Incidental Mutation 'R4357:Rara'
| ID |
324622 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Rara
|
| Ensembl Gene |
ENSMUSG00000037992 |
| Gene Name |
retinoic acid receptor, alpha |
| Synonyms |
RARalpha1, RAR alpha 1 |
| MMRRC Submission |
041109-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R4357 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
11 |
| Chromosomal Location |
98818644-98865768 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to C
at 98858937 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Isoleucine to Leucine
at position 129
(I129L)
|
| 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: I132L
PolyPhen 2
Score 0.487 (Sensitivity: 0.88; Specificity: 0.90)
|
| SMART Domains |
Protein: ENSMUSP00000069744
Gene: ENSMUSG00000037992
AA Change: I132L
| 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 |
probably damaging
Transcript: ENSMUST00000107473
AA Change: I129L
PolyPhen 2
Score 0.980 (Sensitivity: 0.75; Specificity: 0.96)
|
| SMART Domains |
Protein: ENSMUSP00000103097
Gene: ENSMUSG00000037992
AA Change: I129L
| 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: I132L
PolyPhen 2
Score 0.487 (Sensitivity: 0.88; Specificity: 0.90)
|
| SMART Domains |
Protein: ENSMUSP00000103098
Gene: ENSMUSG00000037992
AA Change: I132L
| 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: I132L
PolyPhen 2
Score 0.487 (Sensitivity: 0.88; Specificity: 0.90)
|
| SMART Domains |
Protein: ENSMUSP00000103099
Gene: ENSMUSG00000037992
AA Change: I132L
| 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: I132L
PolyPhen 2
Score 0.487 (Sensitivity: 0.88; Specificity: 0.90)
|
| SMART Domains |
Protein: ENSMUSP00000129791
Gene: ENSMUSG00000037992
AA Change: I132L
| 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 |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.1%
- 20x: 95.0%
|
| 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: 54 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Adam20 |
A |
G |
8: 41,248,084 (GRCm39) |
T65A |
possibly damaging |
Het |
| Alpk1 |
C |
T |
3: 127,523,022 (GRCm39) |
V7M |
probably damaging |
Het |
| Ap4m1 |
A |
G |
5: 138,171,311 (GRCm39) |
E125G |
probably damaging |
Het |
| Atp13a2 |
C |
A |
4: 140,729,215 (GRCm39) |
D599E |
probably benign |
Het |
| Brme1 |
T |
C |
8: 84,886,221 (GRCm39) |
L59P |
probably benign |
Het |
| Camkv |
G |
A |
9: 107,825,145 (GRCm39) |
G354E |
probably benign |
Het |
| Casp8ap2 |
T |
A |
4: 32,646,150 (GRCm39) |
M1741K |
probably benign |
Het |
| Chtf18 |
T |
C |
17: 25,938,106 (GRCm39) |
D119G |
probably benign |
Het |
| Cnga1 |
T |
A |
5: 72,775,595 (GRCm39) |
D42V |
probably damaging |
Het |
| Cysltr2 |
T |
C |
14: 73,267,084 (GRCm39) |
I209V |
probably benign |
Het |
| Defa27 |
A |
T |
8: 21,805,608 (GRCm39) |
Q16L |
probably null |
Het |
| Dnaja3 |
T |
C |
16: 4,517,731 (GRCm39) |
I321T |
probably damaging |
Het |
| Eef2 |
GCCC |
GCCCC |
10: 81,014,601 (GRCm39) |
|
probably null |
Het |
| Eif2ak3 |
T |
A |
6: 70,861,859 (GRCm39) |
I467N |
probably damaging |
Het |
| Eif5b |
T |
A |
1: 38,089,339 (GRCm39) |
V1105E |
probably damaging |
Het |
| Gfod2 |
T |
C |
8: 106,444,177 (GRCm39) |
N122S |
possibly damaging |
Het |
| Gm10803 |
A |
G |
2: 93,394,350 (GRCm39) |
R41G |
unknown |
Het |
| Gm38392 |
A |
T |
3: 88,154,741 (GRCm39) |
I221N |
probably damaging |
Het |
| Grm7 |
G |
T |
6: 110,623,309 (GRCm39) |
V161F |
probably damaging |
Het |
| Hsd17b6 |
G |
T |
10: 127,829,637 (GRCm39) |
|
probably null |
Het |
| Ids |
C |
A |
X: 69,389,950 (GRCm39) |
G506C |
probably damaging |
Het |
| Ifna15 |
G |
T |
4: 88,476,079 (GRCm39) |
T135N |
probably benign |
Het |
| Igsf9b |
G |
A |
9: 27,220,774 (GRCm39) |
V47I |
possibly damaging |
Het |
| Kif24 |
A |
G |
4: 41,413,827 (GRCm39) |
|
probably null |
Het |
| Lats2 |
A |
G |
14: 57,936,840 (GRCm39) |
S550P |
probably damaging |
Het |
| Lmo7 |
A |
G |
14: 102,125,091 (GRCm39) |
R406G |
probably null |
Het |
| Lpcat2 |
C |
A |
8: 93,599,734 (GRCm39) |
P234Q |
probably benign |
Het |
| Lrp10 |
C |
T |
14: 54,705,823 (GRCm39) |
R338C |
probably damaging |
Het |
| Lrrfip2 |
A |
G |
9: 111,028,755 (GRCm39) |
E326G |
probably damaging |
Het |
| Megf8 |
T |
A |
7: 25,055,174 (GRCm39) |
I1969N |
probably benign |
Het |
| Mib1 |
A |
G |
18: 10,751,844 (GRCm39) |
N242S |
probably benign |
Het |
| Ngf |
A |
G |
3: 102,427,521 (GRCm39) |
E94G |
probably benign |
Het |
| Oas2 |
C |
T |
5: 120,876,734 (GRCm39) |
|
probably null |
Het |
| Odf2 |
A |
G |
2: 29,782,256 (GRCm39) |
T75A |
probably benign |
Het |
| Or4f60 |
A |
G |
2: 111,902,583 (GRCm39) |
L115P |
probably damaging |
Het |
| Or5w11 |
T |
A |
2: 87,458,810 (GRCm39) |
M1K |
probably null |
Het |
| Pi4ka |
T |
A |
16: 17,185,303 (GRCm39) |
I266F |
probably benign |
Het |
| Prps2 |
T |
A |
X: 166,146,545 (GRCm39) |
K176* |
probably null |
Het |
| Psmd2 |
T |
G |
16: 20,475,402 (GRCm39) |
D393E |
probably benign |
Het |
| Rabep2 |
A |
G |
7: 126,047,397 (GRCm39) |
I753T |
probably damaging |
Het |
| Rasgrf2 |
C |
A |
13: 92,038,796 (GRCm39) |
D1017Y |
probably damaging |
Het |
| Slc15a4 |
A |
G |
5: 127,681,600 (GRCm39) |
|
probably null |
Het |
| Spmip4 |
T |
C |
6: 50,551,190 (GRCm39) |
T420A |
probably benign |
Het |
| Spsb1 |
T |
C |
4: 149,991,232 (GRCm39) |
H112R |
probably damaging |
Het |
| Sptlc1 |
A |
T |
13: 53,528,068 (GRCm39) |
I32K |
probably damaging |
Het |
| Srd5a3 |
T |
A |
5: 76,295,547 (GRCm39) |
F79Y |
probably damaging |
Het |
| Ssrp1 |
A |
T |
2: 84,871,495 (GRCm39) |
M306L |
probably benign |
Het |
| Sulf2 |
T |
C |
2: 165,919,497 (GRCm39) |
E817G |
probably benign |
Het |
| Tiam2 |
C |
A |
17: 3,501,128 (GRCm39) |
D922E |
probably damaging |
Het |
| Tle4 |
A |
G |
19: 14,445,625 (GRCm39) |
V207A |
probably benign |
Het |
| Ttll12 |
A |
T |
15: 83,465,958 (GRCm39) |
C413S |
probably damaging |
Het |
| Usp45 |
T |
A |
4: 21,834,350 (GRCm39) |
Y809* |
probably null |
Het |
| Vmn2r59 |
G |
A |
7: 41,661,644 (GRCm39) |
P724S |
probably damaging |
Het |
| Vrk3 |
C |
T |
7: 44,424,866 (GRCm39) |
T427M |
probably benign |
Het |
|
| Other mutations in Rara |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00951:Rara
|
APN |
11 |
98,858,992 (GRCm39) |
missense |
probably benign |
0.00 |
|
IGL01155:Rara
|
APN |
11 |
98,859,010 (GRCm39) |
missense |
possibly damaging |
0.92 |
|
IGL02141:Rara
|
APN |
11 |
98,858,907 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL03194:Rara
|
APN |
11 |
98,862,490 (GRCm39) |
missense |
possibly damaging |
0.96 |
|
annie
|
UTSW |
11 |
98,864,452 (GRCm39) |
missense |
unknown |
|
|
kane
|
UTSW |
11 |
98,862,595 (GRCm39) |
missense |
probably damaging |
1.00 |
|
Orphan
|
UTSW |
11 |
98,860,989 (GRCm39) |
missense |
probably damaging |
1.00 |
|
warbucks
|
UTSW |
11 |
98,861,395 (GRCm39) |
missense |
probably damaging |
1.00 |
|
PIT4486001:Rara
|
UTSW |
11 |
98,864,321 (GRCm39) |
missense |
possibly damaging |
0.88 |
|
R0626:Rara
|
UTSW |
11 |
98,862,406 (GRCm39) |
critical splice acceptor site |
probably null |
|
|
R1973:Rara
|
UTSW |
11 |
98,862,496 (GRCm39) |
missense |
possibly damaging |
0.91 |
|
R3975:Rara
|
UTSW |
11 |
98,861,395 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5102:Rara
|
UTSW |
11 |
98,857,185 (GRCm39) |
missense |
possibly damaging |
0.80 |
|
R5147:Rara
|
UTSW |
11 |
98,841,550 (GRCm39) |
missense |
probably benign |
0.35 |
|
R5381:Rara
|
UTSW |
11 |
98,862,410 (GRCm39) |
missense |
possibly damaging |
0.93 |
|
R5570:Rara
|
UTSW |
11 |
98,863,478 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5861:Rara
|
UTSW |
11 |
98,858,987 (GRCm39) |
nonsense |
probably null |
|
|
R6273:Rara
|
UTSW |
11 |
98,861,048 (GRCm39) |
missense |
probably benign |
0.00 |
|
R6404:Rara
|
UTSW |
11 |
98,851,839 (GRCm39) |
missense |
probably benign |
0.16 |
|
R8906:Rara
|
UTSW |
11 |
98,860,989 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8921:Rara
|
UTSW |
11 |
98,864,452 (GRCm39) |
missense |
unknown |
|
|
R8978:Rara
|
UTSW |
11 |
98,862,595 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9224:Rara
|
UTSW |
11 |
98,857,236 (GRCm39) |
frame shift |
probably null |
|
|
R9476:Rara
|
UTSW |
11 |
98,860,983 (GRCm39) |
missense |
probably benign |
0.02 |
|
R9510:Rara
|
UTSW |
11 |
98,860,983 (GRCm39) |
missense |
probably benign |
0.02 |
|
| Predicted Primers |
PCR Primer
(F):5'- TTTCAAAAGAGTCATCCTCCCC -3'
(R):5'- CTTAACTAGAAGCTTGCCCGC -3'
Sequencing Primer
(F):5'- AAAAGAGTCATCCTCCCCCATTTTTC -3'
(R):5'- TGTTCCCACATGTATACACAGG -3'
|
| Posted On |
2015-06-24 |
Incidental Mutation