Mutagenetix > Incidental Mutation

Incidental Mutation 'R2168:Rd3'

235587

Institutional Source

Beutler Lab

Gene Symbol

Rd3

Ensembl Gene

ENSMUSG00000049353

Gene Name

retinal degeneration 3

Synonyms

3322402L07Rik, rd-3, rd3

MMRRC Submission

040171-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R2168 (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 191715488 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Valine at position 88 (I88V)

Ref Sequence

ENSEMBL: ENSMUSP00000138049 (fasta)

Gene Model

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

AlphaFold

Q8BRE0

Predicted Effect

possibly damaging
Transcript: ENSMUST00000053463
AA Change: I203V

PolyPhen 2 Score 0.863 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000050188
Gene: ENSMUSG00000049353
AA Change: I203V

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: I88V

PolyPhen 2 Score 0.968 (Sensitivity: 0.77; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000138049
Gene: ENSMUSG00000049353
AA Change: I88V

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

0.0803

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.4%
20x: 95.5%

Validation Efficiency

100% (62/62)

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: 59 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acoxl	T	A	2: 127,720,701 (GRCm39)	I188N	probably damaging	Het
Akr1c14	T	C	13: 4,131,106 (GRCm39)	V266A	probably damaging	Het
Als2cl	C	A	9: 110,717,810 (GRCm39)	P301H	probably damaging	Het
Arsi	G	A	18: 61,049,723 (GRCm39)	G202E	probably benign	Het
Catspere2	C	T	1: 177,843,477 (GRCm39)		probably benign	Het
Cpsf1	A	T	15: 76,487,937 (GRCm39)	N53K	possibly damaging	Het
Ctsll3	C	T	13: 60,948,749 (GRCm39)	G69R	possibly damaging	Het
F2	C	T	2: 91,458,693 (GRCm39)	R539Q	probably damaging	Het
Fam78b	G	A	1: 166,906,219 (GRCm39)	G126D	probably damaging	Het
Fancd2	A	G	6: 113,568,120 (GRCm39)	I1332V	possibly damaging	Het
Flg2	C	T	3: 93,109,244 (GRCm39)	S424L	probably damaging	Het
Fpr1	T	C	17: 18,097,471 (GRCm39)	T173A	possibly damaging	Het
Gas2l3	A	G	10: 89,249,960 (GRCm39)	V386A	probably benign	Het
Gdap2	A	C	3: 100,095,199 (GRCm39)	E269A	probably benign	Het
Igf2bp2	T	A	16: 21,898,358 (GRCm39)		probably null	Het
Ipo11	T	C	13: 107,016,118 (GRCm39)		probably null	Het
Itpr2	G	T	6: 146,013,176 (GRCm39)	P2667Q	probably benign	Het
Itsn2	G	T	12: 4,683,044 (GRCm39)		probably benign	Het
Jakmip2	A	G	18: 43,698,995 (GRCm39)	L488P	probably damaging	Het
Lrp1b	A	T	2: 41,265,858 (GRCm39)	C248S	probably damaging	Het
Lrrc17	A	T	5: 21,780,046 (GRCm39)	D340V	probably damaging	Het
Megf9	T	C	4: 70,351,679 (GRCm39)	T481A	probably damaging	Het
Mrc1	T	C	2: 14,249,015 (GRCm39)	S184P	possibly damaging	Het
Msh4	A	T	3: 153,573,472 (GRCm39)	Y533*	probably null	Het
Mug1	A	G	6: 121,847,458 (GRCm39)	N612S	probably benign	Het
Nectin2	G	T	7: 19,464,539 (GRCm39)	S288R	probably damaging	Het
Neurog2	A	T	3: 127,427,754 (GRCm39)	H126L	probably damaging	Het
Nol10	A	T	12: 17,423,585 (GRCm39)	E310V	probably damaging	Het
Or1f12	T	G	13: 21,721,422 (GRCm39)	K251T	probably damaging	Het
Or4c29	A	G	2: 88,740,522 (GRCm39)	S72P	probably damaging	Het
Or51h7	A	T	7: 102,591,678 (GRCm39)	F35L	probably benign	Het
Or5h23	T	A	16: 58,905,949 (GRCm39)	K299I	probably benign	Het
Pappa	A	C	4: 65,074,682 (GRCm39)	D412A	probably damaging	Het
Pcdhb7	T	A	18: 37,476,335 (GRCm39)	F490L	probably benign	Het
Pcsk1	T	A	13: 75,260,653 (GRCm39)		probably benign	Het
Plekhn1	T	A	4: 156,306,339 (GRCm39)	D577V	probably damaging	Het
Prrc2c	C	A	1: 162,537,903 (GRCm39)		probably benign	Het
Ptch1	T	G	13: 63,672,773 (GRCm39)	E944A	probably benign	Het
Pzp	G	A	6: 128,465,010 (GRCm39)	T1288M	probably damaging	Het
Radil	A	C	5: 142,492,718 (GRCm39)	H63Q	probably benign	Het
Rai1	T	C	11: 60,078,422 (GRCm39)	S829P	probably benign	Het
Rfesd	T	C	13: 76,156,244 (GRCm39)	D54G	probably damaging	Het
Rnf213	A	C	11: 119,305,896 (GRCm39)	K568T	probably damaging	Het
Scaper	T	A	9: 55,650,923 (GRCm39)	K913N	probably damaging	Het
Serpina3c	T	C	12: 104,115,628 (GRCm39)		probably null	Het
Serpinb6d	A	T	13: 33,850,357 (GRCm39)	K61N	probably benign	Het
Skint4	A	T	4: 111,944,183 (GRCm39)		probably null	Het
Sod1	T	C	16: 90,017,801 (GRCm39)	I19T	possibly damaging	Het
Stfa3	C	A	16: 36,271,042 (GRCm39)	G81*	probably null	Het
Ubr4	A	G	4: 139,137,960 (GRCm39)	T1106A	probably benign	Het
Uggt2	T	A	14: 119,256,917 (GRCm39)	N1106Y	probably damaging	Het
Vmn1r217	G	A	13: 23,298,714 (GRCm39)	Q63*	probably null	Het
Vmn2r129	A	T	4: 156,690,673 (GRCm39)		noncoding transcript	Het
Vps13b	C	A	15: 35,792,334 (GRCm39)	P2201T	probably damaging	Het
Vps13b	C	A	15: 35,792,335 (GRCm39)	P2201Q	probably damaging	Het
Vps13d	G	T	4: 144,813,893 (GRCm39)		probably benign	Het
Zer1	A	G	2: 29,994,887 (GRCm39)	C503R	probably damaging	Het
Zfp369	T	C	13: 65,444,762 (GRCm39)	V635A	probably benign	Het
Zfp608	A	T	18: 55,031,125 (GRCm39)	Y938*	probably null	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
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
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'- TGCTGGAGACGCTCATGATG -3'
(R):5'- CTCTAGAATCTGCCTCCAGC -3'

Sequencing Primer
(F):5'- CTCATGATGGAGCTGGCTG -3'
(R):5'- GATGAAGCCTCCCCCAAGTCTG -3'

Posted On

2014-10-01