Incidental Mutation 'R1555:Rxra'
| ID |
170205 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Rxra
|
| Ensembl Gene |
ENSMUSG00000015846 |
| Gene Name |
retinoid X receptor alpha |
| Synonyms |
RXRalpha1, 9530071D11Rik, RXR alpha 1 |
| MMRRC Submission |
039594-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R1555 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
2 |
| Chromosomal Location |
27566452-27652969 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
C to T
at 27638690 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Alanine to Valine
at position 231
(A231V)
|
| 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 benign
Transcript: ENSMUST00000077257
AA Change: A231V
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
| SMART Domains |
Protein: ENSMUSP00000076491
Gene: ENSMUSG00000015846
AA Change: A231V
| 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 benign
Transcript: ENSMUST00000100251
AA Change: A203V
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000097822
Gene: ENSMUSG00000015846
AA Change: A203V
| 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 benign
Transcript: ENSMUST00000113934
AA Change: A203V
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000109567
Gene: ENSMUSG00000015846
AA Change: A203V
| 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 |
noncoding transcript
Transcript: ENSMUST00000148756
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000166775
AA Change: A231V
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
| SMART Domains |
Protein: ENSMUSP00000133044
Gene: ENSMUSG00000015846
AA Change: A231V
| 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 |
0.0694 |
| Coding Region Coverage |
- 1x: 99.1%
- 3x: 98.3%
- 10x: 96.1%
- 20x: 92.0%
|
| Validation Efficiency |
96% (43/45) |
| 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: 38 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Ace |
A |
G |
11: 105,865,727 (GRCm39) |
|
probably null |
Het |
| Adamts1 |
T |
A |
16: 85,594,776 (GRCm39) |
T358S |
probably benign |
Het |
| Ate1 |
A |
T |
7: 130,110,821 (GRCm39) |
F169I |
probably benign |
Het |
| Cdkl4 |
T |
A |
17: 80,851,043 (GRCm39) |
|
probably benign |
Het |
| Clcnkb |
T |
C |
4: 141,139,050 (GRCm39) |
|
probably null |
Het |
| Col6a4 |
C |
T |
9: 105,878,085 (GRCm39) |
R1964Q |
possibly damaging |
Het |
| Dcakd |
C |
T |
11: 102,891,039 (GRCm39) |
V17I |
probably damaging |
Het |
| Dcdc5 |
T |
G |
2: 106,214,480 (GRCm39) |
|
noncoding transcript |
Het |
| Erc2 |
T |
A |
14: 27,733,622 (GRCm39) |
D557E |
probably damaging |
Het |
| Grid2 |
A |
T |
6: 64,406,668 (GRCm39) |
D676V |
possibly damaging |
Het |
| Hebp2 |
G |
T |
10: 18,420,163 (GRCm39) |
T90K |
possibly damaging |
Het |
| Igkv10-96 |
C |
T |
6: 68,609,365 (GRCm39) |
|
probably benign |
Het |
| Mier3 |
T |
A |
13: 111,844,893 (GRCm39) |
N248K |
probably damaging |
Het |
| Myo5b |
A |
T |
18: 74,702,853 (GRCm39) |
I15F |
probably damaging |
Het |
| Neurl3 |
A |
G |
1: 36,305,613 (GRCm39) |
V198A |
probably benign |
Het |
| Notch2 |
C |
A |
3: 98,038,656 (GRCm39) |
N1266K |
possibly damaging |
Het |
| Nup107 |
A |
G |
10: 117,587,395 (GRCm39) |
|
probably benign |
Het |
| Or52e8b |
T |
C |
7: 104,673,729 (GRCm39) |
I153V |
probably benign |
Het |
| Or6d14 |
A |
T |
6: 116,533,787 (GRCm39) |
I134F |
probably damaging |
Het |
| Phf3 |
G |
T |
1: 30,844,958 (GRCm39) |
H1334N |
possibly damaging |
Het |
| Phyhd1 |
T |
A |
2: 30,164,718 (GRCm39) |
I100N |
probably damaging |
Het |
| Rad21l |
T |
A |
2: 151,500,348 (GRCm39) |
T224S |
probably benign |
Het |
| Sac3d1 |
T |
C |
19: 6,168,435 (GRCm39) |
D61G |
probably damaging |
Het |
| Sbf1 |
A |
G |
15: 89,189,279 (GRCm39) |
Y481H |
probably damaging |
Het |
| Spg11 |
T |
C |
2: 121,927,858 (GRCm39) |
E642G |
probably damaging |
Het |
| Spta1 |
A |
G |
1: 174,006,315 (GRCm39) |
Y159C |
probably damaging |
Het |
| Sry |
C |
G |
Y: 2,662,975 (GRCm39) |
Q228H |
unknown |
Het |
| Tedc1 |
G |
T |
12: 113,120,117 (GRCm39) |
|
probably benign |
Het |
| Tmem200a |
A |
T |
10: 25,869,782 (GRCm39) |
D162E |
probably damaging |
Het |
| Tmprss11e |
T |
A |
5: 86,863,447 (GRCm39) |
Q206L |
probably damaging |
Het |
| Tpra1 |
A |
G |
6: 88,887,185 (GRCm39) |
N175S |
probably damaging |
Het |
| Ttll10 |
T |
C |
4: 156,119,596 (GRCm39) |
E601G |
probably benign |
Het |
| Ttll6 |
G |
T |
11: 96,036,408 (GRCm39) |
D346Y |
probably damaging |
Het |
| U2surp |
A |
G |
9: 95,348,630 (GRCm39) |
V874A |
probably damaging |
Het |
| Vwa5b1 |
T |
C |
4: 138,332,788 (GRCm39) |
K258R |
probably benign |
Het |
| Xkr6 |
A |
G |
14: 64,056,374 (GRCm39) |
Y95C |
unknown |
Het |
| Zfp180 |
T |
C |
7: 23,800,999 (GRCm39) |
|
probably benign |
Het |
| Zfp90 |
A |
G |
8: 107,150,727 (GRCm39) |
T147A |
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 |
|
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'- TGTGACCCATCAGCTCCAGGAAAG -3'
(R):5'- GTGATGTATGCCGAGATCCCACAG -3'
Sequencing Primer
(F):5'- TGTTCAGGGTATACAGCCATC -3'
(R):5'- TCTCACTGCTGGGGACAAAG -3'
|
| Posted On |
2014-04-13 |
Incidental Mutation