Incidental Mutation 'R6404:Rara'
| ID |
518904 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Rara
|
| Ensembl Gene |
ENSMUSG00000037992 |
| Gene Name |
retinoic acid receptor, alpha |
| Synonyms |
RARalpha1, RAR alpha 1 |
| MMRRC Submission |
044549-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R6404 (G1)
|
| Quality Score |
181.009 |
|
Status
|
Validated
|
| Chromosome |
11 |
| Chromosomal Location |
98818644-98865768 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 98851839 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Phenylalanine to Leucine
at position 17
(F17L)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000103097
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000068133]
[ENSMUST00000107473]
[ENSMUST00000107474]
[ENSMUST00000107475]
[ENSMUST00000164748]
|
| AlphaFold |
P11416 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000068133
|
| SMART Domains |
Protein: ENSMUSP00000069744
Gene: ENSMUSG00000037992
| 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 benign
Transcript: ENSMUST00000107473
AA Change: F17L
PolyPhen 2
Score 0.156 (Sensitivity: 0.92; Specificity: 0.87)
|
| SMART Domains |
Protein: ENSMUSP00000103097
Gene: ENSMUSG00000037992
AA Change: F17L
| 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 |
probably benign
Transcript: ENSMUST00000107474
|
| SMART Domains |
Protein: ENSMUSP00000103098
Gene: ENSMUSG00000037992
| 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 benign
Transcript: ENSMUST00000107475
|
| SMART Domains |
Protein: ENSMUSP00000103099
Gene: ENSMUSG00000037992
| 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 benign
Transcript: ENSMUST00000164748
|
| SMART Domains |
Protein: ENSMUSP00000129791
Gene: ENSMUSG00000037992
| 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 |
|
| Meta Mutation Damage Score |
0.0684 |
| Coding Region Coverage |
- 1x: 99.9%
- 3x: 99.6%
- 10x: 97.8%
- 20x: 93.4%
|
| Validation Efficiency |
98% (40/41) |
| 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: 41 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abca17 |
T |
C |
17: 24,484,892 (GRCm39) |
D1540G |
probably benign |
Het |
| Adamts7 |
A |
T |
9: 90,062,509 (GRCm39) |
|
probably null |
Het |
| Apol10a |
C |
A |
15: 77,373,241 (GRCm39) |
F292L |
probably benign |
Het |
| Atp13a4 |
A |
T |
16: 29,290,719 (GRCm39) |
Y243* |
probably null |
Het |
| Cc2d2a |
A |
G |
5: 43,861,416 (GRCm39) |
N660D |
possibly damaging |
Het |
| Ccdc57 |
T |
C |
11: 120,785,538 (GRCm39) |
T466A |
probably benign |
Het |
| Ccdc74a |
A |
T |
16: 17,467,889 (GRCm39) |
N249Y |
possibly damaging |
Het |
| Cd3e |
T |
A |
9: 44,912,426 (GRCm39) |
E106V |
probably damaging |
Het |
| Col4a1 |
G |
T |
8: 11,257,409 (GRCm39) |
|
probably null |
Het |
| Csmd2 |
T |
C |
4: 128,415,743 (GRCm39) |
Y2691H |
possibly damaging |
Het |
| Dmxl2 |
T |
C |
9: 54,282,820 (GRCm39) |
R2786G |
probably damaging |
Het |
| Dpyd |
A |
G |
3: 119,059,606 (GRCm39) |
T768A |
probably benign |
Het |
| Endou |
T |
A |
15: 97,610,012 (GRCm39) |
Q428L |
probably damaging |
Het |
| Fam13c |
T |
C |
10: 70,284,646 (GRCm39) |
|
probably null |
Het |
| Fhip1b |
G |
A |
7: 105,034,198 (GRCm39) |
R478* |
probably null |
Het |
| Frmd5 |
G |
A |
2: 121,379,699 (GRCm39) |
R70* |
probably null |
Het |
| Fsip2 |
A |
G |
2: 82,820,430 (GRCm39) |
T5388A |
possibly damaging |
Het |
| Gm4131 |
T |
A |
14: 62,718,598 (GRCm39) |
R3* |
probably null |
Het |
| Habp4 |
A |
G |
13: 64,330,000 (GRCm39) |
T302A |
possibly damaging |
Het |
| Ift81 |
A |
T |
5: 122,749,069 (GRCm39) |
D27E |
probably damaging |
Het |
| Iqcf3 |
T |
C |
9: 106,430,083 (GRCm39) |
I107V |
probably benign |
Het |
| Iqgap2 |
A |
G |
13: 95,865,985 (GRCm39) |
I298T |
probably benign |
Het |
| Lilrb4b |
A |
G |
10: 51,361,825 (GRCm39) |
D199G |
probably damaging |
Het |
| Lsm8 |
C |
T |
6: 18,848,739 (GRCm39) |
S3F |
possibly damaging |
Het |
| Meox1 |
T |
C |
11: 101,769,482 (GRCm39) |
E238G |
probably benign |
Het |
| Naip1 |
A |
T |
13: 100,559,727 (GRCm39) |
D1092E |
probably benign |
Het |
| Neb |
T |
C |
2: 52,097,737 (GRCm39) |
Y901C |
probably damaging |
Het |
| Nfat5 |
A |
G |
8: 108,097,220 (GRCm39) |
M121V |
probably benign |
Het |
| Notch2 |
G |
A |
3: 97,989,314 (GRCm39) |
G278D |
probably damaging |
Het |
| Or4c121 |
T |
C |
2: 89,023,906 (GRCm39) |
I157M |
probably damaging |
Het |
| Pbld2 |
T |
A |
10: 62,890,107 (GRCm39) |
S172T |
probably damaging |
Het |
| Pla2g7 |
T |
A |
17: 43,905,688 (GRCm39) |
Y83N |
probably damaging |
Het |
| Plxnb1 |
A |
T |
9: 108,945,705 (GRCm39) |
I2079F |
probably damaging |
Het |
| Skint5 |
G |
A |
4: 113,799,806 (GRCm39) |
T121I |
probably damaging |
Het |
| Slco6c1 |
T |
C |
1: 97,046,330 (GRCm39) |
Y251C |
probably damaging |
Het |
| Slmap |
T |
A |
14: 26,143,566 (GRCm39) |
|
probably null |
Het |
| Uba2 |
A |
T |
7: 33,853,985 (GRCm39) |
L319Q |
probably damaging |
Het |
| Vmn2r96 |
A |
T |
17: 18,817,793 (GRCm39) |
I457F |
probably damaging |
Het |
| Zfp57 |
A |
T |
17: 37,320,716 (GRCm39) |
H190L |
probably damaging |
Het |
| Zfp738 |
A |
G |
13: 67,819,179 (GRCm39) |
S271P |
possibly damaging |
Het |
| Zp2 |
A |
T |
7: 119,734,765 (GRCm39) |
H474Q |
possibly damaging |
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 |
|
R4357:Rara
|
UTSW |
11 |
98,858,937 (GRCm39) |
missense |
probably damaging |
0.98 |
|
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 |
|
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'- GAGTGACCTGCAGACTTAGG -3'
(R):5'- TCCGAGTTACAGCGAGACAG -3'
Sequencing Primer
(F):5'- ACTTAGGCGCGGGCAATTC -3'
(R):5'- GTAGAGAGGGCCAGCGC -3'
|
| Posted On |
2018-05-24 |
Incidental Mutation