Incidental Mutation 'R6373:Rxrb'
| ID |
513645 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Rxrb
|
| Ensembl Gene |
ENSMUSG00000039656 |
| Gene Name |
retinoid X receptor beta |
| Synonyms |
Rub, Nr2b2, H-2RIIBP, RCoR-1 |
| MMRRC Submission |
044523-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.829)
|
| Stock # |
R6373 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
17 |
| Chromosomal Location |
34250786-34257373 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 34252533 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Asparagine to Serine
at position 40
(N40S)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000134299
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000025186]
[ENSMUST00000044858]
[ENSMUST00000116612]
[ENSMUST00000169397]
[ENSMUST00000173354]
[ENSMUST00000173554]
[ENSMUST00000171872]
|
| AlphaFold |
P28704 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000025186
|
| SMART Domains |
Protein: ENSMUSP00000025186
Gene: ENSMUSG00000024327
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
27 |
N/A |
INTRINSIC |
|
low complexity region
|
39 |
77 |
N/A |
INTRINSIC |
|
low complexity region
|
80 |
123 |
N/A |
INTRINSIC |
|
Pfam:Zip
|
140 |
473 |
2.4e-83 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000044858
AA Change: N150S
PolyPhen 2
Score 0.027 (Sensitivity: 0.95; Specificity: 0.81)
|
| SMART Domains |
Protein: ENSMUSP00000036585
Gene: ENSMUSG00000039656
AA Change: N150S
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
66 |
85 |
N/A |
INTRINSIC |
|
low complexity region
|
94 |
121 |
N/A |
INTRINSIC |
|
low complexity region
|
124 |
147 |
N/A |
INTRINSIC |
|
low complexity region
|
179 |
186 |
N/A |
INTRINSIC |
|
ZnF_C4
|
189 |
260 |
3.98e-39 |
SMART |
|
low complexity region
|
269 |
282 |
N/A |
INTRINSIC |
|
low complexity region
|
305 |
316 |
N/A |
INTRINSIC |
|
HOLI
|
328 |
491 |
1.91e-50 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000116612
AA Change: N40S
PolyPhen 2
Score 0.027 (Sensitivity: 0.95; Specificity: 0.81)
|
| SMART Domains |
Protein: ENSMUSP00000112311
Gene: ENSMUSG00000039656
AA Change: N40S
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Nuc_recep-AF1
|
2 |
76 |
4.3e-10 |
PFAM |
|
ZnF_C4
|
79 |
150 |
3.98e-39 |
SMART |
|
low complexity region
|
159 |
172 |
N/A |
INTRINSIC |
|
low complexity region
|
195 |
206 |
N/A |
INTRINSIC |
|
HOLI
|
218 |
377 |
1.35e-50 |
SMART |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000167145
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000168978
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000169397
|
| SMART Domains |
Protein: ENSMUSP00000130102
Gene: ENSMUSG00000024327
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
27 |
N/A |
INTRINSIC |
|
low complexity region
|
39 |
77 |
N/A |
INTRINSIC |
|
low complexity region
|
80 |
123 |
N/A |
INTRINSIC |
|
Pfam:Zip
|
140 |
473 |
1.9e-81 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000170491
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000173354
AA Change: N40S
PolyPhen 2
Score 0.060 (Sensitivity: 0.94; Specificity: 0.84)
|
| SMART Domains |
Protein: ENSMUSP00000133661
Gene: ENSMUSG00000039656
AA Change: N40S
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Nuc_recep-AF1
|
2 |
76 |
4.3e-10 |
PFAM |
|
ZnF_C4
|
79 |
150 |
3.98e-39 |
SMART |
|
low complexity region
|
159 |
172 |
N/A |
INTRINSIC |
|
low complexity region
|
195 |
206 |
N/A |
INTRINSIC |
|
HOLI
|
218 |
381 |
1.91e-50 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000173554
AA Change: N40S
PolyPhen 2
Score 0.081 (Sensitivity: 0.93; Specificity: 0.85)
|
| SMART Domains |
Protein: ENSMUSP00000134299
Gene: ENSMUSG00000039656
AA Change: N40S
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Nuc_recep-AF1
|
2 |
76 |
4.9e-11 |
PFAM |
|
ZnF_C4
|
79 |
150 |
3.98e-39 |
SMART |
|
| Predicted Effect |
unknown
Transcript: ENSMUST00000174299
AA Change: N88S
|
| SMART Domains |
Protein: ENSMUSP00000133775
Gene: ENSMUSG00000039656
AA Change: N88S
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
2 |
16 |
N/A |
INTRINSIC |
|
low complexity region
|
25 |
52 |
N/A |
INTRINSIC |
|
low complexity region
|
55 |
78 |
N/A |
INTRINSIC |
|
low complexity region
|
110 |
117 |
N/A |
INTRINSIC |
|
ZnF_C4
|
120 |
191 |
3.98e-39 |
SMART |
|
low complexity region
|
200 |
213 |
N/A |
INTRINSIC |
|
low complexity region
|
236 |
247 |
N/A |
INTRINSIC |
|
HOLI
|
259 |
418 |
1.35e-50 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000171872
|
| SMART Domains |
Protein: ENSMUSP00000133146
Gene: ENSMUSG00000024327
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
27 |
N/A |
INTRINSIC |
|
low complexity region
|
39 |
77 |
N/A |
INTRINSIC |
|
low complexity region
|
80 |
123 |
N/A |
INTRINSIC |
|
Pfam:Zip
|
140 |
246 |
4.7e-25 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000173810
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000174130
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000174740
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000174033
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000174578
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000174645
|
| Meta Mutation Damage Score |
0.0617 |
| Coding Region Coverage |
- 1x: 99.9%
- 3x: 99.6%
- 10x: 98.3%
- 20x: 95.2%
|
| Validation Efficiency |
95% (37/39) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the retinoid X receptor (RXR) family of nuclear receptors which are involved in mediating the effects of retinoic acid (RA). The encoded protein forms homodimers with the retinoic acid, thyroid hormone, and vitamin D receptors, increasing both DNA binding and transcriptional function on their respective response elements. This gene lies within the major histocompatibility complex (MHC) class II region on chromosome 6. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Jul 2012]
PHENOTYPE: Mutant mice homozygous for a null mutation exhibit partial embryonic and perinatal lethality, and surviving adult males are sterile due to defects in spermatogenesis. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 40 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abhd13 |
T |
C |
8: 10,038,240 (GRCm39) |
L279P |
probably damaging |
Het |
| Aldh16a1 |
C |
G |
7: 44,795,695 (GRCm39) |
V373L |
probably benign |
Het |
| Btn2a2 |
T |
C |
13: 23,665,999 (GRCm39) |
K278E |
probably benign |
Het |
| Carns1 |
G |
T |
19: 4,216,515 (GRCm39) |
Q556K |
probably benign |
Het |
| Chd1 |
A |
T |
17: 15,958,898 (GRCm39) |
E650V |
probably damaging |
Het |
| Cobl |
A |
G |
11: 12,203,118 (GRCm39) |
S1195P |
probably damaging |
Het |
| Deup1 |
T |
C |
9: 15,472,638 (GRCm39) |
H464R |
probably damaging |
Het |
| Eva1a |
T |
C |
6: 82,068,847 (GRCm39) |
L58S |
probably damaging |
Het |
| Fign |
A |
C |
2: 63,809,989 (GRCm39) |
M427R |
probably benign |
Het |
| Gm6309 |
A |
T |
5: 146,107,085 (GRCm39) |
I87N |
probably damaging |
Het |
| H2ac7 |
A |
G |
13: 23,759,027 (GRCm39) |
K128R |
probably benign |
Het |
| Helz |
A |
G |
11: 107,486,010 (GRCm39) |
T140A |
probably benign |
Het |
| Helz2 |
C |
T |
2: 180,875,260 (GRCm39) |
E1745K |
probably damaging |
Het |
| Kif16b |
A |
T |
2: 142,541,618 (GRCm39) |
H1227Q |
possibly damaging |
Het |
| Mab21l1 |
A |
T |
3: 55,690,505 (GRCm39) |
I31F |
possibly damaging |
Het |
| Mex3c |
T |
C |
18: 73,723,065 (GRCm39) |
M386T |
probably benign |
Het |
| Myh11 |
T |
A |
16: 14,022,994 (GRCm39) |
I1644F |
possibly damaging |
Het |
| Nav2 |
C |
T |
7: 49,102,923 (GRCm39) |
P513S |
probably damaging |
Het |
| Ncoa3 |
C |
T |
2: 165,901,267 (GRCm39) |
S953F |
possibly damaging |
Het |
| Nmt2 |
A |
G |
2: 3,325,988 (GRCm39) |
T462A |
probably benign |
Het |
| Nrxn2 |
T |
C |
19: 6,559,860 (GRCm39) |
I163T |
probably damaging |
Het |
| Nrxn3 |
G |
C |
12: 89,943,237 (GRCm39) |
G122R |
probably damaging |
Het |
| Or1e26 |
A |
G |
11: 73,479,724 (GRCm39) |
V280A |
probably benign |
Het |
| Or5d20-ps1 |
T |
C |
2: 87,932,189 (GRCm39) |
I47M |
possibly damaging |
Het |
| Parg |
T |
G |
14: 31,931,454 (GRCm39) |
|
probably null |
Het |
| Pcdhb7 |
T |
A |
18: 37,475,264 (GRCm39) |
C133* |
probably null |
Het |
| Ppihl |
A |
G |
5: 44,070,893 (GRCm39) |
T127A |
probably damaging |
Het |
| Rigi |
A |
G |
4: 40,216,487 (GRCm39) |
Y504H |
possibly damaging |
Het |
| Rpe |
T |
C |
1: 66,755,139 (GRCm39) |
F174L |
probably benign |
Het |
| Ryr3 |
C |
A |
2: 112,486,889 (GRCm39) |
G3840W |
probably damaging |
Het |
| Smurf2 |
A |
G |
11: 106,724,595 (GRCm39) |
L529P |
probably damaging |
Het |
| Sntg2 |
C |
T |
12: 30,308,040 (GRCm39) |
R215H |
probably benign |
Het |
| Spata20 |
A |
G |
11: 94,374,226 (GRCm39) |
V348A |
probably benign |
Het |
| Spink5 |
A |
G |
18: 44,123,739 (GRCm39) |
E342G |
probably damaging |
Het |
| St3gal1 |
A |
G |
15: 66,983,195 (GRCm39) |
V187A |
possibly damaging |
Het |
| Syce1l |
T |
A |
8: 114,376,143 (GRCm39) |
M31K |
probably benign |
Het |
| Ttn |
C |
T |
2: 76,618,960 (GRCm39) |
V14394I |
probably damaging |
Het |
| Twnk |
G |
A |
19: 44,997,820 (GRCm39) |
V450M |
probably damaging |
Het |
| Vangl1 |
T |
C |
3: 102,065,764 (GRCm39) |
K407R |
probably benign |
Het |
| Vmn1r19 |
T |
C |
6: 57,382,317 (GRCm39) |
I290T |
unknown |
Het |
|
| Other mutations in Rxrb |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00435:Rxrb
|
APN |
17 |
34,253,049 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL01337:Rxrb
|
APN |
17 |
34,255,605 (GRCm39) |
missense |
probably damaging |
1.00 |
|
concerned
|
UTSW |
17 |
34,255,645 (GRCm39) |
missense |
probably benign |
0.03 |
|
problematic
|
UTSW |
17 |
34,253,134 (GRCm39) |
missense |
probably damaging |
1.00 |
|
BB006:Rxrb
|
UTSW |
17 |
34,255,645 (GRCm39) |
missense |
probably benign |
0.03 |
|
BB016:Rxrb
|
UTSW |
17 |
34,255,645 (GRCm39) |
missense |
probably benign |
0.03 |
|
I2505:Rxrb
|
UTSW |
17 |
34,252,523 (GRCm39) |
splice site |
probably benign |
|
|
R0571:Rxrb
|
UTSW |
17 |
34,251,106 (GRCm39) |
unclassified |
probably benign |
|
|
R1463:Rxrb
|
UTSW |
17 |
34,253,134 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2312:Rxrb
|
UTSW |
17 |
34,251,103 (GRCm39) |
unclassified |
probably benign |
|
|
R2395:Rxrb
|
UTSW |
17 |
34,256,412 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2935:Rxrb
|
UTSW |
17 |
34,251,106 (GRCm39) |
unclassified |
probably benign |
|
|
R3978:Rxrb
|
UTSW |
17 |
34,255,300 (GRCm39) |
missense |
possibly damaging |
0.92 |
|
R5119:Rxrb
|
UTSW |
17 |
34,252,562 (GRCm39) |
missense |
probably benign |
0.10 |
|
R5523:Rxrb
|
UTSW |
17 |
34,255,411 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5638:Rxrb
|
UTSW |
17 |
34,256,381 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5769:Rxrb
|
UTSW |
17 |
34,251,821 (GRCm39) |
utr 5 prime |
probably benign |
|
|
R5894:Rxrb
|
UTSW |
17 |
34,254,718 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7798:Rxrb
|
UTSW |
17 |
34,252,579 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7929:Rxrb
|
UTSW |
17 |
34,255,645 (GRCm39) |
missense |
probably benign |
0.03 |
|
R8087:Rxrb
|
UTSW |
17 |
34,254,763 (GRCm39) |
missense |
probably benign |
0.00 |
|
R8233:Rxrb
|
UTSW |
17 |
34,255,879 (GRCm39) |
missense |
possibly damaging |
0.48 |
|
R8268:Rxrb
|
UTSW |
17 |
34,254,750 (GRCm39) |
missense |
probably benign |
0.01 |
|
R8886:Rxrb
|
UTSW |
17 |
34,256,428 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R9211:Rxrb
|
UTSW |
17 |
34,255,626 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9671:Rxrb
|
UTSW |
17 |
34,252,020 (GRCm39) |
critical splice donor site |
probably null |
|
|
Z1177:Rxrb
|
UTSW |
17 |
34,251,101 (GRCm39) |
missense |
unknown |
|
|
| Predicted Primers |
PCR Primer
(F):5'- ATGCCTGCCCTTCTAAGACC -3'
(R):5'- TCTTCTACGGCTGTGCTGAG -3'
Sequencing Primer
(F):5'- GGGCCACTGTAGCACAATTAC -3'
(R):5'- TGCTGAGCCCCATACCTGAG -3'
|
| Posted On |
2018-04-27 |
Incidental Mutation