Incidental Mutation 'R1344:Rd3'
ID 200697
Institutional Source Beutler Lab
Gene Symbol Rd3
Ensembl Gene ENSMUSG00000049353
Gene Name retinal degeneration 3
Synonyms 3322402L07Rik, rd-3, rd3
MMRRC Submission 039409-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R1344 (G1)
Quality Score 128
Status Not validated
Chromosome 1
Chromosomal Location 191709331-191720244 bp(+) (GRCm39)
Type of Mutation makesense
DNA Base Change (assembly) T to C at 191717262 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Stop codon to Arginine at position 106 (*106R)
Ref Sequence ENSEMBL: ENSMUSP00000137756 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000175680] [ENSMUST00000180463] [ENSMUST00000181512]
AlphaFold Q8BRE0
Predicted Effect probably benign
Transcript: ENSMUST00000053463
AA Change: M244T

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000050188
Gene: ENSMUSG00000049353
AA Change: M244T

DomainStartEndE-ValueType
Pfam:RD3 120 248 3.3e-48 PFAM
Predicted Effect probably null
Transcript: ENSMUST00000175680
AA Change: *106R
SMART Domains Protein: ENSMUSP00000135650
Gene: ENSMUSG00000049353
AA Change: *106R

DomainStartEndE-ValueType
Pfam:RD3 4 79 4.7e-24 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000180429
Predicted Effect probably benign
Transcript: ENSMUST00000180463
AA Change: M129T

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000138049
Gene: ENSMUSG00000049353
AA Change: M129T

DomainStartEndE-ValueType
Pfam:RD3 4 134 2.2e-50 PFAM
Predicted Effect probably null
Transcript: ENSMUST00000181512
AA Change: *106R
SMART Domains Protein: ENSMUSP00000137756
Gene: ENSMUSG00000049353
AA Change: *106R

DomainStartEndE-ValueType
Pfam:RD3 4 79 4.7e-24 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000192547
Predicted Effect noncoding transcript
Transcript: ENSMUST00000226862
Coding Region Coverage
  • 1x: 97.4%
  • 3x: 96.8%
  • 10x: 95.2%
  • 20x: 92.2%
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: 79 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
5730596B20Rik T G 6: 52,156,131 (GRCm39) probably benign Het
Aco1 T C 4: 40,179,008 (GRCm39) Y336H probably damaging Het
Adamts12 T A 15: 11,286,890 (GRCm39) W832R probably damaging Het
Asxl2 A G 12: 3,543,790 (GRCm39) K320E probably damaging Het
Atrnl1 G A 19: 57,924,137 (GRCm39) probably null Het
B4galnt2 A C 11: 95,760,181 (GRCm39) I282S probably benign Het
Bcl2l13 T C 6: 120,853,288 (GRCm39) I191T probably benign Het
Bltp3a A G 17: 28,113,551 (GRCm39) K1241R probably benign Het
Cd101 A T 3: 100,926,091 (GRCm39) Y209* probably null Het
Cd109 A T 9: 78,579,832 (GRCm39) probably null Het
Cdc34 G A 10: 79,521,134 (GRCm39) A128T probably damaging Het
Cdk12 T A 11: 98,132,611 (GRCm39) S1013R unknown Het
Cntd1 T A 11: 101,176,566 (GRCm39) L221Q possibly damaging Het
Cntn4 G A 6: 106,321,831 (GRCm39) probably null Het
Col12a1 T A 9: 79,606,837 (GRCm39) K529* probably null Het
Col17a1 T A 19: 47,659,944 (GRCm39) D336V probably damaging Het
Creb3l4 A G 3: 90,146,045 (GRCm39) I193T possibly damaging Het
Cyp2d10 A T 15: 82,290,106 (GRCm39) probably null Het
Dcun1d3 A G 7: 119,457,158 (GRCm39) F185L probably damaging Het
Dlec1 G A 9: 118,959,085 (GRCm39) E910K probably benign Het
Dnajc19 T A 3: 34,112,161 (GRCm39) N128I probably damaging Het
Dusp1 A G 17: 26,727,293 (GRCm39) V2A probably benign Het
Eea1 G A 10: 95,830,861 (GRCm39) probably null Het
Elf1 T C 14: 79,798,215 (GRCm39) V34A probably damaging Het
Extl1 T C 4: 134,086,552 (GRCm39) D501G probably damaging Het
Fcgr2b T C 1: 170,788,650 (GRCm39) Y319C probably damaging Het
Fhip2a G A 19: 57,359,594 (GRCm39) A45T possibly damaging Het
Fxr2 A G 11: 69,539,710 (GRCm39) H247R possibly damaging Het
Gask1a A T 9: 121,807,452 (GRCm39) H532L probably damaging Het
Gfra1 A C 19: 58,226,849 (GRCm39) S461A possibly damaging Het
Gli2 T G 1: 118,769,666 (GRCm39) I629L probably damaging Het
Gpx3 G A 11: 54,800,422 (GRCm39) V207I probably damaging Het
Helz2 T C 2: 180,879,389 (GRCm39) D743G possibly damaging Het
Hormad2 A G 11: 4,359,005 (GRCm39) probably null Het
Ifitm1 C T 7: 140,548,263 (GRCm39) T32M probably benign Het
Iqca1 C A 1: 90,070,453 (GRCm39) G133V probably null Het
Lrit2 A G 14: 36,790,513 (GRCm39) N64S probably benign Het
Lsm14a A T 7: 34,052,982 (GRCm39) D322E probably damaging Het
Macf1 T G 4: 123,327,246 (GRCm39) R4752S probably damaging Het
Mark3 T C 12: 111,594,271 (GRCm39) I307T possibly damaging Het
Mpdz T A 4: 81,226,556 (GRCm39) T1360S probably benign Het
Mtif2 G A 11: 29,495,002 (GRCm39) V701I probably benign Het
Myh3 A G 11: 66,983,158 (GRCm39) E895G probably benign Het
Ncan A C 8: 70,560,819 (GRCm39) I716R probably benign Het
Ncor2 C T 5: 125,102,510 (GRCm39) R1867K probably damaging Het
Oas1d C T 5: 121,052,959 (GRCm39) L5F probably damaging Het
Or10s1 T A 9: 39,985,768 (GRCm39) L59H probably damaging Het
Or11h4b T A 14: 50,918,315 (GRCm39) M259L probably benign Het
Or13a17 T C 7: 140,271,712 (GRCm39) V298A probably damaging Het
Or3a4 A T 11: 73,945,038 (GRCm39) C182* probably null Het
Otog G T 7: 45,924,039 (GRCm39) A1133S probably damaging Het
Oxtr C T 6: 112,454,138 (GRCm39) R42Q probably benign Het
Pcdhb2 G A 18: 37,428,710 (GRCm39) V228I possibly damaging Het
Pdcd11 A G 19: 47,118,516 (GRCm39) D1794G probably damaging Het
Pde1c T C 6: 56,338,752 (GRCm39) I27V probably benign Het
Pde4d C A 13: 110,086,921 (GRCm39) S609* probably null Het
Piezo2 T A 18: 63,154,325 (GRCm39) I2485F probably damaging Het
Plekhd1 A G 12: 80,739,659 (GRCm39) T3A probably benign Het
Plscr1 C T 9: 92,141,357 (GRCm39) T15I unknown Het
Rnf125 A G 18: 21,114,288 (GRCm39) I97V possibly damaging Het
Sec24b T C 3: 129,801,072 (GRCm39) N408S probably damaging Het
Sf3b3 G C 8: 111,564,935 (GRCm39) A291G probably damaging Het
Simc1 T C 13: 54,698,292 (GRCm39) V403A probably damaging Het
Slc38a9 T C 13: 112,826,714 (GRCm39) C151R probably benign Het
Slco1a8 A G 6: 141,931,344 (GRCm39) S474P probably damaging Het
Slitrk5 A G 14: 111,917,821 (GRCm39) S482G probably benign Het
Smyd1 G A 6: 71,239,151 (GRCm39) T13I probably benign Het
Speer4a3 T A 5: 26,158,107 (GRCm39) T82S probably benign Het
Stoml2 T A 4: 43,028,197 (GRCm39) I344F probably benign Het
Tet1 C T 10: 62,650,300 (GRCm39) R1636H probably damaging Het
Thap12 A G 7: 98,366,037 (GRCm39) D735G probably damaging Het
Tnip3 T C 6: 65,574,413 (GRCm39) V88A probably benign Het
Ttn A G 2: 76,565,755 (GRCm39) V28199A possibly damaging Het
Ube3b T C 5: 114,556,636 (GRCm39) F989S probably damaging Het
Ubox5 A G 2: 130,442,210 (GRCm39) L159P probably damaging Het
Uevld A T 7: 46,587,758 (GRCm39) V314E possibly damaging Het
Urb1 T C 16: 90,566,354 (GRCm39) M1478V probably damaging Het
Ust C A 10: 8,173,954 (GRCm39) V184F possibly damaging Het
Wdr95 G A 5: 149,511,563 (GRCm39) C421Y 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
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
R9541:Rd3 UTSW 1 191,717,294 (GRCm39) missense possibly damaging 0.84
Predicted Primers PCR Primer
(F):5'- AGGCTCCTTGCATATGAGCACAC -3'
(R):5'- ACAGAGTCACCAGCCCGTTATTCC -3'

Sequencing Primer
(F):5'- acaggtgagaaaactgaggc -3'
(R):5'- CCGTTATTCCTCCTGAGGGTG -3'
Posted On 2014-05-23