 0.986 (Sensitivity: 0.74; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000115165
Gene: ENSMUSG00000015846
AA Change: N151I

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: N179I

PolyPhen 2 Score 0.986 (Sensitivity: 0.74; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000133044
Gene: ENSMUSG00000015846
AA Change: N179I

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: 99.7%
20x: 99.1%

Validation Efficiency

99% (92/93)

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: 93 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Ablim3	C	T	18: 61,955,099 (GRCm39)	A297T	probably damaging	Het
Adprhl1	T	A	8: 13,275,118 (GRCm39)	S547C	probably damaging	Het
Ankrd63	G	C	2: 118,533,793 (GRCm39)	R43G	unknown	Het
Asah2	T	C	19: 32,035,254 (GRCm39)	T24A	probably benign	Het
Asb17	G	A	3: 153,550,447 (GRCm39)		probably null	Het
Atp8b5	C	T	4: 43,342,640 (GRCm39)	T437I	probably benign	Het
Bbs2	T	C	8: 94,808,992 (GRCm39)	D311G	probably damaging	Het
Birc6	C	T	17: 74,946,789 (GRCm39)	T2851I	possibly damaging	Het
Bnip5	G	A	17: 29,124,298 (GRCm39)	R335W	probably damaging	Het
Cchcr1	T	C	17: 35,835,693 (GRCm39)	W266R	probably benign	Het
Col14a1	C	A	15: 55,252,024 (GRCm39)	S560*	probably null	Het
Crocc	G	A	4: 140,753,497 (GRCm39)	T1317M	possibly damaging	Het
Cxxc1	T	A	18: 74,352,278 (GRCm39)	V334E	possibly damaging	Het
Cyp3a25	T	A	5: 145,923,635 (GRCm39)	D336V	probably damaging	Het
Dapk1	A	G	13: 60,867,455 (GRCm39)	T221A	probably benign	Het
Dnah11	G	T	12: 118,068,543 (GRCm39)	T1605K	probably benign	Het
Dnah7c	T	C	1: 46,705,223 (GRCm39)	V2412A	possibly damaging	Het
Ect2l	T	A	10: 18,035,529 (GRCm39)	D524V	probably damaging	Het
Ehbp1l1	T	C	19: 5,770,872 (GRCm39)	E223G	possibly damaging	Het
Ephb2	A	T	4: 136,498,524 (GRCm39)	M185K	probably damaging	Het
Fcer1a	T	C	1: 173,049,083 (GRCm39)	K243E	probably damaging	Het
Fcgbp	T	A	7: 27,800,932 (GRCm39)	I1326N	probably damaging	Het
Fgfr1	T	C	8: 26,045,566 (GRCm39)	V45A	probably benign	Het
Filip1	T	A	9: 79,727,380 (GRCm39)	E413V	possibly damaging	Het
Frs3	T	C	17: 48,013,651 (GRCm39)		probably null	Het
Fstl4	A	G	11: 53,024,898 (GRCm39)	T257A	probably benign	Het
Golga5	A	T	12: 102,450,778 (GRCm39)	K477M	probably damaging	Het
Gpr171	A	T	3: 59,005,622 (GRCm39)	I51K	probably damaging	Het
H1f0	T	A	15: 78,913,080 (GRCm39)	Y53*	probably null	Het
Hephl1	A	G	9: 14,981,047 (GRCm39)	V795A	possibly damaging	Het
Hmcn1	A	T	1: 150,596,510 (GRCm39)	D1775E	probably benign	Het
Hs3st2	A	G	7: 121,100,168 (GRCm39)	D338G	possibly damaging	Het
Hsd3b6	T	A	3: 98,713,534 (GRCm39)	Y255F	probably benign	Het
Hspa9	T	C	18: 35,076,329 (GRCm39)	N328D	possibly damaging	Het
Hvcn1	T	A	5: 122,375,748 (GRCm39)	I100N	probably damaging	Het
Ifi207	C	T	1: 173,556,494 (GRCm39)	S748N	possibly damaging	Het
Katnip	A	T	7: 125,464,434 (GRCm39)	N1267I	probably damaging	Het
Kcnma1	G	T	14: 24,052,902 (GRCm39)	T180K	unknown	Het
Kctd16	A	G	18: 40,391,826 (GRCm39)	D138G	probably damaging	Het
Kifc3	A	G	8: 95,830,092 (GRCm39)	Y605H	probably benign	Het
Kmt2d	T	A	15: 98,743,376 (GRCm39)	Q3928L	unknown	Het
Lamb2	C	T	9: 108,364,782 (GRCm39)	R1179C	probably damaging	Het
Layn	T	A	9: 50,968,670 (GRCm39)	I358F	possibly damaging	Het
Lrig1	G	A	6: 94,603,452 (GRCm39)	T232M	probably damaging	Het
Lrp1	T	C	10: 127,418,577 (GRCm39)	T38A		Het
Map3k14	A	G	11: 103,129,918 (GRCm39)	V333A	probably benign	Het
Med13	T	C	11: 86,177,272 (GRCm39)	D1608G	possibly damaging	Het
Mrps31	T	G	8: 22,911,429 (GRCm39)	S224A	probably benign	Het
Msh6	G	T	17: 88,282,548 (GRCm39)			Het
Ncapd3	A	G	9: 26,978,315 (GRCm39)	D838G	probably benign	Het
Nlrp1a	C	A	11: 70,987,919 (GRCm39)	E1184*	probably null	Het
Npat	T	A	9: 53,466,233 (GRCm39)		probably null	Het
Nup210	A	T	6: 91,050,227 (GRCm39)	I414N	probably benign	Het
Or1e19	A	T	11: 73,316,419 (GRCm39)	L130H	probably damaging	Het
Or52n2	A	T	7: 104,542,181 (GRCm39)	V218E	possibly damaging	Het
Or5b122	T	A	19: 13,562,752 (GRCm39)	I28N	possibly damaging	Het
Or5h19	T	C	16: 58,856,603 (GRCm39)	T166A	possibly damaging	Het
Or6z5	T	C	7: 6,477,163 (GRCm39)	L18P	probably damaging	Het
Or8b12c	A	T	9: 37,715,257 (GRCm39)	T17S	possibly damaging	Het
Or8h7	A	C	2: 86,721,217 (GRCm39)	L101V	probably benign	Het
Otud7b	G	C	3: 96,043,936 (GRCm39)		probably null	Het
Phf11d	A	C	14: 59,596,942 (GRCm39)	W86G	probably benign	Het
Pik3c2b	T	A	1: 133,018,444 (GRCm39)	S964T	probably damaging	Het
Pira1	T	C	7: 3,742,344 (GRCm39)	Y61C	probably damaging	Het
Plod3	G	A	5: 137,023,901 (GRCm39)	V687I	probably benign	Het
Poglut1	T	G	16: 38,358,284 (GRCm39)	Y208S	possibly damaging	Het
Pou1f1	T	A	16: 65,330,749 (GRCm39)	L253H	probably damaging	Het
Pou2f1	C	T	1: 165,738,955 (GRCm39)	A166T	unknown	Het
Rhbdl3	C	T	11: 80,237,659 (GRCm39)	S297L	probably damaging	Het
Ryr2	C	T	13: 11,750,506 (GRCm39)	E1922K	probably damaging	Het
Scube1	T	C	15: 83,499,211 (GRCm39)	Y668C	probably damaging	Het
Sec16b	A	G	1: 157,358,927 (GRCm39)	Y120C	probably damaging	Het
Sec61b	G	T	4: 47,483,047 (GRCm39)	K92N	probably damaging	Het
Skic3	T	A	13: 76,296,866 (GRCm39)	Y1074*	probably null	Het
Slc13a3	T	C	2: 165,275,984 (GRCm39)	N254S	possibly damaging	Het
Slc17a7	T	A	7: 44,822,354 (GRCm39)	Y397N	probably benign	Het
Slc25a3	A	G	10: 90,952,902 (GRCm39)	V333A	possibly damaging	Het
Slc7a8	A	T	14: 54,964,283 (GRCm39)	V390E	probably damaging	Het
Sorbs2	G	A	8: 46,212,233 (GRCm39)		probably null	Het
Srgap1	T	C	10: 121,621,650 (GRCm39)	N948D	probably benign	Het
Tacc2	A	T	7: 130,225,066 (GRCm39)	T584S	probably benign	Het
Tec	A	T	5: 72,920,961 (GRCm39)	D471E	probably damaging	Het
Tecpr2	C	T	12: 110,898,038 (GRCm39)	A430V	probably benign	Het
Tmcc2	A	T	1: 132,288,759 (GRCm39)	D309E	probably damaging	Het
Tmem82	G	A	4: 141,344,742 (GRCm39)	A67V	possibly damaging	Het
Ttc23l	T	C	15: 10,551,663 (GRCm39)	Q21R	probably damaging	Het
Ubl3	A	G	5: 148,448,764 (GRCm39)	F26L	probably damaging	Het
Upf2	A	G	2: 6,045,014 (GRCm39)	E1088G	unknown	Het
Usp9y	T	A	Y: 1,341,780 (GRCm39)	I1362F	probably benign	Het
Wnk4	T	A	11: 101,159,318 (GRCm39)		probably null	Het
Wrn	C	G	8: 33,738,994 (GRCm39)	W1278S	probably benign	Het
Zfc3h1	T	A	10: 115,251,153 (GRCm39)	V1248D	probably damaging	Het
Zfp12	T	A	5: 143,226,099 (GRCm39)	V56D	probably damaging	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
R6913:Rxra	UTSW	2	27,631,186 (GRCm39)	missense	probably damaging	1.00
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'- TAGTAGCGGTGGACCTGTTC -3'
(R):5'- CCCCACATAAAGAATGCTGAGG -3'

Sequencing Primer
(F):5'- TGGACCTGTTCTCTGATGAAC -3'
(R):5'- GAAGGGACAATGGAGGCCCC -3'

Posted On

2019-09-13