Incidental Mutation 'N/A:Pde6b'
| ID |
39 |
| 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 |
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
N/A
of strain
294
|
| Quality Score |
|
|
Status
|
Validated
|
| Chromosome |
5 |
| Chromosomal Location |
108536239-108579609 bp(+) (GRCm39) |
| Type of Mutation |
unclassified |
| DNA Base Change (assembly) |
A to T
at 108576969 bp (GRCm39)
|
| Zygosity |
Homozygous |
| Amino Acid Change |
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000113882
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000031456]
[ENSMUST00000049628]
[ENSMUST00000118632]
|
| AlphaFold |
P23440 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000031456
|
| SMART Domains |
Protein: ENSMUSP00000031456
Gene: ENSMUSG00000029491
| 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 |
probably benign
Transcript: ENSMUST00000049628
|
| SMART Domains |
Protein: ENSMUSP00000051222
Gene: ENSMUSG00000050856
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:ATP-synt_E
|
2 |
69 |
6.3e-18 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000118632
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000123184
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000130448
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000134865
|
| Coding Region Coverage |
|
| Validation Efficiency |
91% (106/116) |
| 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: 18 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 1700016P04Rik |
T |
A |
6: 13,415,772 (GRCm39) |
|
noncoding transcript |
Homo |
| Aif1 |
A |
G |
17: 35,391,496 (GRCm39) |
L7S |
possibly damaging |
Homo |
| Ankrd26 |
T |
C |
6: 118,506,535 (GRCm39) |
D646G |
probably benign |
Homo |
| Cacna1s |
A |
G |
1: 136,001,247 (GRCm39) |
I233V |
probably benign |
Homo |
| Cfap92 |
A |
T |
6: 87,667,773 (GRCm39) |
|
noncoding transcript |
Homo |
| Chchd4 |
T |
C |
6: 91,442,187 (GRCm39) |
Y77C |
probably damaging |
Homo |
| Crocc |
G |
A |
4: 140,749,057 (GRCm39) |
R1419C |
probably damaging |
Homo |
| Cyp4f39 |
A |
C |
17: 32,687,655 (GRCm39) |
M74L |
probably benign |
Homo |
| Fgf9 |
C |
A |
14: 58,327,421 (GRCm39) |
|
probably benign |
Homo |
| Gimap6 |
T |
C |
6: 48,679,349 (GRCm39) |
D229G |
probably damaging |
Homo |
| Glp1r |
T |
C |
17: 31,150,257 (GRCm39) |
F393S |
probably damaging |
Homo |
| Lrrc7 |
T |
G |
3: 157,865,977 (GRCm39) |
I1255L |
probably benign |
Homo |
| Mtrr |
C |
A |
13: 68,723,516 (GRCm39) |
|
probably benign |
Homo |
| Rbm19 |
A |
T |
5: 120,282,162 (GRCm39) |
I840F |
probably damaging |
Homo |
| Serpina3c |
A |
C |
12: 104,115,864 (GRCm39) |
S227A |
probably benign |
Homo |
| Spag17 |
G |
A |
3: 99,889,570 (GRCm39) |
|
probably benign |
Homo |
| Spmip3 |
G |
A |
1: 177,561,100 (GRCm39) |
R13H |
probably damaging |
Homo |
| Zbtb8b |
T |
C |
4: 129,326,361 (GRCm39) |
D268G |
probably benign |
Homo |
|
| 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 |
|
|
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 |
|
R4972:Pde6b
|
UTSW |
5 |
108,573,130 (GRCm39) |
missense |
probably benign |
0.00 |
|
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 |
|
| Nature of Mutation |
 DNA sequencing using the SOLiD technique identified identified an A to T transversion at position 40731 in the Genbank genomic region NC_000071 for the Pde6b gene on chromosome 5 (TCTTTACAAG->TCTTTACTAG). The mutation is located within intron 19, three nucleotides upstream from the start of exon 20, and may impair the acceptor splice site of intron 19. Pde6b contains 22 exons. The mutation has been confirmed by DNA sequencing using the Sanger method (Figure 1).
|
| Protein Function and Prediction |
Pde6b encodes the 856 amino acid rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta (PDE6B). PDE6 is the rod-specific cGMP phosphodiesterase, and is a critical component of the phototransduction cascade in rod photoreceptors downstream of rhodopsin. PDE6B is one of the catalytic subunits of PDE6 (Uniprot P23440). Mutations in the Pde6b gene in both mouse and humans cause retinitis pigmentosa with severe retinal degeneration and vision loss (OMIM #268000).
|
| Posted On |
2009-11-11 |
Incidental Mutation