Mutagenetix > Incidental Mutation

Incidental Mutation 'R3899:Rd3'

308854

Institutional Source

Beutler Lab

Gene Symbol

Rd3

Ensembl Gene

ENSMUSG00000049353

Gene Name

retinal degeneration 3

Synonyms

3322402L07Rik, rd-3, rd3

MMRRC Submission

040809-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R3899 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

191709331-191720244 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 191717217 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 114 (V114A)

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: V229A

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000050188
Gene: ENSMUSG00000049353
AA Change: V229A

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

Predicted Effect

unknown
Transcript: ENSMUST00000175680
AA Change: W91R

SMART Domains

Protein: ENSMUSP00000135650
Gene: ENSMUSG00000049353
AA Change: W91R

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: V114A

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000138049
Gene: ENSMUSG00000049353
AA Change: V114A

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

Predicted Effect

unknown
Transcript: ENSMUST00000181512
AA Change: W91R

SMART Domains

Protein: ENSMUSP00000137756
Gene: ENSMUSG00000049353
AA Change: W91R

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

0.3394

Coding Region Coverage

1x: 99.3%
3x: 98.7%
10x: 97.5%
20x: 95.8%

Validation Efficiency

98% (62/63)

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: 61 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acss2	A	G	2: 155,399,157 (GRCm39)		probably benign	Het
Ahctf1	A	G	1: 179,605,345 (GRCm39)	S730P	possibly damaging	Het
Ankrd26	T	A	6: 118,526,389 (GRCm39)	R327S	probably benign	Het
Anpep	A	G	7: 79,488,973 (GRCm39)	S372P	probably benign	Het
Apob	A	T	12: 8,065,849 (GRCm39)	I4273F	possibly damaging	Het
Ascl1	G	T	10: 87,328,435 (GRCm39)	H172Q	probably benign	Het
Azi2	A	G	9: 117,876,571 (GRCm39)	Y29C	probably damaging	Het
Baz1a	A	G	12: 54,981,589 (GRCm39)	M355T	probably benign	Het
Brs3	G	A	X: 56,092,616 (GRCm39)	V367M	possibly damaging	Het
Ccdc33	T	C	9: 57,940,200 (GRCm39)	D524G	probably damaging	Het
Cd300lf	T	C	11: 115,015,177 (GRCm39)	T138A	probably damaging	Het
Cemip2	A	G	19: 21,829,598 (GRCm39)	T1236A	probably benign	Het
Ces1g	T	C	8: 94,029,678 (GRCm39)	Y518C	probably damaging	Het
Chek2	C	T	5: 111,013,479 (GRCm39)		probably benign	Het
Cherp	A	G	8: 73,223,780 (GRCm39)	I201T	possibly damaging	Het
Cntnap2	A	T	6: 45,968,837 (GRCm39)	H193L	probably benign	Het
Crim1	C	A	17: 78,588,783 (GRCm39)	T286N	probably benign	Het
Cwc27	T	A	13: 104,929,023 (GRCm39)	K307*	probably null	Het
Dbx2	T	C	15: 95,530,313 (GRCm39)	D218G	possibly damaging	Het
Dclk1	G	A	3: 55,154,750 (GRCm39)	R60Q	probably damaging	Het
Dnah17	A	T	11: 117,985,634 (GRCm39)	I1481N	possibly damaging	Het
Dnah8	G	A	17: 31,073,872 (GRCm39)	R4514H	probably damaging	Het
Dpp10	A	T	1: 123,281,286 (GRCm39)	W588R	probably damaging	Het
Epg5	G	A	18: 78,000,725 (GRCm39)	E554K	probably damaging	Het
Eya1	T	C	1: 14,340,971 (GRCm39)	T139A	probably benign	Het
Fchsd2	A	G	7: 100,841,006 (GRCm39)	K172E	possibly damaging	Het
Foxd3	A	G	4: 99,545,736 (GRCm39)	Y292C	unknown	Het
Gli1	C	T	10: 127,172,535 (GRCm39)	M202I	possibly damaging	Het
Gm973	T	C	1: 59,664,299 (GRCm39)	Y634H	probably benign	Het
Gpr132	G	T	12: 112,815,728 (GRCm39)	A366E	probably benign	Het
Kcnd3	C	T	3: 105,566,082 (GRCm39)	A421V	probably damaging	Het
Kcnq3	C	T	15: 65,902,372 (GRCm39)	M201I	probably benign	Het
Khdc3	T	C	9: 73,011,628 (GRCm39)		probably benign	Het
Lrrc37a	A	G	11: 103,388,372 (GRCm39)	V2351A	unknown	Het
Mmrn2	G	T	14: 34,121,517 (GRCm39)		probably null	Het
Mtr	A	T	13: 12,231,735 (GRCm39)	N656K	probably benign	Het
Mtus1	T	C	8: 41,536,166 (GRCm39)	T517A	probably benign	Het
Osgep	G	C	14: 51,162,200 (GRCm39)	N12K	probably damaging	Het
Pcare	A	T	17: 72,057,155 (GRCm39)	C841S	probably benign	Het
Prdx3	T	A	19: 60,853,621 (GRCm39)	T235S	probably benign	Het
Rasa3	G	A	8: 13,628,635 (GRCm39)	H608Y	probably benign	Het
Setd2	C	T	9: 110,421,586 (GRCm39)	R273W	probably damaging	Het
Slc24a1	A	T	9: 64,835,426 (GRCm39)	S900R	probably damaging	Het
Slc30a5	T	C	13: 100,954,655 (GRCm39)	M170V	probably benign	Het
Slc4a9	T	C	18: 36,668,616 (GRCm39)	V732A	probably benign	Het
Slc7a2	C	T	8: 41,358,590 (GRCm39)	T311M	possibly damaging	Het
Smarcc1	T	C	9: 109,947,586 (GRCm39)		probably benign	Het
Stk32b	A	G	5: 37,614,498 (GRCm39)	S337P	probably damaging	Het
Thop1	G	A	10: 80,916,278 (GRCm39)	G429S	probably damaging	Het
Timp2	C	T	11: 118,194,542 (GRCm39)	D139N	probably damaging	Het
Tmem45a	T	C	16: 56,627,101 (GRCm39)	E256G	probably damaging	Het
Tox4	T	A	14: 52,517,299 (GRCm39)	Y10N	probably damaging	Het
Trpm3	A	G	19: 22,878,524 (GRCm39)	M642V	possibly damaging	Het
Ttll10	T	C	4: 156,120,257 (GRCm39)	T508A	probably damaging	Het
Tut7	T	A	13: 59,937,069 (GRCm39)	K791*	probably null	Het
Ubash3b	C	T	9: 40,942,860 (GRCm39)	D211N	probably benign	Het
Usp36	T	A	11: 118,170,650 (GRCm39)	D28V	possibly damaging	Het
Vmn2r97	T	C	17: 19,167,873 (GRCm39)	I709T	probably damaging	Het
Zfp936	T	A	7: 42,839,158 (GRCm39)	N207K	possibly damaging	Het
Zfp946	T	G	17: 22,673,531 (GRCm39)	I95S	probably benign	Het
Zhx3	A	T	2: 160,622,371 (GRCm39)	S599T	possibly 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
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
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'- GCTTCAGGCTCCTTGCATATG -3'
(R):5'- CGAGATGGTTCGGATGTCACTG -3'

Sequencing Primer
(F):5'- AAGGCAGGTGTACCCTTTTACAG -3'
(R):5'- TTCGGATGTCACTGGCAAAG -3'

Posted On

2015-04-17