Incidental Mutation 'R0055:Rarb'
| ID |
58986 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Rarb
|
| Ensembl Gene |
ENSMUSG00000017491 |
| Gene Name |
retinoic acid receptor, beta |
| Synonyms |
RARbeta2, RAR beta 2, Hap |
| MMRRC Submission |
038349-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R0055 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
14 |
| Chromosomal Location |
5650540-6038924 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
G to A
at 16509066 bp (GRCm38)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Arginine to Cysteine
at position 106
(R106C)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000153178
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000063750]
[ENSMUST00000223576]
[ENSMUST00000223976]
[ENSMUST00000225594]
[ENSMUST00000225921]
|
| AlphaFold |
no structure available at present |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000063750
AA Change: R106C
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000067694
Gene: ENSMUSG00000017491
AA Change: R106C
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
52 |
75 |
N/A |
INTRINSIC |
|
ZnF_C4
|
78 |
149 |
3.77e-40 |
SMART |
|
HOLI
|
223 |
381 |
1.72e-34 |
SMART |
|
low complexity region
|
428 |
445 |
N/A |
INTRINSIC |
|
| Predicted Effect |
silent
Transcript: ENSMUST00000223576
|
| Predicted Effect |
silent
Transcript: ENSMUST00000223976
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000225594
AA Change: R106C
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000225921
AA Change: R106C
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| Meta Mutation Damage Score |
0.7764 |
| Coding Region Coverage |
- 1x: 99.4%
- 3x: 98.9%
- 10x: 97.6%
- 20x: 95.6%
|
| Validation Efficiency |
98% (59/60) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes retinoic acid receptor beta, a member of the thyroid-steroid hormone receptor superfamily of nuclear transcriptional regulators. This receptor localizes to the cytoplasm and to subnuclear compartments. It binds retinoic acid, the biologically active form of vitamin A which mediates cellular signalling in embryonic morphogenesis, cell growth and differentiation. It is thought that this protein limits growth of many cell types by regulating gene expression. The gene was first identified in a hepatocellular carcinoma where it flanks a hepatitis B virus integration site. Alternate promoter usage and differential splicing result in multiple transcript variants. [provided by RefSeq, Mar 2014]
PHENOTYPE: Homozygotes for a targeted null mutation exhibit reduced growth, but are otherwise normal. Rarb/Rara double knockouts exhibit impaired vitamin A signaling and develop urogenital malformations, including renal hypoplasia and hydronephrosis. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 57 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| A2ml1 |
T |
C |
6: 128,547,057 (GRCm39) |
|
probably benign |
Het |
| Atp6v1h |
A |
T |
1: 5,154,677 (GRCm39) |
T2S |
probably benign |
Het |
| Bcl11b |
G |
A |
12: 107,932,036 (GRCm39) |
P179S |
probably benign |
Het |
| Cacna1a |
C |
T |
8: 85,306,687 (GRCm39) |
|
probably benign |
Het |
| Ccdc146 |
C |
T |
5: 21,502,004 (GRCm39) |
|
probably null |
Het |
| Ccdc61 |
T |
C |
7: 18,626,461 (GRCm39) |
D128G |
probably damaging |
Het |
| Cd55 |
A |
G |
1: 130,387,313 (GRCm39) |
|
probably benign |
Het |
| Cdk7 |
C |
A |
13: 100,855,812 (GRCm39) |
E99* |
probably null |
Het |
| Cfap96 |
A |
T |
8: 46,421,198 (GRCm39) |
S108R |
probably damaging |
Het |
| Cox8a |
A |
T |
19: 7,194,874 (GRCm39) |
S2T |
probably damaging |
Het |
| Cracdl |
A |
C |
1: 37,663,337 (GRCm39) |
S854A |
probably benign |
Het |
| Dennd5a |
A |
G |
7: 109,498,998 (GRCm39) |
I955T |
possibly damaging |
Het |
| Dop1a |
A |
C |
9: 86,394,705 (GRCm39) |
E602A |
probably benign |
Het |
| Ephx4 |
T |
C |
5: 107,560,944 (GRCm39) |
L32S |
probably damaging |
Het |
| Fbxo21 |
T |
A |
5: 118,138,555 (GRCm39) |
D493E |
probably benign |
Het |
| Frmd4b |
A |
T |
6: 97,300,610 (GRCm39) |
|
probably benign |
Het |
| Fzd1 |
A |
T |
5: 4,806,037 (GRCm39) |
M515K |
possibly damaging |
Het |
| Gli2 |
A |
G |
1: 118,818,138 (GRCm39) |
|
probably benign |
Het |
| Gm12887 |
T |
A |
4: 121,473,666 (GRCm39) |
K61N |
probably damaging |
Het |
| Grin2a |
A |
T |
16: 9,487,671 (GRCm39) |
V409D |
probably damaging |
Het |
| Grin2b |
T |
C |
6: 135,900,201 (GRCm39) |
I227V |
probably benign |
Het |
| Helz2 |
T |
G |
2: 180,870,614 (GRCm39) |
D2879A |
possibly damaging |
Het |
| Itpr2 |
T |
C |
6: 146,224,631 (GRCm39) |
N1453S |
probably benign |
Het |
| Itpr3 |
C |
A |
17: 27,317,296 (GRCm39) |
S817Y |
probably damaging |
Het |
| Lin7c |
T |
A |
2: 109,726,798 (GRCm39) |
|
probably benign |
Het |
| Ly75 |
T |
C |
2: 60,152,262 (GRCm39) |
E1097G |
probably benign |
Het |
| Mcm10 |
T |
C |
2: 4,996,218 (GRCm39) |
N882D |
probably damaging |
Het |
| Mettl13 |
A |
T |
1: 162,373,750 (GRCm39) |
L167Q |
probably damaging |
Het |
| Morn2 |
A |
T |
17: 80,602,942 (GRCm39) |
M1L |
probably benign |
Het |
| Mybph |
G |
T |
1: 134,121,590 (GRCm39) |
V88L |
probably damaging |
Het |
| Nefm |
T |
A |
14: 68,358,648 (GRCm39) |
|
probably benign |
Het |
| Nf1 |
A |
G |
11: 79,362,377 (GRCm39) |
E1497G |
probably damaging |
Het |
| Or2j3 |
T |
C |
17: 38,615,702 (GRCm39) |
S217G |
possibly damaging |
Het |
| Or4k37 |
T |
A |
2: 111,158,870 (GRCm39) |
Y35* |
probably null |
Het |
| Or51ah3 |
A |
G |
7: 103,210,244 (GRCm39) |
K187E |
probably damaging |
Het |
| Or52e18 |
T |
A |
7: 104,609,703 (GRCm39) |
T79S |
possibly damaging |
Het |
| Phf8-ps |
A |
T |
17: 33,285,696 (GRCm39) |
W369R |
probably damaging |
Het |
| Plcd3 |
C |
G |
11: 102,968,411 (GRCm39) |
W382S |
probably damaging |
Het |
| Plxna1 |
T |
A |
6: 89,306,721 (GRCm39) |
I1370F |
possibly damaging |
Het |
| Qng1 |
T |
C |
13: 58,531,980 (GRCm39) |
D192G |
probably damaging |
Het |
| Rps6ka5 |
G |
A |
12: 100,644,839 (GRCm39) |
T37I |
probably damaging |
Het |
| Runx1 |
G |
T |
16: 92,441,029 (GRCm39) |
|
probably benign |
Het |
| Scube1 |
A |
G |
15: 83,518,937 (GRCm39) |
V301A |
probably damaging |
Het |
| Sema3a |
A |
T |
5: 13,450,004 (GRCm39) |
N27I |
possibly damaging |
Het |
| Slc15a3 |
G |
T |
19: 10,820,406 (GRCm39) |
E8* |
probably null |
Het |
| Slc22a5 |
T |
C |
11: 53,782,032 (GRCm39) |
S112G |
probably benign |
Het |
| Slc25a45 |
T |
C |
19: 5,930,495 (GRCm39) |
F3L |
probably damaging |
Het |
| Slc4a4 |
A |
C |
5: 89,304,195 (GRCm39) |
H502P |
possibly damaging |
Het |
| Slfn10-ps |
A |
G |
11: 82,921,126 (GRCm39) |
|
noncoding transcript |
Het |
| Slit2 |
C |
A |
5: 48,439,068 (GRCm39) |
C1077* |
probably null |
Het |
| Spn |
A |
G |
7: 126,735,494 (GRCm39) |
F82L |
possibly damaging |
Het |
| Tbccd1 |
A |
G |
16: 22,660,655 (GRCm39) |
W54R |
probably damaging |
Het |
| Ucp1 |
G |
T |
8: 84,017,233 (GRCm39) |
E8* |
probably null |
Het |
| Unc80 |
A |
T |
1: 66,545,782 (GRCm39) |
|
probably benign |
Het |
| Vsnl1 |
A |
T |
12: 11,436,987 (GRCm39) |
|
probably null |
Het |
| Zdhhc11 |
C |
T |
13: 74,130,805 (GRCm39) |
Q295* |
probably null |
Het |
| Zfp457 |
T |
A |
13: 67,442,098 (GRCm39) |
H63L |
probably damaging |
Het |
|
| Other mutations in Rarb |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00756:Rarb
|
APN |
14 |
16,443,791 (GRCm38) |
nonsense |
probably null |
|
|
IGL01483:Rarb
|
APN |
14 |
16,432,273 (GRCm38) |
splice site |
probably benign |
|
|
IGL01591:Rarb
|
APN |
14 |
16,434,207 (GRCm38) |
missense |
possibly damaging |
0.93 |
|
IGL01769:Rarb
|
APN |
14 |
16,443,760 (GRCm38) |
missense |
probably damaging |
0.97 |
|
IGL01782:Rarb
|
APN |
14 |
16,434,180 (GRCm38) |
missense |
probably damaging |
1.00 |
|
IGL01866:Rarb
|
APN |
14 |
16,443,751 (GRCm38) |
missense |
probably benign |
0.17 |
|
IGL03299:Rarb
|
APN |
14 |
16,434,168 (GRCm38) |
missense |
probably damaging |
1.00 |
|
IGL03134:Rarb
|
UTSW |
14 |
16,436,910 (GRCm38) |
missense |
probably damaging |
0.99 |
|
R0055:Rarb
|
UTSW |
14 |
16,509,066 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R0849:Rarb
|
UTSW |
14 |
16,434,293 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R1067:Rarb
|
UTSW |
14 |
16,436,769 (GRCm38) |
missense |
probably damaging |
0.98 |
|
R1314:Rarb
|
UTSW |
14 |
16,508,932 (GRCm38) |
critical splice donor site |
probably null |
|
|
R1416:Rarb
|
UTSW |
14 |
16,435,177 (GRCm38) |
missense |
possibly damaging |
0.82 |
|
R2894:Rarb
|
UTSW |
14 |
16,435,146 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R4637:Rarb
|
UTSW |
14 |
16,574,875 (GRCm38) |
missense |
possibly damaging |
0.51 |
|
R4950:Rarb
|
UTSW |
14 |
16,432,085 (GRCm38) |
unclassified |
probably benign |
|
|
R5420:Rarb
|
UTSW |
14 |
16,434,249 (GRCm38) |
missense |
possibly damaging |
0.89 |
|
R5456:Rarb
|
UTSW |
14 |
16,436,843 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R5635:Rarb
|
UTSW |
14 |
16,443,788 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R5689:Rarb
|
UTSW |
14 |
16,434,177 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R5708:Rarb
|
UTSW |
14 |
16,548,545 (GRCm38) |
missense |
probably damaging |
0.99 |
|
R5819:Rarb
|
UTSW |
14 |
16,443,820 (GRCm38) |
missense |
possibly damaging |
0.68 |
|
R5935:Rarb
|
UTSW |
14 |
16,434,264 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R6264:Rarb
|
UTSW |
14 |
16,818,819 (GRCm38) |
missense |
probably benign |
0.31 |
|
R6823:Rarb
|
UTSW |
14 |
16,443,824 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R6975:Rarb
|
UTSW |
14 |
16,574,942 (GRCm38) |
missense |
possibly damaging |
0.92 |
|
R7295:Rarb
|
UTSW |
14 |
16,508,932 (GRCm38) |
critical splice donor site |
probably null |
|
|
R7402:Rarb
|
UTSW |
14 |
16,548,419 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R7849:Rarb
|
UTSW |
14 |
16,548,473 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R8471:Rarb
|
UTSW |
14 |
16,548,456 (GRCm38) |
unclassified |
probably benign |
|
|
R8833:Rarb
|
UTSW |
14 |
16,819,015 (GRCm38) |
unclassified |
probably benign |
|
|
R8835:Rarb
|
UTSW |
14 |
16,575,011 (GRCm38) |
missense |
probably benign |
0.23 |
|
R8896:Rarb
|
UTSW |
14 |
16,436,804 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R9011:Rarb
|
UTSW |
14 |
16,435,140 (GRCm38) |
missense |
probably damaging |
0.98 |
|
R9090:Rarb
|
UTSW |
14 |
16,435,235 (GRCm38) |
nonsense |
probably null |
|
|
R9184:Rarb
|
UTSW |
14 |
16,818,882 (GRCm38) |
start gained |
probably benign |
|
|
R9184:Rarb
|
UTSW |
14 |
16,818,881 (GRCm38) |
start gained |
probably benign |
|
|
R9271:Rarb
|
UTSW |
14 |
16,435,235 (GRCm38) |
nonsense |
probably null |
|
|
R9574:Rarb
|
UTSW |
14 |
16,574,858 (GRCm38) |
missense |
probably damaging |
0.96 |
|
X0065:Rarb
|
UTSW |
14 |
16,434,303 (GRCm38) |
missense |
possibly damaging |
0.89 |
|
Z1177:Rarb
|
UTSW |
14 |
16,818,725 (GRCm38) |
missense |
possibly damaging |
0.50 |
|
| Predicted Primers |
PCR Primer
(F):5'- AGCTAGGGAGCCCCACTAAGTAAAG -3'
(R):5'- GCATGGATTCCAGCTCTGTCTGATG -3'
Sequencing Primer
(F):5'- ATGGTAGCGTGCCATTCC -3'
(R):5'- gtgagaagagagtgtcccag -3'
|
| Posted On |
2013-07-11 |
Incidental Mutation