Incidental Mutation 'R0265:Rxra'
ID 155848
Institutional Source Beutler Lab
Gene Symbol Rxra
Ensembl Gene ENSMUSG00000015846
Gene Name retinoid X receptor alpha
Synonyms RXRalpha1, 9530071D11Rik, RXR alpha 1
MMRRC Submission 038491-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R0265 (G1)
Quality Score 60
Status Validated
Chromosome 2
Chromosomal Location 27566452-27652969 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 27642442 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Leucine to Proline at position 305 (L305P)
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: L305P

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000076491
Gene: ENSMUSG00000015846
AA Change: L305P

DomainStartEndE-ValueType
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: L277P

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000097822
Gene: ENSMUSG00000015846
AA Change: L277P

DomainStartEndE-ValueType
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: L277P

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000109567
Gene: ENSMUSG00000015846
AA Change: L277P

DomainStartEndE-ValueType
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 noncoding transcript
Transcript: ENSMUST00000148756
Predicted Effect probably damaging
Transcript: ENSMUST00000166775
AA Change: L305P

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000133044
Gene: ENSMUSG00000015846
AA Change: L305P

DomainStartEndE-ValueType
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 0.9752 question?
Coding Region Coverage
  • 1x: 98.5%
  • 3x: 97.4%
  • 10x: 95.6%
  • 20x: 92.0%
Validation Efficiency 99% (83/84)
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: 82 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca14 A G 7: 119,822,850 (GRCm39) I321V probably benign Het
Adcy7 A G 8: 89,051,391 (GRCm39) D837G probably damaging Het
Aldh1a1 T A 19: 20,617,440 (GRCm39) Y457* probably null Het
Alox5 T C 6: 116,397,323 (GRCm39) Y287C probably benign Het
Ano8 T C 8: 71,933,168 (GRCm39) probably benign Het
Ap3b1 A G 13: 94,630,189 (GRCm39) K815E unknown Het
Atp11a A T 8: 12,906,930 (GRCm39) probably benign Het
Atp6v0a1 A T 11: 100,939,341 (GRCm39) D702V possibly damaging Het
Cacna1b T A 2: 24,651,856 (GRCm39) N108Y probably damaging Het
Ccdc57 G C 11: 120,812,637 (GRCm39) A39G probably benign Het
Cdhr1 A T 14: 36,803,333 (GRCm39) V581D probably benign Het
Cfap20dc T G 14: 8,431,667 (GRCm38) Y655S probably damaging Het
Cyp2b23 A G 7: 26,372,304 (GRCm39) probably benign Het
D430041D05Rik G C 2: 103,998,295 (GRCm39) P1836R probably damaging Het
Ddit4l C T 3: 137,330,048 (GRCm39) probably benign Het
Dnah8 A T 17: 30,909,245 (GRCm39) I1024F probably benign Het
Dync2i1 T C 12: 116,221,026 (GRCm39) probably benign Het
Edc3 T A 9: 57,634,621 (GRCm39) F213I probably damaging Het
Edrf1 G A 7: 133,258,774 (GRCm39) D717N probably damaging Het
Efna5 G A 17: 62,958,068 (GRCm39) P63S probably damaging Het
Elapor2 T C 5: 9,484,681 (GRCm39) L486P probably damaging Het
Entpd3 A G 9: 120,387,547 (GRCm39) Y248C probably damaging Het
Flcn G A 11: 59,686,635 (GRCm39) Q373* probably null Het
Fry T C 5: 150,358,241 (GRCm39) V1908A probably damaging Het
Gabrg3 A T 7: 57,031,365 (GRCm39) Y58* probably null Het
Gabrp A T 11: 33,502,614 (GRCm39) Y417N probably damaging Het
Golga2 C A 2: 32,194,964 (GRCm39) probably null Het
Grip2 C A 6: 91,750,773 (GRCm39) probably null Het
Gsx2 A G 5: 75,237,729 (GRCm39) Y227C probably damaging Het
H2ac1 T C 13: 24,118,632 (GRCm39) V63A probably benign Het
Hif3a T C 7: 16,769,793 (GRCm39) *665W probably null Het
Hsd3b1 C A 3: 98,760,089 (GRCm39) V301L probably damaging Het
Ifitm5 T C 7: 140,529,921 (GRCm39) probably benign Het
Inpp4a A T 1: 37,418,067 (GRCm39) D498V probably damaging Het
Itga1 A T 13: 115,128,995 (GRCm39) D554E probably benign Het
Itk G A 11: 46,280,285 (GRCm39) probably benign Het
Kdm3b T A 18: 34,928,716 (GRCm39) probably benign Het
Klhl6 A G 16: 19,766,984 (GRCm39) V470A probably benign Het
Lamb3 T A 1: 193,002,839 (GRCm39) W95R probably damaging Het
Lbhd2 T A 12: 111,376,676 (GRCm39) I41N probably damaging Het
Lrp4 A T 2: 91,321,015 (GRCm39) S1014C probably damaging Het
Ltbp2 C T 12: 84,832,743 (GRCm39) probably null Het
Map3k19 A G 1: 127,749,919 (GRCm39) I1144T possibly damaging Het
Mfsd10 T C 5: 34,792,507 (GRCm39) probably benign Het
Mocos A G 18: 24,799,333 (GRCm39) D189G probably benign Het
Mvb12a T A 8: 71,999,654 (GRCm39) F224L probably damaging Het
Myo15a A T 11: 60,405,723 (GRCm39) probably null Het
Nos2 A T 11: 78,828,428 (GRCm39) H249L probably damaging Het
Notum A G 11: 120,549,160 (GRCm39) M184T probably benign Het
Nvl C A 1: 180,962,395 (GRCm39) D192Y probably damaging Het
Or10j3 A G 1: 173,031,484 (GRCm39) K187R probably benign Het
Or4f57 T C 2: 111,790,839 (GRCm39) Y193C probably damaging Het
Or5ac22 A T 16: 59,135,434 (GRCm39) F112Y probably damaging Het
Or5m12 T A 2: 85,734,591 (GRCm39) N269I probably benign Het
Or8k27 C A 2: 86,276,303 (GRCm39) V8L probably benign Het
Osgin1 A G 8: 120,172,396 (GRCm39) I397V possibly damaging Het
Otulin A G 15: 27,616,510 (GRCm39) V123A probably damaging Het
P4ha1 A G 10: 59,184,081 (GRCm39) Y181C probably damaging Het
Pcdhgc5 A T 18: 37,954,403 (GRCm39) D559V probably damaging Het
Phf2 T C 13: 48,982,270 (GRCm39) N151S unknown Het
Plxnc1 C A 10: 94,648,991 (GRCm39) G1263C probably benign Het
Rad51ap1 A G 6: 126,901,160 (GRCm39) *338Q probably null Het
Raver1 A G 9: 20,986,955 (GRCm39) S676P probably benign Het
Rfx8 T C 1: 39,727,737 (GRCm39) E196G possibly damaging Het
Rreb1 A T 13: 38,100,131 (GRCm39) K187* probably null Het
Rxfp1 T C 3: 79,574,961 (GRCm39) T217A probably benign Het
Sardh T C 2: 27,117,078 (GRCm39) probably benign Het
Skor2 A T 18: 76,964,293 (GRCm39) E952D probably damaging Het
Slc22a29 A T 19: 8,147,334 (GRCm39) S343T probably benign Het
Sorbs2 T C 8: 46,238,374 (GRCm39) probably benign Het
Supt7l C T 5: 31,673,262 (GRCm39) V329I probably benign Het
Taar2 G A 10: 23,817,393 (GRCm39) R311H probably benign Het
Tac1 T C 6: 7,559,165 (GRCm39) probably benign Het
Tcn2 A T 11: 3,872,044 (GRCm39) V361D probably damaging Het
Tm2d3 G A 7: 65,347,582 (GRCm39) A170T possibly damaging Het
Tnks G A 8: 35,307,124 (GRCm39) R1142* probably null Het
Ttll7 C A 3: 146,649,915 (GRCm39) Y648* probably null Het
Umod G T 7: 119,065,296 (GRCm39) Q578K probably benign Het
Upf2 G A 2: 6,032,015 (GRCm39) probably benign Het
Vmn2r92 C T 17: 18,388,219 (GRCm39) A408V probably damaging Het
Washc5 A G 15: 59,210,809 (GRCm39) I1013T probably benign Het
Zfp704 C A 3: 9,630,217 (GRCm39) R48L probably damaging Het
Other mutations in Rxra
AlleleSourceChrCoordTypePredicted EffectPPH 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
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
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'- CTCAGAGTCCTTTCACTGTGCCAG -3'
(R):5'- CCAAGTTCCAAGGCTACACTCCTTC -3'

Sequencing Primer
(F):5'- CCTCCGATGGTTTGGGATG -3'
(R):5'- AGTCCCCTTGGCTATGAGAGAC -3'
Posted On 2014-02-10