Mutagenetix > Incidental Mutation

Incidental Mutation 'R0537:Rd3'

49482

Institutional Source

Beutler Lab

Gene Symbol

Rd3

Ensembl Gene

ENSMUSG00000049353

Gene Name

retinal degeneration 3

Synonyms

3322402L07Rik, rd-3, rd3

MMRRC Submission

038729-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R0537 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

191709331-191720244 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 191715501 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Cysteine at position 92 (Y92C)

Ref Sequence

ENSEMBL: ENSMUSP00000138049 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000175680] [ENSMUST00000180463] [ENSMUST00000181512]

AlphaFold

Q8BRE0

Predicted Effect

probably damaging
Transcript: ENSMUST00000053463
AA Change: Y207C

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000050188
Gene: ENSMUSG00000049353
AA Change: Y207C

Domain	Start	End	E-Value	Type
Pfam:RD3	120	248	3.3e-48	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000175680

SMART Domains

Protein: ENSMUSP00000135650
Gene: ENSMUSG00000049353

Domain	Start	End	E-Value	Type
Pfam:RD3	4	79	4.7e-24	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000180429

Predicted Effect

probably damaging
Transcript: ENSMUST00000180463
AA Change: Y92C

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000138049
Gene: ENSMUSG00000049353
AA Change: Y92C

Domain	Start	End	E-Value	Type
Pfam:RD3	4	134	2.2e-50	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000181512

SMART Domains

Protein: ENSMUSP00000137756
Gene: ENSMUSG00000049353

Domain	Start	End	E-Value	Type
Pfam:RD3	4	79	4.7e-24	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000192547

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000226862

Meta Mutation Damage Score

0.0659

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 96.7%
20x: 93.9%

Validation Efficiency

100% (53/53)

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
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930474N05Rik	A	T	14: 35,818,657 (GRCm39)	K218N	probably benign	Het
Acot11	T	C	4: 106,619,652 (GRCm39)	E156G	probably benign	Het
Arhgef28	A	T	13: 98,094,224 (GRCm39)	N973K	probably damaging	Het
B4galt3	T	C	1: 171,101,821 (GRCm39)		probably benign	Het
Bmpr1a	T	C	14: 34,165,769 (GRCm39)		probably benign	Het
Camkmt	A	T	17: 85,702,087 (GRCm39)	I184F	probably benign	Het
Ccdc33	T	C	9: 58,024,737 (GRCm39)	Y163C	probably damaging	Het
Ccdc9	A	G	7: 16,014,701 (GRCm39)		probably benign	Het
Dars2	A	T	1: 160,888,318 (GRCm39)	C201S	possibly damaging	Het
Dnajc1	A	T	2: 18,312,767 (GRCm39)	S194R	possibly damaging	Het
Dock8	A	G	19: 25,148,941 (GRCm39)	D1473G	probably benign	Het
Dpm2	T	A	2: 32,462,961 (GRCm39)		probably null	Het
Dsg4	T	C	18: 20,591,628 (GRCm39)	S456P	probably damaging	Het
Gys1	T	C	7: 45,089,425 (GRCm39)	S195P	probably damaging	Het
Heatr6	G	T	11: 83,670,290 (GRCm39)	E948*	probably null	Het
Itgal	G	A	7: 126,910,445 (GRCm39)	R518Q	possibly damaging	Het
Klhdc8b	G	C	9: 108,326,422 (GRCm39)	R158G	possibly damaging	Het
Klhl41	G	A	2: 69,500,554 (GRCm39)	R5Q	probably benign	Het
Lrrtm4	A	T	6: 79,999,103 (GRCm39)	T172S	probably benign	Het
Lypd1	A	G	1: 125,840,604 (GRCm39)		probably benign	Het
Mei1	T	C	15: 81,975,562 (GRCm39)	F121S	possibly damaging	Het
Mtor	C	T	4: 148,622,817 (GRCm39)	R1966W	probably damaging	Het
Myh7	A	G	14: 55,228,256 (GRCm39)	F247L	possibly damaging	Het
Nebl	G	T	2: 17,409,026 (GRCm39)	D392E	possibly damaging	Het
Notch2	C	A	3: 98,024,057 (GRCm39)	N840K	possibly damaging	Het
Nubp1	T	C	16: 10,240,678 (GRCm39)		probably benign	Het
Or5w16	A	T	2: 87,577,017 (GRCm39)	Q159L	probably benign	Het
Or7g19	T	C	9: 18,856,444 (GRCm39)	S167P	probably damaging	Het
Pcdh17	T	A	14: 84,684,897 (GRCm39)	S455T	probably damaging	Het
Picalm	C	A	7: 89,779,876 (GRCm39)	H32Q	probably benign	Het
Pold1	T	C	7: 44,184,516 (GRCm39)	E828G	probably damaging	Het
Ptpro	T	A	6: 137,420,592 (GRCm39)	V1007D	probably damaging	Het
Rala	A	T	13: 18,063,233 (GRCm39)	N119K	probably benign	Het
Rasal2	A	T	1: 156,975,362 (GRCm39)	V1149E	possibly damaging	Het
Rps18-ps6	A	T	13: 97,897,071 (GRCm39)	F9Y	probably benign	Het
Sart1	A	T	19: 5,431,752 (GRCm39)	D635E	probably damaging	Het
Sec16b	A	G	1: 157,365,116 (GRCm39)	T335A	possibly damaging	Het
Slc11a2	C	T	15: 100,303,679 (GRCm39)	G185R	probably damaging	Het
Slc2a12	G	A	10: 22,540,967 (GRCm39)	R274H	probably damaging	Het
Spag17	T	C	3: 100,032,618 (GRCm39)	V2276A	probably damaging	Het
Tcam1	G	A	11: 106,174,904 (GRCm39)	E120K	probably benign	Het
Tenm2	T	C	11: 36,054,557 (GRCm39)	D601G	probably damaging	Het
Tmem168	C	A	6: 13,603,360 (GRCm39)	C2F	probably damaging	Het
Tmem80	A	G	7: 140,913,609 (GRCm39)	Y13C	probably damaging	Het
Try4	T	A	6: 41,281,296 (GRCm39)	N79K	probably benign	Het
Vldlr	C	A	19: 27,225,318 (GRCm39)	N798K	probably damaging	Het
Wdr41	A	G	13: 95,131,813 (GRCm39)		probably benign	Het
Zfp30	A	T	7: 29,492,160 (GRCm39)	E138V	probably damaging	Het
Zfp366	A	C	13: 99,365,786 (GRCm39)	T316P	probably damaging	Het
Zfp563	A	T	17: 33,323,659 (GRCm39)	S85C	possibly damaging	Het
Znfx1	T	C	2: 166,883,621 (GRCm39)	H162R	probably damaging	Het

Other mutations in Rd3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH 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
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
R9541:Rd3	UTSW	1	191,717,294 (GRCm39)	missense	possibly damaging	0.84

Predicted Primers

PCR Primer
(F):5'- GACAAGGGACACATTCCCCTTCTTC -3'
(R):5'- GTTGACATGCATACTTGCAACCACC -3'

Sequencing Primer
(F):5'- ACGCTCATGATGGAGCTG -3'
(R):5'- TGAGGGCCTCTAGAATCTGC -3'

Posted On

2013-06-12