Incidental Mutation 'R4972:Pde6b'
| ID |
384512 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Pde6b
|
| Ensembl Gene |
ENSMUSG00000029491 |
| Gene Name |
phosphodiesterase 6B, cGMP, rod receptor, beta polypeptide |
| Synonyms |
rd, rd10, rd1, r, Pdeb |
| MMRRC Submission |
042567-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R4972 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
5 |
| Chromosomal Location |
108536239-108579609 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 108573130 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Aspartic acid to Glycine
at position 500
(D500G)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000031456
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000031456]
|
| AlphaFold |
P23440 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000031456
AA Change: D500G
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
| SMART Domains |
Protein: ENSMUSP00000031456
Gene: ENSMUSG00000029491
AA Change: D500G
| Domain | Start | End | E-Value | Type |
|---|
|
GAF
|
71 |
230 |
1.29e-27 |
SMART |
|
GAF
|
252 |
439 |
5.76e-25 |
SMART |
|
Blast:HDc
|
484 |
538 |
1e-24 |
BLAST |
|
HDc
|
554 |
732 |
1.25e-9 |
SMART |
|
Blast:HDc
|
757 |
792 |
8e-13 |
BLAST |
|
low complexity region
|
813 |
837 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000134865
|
| Meta Mutation Damage Score |
0.0703 |
| Coding Region Coverage |
- 1x: 99.1%
- 3x: 98.2%
- 10x: 96.0%
- 20x: 91.2%
|
| Validation Efficiency |
93% (82/88) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] Photon absorption triggers a signaling cascade in rod photoreceptors that activates cGMP phosphodiesterase (PDE), resulting in the rapid hydrolysis of cGMP, closure of cGMP-gated cation channels, and hyperpolarization of the cell. PDE is a peripheral membrane heterotrimeric enzyme made up of alpha, beta, and gamma subunits. This gene encodes the beta subunit. Mutations in this gene result in retinitis pigmentosa and autosomal dominant congenital stationary night blindness. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2009]
PHENOTYPE: Homozygotes for the rd1 mutation have severe retinal degeneration and vision loss. Rod cells are lost by 35 days of age; cone cells degenerate slower and some light sensitivity persists. Other allelic mutations produce similar or milder phenotypes. [provided by MGI curators]
|
| Allele List at MGI |
All alleles(13) : Targeted, knock-out(1) Targeted, other(1) Spontaneous(2) Chemically induced(9) |
| Other mutations in this stock |
Total: 72 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 3425401B19Rik |
A |
T |
14: 32,383,361 (GRCm39) |
I868N |
possibly damaging |
Het |
| A730013G03Rik |
C |
G |
1: 192,516,081 (GRCm39) |
|
noncoding transcript |
Het |
| Actl11 |
A |
G |
9: 107,807,155 (GRCm39) |
T493A |
probably benign |
Het |
| Actn1 |
T |
C |
12: 80,219,813 (GRCm39) |
D686G |
probably benign |
Het |
| Adamts1 |
G |
A |
16: 85,592,833 (GRCm39) |
T525I |
probably damaging |
Het |
| Adcy10 |
T |
A |
1: 165,384,431 (GRCm39) |
L1064H |
probably damaging |
Het |
| AI661453 |
A |
T |
17: 47,777,324 (GRCm39) |
|
probably benign |
Het |
| Apba1 |
T |
A |
19: 23,889,900 (GRCm39) |
S433T |
probably benign |
Het |
| Arid4b |
T |
A |
13: 14,334,857 (GRCm39) |
N355K |
probably benign |
Het |
| Bsn |
A |
T |
9: 107,992,377 (GRCm39) |
M1125K |
probably damaging |
Het |
| C2cd5 |
A |
T |
6: 142,958,950 (GRCm39) |
M1003K |
probably damaging |
Het |
| Ccdc18 |
A |
G |
5: 108,339,869 (GRCm39) |
M805V |
probably benign |
Het |
| Cep89 |
T |
G |
7: 35,131,977 (GRCm39) |
L637R |
probably damaging |
Het |
| Col24a1 |
A |
T |
3: 145,215,439 (GRCm39) |
I1444F |
probably benign |
Het |
| Commd4 |
A |
T |
9: 57,062,732 (GRCm39) |
S175T |
probably benign |
Het |
| Coq7 |
A |
G |
7: 118,109,340 (GRCm39) |
V236A |
unknown |
Het |
| Dctn2 |
C |
T |
10: 127,112,572 (GRCm39) |
R176C |
probably damaging |
Het |
| Ddx31 |
T |
C |
2: 28,750,782 (GRCm39) |
F389L |
probably damaging |
Het |
| Dgkz |
C |
T |
2: 91,776,047 (GRCm39) |
R72H |
probably benign |
Het |
| Dpysl4 |
A |
G |
7: 138,670,206 (GRCm39) |
D24G |
probably damaging |
Het |
| Dydc1 |
A |
G |
14: 40,804,295 (GRCm39) |
T106A |
probably benign |
Het |
| F13b |
A |
G |
1: 139,438,661 (GRCm39) |
Y355C |
probably damaging |
Het |
| Fcrl5 |
A |
G |
3: 87,361,957 (GRCm39) |
M407V |
probably benign |
Het |
| Fzd5 |
C |
A |
1: 64,775,171 (GRCm39) |
V197L |
probably benign |
Het |
| Galnt16 |
G |
T |
12: 80,619,103 (GRCm39) |
E70* |
probably null |
Het |
| Gpr171 |
A |
T |
3: 59,005,386 (GRCm39) |
F130I |
probably damaging |
Het |
| Grin3a |
T |
C |
4: 49,770,484 (GRCm39) |
N763D |
probably damaging |
Het |
| Gsta2 |
A |
T |
9: 78,244,961 (GRCm39) |
M51K |
probably damaging |
Het |
| Gvin-ps3 |
T |
C |
7: 105,682,521 (GRCm39) |
|
noncoding transcript |
Het |
| Hacd3 |
A |
T |
9: 64,897,718 (GRCm39) |
I298N |
probably damaging |
Het |
| Il18r1 |
C |
T |
1: 40,530,224 (GRCm39) |
P317L |
probably benign |
Het |
| Iscu |
T |
A |
5: 113,915,037 (GRCm39) |
|
probably benign |
Het |
| Kif6 |
A |
G |
17: 50,014,647 (GRCm39) |
D250G |
probably damaging |
Het |
| Klk14 |
G |
A |
7: 43,341,501 (GRCm39) |
C51Y |
probably damaging |
Het |
| Lcn6 |
T |
A |
2: 25,570,079 (GRCm39) |
C82S |
probably damaging |
Het |
| Mob4 |
C |
G |
1: 55,190,161 (GRCm39) |
L135V |
possibly damaging |
Het |
| Mpzl3 |
T |
A |
9: 44,973,554 (GRCm39) |
|
probably benign |
Het |
| Mvp |
T |
C |
7: 126,588,970 (GRCm39) |
D599G |
probably damaging |
Het |
| Myo1a |
T |
C |
10: 127,552,178 (GRCm39) |
Y766H |
probably benign |
Het |
| Myo5b |
A |
G |
18: 74,760,264 (GRCm39) |
H260R |
probably damaging |
Het |
| Nbea |
C |
T |
3: 55,992,667 (GRCm39) |
R313H |
probably damaging |
Het |
| Necab1 |
T |
A |
4: 14,978,216 (GRCm39) |
D211V |
probably damaging |
Het |
| Nefl |
G |
T |
14: 68,324,212 (GRCm39) |
|
probably benign |
Het |
| Nfx1 |
T |
A |
4: 40,976,375 (GRCm39) |
D16E |
probably benign |
Het |
| Nlrp9a |
G |
T |
7: 26,269,964 (GRCm39) |
C797F |
probably damaging |
Het |
| Or4k36 |
T |
A |
2: 111,146,163 (GRCm39) |
V113E |
probably damaging |
Het |
| Or5p5 |
A |
G |
7: 107,413,953 (GRCm39) |
Q56R |
probably benign |
Het |
| Pgs1 |
T |
C |
11: 117,896,719 (GRCm39) |
|
probably null |
Het |
| Polr3b |
T |
A |
10: 84,473,988 (GRCm39) |
I189N |
probably damaging |
Het |
| Ppwd1 |
A |
T |
13: 104,356,616 (GRCm39) |
S300T |
probably benign |
Het |
| Prl2c2 |
A |
C |
13: 13,176,755 (GRCm39) |
N55K |
possibly damaging |
Het |
| Prpf19 |
C |
T |
19: 10,876,709 (GRCm39) |
|
probably benign |
Het |
| Prph2 |
G |
T |
17: 47,221,733 (GRCm39) |
L37F |
possibly damaging |
Het |
| Ptprg |
G |
T |
14: 12,226,427 (GRCm38) |
R565L |
possibly damaging |
Het |
| Rab8a |
C |
T |
8: 72,925,119 (GRCm39) |
T74M |
probably damaging |
Het |
| Rexo1 |
A |
T |
10: 80,385,527 (GRCm39) |
F510L |
probably damaging |
Het |
| Rexo2 |
G |
T |
9: 48,390,689 (GRCm39) |
T51K |
probably damaging |
Het |
| Sh3d21 |
T |
C |
4: 126,046,209 (GRCm39) |
K147R |
possibly damaging |
Het |
| Skint6 |
A |
G |
4: 112,692,265 (GRCm39) |
I1062T |
probably benign |
Het |
| Spag16 |
C |
T |
1: 70,764,087 (GRCm39) |
R636W |
probably damaging |
Het |
| Spata16 |
T |
C |
3: 26,894,872 (GRCm39) |
I307T |
possibly damaging |
Het |
| Speer4f2 |
T |
G |
5: 17,579,423 (GRCm39) |
I74S |
probably benign |
Het |
| Svep1 |
T |
A |
4: 58,087,778 (GRCm39) |
Y1767F |
possibly damaging |
Het |
| Swt1 |
T |
C |
1: 151,299,293 (GRCm39) |
S7G |
probably benign |
Het |
| Tex9 |
A |
G |
9: 72,385,620 (GRCm39) |
|
probably null |
Het |
| Thsd7b |
C |
A |
1: 130,116,309 (GRCm39) |
P1354H |
probably damaging |
Het |
| Ticrr |
A |
G |
7: 79,319,416 (GRCm39) |
D467G |
probably damaging |
Het |
| Tmco5b |
A |
C |
2: 113,127,338 (GRCm39) |
D303A |
probably damaging |
Het |
| Trpm7 |
A |
G |
2: 126,665,978 (GRCm39) |
V876A |
probably damaging |
Het |
| Ttc21a |
G |
A |
9: 119,774,027 (GRCm39) |
E245K |
probably benign |
Het |
| Vezt |
C |
T |
10: 93,836,212 (GRCm39) |
|
probably null |
Het |
| Zscan20 |
G |
A |
4: 128,486,152 (GRCm39) |
P183S |
probably benign |
Het |
|
| Other mutations in Pde6b |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00534:Pde6b
|
APN |
5 |
108,574,437 (GRCm39) |
splice site |
probably benign |
|
|
IGL01071:Pde6b
|
APN |
5 |
108,567,581 (GRCm39) |
nonsense |
probably null |
|
|
IGL01335:Pde6b
|
APN |
5 |
108,571,379 (GRCm39) |
missense |
probably benign |
0.03 |
|
IGL01611:Pde6b
|
APN |
5 |
108,551,262 (GRCm39) |
missense |
possibly damaging |
0.90 |
|
IGL01881:Pde6b
|
APN |
5 |
108,569,366 (GRCm39) |
missense |
probably benign |
0.01 |
|
IGL01941:Pde6b
|
APN |
5 |
108,570,902 (GRCm39) |
missense |
probably benign |
0.11 |
|
IGL02616:Pde6b
|
APN |
5 |
108,579,407 (GRCm39) |
missense |
probably benign |
0.05 |
|
IGL02657:Pde6b
|
APN |
5 |
108,568,142 (GRCm39) |
splice site |
probably benign |
|
|
IGL03217:Pde6b
|
APN |
5 |
108,567,432 (GRCm39) |
missense |
probably damaging |
1.00 |
|
Bemr28
|
UTSW |
5 |
0 () |
unclassified |
|
|
|
D4043:Pde6b
|
UTSW |
5 |
108,573,222 (GRCm39) |
nonsense |
probably null |
|
|
N/A:Pde6b
|
UTSW |
5 |
108,576,969 (GRCm39) |
unclassified |
probably benign |
|
|
PIT4362001:Pde6b
|
UTSW |
5 |
108,571,451 (GRCm39) |
critical splice donor site |
probably null |
|
|
PIT4581001:Pde6b
|
UTSW |
5 |
108,576,374 (GRCm39) |
missense |
probably benign |
0.01 |
|
R0940:Pde6b
|
UTSW |
5 |
108,568,203 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
R0963:Pde6b
|
UTSW |
5 |
108,578,534 (GRCm39) |
missense |
probably benign |
|
|
R1738:Pde6b
|
UTSW |
5 |
108,578,425 (GRCm39) |
nonsense |
probably null |
|
|
R1753:Pde6b
|
UTSW |
5 |
108,536,557 (GRCm39) |
nonsense |
probably null |
|
|
R1801:Pde6b
|
UTSW |
5 |
108,575,713 (GRCm39) |
missense |
possibly damaging |
0.51 |
|
R1913:Pde6b
|
UTSW |
5 |
108,575,056 (GRCm39) |
missense |
probably benign |
0.05 |
|
R2131:Pde6b
|
UTSW |
5 |
108,576,069 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2282:Pde6b
|
UTSW |
5 |
108,571,452 (GRCm39) |
splice site |
probably null |
|
|
R3713:Pde6b
|
UTSW |
5 |
108,570,928 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4385:Pde6b
|
UTSW |
5 |
108,575,508 (GRCm39) |
missense |
probably benign |
0.08 |
|
R4562:Pde6b
|
UTSW |
5 |
108,551,234 (GRCm39) |
missense |
probably benign |
0.23 |
|
R4582:Pde6b
|
UTSW |
5 |
108,573,097 (GRCm39) |
critical splice acceptor site |
probably null |
|
|
R4939:Pde6b
|
UTSW |
5 |
108,569,363 (GRCm39) |
missense |
probably benign |
0.01 |
|
R4950:Pde6b
|
UTSW |
5 |
108,578,569 (GRCm39) |
missense |
probably benign |
0.16 |
|
R4983:Pde6b
|
UTSW |
5 |
108,573,196 (GRCm39) |
missense |
probably benign |
0.21 |
|
R5056:Pde6b
|
UTSW |
5 |
108,571,357 (GRCm39) |
nonsense |
probably null |
|
|
R5514:Pde6b
|
UTSW |
5 |
108,571,317 (GRCm39) |
missense |
probably benign |
0.06 |
|
R5528:Pde6b
|
UTSW |
5 |
108,571,424 (GRCm39) |
missense |
probably benign |
0.04 |
|
R5937:Pde6b
|
UTSW |
5 |
108,572,193 (GRCm39) |
missense |
probably benign |
0.00 |
|
R6556:Pde6b
|
UTSW |
5 |
108,569,367 (GRCm39) |
missense |
possibly damaging |
0.56 |
|
R6826:Pde6b
|
UTSW |
5 |
108,578,458 (GRCm39) |
nonsense |
probably null |
|
|
R6884:Pde6b
|
UTSW |
5 |
108,536,574 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R7213:Pde6b
|
UTSW |
5 |
108,551,956 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7444:Pde6b
|
UTSW |
5 |
108,575,008 (GRCm39) |
nonsense |
probably null |
|
|
R7690:Pde6b
|
UTSW |
5 |
108,567,384 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7909:Pde6b
|
UTSW |
5 |
108,551,288 (GRCm39) |
missense |
probably benign |
0.01 |
|
R7937:Pde6b
|
UTSW |
5 |
108,567,639 (GRCm39) |
critical splice donor site |
probably null |
|
|
R8049:Pde6b
|
UTSW |
5 |
108,573,118 (GRCm39) |
missense |
probably benign |
0.04 |
|
R8087:Pde6b
|
UTSW |
5 |
108,536,328 (GRCm39) |
missense |
probably benign |
0.00 |
|
R8698:Pde6b
|
UTSW |
5 |
108,576,105 (GRCm39) |
missense |
possibly damaging |
0.87 |
|
R8822:Pde6b
|
UTSW |
5 |
108,551,328 (GRCm39) |
missense |
probably benign |
0.00 |
|
R8985:Pde6b
|
UTSW |
5 |
108,578,503 (GRCm39) |
missense |
probably benign |
0.02 |
|
R9016:Pde6b
|
UTSW |
5 |
108,536,592 (GRCm39) |
missense |
possibly damaging |
0.88 |
|
R9292:Pde6b
|
UTSW |
5 |
108,536,751 (GRCm39) |
missense |
probably benign |
0.00 |
|
R9323:Pde6b
|
UTSW |
5 |
108,551,298 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9414:Pde6b
|
UTSW |
5 |
108,567,592 (GRCm39) |
missense |
possibly damaging |
0.82 |
|
R9486:Pde6b
|
UTSW |
5 |
108,551,241 (GRCm39) |
missense |
probably damaging |
0.97 |
|
| Predicted Primers |
PCR Primer
(F):5'- TTACCTGGTGCAAGGAAACAG -3'
(R):5'- ACATATACACTTCACCTCTTGGGG -3'
Sequencing Primer
(F):5'- CAGTAGGATAAGATAAACAGTGGCC -3'
(R):5'- GGGACCTGTAACCTTTACCAC -3'
|
| Posted On |
2016-04-27 |
Incidental Mutation