Incidental Mutation 'R3085:Pde6d'
ID 265555
Institutional Source Beutler Lab
Gene Symbol Pde6d
Ensembl Gene ENSMUSG00000026239
Gene Name phosphodiesterase 6D, cGMP-specific, rod, delta
Synonyms
MMRRC Submission 040574-MU
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.374) question?
Stock # R3085 (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

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
Pfam:GMP_PDE_delta 7 64 4e-9 PFAM
Predicted Effect probably null
Transcript: ENSMUST00000146220
SMART Domains Protein: ENSMUSP00000137820
Gene: ENSMUSG00000026239

DomainStartEndE-ValueType
Pfam:GMP_PDE_delta 7 124 6.9e-41 PFAM
Predicted Effect probably null
Transcript: ENSMUST00000146220
SMART Domains Protein: ENSMUSP00000137820
Gene: ENSMUSG00000026239

DomainStartEndE-ValueType
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 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.4%
  • 20x: 95.4%
Validation Efficiency 100% (63/63)
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: 64 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcc12 T A 8: 87,270,536 (GRCm39) probably benign Het
Adrm1 T C 2: 179,816,094 (GRCm39) probably null Het
Aldh18a1 T C 19: 40,562,813 (GRCm39) I76V probably benign Het
Atp1b2 T C 11: 69,493,705 (GRCm39) K125E possibly damaging Het
Cabyr T C 18: 12,884,023 (GRCm39) V170A probably damaging Het
Cdh8 T C 8: 99,923,018 (GRCm39) T293A probably benign Het
Cenpc1 A T 5: 86,185,476 (GRCm39) V345D probably benign Het
Col4a3 A G 1: 82,628,979 (GRCm39) E131G unknown Het
Col4a4 C T 1: 82,507,285 (GRCm39) probably null Het
Creb3l1 G T 2: 91,825,789 (GRCm39) probably null Het
Dhx9 T C 1: 153,341,445 (GRCm39) D601G probably benign Het
Dipk1a G T 5: 108,062,290 (GRCm39) D28E probably damaging Het
Dnaaf4 T A 9: 72,879,688 (GRCm39) N289K probably benign Het
Eml6 T C 11: 29,759,332 (GRCm39) E807G probably damaging Het
Exog C A 9: 119,291,518 (GRCm39) T241K probably benign Het
Eya1 T C 1: 14,344,314 (GRCm39) D109G probably benign Het
Fat2 C T 11: 55,142,997 (GRCm39) R4284H possibly damaging Het
Fbxw13 C A 9: 109,013,299 (GRCm39) G130* probably null Het
Fcrl5 A G 3: 87,353,771 (GRCm39) Y372C probably damaging Het
Gli3 T C 13: 15,835,526 (GRCm39) S435P probably damaging Het
Gsg1l C T 7: 125,490,852 (GRCm39) R284H probably benign Het
Havcr1 C T 11: 46,647,052 (GRCm39) T162I probably damaging Het
Igdcc4 T C 9: 65,039,340 (GRCm39) F947S probably damaging Het
Irx1 G T 13: 72,111,411 (GRCm39) A66E probably damaging Het
Klf11 T C 12: 24,705,490 (GRCm39) S315P probably benign Het
Kynu A G 2: 43,492,312 (GRCm39) M190V probably benign Het
Lrp2 T C 2: 69,297,479 (GRCm39) T3161A probably benign Het
Macrod1 G T 19: 7,173,859 (GRCm39) A208S probably damaging Het
Mamdc2 G A 19: 23,288,296 (GRCm39) H581Y possibly damaging Het
Megf8 T A 7: 25,048,444 (GRCm39) Y1706N probably damaging Het
Mthfd1l G A 10: 4,040,007 (GRCm39) R806H probably benign Het
Nags T A 11: 102,036,810 (GRCm39) V133D probably damaging Het
Nrg3 C A 14: 38,092,906 (GRCm39) D560Y 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
Or4p23 A G 2: 88,576,488 (GRCm39) F248S probably damaging Het
Or5af2 T C 11: 58,708,553 (GRCm39) S240P probably damaging Het
Orc4 G A 2: 48,827,501 (GRCm39) P31S probably benign Het
Plekhf1 T C 7: 37,921,001 (GRCm39) E189G probably benign Het
Ppm1b A T 17: 85,321,288 (GRCm39) I477L probably benign Het
Rad51ap2 C A 12: 11,506,758 (GRCm39) Q227K possibly damaging Het
Rnf125 T C 18: 21,110,787 (GRCm39) V15A probably benign Het
Rnps1 C T 17: 24,631,393 (GRCm39) probably benign Het
Robo1 A G 16: 72,798,898 (GRCm39) I953V possibly damaging Het
Sash1 A T 10: 8,618,186 (GRCm39) probably null Het
Smarcc2 T C 10: 128,324,028 (GRCm39) probably benign Het
Stx12 T A 4: 132,584,672 (GRCm39) E224V probably damaging Het
Sun1 T C 5: 139,221,356 (GRCm39) V357A probably benign Het
Synpo2l T C 14: 20,712,248 (GRCm39) D350G probably damaging Het
Tex15 A T 8: 34,064,913 (GRCm39) N1448Y probably benign Het
Tfpi A G 2: 84,273,227 (GRCm39) probably benign Het
Tktl2 T A 8: 66,965,858 (GRCm39) M472K possibly damaging Het
Tmem40 T C 6: 115,718,576 (GRCm39) D43G possibly damaging Het
Tshz2 T A 2: 169,725,871 (GRCm39) C156S probably benign Het
Vmn2r101 T A 17: 19,809,077 (GRCm39) probably null Het
Vmn2r85 T C 10: 130,261,081 (GRCm39) M419V probably benign Het
Wdr73 G A 7: 80,550,990 (GRCm39) probably benign Het
Zc3hc1 C T 6: 30,374,763 (GRCm39) probably null Het
Zfhx3 T C 8: 109,682,664 (GRCm39) Y3368H unknown Het
Zfp263 G A 16: 3,567,580 (GRCm39) E632K probably damaging Het
Zfp266 A G 9: 20,412,240 (GRCm39) L111P probably damaging Het
Zfp626 T A 7: 27,517,587 (GRCm39) S189R probably benign Het
Zfp772 T C 7: 7,206,699 (GRCm39) R331G possibly damaging Het
Zkscan5 G A 5: 145,157,889 (GRCm39) C797Y probably damaging Het
Other mutations in Pde6d
AlleleSourceChrCoordTypePredicted EffectPPH 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
R3084: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'- TCTCTCTGTGCAGCTGTCAG -3'
(R):5'- AGTTCATGTCTCAGATGTTATGTAAC -3'

Sequencing Primer
(F):5'- CTCAATCTGCAAAGTGCTGG -3'
(R):5'- TTAAAAACCTCTGGAGTCAGCTGG -3'
Posted On 2015-02-05