Incidental Mutation 'R3900:Rd3'
| ID |
308916 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Rd3
|
| Ensembl Gene |
ENSMUSG00000049353 |
| Gene Name |
retinal degeneration 3 |
| Synonyms |
3322402L07Rik, rd-3, rd3 |
| MMRRC Submission |
041607-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R3900 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
1 |
| Chromosomal Location |
191709331-191720244 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 191717217 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Valine to Alanine
at position 114
(V114A)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000138049
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000175680]
[ENSMUST00000180463]
[ENSMUST00000181512]
|
| AlphaFold |
Q8BRE0 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000053463
AA Change: V229A
PolyPhen 2
Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000050188
Gene: ENSMUSG00000049353
AA Change: V229A
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:RD3
|
120 |
248 |
3.3e-48 |
PFAM |
|
| Predicted Effect |
unknown
Transcript: ENSMUST00000175680
AA Change: W91R
|
| SMART Domains |
Protein: ENSMUSP00000135650
Gene: ENSMUSG00000049353
AA Change: W91R
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:RD3
|
4 |
79 |
4.7e-24 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000180429
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000180463
AA Change: V114A
PolyPhen 2
Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000138049
Gene: ENSMUSG00000049353
AA Change: V114A
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:RD3
|
4 |
134 |
2.2e-50 |
PFAM |
|
| Predicted Effect |
unknown
Transcript: ENSMUST00000181512
AA Change: W91R
|
| SMART Domains |
Protein: ENSMUSP00000137756
Gene: ENSMUSG00000049353
AA Change: W91R
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:RD3
|
4 |
79 |
4.7e-24 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000192547
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000226862
|
| Meta Mutation Damage Score |
0.3394 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.7%
- 10x: 97.4%
- 20x: 95.4%
|
| Validation Efficiency |
98% (45/46) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a retinal protein that is associated with promyelocytic leukemia-gene product (PML) bodies in the nucleus. Mutations in this gene cause Leber congenital amaurosis type 12, a disease that results in retinal degeneration. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2009]
PHENOTYPE: Homozygotes for a spontaneous mutation exhibit retinal degeneration, beginning at 3 weeks of age, characterized by complete loss of photoreceptor rod cells by 5 weeks, and cones by 8 weeks. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 42 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 4833439L19Rik |
A |
T |
13: 54,700,781 (GRCm39) |
S212R |
probably damaging |
Het |
| AI182371 |
T |
C |
2: 34,975,228 (GRCm39) |
I334V |
probably benign |
Het |
| Anpep |
A |
G |
7: 79,488,973 (GRCm39) |
S372P |
probably benign |
Het |
| Apc2 |
C |
A |
10: 80,131,806 (GRCm39) |
|
probably null |
Het |
| Bcl6 |
T |
G |
16: 23,796,304 (GRCm39) |
E41A |
possibly damaging |
Het |
| Brpf1 |
A |
G |
6: 113,295,394 (GRCm39) |
I674V |
probably benign |
Het |
| Cherp |
A |
G |
8: 73,223,780 (GRCm39) |
I201T |
possibly damaging |
Het |
| Cluh |
A |
G |
11: 74,557,930 (GRCm39) |
H1056R |
probably benign |
Het |
| Csgalnact2 |
A |
T |
6: 118,097,975 (GRCm39) |
F122I |
probably damaging |
Het |
| Cubn |
C |
A |
2: 13,291,791 (GRCm39) |
|
probably null |
Het |
| Dnah17 |
A |
T |
11: 117,985,634 (GRCm39) |
I1481N |
possibly damaging |
Het |
| Eif2ak4 |
A |
G |
2: 118,305,510 (GRCm39) |
Y1561C |
probably damaging |
Het |
| Elfn1 |
G |
A |
5: 139,957,719 (GRCm39) |
R241H |
probably damaging |
Het |
| Eml5 |
G |
A |
12: 98,791,782 (GRCm39) |
R1245C |
probably damaging |
Het |
| Fchsd2 |
A |
G |
7: 100,841,006 (GRCm39) |
K172E |
possibly damaging |
Het |
| Gm10608 |
CAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA |
CAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA |
9: 118,989,784 (GRCm39) |
|
probably null |
Het |
| Gm6133 |
A |
G |
18: 78,393,365 (GRCm39) |
N120D |
probably benign |
Het |
| Hivep2 |
C |
A |
10: 14,004,713 (GRCm39) |
T437K |
probably benign |
Het |
| Igsf9 |
T |
C |
1: 172,317,125 (GRCm39) |
L35P |
probably damaging |
Het |
| Khdc3 |
T |
C |
9: 73,011,628 (GRCm39) |
|
probably benign |
Het |
| Mmrn2 |
G |
T |
14: 34,121,517 (GRCm39) |
|
probably null |
Het |
| Mrgpra1 |
G |
T |
7: 46,985,275 (GRCm39) |
R135S |
possibly damaging |
Het |
| Or4c11b |
A |
T |
2: 88,625,273 (GRCm39) |
L182F |
possibly damaging |
Het |
| Or8g2b |
A |
G |
9: 39,750,698 (GRCm39) |
|
probably null |
Het |
| Otud3 |
T |
C |
4: 138,624,196 (GRCm39) |
N282S |
probably benign |
Het |
| Prkar1a |
A |
G |
11: 109,551,901 (GRCm39) |
K130R |
probably benign |
Het |
| Rictor |
T |
G |
15: 6,818,954 (GRCm39) |
D1392E |
probably benign |
Het |
| Setd2 |
C |
T |
9: 110,421,586 (GRCm39) |
R273W |
probably damaging |
Het |
| Slc22a18 |
C |
A |
7: 143,033,507 (GRCm39) |
A86E |
probably damaging |
Het |
| Slc24a1 |
A |
T |
9: 64,835,426 (GRCm39) |
S900R |
probably damaging |
Het |
| Smarcc1 |
T |
C |
9: 109,947,586 (GRCm39) |
|
probably benign |
Het |
| Smoc1 |
T |
C |
12: 81,214,287 (GRCm39) |
V234A |
probably damaging |
Het |
| Stard9 |
A |
G |
2: 120,544,030 (GRCm39) |
T4443A |
possibly damaging |
Het |
| Timp2 |
C |
T |
11: 118,194,542 (GRCm39) |
D139N |
probably damaging |
Het |
| Trim69 |
A |
G |
2: 122,009,322 (GRCm39) |
T461A |
probably benign |
Het |
| Ubash3b |
C |
T |
9: 40,942,860 (GRCm39) |
D211N |
probably benign |
Het |
| Ubr4 |
T |
C |
4: 139,206,373 (GRCm39) |
|
probably null |
Het |
| Ubr5 |
T |
C |
15: 38,019,486 (GRCm39) |
D752G |
probably damaging |
Het |
| Urb1 |
A |
T |
16: 90,580,264 (GRCm39) |
I633N |
possibly damaging |
Het |
| Usp36 |
T |
A |
11: 118,170,650 (GRCm39) |
D28V |
possibly damaging |
Het |
| Wdr6 |
G |
A |
9: 108,452,968 (GRCm39) |
A305V |
probably damaging |
Het |
| Zfp248 |
T |
C |
6: 118,406,527 (GRCm39) |
N253S |
probably damaging |
Het |
|
| Other mutations in Rd3 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL01520:Rd3
|
APN |
1 |
191,717,283 (GRCm39) |
missense |
possibly damaging |
0.84 |
|
IGL02319:Rd3
|
APN |
1 |
191,715,452 (GRCm39) |
missense |
probably null |
1.00 |
|
R0098:Rd3
|
UTSW |
1 |
191,717,261 (GRCm39) |
missense |
probably benign |
0.05 |
|
R0098:Rd3
|
UTSW |
1 |
191,717,261 (GRCm39) |
missense |
probably benign |
0.05 |
|
R0458:Rd3
|
UTSW |
1 |
191,709,414 (GRCm39) |
missense |
probably damaging |
0.96 |
|
R0537:Rd3
|
UTSW |
1 |
191,715,501 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0991:Rd3
|
UTSW |
1 |
191,717,199 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R1344:Rd3
|
UTSW |
1 |
191,717,262 (GRCm39) |
makesense |
probably null |
|
|
R2168:Rd3
|
UTSW |
1 |
191,715,488 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R3898:Rd3
|
UTSW |
1 |
191,717,217 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R3899:Rd3
|
UTSW |
1 |
191,717,217 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5870:Rd3
|
UTSW |
1 |
191,717,261 (GRCm39) |
missense |
probably benign |
0.00 |
|
R8047:Rd3
|
UTSW |
1 |
191,709,620 (GRCm39) |
start gained |
probably benign |
|
|
R8506:Rd3
|
UTSW |
1 |
191,715,228 (GRCm39) |
start codon destroyed |
probably null |
0.98 |
|
R9541:Rd3
|
UTSW |
1 |
191,717,294 (GRCm39) |
missense |
possibly damaging |
0.84 |
|
| Predicted Primers |
PCR Primer
(F):5'- GGCTTCAGGCTCCTTGCATATG -3'
(R):5'- AGATGGTTCGGATGTCACTG -3'
Sequencing Primer
(F):5'- AAGGCAGGTGTACCCTTTTACAG -3'
(R):5'- TTCGGATGTCACTGGCAAAG -3'
|
| Posted On |
2015-04-17 |
Incidental Mutation