Incidental Mutation 'R9541:Rd3'
ID 719855
Institutional Source Beutler Lab
Gene Symbol Rd3
Ensembl Gene ENSMUSG00000049353
Gene Name retinal degeneration 3
Synonyms 3322402L07Rik, rd-3, rd3
MMRRC Submission
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R9541 (G1)
Quality Score 192.009
Status Not validated
Chromosome 1
Chromosomal Location 191709331-191720244 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to A at 191717294 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Arginine to Serine at position 140 (R140S)
Ref Sequence ENSEMBL: ENSMUSP00000138049 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000175680] [ENSMUST00000180463] [ENSMUST00000181512]
AlphaFold Q8BRE0
Predicted Effect probably benign
Transcript: ENSMUST00000175680
SMART Domains Protein: ENSMUSP00000135650
Gene: ENSMUSG00000049353

DomainStartEndE-ValueType
Pfam:RD3 4 79 4.7e-24 PFAM
Predicted Effect possibly damaging
Transcript: ENSMUST00000180463
AA Change: R140S

PolyPhen 2 Score 0.841 (Sensitivity: 0.84; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000138049
Gene: ENSMUSG00000049353
AA Change: R140S

DomainStartEndE-ValueType
Pfam:RD3 4 134 2.2e-50 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000181512
SMART Domains Protein: ENSMUSP00000137756
Gene: ENSMUSG00000049353

DomainStartEndE-ValueType
Pfam:RD3 4 79 4.7e-24 PFAM
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.1%
  • 20x: 96.5%
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a retinal protein that is associated with promyelocytic leukemia-gene product (PML) bodies in the nucleus. Mutations in this gene cause Leber congenital amaurosis type 12, a disease that results in retinal degeneration. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2009]
PHENOTYPE: Homozygotes for a spontaneous mutation exhibit retinal degeneration, beginning at 3 weeks of age, characterized by complete loss of photoreceptor rod cells by 5 weeks, and cones by 8 weeks. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 51 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcc8 T C 7: 45,801,079 (GRCm39) I450V probably benign Het
Adam21 T C 12: 81,607,724 (GRCm39) T13A probably benign Het
Adamts4 C A 1: 171,084,695 (GRCm39) P644H probably damaging Het
Ak9 C T 10: 41,243,173 (GRCm39) A689V Het
Ankhd1 G A 18: 36,757,697 (GRCm39) S209N Het
Anks1b A T 10: 90,412,947 (GRCm39) T32S probably benign Het
Atp13a4 G T 16: 29,241,544 (GRCm39) T708K Het
B4gat1 C T 19: 5,089,896 (GRCm39) P298S probably damaging Het
Btbd9 A G 17: 30,439,438 (GRCm39) L583P possibly damaging Het
Ciart C A 3: 95,788,527 (GRCm39) C104F possibly damaging Het
Coq5 T C 5: 115,417,901 (GRCm39) S44P probably benign Het
Dennd5b A G 6: 148,899,872 (GRCm39) V1175A probably benign Het
Filip1 T A 9: 79,727,135 (GRCm39) K495* probably null Het
Fscn2 G A 11: 120,258,771 (GRCm39) V439M probably damaging Het
Gcn1 A G 5: 115,754,416 (GRCm39) I2339V probably benign Het
Gmppa T A 1: 75,417,094 (GRCm39) S176R probably damaging Het
Gpatch3 G A 4: 133,305,595 (GRCm39) E277K probably benign Het
Hcn4 A G 9: 58,767,685 (GRCm39) D1082G probably damaging Het
Hdgfl2 T A 17: 56,405,976 (GRCm39) D487E unknown Het
Ifna14 A T 4: 88,490,010 (GRCm39) M9K probably null Het
Igkv4-81 A G 6: 68,967,925 (GRCm39) Y59H Het
Il2rb T A 15: 78,372,393 (GRCm39) N108I probably benign Het
Jarid2 C T 13: 45,068,253 (GRCm39) R1092W possibly damaging Het
Kdm5d T G Y: 910,801 (GRCm39) C304W probably damaging Het
Khnyn T C 14: 56,124,109 (GRCm39) I121T possibly damaging Het
Lmcd1 A T 6: 112,306,824 (GRCm39) H332L probably damaging Het
Lrp1b T C 2: 41,234,600 (GRCm39) D1117G Het
Med25 A G 7: 44,541,267 (GRCm39) V82A possibly damaging Het
Mindy2 G A 9: 70,512,508 (GRCm39) R581C possibly damaging Het
Mindy3 T C 2: 12,391,449 (GRCm39) T257A probably damaging Het
Myo1e A T 9: 70,204,628 (GRCm39) Y76F probably damaging Het
Npas2 A T 1: 39,377,194 (GRCm39) I519F possibly damaging Het
Or2h2c C T 17: 37,422,824 (GRCm39) D17N probably benign Het
Or4f52 T A 2: 111,061,275 (GRCm39) T288S probably damaging Het
Or5ak25 T A 2: 85,269,025 (GRCm39) H159L possibly damaging Het
Otx1 A G 11: 21,947,052 (GRCm39) F86L probably damaging Het
Pcm1 A G 8: 41,780,616 (GRCm39) D1856G probably benign Het
Pcsk7 G A 9: 45,820,768 (GRCm39) E67K probably benign Het
Pkd2 A G 5: 104,607,927 (GRCm39) Y142C probably damaging Het
Ptpre A G 7: 135,266,740 (GRCm39) D236G probably benign Het
Rasd2 T C 8: 75,945,200 (GRCm39) C10R probably benign Het
Rusc1 T G 3: 88,998,922 (GRCm39) T287P possibly damaging Het
Slc22a7 T C 17: 46,749,084 (GRCm39) S78G probably damaging Het
Sltm A T 9: 70,481,057 (GRCm39) H303L unknown Het
Syne4 G A 7: 30,016,343 (GRCm39) V228I probably benign Het
Timm22 T A 11: 76,300,641 (GRCm39) C138S possibly damaging Het
Trib2 T A 12: 15,866,827 (GRCm39) I15L unknown Het
Ttn C T 2: 76,715,357 (GRCm39) E7912K unknown Het
Tyro3 T C 2: 119,642,589 (GRCm39) V591A possibly damaging Het
Vmn2r69 A G 7: 85,056,209 (GRCm39) V643A probably benign Het
Zfp281 G T 1: 136,555,303 (GRCm39) Q760H probably damaging Het
Other mutations in Rd3
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01520:Rd3 APN 1 191,717,283 (GRCm39) missense possibly damaging 0.84
IGL02319:Rd3 APN 1 191,715,452 (GRCm39) missense probably null 1.00
R0098:Rd3 UTSW 1 191,717,261 (GRCm39) missense probably benign 0.05
R0098:Rd3 UTSW 1 191,717,261 (GRCm39) missense probably benign 0.05
R0458:Rd3 UTSW 1 191,709,414 (GRCm39) missense probably damaging 0.96
R0537:Rd3 UTSW 1 191,715,501 (GRCm39) missense probably damaging 1.00
R0991:Rd3 UTSW 1 191,717,199 (GRCm39) missense probably damaging 0.98
R1344:Rd3 UTSW 1 191,717,262 (GRCm39) makesense probably null
R2168:Rd3 UTSW 1 191,715,488 (GRCm39) missense probably damaging 0.97
R3898:Rd3 UTSW 1 191,717,217 (GRCm39) missense probably damaging 1.00
R3899:Rd3 UTSW 1 191,717,217 (GRCm39) missense probably damaging 1.00
R3900:Rd3 UTSW 1 191,717,217 (GRCm39) missense probably damaging 1.00
R5870:Rd3 UTSW 1 191,717,261 (GRCm39) missense probably benign 0.00
R8047:Rd3 UTSW 1 191,709,620 (GRCm39) start gained probably benign
R8506:Rd3 UTSW 1 191,715,228 (GRCm39) start codon destroyed probably null 0.98
Predicted Primers PCR Primer
(F):5'- AGAGCAAGGTTGGGAGTTTC -3'
(R):5'- AGTCACCAGCCCGTTATTCC -3'

Sequencing Primer
(F):5'- CTGGCTTGTGAGATGCTCAGTC -3'
(R):5'- CCTCCTGAGGGTGATTGC -3'
Posted On 2022-07-18