Incidental Mutation 'R3084:Pde6d'
| ID |
265511 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Pde6d
|
| Ensembl Gene |
ENSMUSG00000026239 |
| Gene Name |
phosphodiesterase 6D, cGMP-specific, rod, delta |
| Synonyms |
|
| MMRRC Submission |
040573-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly non essential
(E-score: 0.374)
|
| Stock # |
R3084 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
1 |
| Chromosomal Location |
86470716-86510351 bp(-) (GRCm39) |
| Type of Mutation |
splice site (3 bp from exon) |
| DNA Base Change (assembly) |
T to C
at 86475248 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000137820
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000027444]
[ENSMUST00000143674]
[ENSMUST00000146220]
[ENSMUST00000146220]
|
| AlphaFold |
O55057 |
| Predicted Effect |
probably null
Transcript: ENSMUST00000027444
|
| SMART Domains |
Protein: ENSMUSP00000027444
Gene: ENSMUSG00000026239
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:GMP_PDE_delta
|
9 |
149 |
1e-48 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000143674
AA Change: T48A
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
| SMART Domains |
Protein: ENSMUSP00000137956
Gene: ENSMUSG00000026239
AA Change: T48A
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:GMP_PDE_delta
|
7 |
64 |
4e-9 |
PFAM |
|
| Predicted Effect |
probably null
Transcript: ENSMUST00000146220
|
| SMART Domains |
Protein: ENSMUSP00000137820
Gene: ENSMUSG00000026239
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:GMP_PDE_delta
|
7 |
124 |
6.9e-41 |
PFAM |
|
| Predicted Effect |
probably null
Transcript: ENSMUST00000146220
|
| SMART Domains |
Protein: ENSMUSP00000137820
Gene: ENSMUSG00000026239
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:GMP_PDE_delta
|
7 |
124 |
6.9e-41 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000148683
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000150653
|
| Meta Mutation Damage Score |
0.9755 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.4%
- 20x: 95.5%
|
| Validation Efficiency |
100% (43/43) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes the delta subunit of rod-specific photoreceptor phosphodiesterase (PDE), a key enzyme in the phototransduction cascade. A similar protein in cow functions in solubilizing membrane-bound PDE. In addition to its role in the PDE complex, the encoded protein is thought to bind to prenyl groups of proteins to target them to subcellular organelles called cilia. Mutations in this gene are associated with Joubert syndrome-22. Alternative splicing results in multiple splice variants. [provided by RefSeq, Mar 2014]
PHENOTYPE: Homozygous null mice exhibit progressive retinal degeneration with progressive loss of rod and cone neurons. [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 |
|---|
| Adgra3 |
A |
T |
5: 50,170,733 (GRCm39) |
|
probably null |
Het |
| Alms1 |
A |
G |
6: 85,655,122 (GRCm39) |
R3223G |
probably benign |
Het |
| Arhgef26 |
T |
C |
3: 62,285,037 (GRCm39) |
V431A |
probably benign |
Het |
| Cabyr |
T |
C |
18: 12,884,023 (GRCm39) |
V170A |
probably damaging |
Het |
| Cenpe |
A |
G |
3: 134,946,782 (GRCm39) |
E1099G |
probably damaging |
Het |
| Creb3l1 |
G |
T |
2: 91,825,789 (GRCm39) |
|
probably null |
Het |
| Cyp2c38 |
T |
C |
19: 39,390,145 (GRCm39) |
I352V |
probably benign |
Het |
| Dhrs2 |
G |
T |
14: 55,477,301 (GRCm39) |
V179L |
probably benign |
Het |
| Dhx9 |
T |
C |
1: 153,341,445 (GRCm39) |
D601G |
probably benign |
Het |
| Dlg5 |
T |
C |
14: 24,216,258 (GRCm39) |
T595A |
probably damaging |
Het |
| Fhip1a |
T |
A |
3: 85,573,275 (GRCm39) |
|
probably null |
Het |
| Frk |
G |
A |
10: 34,483,950 (GRCm39) |
G437D |
probably damaging |
Het |
| Gm10608 |
CAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA |
CAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA |
9: 118,989,784 (GRCm39) |
|
probably null |
Het |
| Gm5699 |
G |
T |
1: 31,037,873 (GRCm39) |
|
noncoding transcript |
Het |
| Gsg1l |
C |
T |
7: 125,490,852 (GRCm39) |
R284H |
probably benign |
Het |
| Ifit3 |
A |
T |
19: 34,564,640 (GRCm39) |
H62L |
probably damaging |
Het |
| Krt34 |
T |
C |
11: 99,931,847 (GRCm39) |
N124S |
probably damaging |
Het |
| Megf8 |
T |
A |
7: 25,048,444 (GRCm39) |
Y1706N |
probably damaging |
Het |
| Mmd |
C |
T |
11: 90,156,911 (GRCm39) |
R129C |
probably damaging |
Het |
| Or4f60 |
C |
A |
2: 111,902,320 (GRCm39) |
G203* |
probably null |
Het |
| Or4k36 |
A |
G |
2: 111,146,461 (GRCm39) |
I212M |
probably benign |
Het |
| Pomt1 |
G |
T |
2: 32,134,252 (GRCm39) |
V258L |
probably benign |
Het |
| Ppp2r5e |
T |
C |
12: 75,515,390 (GRCm39) |
I215V |
probably benign |
Het |
| Ranbp10 |
A |
T |
8: 106,501,263 (GRCm39) |
L329Q |
probably damaging |
Het |
| Robo1 |
T |
A |
16: 72,801,625 (GRCm39) |
L1083Q |
probably benign |
Het |
| Rsph4a |
G |
C |
10: 33,785,198 (GRCm39) |
V370L |
probably damaging |
Het |
| Smarcc2 |
T |
C |
10: 128,324,028 (GRCm39) |
|
probably benign |
Het |
| Sun1 |
T |
C |
5: 139,221,356 (GRCm39) |
V357A |
probably benign |
Het |
| Svop |
T |
C |
5: 114,180,299 (GRCm39) |
T283A |
probably benign |
Het |
| Tep1 |
A |
T |
14: 51,064,511 (GRCm39) |
|
probably null |
Het |
| Tet1 |
T |
C |
10: 62,715,400 (GRCm39) |
K132E |
probably benign |
Het |
| Tex15 |
A |
T |
8: 34,064,913 (GRCm39) |
N1448Y |
probably benign |
Het |
| Tktl2 |
T |
A |
8: 66,965,858 (GRCm39) |
M472K |
possibly damaging |
Het |
| Tnrc6b |
T |
G |
15: 80,764,448 (GRCm39) |
L650W |
probably damaging |
Het |
| Ttf2 |
C |
T |
3: 100,855,580 (GRCm39) |
G872R |
possibly damaging |
Het |
| Vmn1r17 |
A |
G |
6: 57,337,768 (GRCm39) |
V199A |
probably damaging |
Het |
| Vmn1r178 |
A |
G |
7: 23,593,331 (GRCm39) |
I126M |
possibly damaging |
Het |
| Vmn2r85 |
T |
C |
10: 130,261,081 (GRCm39) |
M419V |
probably benign |
Het |
| Washc2 |
A |
G |
6: 116,204,454 (GRCm39) |
N454S |
probably benign |
Het |
| Xirp2 |
T |
G |
2: 67,339,393 (GRCm39) |
F545V |
probably damaging |
Het |
| Zfyve26 |
G |
T |
12: 79,312,457 (GRCm39) |
|
probably benign |
Het |
|
| Other mutations in Pde6d |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
costume
|
UTSW |
1 |
86,475,248 (GRCm39) |
splice site |
probably null |
|
|
R0879:Pde6d
|
UTSW |
1 |
86,473,523 (GRCm39) |
missense |
probably benign |
0.04 |
|
R1446:Pde6d
|
UTSW |
1 |
86,474,414 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R2018:Pde6d
|
UTSW |
1 |
86,474,438 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2118:Pde6d
|
UTSW |
1 |
86,473,524 (GRCm39) |
missense |
probably benign |
0.10 |
|
R2119:Pde6d
|
UTSW |
1 |
86,473,524 (GRCm39) |
missense |
probably benign |
0.10 |
|
R2120:Pde6d
|
UTSW |
1 |
86,473,524 (GRCm39) |
missense |
probably benign |
0.10 |
|
R2122:Pde6d
|
UTSW |
1 |
86,473,524 (GRCm39) |
missense |
probably benign |
0.10 |
|
R3085:Pde6d
|
UTSW |
1 |
86,475,248 (GRCm39) |
splice site |
probably null |
|
|
R6824:Pde6d
|
UTSW |
1 |
86,473,485 (GRCm39) |
missense |
possibly damaging |
0.49 |
|
R7775:Pde6d
|
UTSW |
1 |
86,471,250 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7778:Pde6d
|
UTSW |
1 |
86,471,250 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8444:Pde6d
|
UTSW |
1 |
86,471,250 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8794:Pde6d
|
UTSW |
1 |
86,475,209 (GRCm39) |
nonsense |
probably null |
|
|
R9608:Pde6d
|
UTSW |
1 |
86,473,424 (GRCm39) |
missense |
possibly damaging |
0.82 |
|
| Predicted Primers |
PCR Primer
(F):5'- CTCTCTGTGCAGCTGTCAGA -3'
(R):5'- AGTTCATGTCTCAGATGTTATGTAAC -3'
Sequencing Primer
(F):5'- CTCAATCTGCAAAGTGCTGG -3'
(R):5'- TTAAAAACCTCTGGAGTCAGCTGG -3'
|
| Posted On |
2015-02-05 |
Incidental Mutation