Incidental Mutation 'R5870:Rd3'
ID502019
Institutional Source Beutler Lab
Gene Symbol Rd3
Ensembl Gene ENSMUSG00000049353
Gene Nameretinal degeneration 3
Synonymsrd3, rd-3
MMRRC Submission 044078-MU
Accession Numbers
Is this an essential gene? Non essential (E-score: 0.000) question?
Stock #R5870 (G1)
Quality Score41
Status Validated
Chromosome1
Chromosomal Location191977370-191988283 bp(+) (GRCm38)
Type of Mutationmissense
DNA Base Change (assembly) A to T at 191985300 bp
ZygosityHeterozygous
Amino Acid Change Methionine to Leucine at position 244 (M244L)
Gene Model predicted gene model for transcript(s): [ENSMUST00000175680] [ENSMUST00000180463] [ENSMUST00000181512]
Predicted Effect probably benign
Transcript: ENSMUST00000053463
AA Change: M244L

PolyPhen 2 Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)
SMART Domains Protein: ENSMUSP00000050188
Gene: ENSMUSG00000049353
AA Change: M244L

DomainStartEndE-ValueType
Pfam:RD3 120 248 3.3e-48 PFAM
Predicted Effect unknown
Transcript: ENSMUST00000175680
AA Change: R105S
SMART Domains Protein: ENSMUSP00000135650
Gene: ENSMUSG00000049353
AA Change: R105S

DomainStartEndE-ValueType
Pfam:RD3 4 79 4.7e-24 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000180429
Predicted Effect probably benign
Transcript: ENSMUST00000180463
AA Change: M129L

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000138049
Gene: ENSMUSG00000049353
AA Change: M129L

DomainStartEndE-ValueType
Pfam:RD3 4 134 2.2e-50 PFAM
Predicted Effect unknown
Transcript: ENSMUST00000181512
AA Change: R105S
SMART Domains Protein: ENSMUSP00000137756
Gene: ENSMUSG00000049353
AA Change: R105S

DomainStartEndE-ValueType
Pfam:RD3 4 79 4.7e-24 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000192547
Predicted Effect noncoding transcript
Transcript: ENSMUST00000226862
Meta Mutation Damage Score 0.0587 question?
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.4%
  • 10x: 97.2%
  • 20x: 91.1%
Validation Efficiency 93% (84/90)
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: 71 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adcy9 A G 16: 4,418,368 V156A probably damaging Het
Ak6 C A 13: 100,655,424 P125Q probably damaging Het
Aqp4 A C 18: 15,399,889 V49G probably damaging Het
Arfgef1 A G 1: 10,180,938 I874T probably damaging Het
Arid1a T C 4: 133,681,076 D2040G unknown Het
Atp1a3 T G 7: 24,997,578 D220A probably benign Het
C2cd4c A T 10: 79,612,209 I368N possibly damaging Het
Ccnt1 G A 15: 98,543,513 Q625* probably null Het
Cd177 T A 7: 24,756,332 H255L probably benign Het
Cdipt G A 7: 126,978,922 V114M probably benign Het
Coro1b T A 19: 4,149,385 H14Q probably damaging Het
Ctdp1 T A 18: 80,408,686 D158V unknown Het
Cts7 A T 13: 61,355,731 S140T probably damaging Het
Dlgap3 T A 4: 127,195,709 L366* probably null Het
Dnah9 C T 11: 66,085,210 A1338T probably benign Het
Dock7 T C 4: 99,063,962 I424V probably benign Het
Dock8 G T 19: 25,132,126 A891S probably benign Het
Elmod3 A G 6: 72,594,738 probably null Het
Eps15 G A 4: 109,361,310 E107K probably damaging Het
Esco1 A T 18: 10,593,744 probably null Het
Fuz A G 7: 44,900,318 T407A probably damaging Het
Galr1 A T 18: 82,406,072 F27I probably benign Het
Glt1d1 A G 5: 127,677,280 Y182C probably damaging Het
Gm37240 A T 3: 84,690,521 probably benign Het
Gm37610 A G 6: 41,084,914 noncoding transcript Het
Gm6658 G T 8: 90,908,392 probably benign Het
Gm9376 A G 14: 118,267,377 T74A possibly damaging Het
Hadha G A 5: 30,144,286 S109F possibly damaging Het
Herc3 A T 6: 58,916,450 Q899L probably benign Het
Ift172 C T 5: 31,276,940 E485K probably benign Het
Lrrc8e A G 8: 4,235,725 K650R possibly damaging Het
Ly6d A T 15: 74,763,532 V10D possibly damaging Het
Med27 A G 2: 29,389,811 probably null Het
Med29 A T 7: 28,392,497 V56E probably damaging Het
Mobp A G 9: 120,167,853 K17E probably damaging Het
Mrpl37 G A 4: 107,066,722 T25I probably benign Het
Myh1 A G 11: 67,201,979 D33G possibly damaging Het
Nrg3 T A 14: 39,472,629 I58F possibly damaging Het
Olfr589 A G 7: 103,155,741 I2T probably benign Het
Olfr872 A G 9: 20,260,578 D246G probably benign Het
Padi1 T A 4: 140,826,581 D359V probably benign Het
Pcdh7 T C 5: 57,720,411 V436A possibly damaging Het
Pgm3 C A 9: 86,570,361 K15N probably damaging Het
Phip A T 9: 82,908,677 probably benign Het
Pot1a G A 6: 25,778,951 T48I possibly damaging Het
Ppic T C 18: 53,409,261 K125R probably benign Het
Ppm1j T C 3: 104,785,495 V440A possibly damaging Het
Prg4 T A 1: 150,455,549 K458* probably null Het
Rflnb A G 11: 76,022,038 Y175H probably benign Het
Rnf157 T A 11: 116,347,074 S574C probably benign Het
Sardh A G 2: 27,220,641 probably null Het
Senp3 C T 11: 69,678,222 probably null Het
Siglec1 G A 2: 131,072,847 R1450C probably damaging Het
Sim2 A G 16: 94,123,334 H446R probably damaging Het
Spon1 T C 7: 114,031,786 I444T probably damaging Het
Srebf1 T A 11: 60,203,584 Q568H possibly damaging Het
Stxbp4 A T 11: 90,537,956 I441N possibly damaging Het
Sugt1 G A 14: 79,609,011 V163I probably benign Het
Surf1 G T 2: 26,916,259 probably benign Het
Synj2 A G 17: 6,037,853 E1348G probably benign Het
Tc2n A T 12: 101,652,852 V349D probably damaging Het
Ten1 A G 11: 116,214,925 R112G possibly damaging Het
Tm9sf4 A G 2: 153,194,281 D321G probably damaging Het
Ttll12 A T 15: 83,577,036 M594K probably damaging Het
Ttn T A 2: 76,872,714 probably benign Het
Usp28 C T 9: 49,025,985 Q185* probably null Het
Vmn2r112 A G 17: 22,619,023 I822V probably benign Het
Wdr60 A G 12: 116,256,245 S26P possibly damaging Het
Zc3hc1 A T 6: 30,382,683 L88* probably null Het
Zfr T A 15: 12,160,615 V758D probably damaging Het
Zfyve27 T G 19: 42,171,671 L42R probably benign Het
Other mutations in Rd3
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01520:Rd3 APN 1 191985322 missense possibly damaging 0.84
IGL02319:Rd3 APN 1 191983491 missense probably null 1.00
R0098:Rd3 UTSW 1 191985300 missense probably benign 0.05
R0098:Rd3 UTSW 1 191985300 missense probably benign 0.05
R0458:Rd3 UTSW 1 191977453 missense probably damaging 0.96
R0537:Rd3 UTSW 1 191983540 missense probably damaging 1.00
R0991:Rd3 UTSW 1 191985238 missense probably damaging 0.98
R1344:Rd3 UTSW 1 191985301 makesense probably null
R2168:Rd3 UTSW 1 191983527 missense probably damaging 0.97
R3898:Rd3 UTSW 1 191985256 missense probably damaging 1.00
R3899:Rd3 UTSW 1 191985256 missense probably damaging 1.00
R3900:Rd3 UTSW 1 191985256 missense probably damaging 1.00
R8047:Rd3 UTSW 1 191977659 start gained probably benign
R8506:Rd3 UTSW 1 191983267 start codon destroyed probably null 0.98
Predicted Primers PCR Primer
(F):5'- AGCTCAAGATTGACTGGGAC -3'
(R):5'- AGCCCGTTATTCCTCCTGAG -3'

Sequencing Primer
(F):5'- CTCAAGATTGACTGGGACAAGAGC -3'
(R):5'- TGAACTCCGGCATGCTCCAG -3'
Posted On2018-02-19