Incidental Mutation 'IGL01155:Rara'
| ID |
52412 |
| Institutional Source |
Australian Phenomics Network
(link to record)
|
| Gene Symbol |
Rara
|
| Ensembl Gene |
ENSMUSG00000037992 |
| Gene Name |
retinoic acid receptor, alpha |
| Synonyms |
RAR alpha 1, RARalpha1 |
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
IGL01155
|
| Quality Score |
|
|
Status
|
|
| Chromosome |
11 |
| Chromosomal Location |
98927818-98974942 bp(+) (GRCm38) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 98968184 bp (GRCm38)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Glutamic Acid to Glycine
at position 153
(E153G)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000103097
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000068133]
[ENSMUST00000107473]
[ENSMUST00000107474]
[ENSMUST00000107475]
[ENSMUST00000164748]
|
| AlphaFold |
P11416 |
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000068133
AA Change: E156G
PolyPhen 2
Score 0.850 (Sensitivity: 0.83; Specificity: 0.93)
|
| SMART Domains |
Protein: ENSMUSP00000069744
Gene: ENSMUSG00000037992
AA Change: E156G
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
19 |
30 |
N/A |
INTRINSIC |
|
low complexity region
|
65 |
80 |
N/A |
INTRINSIC |
|
ZnF_C4
|
85 |
156 |
7.53e-40 |
SMART |
|
HOLI
|
230 |
388 |
1.22e-34 |
SMART |
|
low complexity region
|
425 |
436 |
N/A |
INTRINSIC |
|
low complexity region
|
439 |
462 |
N/A |
INTRINSIC |
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000107473
AA Change: E153G
PolyPhen 2
Score 0.915 (Sensitivity: 0.81; Specificity: 0.94)
|
| SMART Domains |
Protein: ENSMUSP00000103097
Gene: ENSMUSG00000037992
AA Change: E153G
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
54 |
77 |
N/A |
INTRINSIC |
|
ZnF_C4
|
82 |
153 |
7.53e-40 |
SMART |
|
HOLI
|
227 |
385 |
1.22e-34 |
SMART |
|
low complexity region
|
422 |
433 |
N/A |
INTRINSIC |
|
low complexity region
|
436 |
459 |
N/A |
INTRINSIC |
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000107474
AA Change: E156G
PolyPhen 2
Score 0.850 (Sensitivity: 0.83; Specificity: 0.93)
|
| SMART Domains |
Protein: ENSMUSP00000103098
Gene: ENSMUSG00000037992
AA Change: E156G
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
19 |
30 |
N/A |
INTRINSIC |
|
low complexity region
|
65 |
80 |
N/A |
INTRINSIC |
|
ZnF_C4
|
85 |
156 |
7.53e-40 |
SMART |
|
HOLI
|
230 |
388 |
1.22e-34 |
SMART |
|
low complexity region
|
425 |
436 |
N/A |
INTRINSIC |
|
low complexity region
|
439 |
462 |
N/A |
INTRINSIC |
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000107475
AA Change: E156G
PolyPhen 2
Score 0.850 (Sensitivity: 0.83; Specificity: 0.93)
|
| SMART Domains |
Protein: ENSMUSP00000103099
Gene: ENSMUSG00000037992
AA Change: E156G
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
19 |
30 |
N/A |
INTRINSIC |
|
low complexity region
|
65 |
80 |
N/A |
INTRINSIC |
|
ZnF_C4
|
85 |
156 |
7.53e-40 |
SMART |
|
HOLI
|
230 |
388 |
1.22e-34 |
SMART |
|
low complexity region
|
425 |
436 |
N/A |
INTRINSIC |
|
low complexity region
|
439 |
462 |
N/A |
INTRINSIC |
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000164748
AA Change: E156G
PolyPhen 2
Score 0.850 (Sensitivity: 0.83; Specificity: 0.93)
|
| SMART Domains |
Protein: ENSMUSP00000129791
Gene: ENSMUSG00000037992
AA Change: E156G
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
19 |
30 |
N/A |
INTRINSIC |
|
low complexity region
|
65 |
80 |
N/A |
INTRINSIC |
|
ZnF_C4
|
85 |
156 |
7.53e-40 |
SMART |
|
HOLI
|
230 |
388 |
1.22e-34 |
SMART |
|
low complexity region
|
425 |
436 |
N/A |
INTRINSIC |
|
low complexity region
|
439 |
462 |
N/A |
INTRINSIC |
|
| Coding Region Coverage |
|
| Validation Efficiency |
|
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene represents a nuclear retinoic acid receptor. The encoded protein, retinoic acid receptor alpha, regulates transcription in a ligand-dependent manner. This gene has been implicated in regulation of development, differentiation, apoptosis, granulopoeisis, and transcription of clock genes. Translocations between this locus and several other loci have been associated with acute promyelocytic leukemia. Alternatively spliced transcript variants have been found for this locus.[provided by RefSeq, Sep 2010]
PHENOTYPE: Homozygotes for targeted null mutations show high neonatal mortality due to maternal cannibalization, failure to thrive, and excess mortality during the postnatal period. Male survivors exhibit testicular degeneration. [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 |
|---|
| 1110038F14Rik |
G |
A |
15: 76,950,275 (GRCm38) |
V124I |
probably damaging |
Het |
| Adgrl3 |
T |
A |
5: 81,560,893 (GRCm38) |
I409N |
probably benign |
Het |
| Akap13 |
A |
G |
7: 75,569,936 (GRCm38) |
D29G |
probably damaging |
Het |
| Ap4e1 |
C |
A |
2: 127,043,445 (GRCm38) |
T322K |
probably damaging |
Het |
| Arfgef1 |
G |
A |
1: 10,198,982 (GRCm38) |
|
probably benign |
Het |
| Asic5 |
A |
G |
3: 82,008,588 (GRCm38) |
T282A |
probably benign |
Het |
| Bptf |
T |
C |
11: 107,080,727 (GRCm38) |
T985A |
probably damaging |
Het |
| Btnl9 |
A |
G |
11: 49,175,691 (GRCm38) |
F349L |
probably damaging |
Het |
| Bves |
T |
A |
10: 45,353,859 (GRCm38) |
I253K |
probably damaging |
Het |
| Cars |
T |
A |
7: 143,569,849 (GRCm38) |
Y455F |
probably benign |
Het |
| Cfap206 |
C |
T |
4: 34,721,562 (GRCm38) |
S162N |
probably damaging |
Het |
| Cuedc2 |
C |
A |
19: 46,332,649 (GRCm38) |
V15F |
probably damaging |
Het |
| Defa22 |
T |
A |
8: 21,163,037 (GRCm38) |
|
probably null |
Het |
| Fat1 |
G |
A |
8: 45,023,949 (GRCm38) |
A2011T |
probably damaging |
Het |
| Fyb2 |
C |
T |
4: 104,999,386 (GRCm38) |
T533I |
probably benign |
Het |
| Gm1043 |
T |
C |
5: 37,187,089 (GRCm38) |
L182P |
probably damaging |
Het |
| Ice1 |
A |
T |
13: 70,604,082 (GRCm38) |
V1295E |
possibly damaging |
Het |
| Il12b |
T |
A |
11: 44,404,088 (GRCm38) |
S18T |
probably benign |
Het |
| Iqcg |
A |
G |
16: 33,040,875 (GRCm38) |
V157A |
probably damaging |
Het |
| Itgax |
T |
A |
7: 128,145,035 (GRCm38) |
M937K |
probably benign |
Het |
| Large1 |
T |
C |
8: 73,131,989 (GRCm38) |
S84G |
probably benign |
Het |
| Lrp1b |
T |
C |
2: 41,770,935 (GRCm38) |
T54A |
probably benign |
Het |
| Mfn1 |
A |
G |
3: 32,542,836 (GRCm38) |
M148V |
probably damaging |
Het |
| Mobp |
C |
A |
9: 120,168,234 (GRCm38) |
T73K |
probably benign |
Het |
| Ms4a3 |
T |
C |
19: 11,629,655 (GRCm38) |
|
probably benign |
Het |
| Muc5ac |
C |
T |
7: 141,806,943 (GRCm38) |
|
probably benign |
Het |
| Mzt2 |
A |
C |
16: 15,862,410 (GRCm38) |
S104A |
possibly damaging |
Het |
| Naa16 |
T |
A |
14: 79,384,715 (GRCm38) |
K27N |
probably damaging |
Het |
| Nos1 |
T |
A |
5: 117,945,926 (GRCm38) |
I1267N |
probably damaging |
Het |
| Olfr16 |
T |
A |
1: 172,956,924 (GRCm38) |
I43N |
probably benign |
Het |
| Scn2a |
T |
G |
2: 65,717,748 (GRCm38) |
S66A |
probably damaging |
Het |
| Slc6a1 |
A |
T |
6: 114,314,465 (GRCm38) |
|
probably null |
Het |
| Sorbs3 |
A |
G |
14: 70,199,341 (GRCm38) |
V136A |
probably damaging |
Het |
| Spink5 |
T |
A |
18: 43,981,147 (GRCm38) |
H143Q |
probably benign |
Het |
| Susd2 |
G |
A |
10: 75,640,892 (GRCm38) |
T99I |
possibly damaging |
Het |
| T |
C |
T |
17: 8,441,745 (GRCm38) |
|
probably null |
Het |
| Tac2 |
G |
A |
10: 127,726,134 (GRCm38) |
|
probably null |
Het |
| Tfap4 |
G |
T |
16: 4,547,359 (GRCm38) |
P180T |
probably damaging |
Het |
| Trap1 |
G |
A |
16: 4,043,978 (GRCm38) |
Q641* |
probably null |
Het |
| Unc119 |
A |
G |
11: 78,348,609 (GRCm38) |
N252S |
probably damaging |
Het |
|
| Other mutations in Rara |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00951:Rara
|
APN |
11 |
98,968,166 (GRCm38) |
missense |
probably benign |
0.00 |
|
IGL02141:Rara
|
APN |
11 |
98,968,081 (GRCm38) |
missense |
probably damaging |
1.00 |
|
IGL03194:Rara
|
APN |
11 |
98,971,664 (GRCm38) |
missense |
possibly damaging |
0.96 |
|
annie
|
UTSW |
11 |
98,973,626 (GRCm38) |
missense |
unknown |
|
|
kane
|
UTSW |
11 |
98,971,769 (GRCm38) |
missense |
probably damaging |
1.00 |
|
Orphan
|
UTSW |
11 |
98,970,163 (GRCm38) |
missense |
probably damaging |
1.00 |
|
warbucks
|
UTSW |
11 |
98,970,569 (GRCm38) |
missense |
probably damaging |
1.00 |
|
PIT4486001:Rara
|
UTSW |
11 |
98,973,495 (GRCm38) |
missense |
possibly damaging |
0.88 |
|
R0626:Rara
|
UTSW |
11 |
98,971,580 (GRCm38) |
critical splice acceptor site |
probably null |
|
|
R1973:Rara
|
UTSW |
11 |
98,971,670 (GRCm38) |
missense |
possibly damaging |
0.91 |
|
R3975:Rara
|
UTSW |
11 |
98,970,569 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R4357:Rara
|
UTSW |
11 |
98,968,111 (GRCm38) |
missense |
probably damaging |
0.98 |
|
R5102:Rara
|
UTSW |
11 |
98,966,359 (GRCm38) |
missense |
possibly damaging |
0.80 |
|
R5147:Rara
|
UTSW |
11 |
98,950,724 (GRCm38) |
missense |
probably benign |
0.35 |
|
R5381:Rara
|
UTSW |
11 |
98,971,584 (GRCm38) |
missense |
possibly damaging |
0.93 |
|
R5570:Rara
|
UTSW |
11 |
98,972,652 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R5861:Rara
|
UTSW |
11 |
98,968,161 (GRCm38) |
nonsense |
probably null |
|
|
R6273:Rara
|
UTSW |
11 |
98,970,222 (GRCm38) |
missense |
probably benign |
0.00 |
|
R6404:Rara
|
UTSW |
11 |
98,961,013 (GRCm38) |
missense |
probably benign |
0.16 |
|
R8906:Rara
|
UTSW |
11 |
98,970,163 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R8921:Rara
|
UTSW |
11 |
98,973,626 (GRCm38) |
missense |
unknown |
|
|
R8978:Rara
|
UTSW |
11 |
98,971,769 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R9224:Rara
|
UTSW |
11 |
98,966,410 (GRCm38) |
frame shift |
probably null |
|
|
R9476:Rara
|
UTSW |
11 |
98,970,157 (GRCm38) |
missense |
probably benign |
0.02 |
|
R9510:Rara
|
UTSW |
11 |
98,970,157 (GRCm38) |
missense |
probably benign |
0.02 |
|
| Posted On |
2013-06-21 |
Incidental Mutation