Incidental Mutation 'R6824:Pde6d'
ID 534033
Institutional Source Beutler Lab
Gene Symbol Pde6d
Ensembl Gene ENSMUSG00000026239
Gene Name phosphodiesterase 6D, cGMP-specific, rod, delta
Synonyms
MMRRC Submission 044936-MU
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.385) question?
Stock # R6824 (G1)
Quality Score 225.009
Status Validated
Chromosome 1
Chromosomal Location 86470716-86510351 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 86473485 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Alanine at position 104 (T104A)
Ref Sequence ENSEMBL: ENSMUSP00000137820 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000027444] [ENSMUST00000143674] [ENSMUST00000146220]
AlphaFold O55057
Predicted Effect possibly damaging
Transcript: ENSMUST00000027444
AA Change: T104A

PolyPhen 2 Score 0.488 (Sensitivity: 0.88; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000027444
Gene: ENSMUSG00000026239
AA Change: T104A

DomainStartEndE-ValueType
Pfam:GMP_PDE_delta 9 149 1e-48 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000143674
SMART Domains Protein: ENSMUSP00000137956
Gene: ENSMUSG00000026239

DomainStartEndE-ValueType
Pfam:GMP_PDE_delta 7 64 4e-9 PFAM
Predicted Effect possibly damaging
Transcript: ENSMUST00000146220
AA Change: T104A

PolyPhen 2 Score 0.488 (Sensitivity: 0.88; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000137820
Gene: ENSMUSG00000026239
AA Change: T104A

DomainStartEndE-ValueType
Pfam:GMP_PDE_delta 7 124 6.9e-41 PFAM
Meta Mutation Damage Score 0.9126 question?
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.5%
  • 20x: 98.5%
Validation Efficiency 100% (47/47)
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: 46 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adck2 A G 6: 39,552,058 (GRCm39) D275G probably benign Het
Cdh4 G A 2: 179,439,351 (GRCm39) R166H probably damaging Het
Chl1 A G 6: 103,691,510 (GRCm39) K1051E probably damaging Het
Chn2 A T 6: 54,249,938 (GRCm39) M16L probably benign Het
Cmas A G 6: 142,716,962 (GRCm39) T285A possibly damaging Het
Cnga4 A T 7: 105,056,036 (GRCm39) M213L probably benign Het
Ctif C T 18: 75,654,782 (GRCm39) R248Q probably damaging Het
Cyth3 T C 5: 143,672,265 (GRCm39) I60T probably damaging Het
Dach1 A G 14: 98,256,328 (GRCm39) I310T possibly damaging Het
Defb6 T C 8: 19,278,099 (GRCm39) I57T probably benign Het
Dnajc27 T C 12: 4,156,897 (GRCm39) V262A possibly damaging Het
Emsy G A 7: 98,242,614 (GRCm39) T1175M probably benign Het
Enpp5 G A 17: 44,396,155 (GRCm39) G356S probably damaging Het
Fam50b G A 13: 34,931,084 (GRCm39) E187K possibly damaging Het
Fat4 T A 3: 39,011,674 (GRCm39) V2258E probably benign Het
Gm136 G A 4: 34,746,591 (GRCm39) T140I probably benign Het
Gps1 T C 11: 120,678,254 (GRCm39) F265S probably damaging Het
Grik5 C T 7: 24,745,780 (GRCm39) R431Q possibly damaging Het
Hnrnpul2 T C 19: 8,804,081 (GRCm39) V560A possibly damaging Het
Kmt2b A G 7: 30,285,701 (GRCm39) probably benign Het
Krt8 T C 15: 101,906,875 (GRCm39) N317S possibly damaging Het
Lad1 A G 1: 135,755,479 (GRCm39) T252A probably benign Het
Maml2 G A 9: 13,608,513 (GRCm39) S743N possibly damaging Het
Mrpl9 C A 3: 94,350,677 (GRCm39) P7H possibly damaging Het
Myb T A 10: 21,021,019 (GRCm39) H470L probably benign Het
Nicol1 T C 5: 34,141,069 (GRCm39) probably benign Het
Nr1i3 T C 1: 171,042,542 (GRCm39) I56T probably benign Het
Nrdc A G 4: 108,900,622 (GRCm39) Y338C probably damaging Het
Or13n4 A G 7: 106,423,664 (GRCm39) V23A probably benign Het
Pcdhb20 T A 18: 37,638,752 (GRCm39) M426K probably benign Het
Ptprz1 A T 6: 23,002,130 (GRCm39) T1407S probably benign Het
Recql5 C T 11: 115,814,038 (GRCm39) R369Q possibly damaging Het
Rnf180 T A 13: 105,318,023 (GRCm39) D463V probably damaging Het
Sart3 C T 5: 113,882,600 (GRCm39) probably null Het
Sdk2 T C 11: 113,758,760 (GRCm39) D488G probably benign Het
Slc9a9 C T 9: 95,109,251 (GRCm39) P538S probably damaging Het
Snap29 A G 16: 17,240,370 (GRCm39) K159E probably benign Het
Spaca1 A G 4: 34,049,869 (GRCm39) V43A probably benign Het
Stk10 T C 11: 32,537,363 (GRCm39) S191P probably damaging Het
Tbc1d1 A G 5: 64,414,245 (GRCm39) H73R probably benign Het
Tcerg1l A G 7: 137,995,844 (GRCm39) probably null Het
Tmem67 T C 4: 12,051,449 (GRCm39) Y793C probably damaging Het
Ttll12 A T 15: 83,475,578 (GRCm39) probably null Het
Vmn2r61 G T 7: 41,949,403 (GRCm39) V608L probably benign Het
Xpo4 A T 14: 57,850,860 (GRCm39) I348N probably damaging Het
Zfp941 G A 7: 140,392,612 (GRCm39) T249M probably benign 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
R3085:Pde6d UTSW 1 86,475,248 (GRCm39) splice site probably null
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'- AAGGTTAGGTGGCAGTTACTGAC -3'
(R):5'- TCGTGTAACTCTCTGATTTAGGAGG -3'

Sequencing Primer
(F):5'- CTGGAACTCACTTTGTAGACCAGG -3'
(R):5'- AACTCTCTGATTTAGGAGGTATCTG -3'
Posted On 2018-09-12