Incidental Mutation 'R2119:Pde6d'
ID 231251
Institutional Source Beutler Lab
Gene Symbol Pde6d
Ensembl Gene ENSMUSG00000026239
Gene Name phosphodiesterase 6D, cGMP-specific, rod, delta
Synonyms
MMRRC Submission 040123-MU
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.374) question?
Stock # R2119 (G1)
Quality Score 225
Status Not validated
Chromosome 1
Chromosomal Location 86470716-86510351 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 86473524 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Phenylalanine to Leucine at position 91 (F91L)
Ref Sequence ENSEMBL: ENSMUSP00000137820 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000027444] [ENSMUST00000143674] [ENSMUST00000146220]
AlphaFold O55057
Predicted Effect probably benign
Transcript: ENSMUST00000027444
AA Change: F91L

PolyPhen 2 Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)
SMART Domains Protein: ENSMUSP00000027444
Gene: ENSMUSG00000026239
AA Change: F91L

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 probably benign
Transcript: ENSMUST00000146220
AA Change: F91L

PolyPhen 2 Score 0.103 (Sensitivity: 0.93; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000137820
Gene: ENSMUSG00000026239
AA Change: F91L

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 0.0624 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.5%
  • 20x: 95.8%
Validation Efficiency
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: 74 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4933430I17Rik T A 4: 62,457,109 (GRCm39) L143M possibly damaging Het
Actbl2 G A 13: 111,391,694 (GRCm39) V10I probably benign Het
Adamts12 C T 15: 11,310,665 (GRCm39) T974I probably damaging Het
Aifm2 G A 10: 61,571,383 (GRCm39) V306M possibly damaging Het
Arhgef38 T C 3: 132,866,514 (GRCm39) K208E probably benign Het
Atxn7l3 C A 11: 102,182,807 (GRCm39) R278L possibly damaging Het
Bcl9 A G 3: 97,116,231 (GRCm39) L821P probably benign Het
Cdh19 C T 1: 110,847,320 (GRCm39) V430I probably benign Het
Clns1a T A 7: 97,363,111 (GRCm39) probably null Het
Col3a1 T A 1: 45,385,281 (GRCm39) C133S probably damaging Het
Csmd1 G A 8: 17,266,749 (GRCm39) T59I probably damaging Het
Cyp2a12 A G 7: 26,736,071 (GRCm39) *493W probably null Het
Cyp2j8 A T 4: 96,395,438 (GRCm39) D62E probably benign Het
Dcbld1 A T 10: 52,196,075 (GRCm39) M428L probably benign Het
Dhx32 A T 7: 133,323,976 (GRCm39) Y523* probably null Het
Dlgap2 C T 8: 14,828,206 (GRCm39) A538V possibly damaging Het
Dlgap3 T C 4: 127,129,982 (GRCm39) S919P probably benign Het
Dmd G C X: 83,356,089 (GRCm39) A2257P probably benign Het
Dsc1 A T 18: 20,243,209 (GRCm39) H81Q probably benign Het
Dusp8 A T 7: 141,636,298 (GRCm39) S431T possibly damaging Het
Dync1i1 A T 6: 5,767,096 (GRCm39) T59S probably damaging Het
Ecel1 A G 1: 87,075,997 (GRCm39) S727P probably damaging Het
Ednrb T A 14: 104,059,204 (GRCm39) D274V probably benign Het
Eef1d G T 15: 75,775,062 (GRCm39) A199E probably benign Het
Eml3 T A 19: 8,911,718 (GRCm39) probably null Het
Enah G T 1: 181,749,318 (GRCm39) A138E probably damaging Het
Fgf18 A C 11: 33,068,003 (GRCm39) F129C probably damaging Het
Gba1 A T 3: 89,112,868 (GRCm39) E170V probably benign Het
Hdac1 C T 4: 129,416,157 (GRCm39) R212Q probably benign Het
Heatr1 T A 13: 12,447,527 (GRCm39) L1740Q probably null Het
Inhbb T A 1: 119,348,431 (GRCm39) H129L probably benign Het
Inpp5b T A 4: 124,691,662 (GRCm39) H862Q probably benign Het
Itsn2 C A 12: 4,757,025 (GRCm39) R1372S probably benign Het
Jaml T A 9: 45,012,362 (GRCm39) I283N probably damaging Het
Klk1b21 A T 7: 43,755,193 (GRCm39) T163S probably benign Het
Lmo3 A T 6: 138,393,492 (GRCm39) C43S probably damaging Het
Metrn C T 17: 26,014,197 (GRCm39) V210I probably benign Het
Ndufaf7 A T 17: 79,252,442 (GRCm39) I284F possibly damaging Het
Nlrp6 T C 7: 140,506,357 (GRCm39) V766A probably benign Het
Or10a5 A G 7: 106,635,938 (GRCm39) D192G probably damaging Het
Osbpl7 T C 11: 96,946,905 (GRCm39) S403P probably benign Het
Pabpc4l T C 3: 46,401,276 (GRCm39) T123A probably benign Het
Psg20 T A 7: 18,414,947 (GRCm39) Y316F probably benign Het
Psmd1 T A 1: 86,006,422 (GRCm39) S263T possibly damaging Het
Pum1 C A 4: 130,396,581 (GRCm39) T112K possibly damaging Het
Rasgrp2 T A 19: 6,454,425 (GRCm39) M156K probably benign Het
Reln T A 5: 22,223,998 (GRCm39) E917V probably damaging Het
Rfc4 A T 16: 22,943,314 (GRCm39) V61E probably damaging Het
Rnf112 C T 11: 61,341,854 (GRCm39) V317I possibly damaging Het
Rpe T C 1: 66,754,387 (GRCm39) M153T probably damaging Het
Rtn4ip1 A G 10: 43,811,993 (GRCm39) probably null Het
Sap18 T A 14: 58,036,011 (GRCm39) S66T probably damaging Het
Scamp5 C A 9: 57,354,508 (GRCm39) V49F possibly damaging Het
Serhl A G 15: 82,999,776 (GRCm39) Q252R probably benign Het
Sestd1 T C 2: 77,042,867 (GRCm39) D229G probably benign Het
Slc35g1 T C 19: 38,391,735 (GRCm39) V339A probably benign Het
Slc9b2 T A 3: 135,034,743 (GRCm39) probably null Het
Stk40 C T 4: 126,022,640 (GRCm39) T138I probably benign Het
Syt10 C T 15: 89,674,979 (GRCm39) D456N probably damaging Het
Tep1 T G 14: 51,076,443 (GRCm39) K1664Q probably benign Het
Tmod2 T C 9: 75,493,377 (GRCm39) K193E possibly damaging Het
Trak1 T A 9: 121,302,063 (GRCm39) *940R probably null Het
Ttc5 A T 14: 51,012,822 (GRCm39) Y189N probably damaging Het
Ugt2a3 A T 5: 87,484,430 (GRCm39) M198K probably damaging Het
Uox A G 3: 146,318,297 (GRCm39) H66R probably benign Het
Usp9y A T Y: 1,303,451 (GRCm39) D2487E probably benign Het
Vnn3 G A 10: 23,740,311 (GRCm39) G205R probably damaging Het
Vps11 T C 9: 44,260,294 (GRCm39) D856G probably benign Het
Zdhhc17 T C 10: 110,817,909 (GRCm39) N90D possibly damaging Het
Zfp105 T A 9: 122,758,743 (GRCm39) L138* probably null Het
Zfp28 A G 7: 6,397,875 (GRCm39) Y770C probably benign Het
Zfp655 T A 5: 145,181,594 (GRCm39) L484Q probably damaging Het
Zfp868 C A 8: 70,064,646 (GRCm39) E230* probably null Het
Zfpm2 A G 15: 40,966,419 (GRCm39) Y836C 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
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
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'- TGTGAGTAGGACCTGGAGTC -3'
(R):5'- CATAAGGAACAGCCCAGTGTC -3'

Sequencing Primer
(F):5'- AGTCCCGCCTGCCTGAATG -3'
(R):5'- TCTACAAGTGAGTTCCAGGATAGCC -3'
Posted On 2014-09-18