Mutagenetix > Incidental Mutation

Incidental Mutation 'R3898:Rd3'

309037

Institutional Source

Beutler Lab

Gene Symbol

Rd3

Ensembl Gene

ENSMUSG00000049353

Gene Name

retinal degeneration 3

Synonyms

3322402L07Rik, rd-3, rd3

MMRRC Submission

040906-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R3898 (G1)

Quality Score

225

Status

Not 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: 99.2%
3x: 98.6%
10x: 97.2%
20x: 94.8%

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: 44 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Alg1	A	C	16: 5,054,253 (GRCm39)	I154L	possibly damaging	Het
Ankra2	C	T	13: 98,410,317 (GRCm39)	L136F	probably benign	Het
Anpep	A	G	7: 79,488,973 (GRCm39)	S372P	probably benign	Het
Cabyr	T	C	18: 12,884,580 (GRCm39)	S356P	probably benign	Het
Cad	G	T	5: 31,231,366 (GRCm39)	C1633F	probably benign	Het
Cadps2	G	A	6: 23,528,125 (GRCm39)	R425W	probably damaging	Het
Ccdc180	A	G	4: 45,912,799 (GRCm39)	K593E	possibly damaging	Het
Cdh8	T	A	8: 99,898,005 (GRCm39)	E436V	probably damaging	Het
Cfap95	A	G	19: 23,570,466 (GRCm39)	V101A	probably benign	Het
Cln6	T	G	9: 62,757,934 (GRCm39)	F231C	probably damaging	Het
Cul2	A	G	18: 3,434,033 (GRCm39)	K677E	probably benign	Het
Cyp2c69	T	C	19: 39,864,834 (GRCm39)	I215V	probably benign	Het
Dhx36	T	C	3: 62,399,790 (GRCm39)	D393G	probably damaging	Het
Dnah7b	T	C	1: 46,282,417 (GRCm39)	V2850A	probably damaging	Het
Dnah8	G	A	17: 31,073,872 (GRCm39)	R4514H	probably damaging	Het
Drg2	T	A	11: 60,347,460 (GRCm39)	S50T	probably benign	Het
Ecscr	A	G	18: 35,846,705 (GRCm39)	S230P	possibly damaging	Het
Eif2ak4	T	C	2: 118,261,404 (GRCm39)	V527A	probably damaging	Het
Elfn1	G	A	5: 139,957,719 (GRCm39)	R241H	probably damaging	Het
Fchsd2	A	G	7: 100,841,006 (GRCm39)	K172E	possibly damaging	Het
Fli1	C	T	9: 32,388,018 (GRCm39)	G24R	possibly damaging	Het
Frmd3	A	G	4: 73,992,346 (GRCm39)	D71G	probably damaging	Het
Ggnbp1	A	G	17: 27,244,312 (GRCm39)		probably benign	Het
Gpat2	T	C	2: 127,277,018 (GRCm39)	F713S	probably damaging	Het
H2-Q2	C	T	17: 35,561,743 (GRCm39)	P78S	probably damaging	Het
Kcnq2	C	T	2: 180,751,479 (GRCm39)	A306T	probably damaging	Het
Lmntd1	G	A	6: 145,359,152 (GRCm39)	P333S	probably benign	Het
Lrp1	G	A	10: 127,427,969 (GRCm39)	R535*	probably null	Het
Mmrn2	G	T	14: 34,121,517 (GRCm39)		probably null	Het
Nlrp1a	G	A	11: 71,013,700 (GRCm39)	P517S	probably benign	Het
Or2y13	A	T	11: 49,415,386 (GRCm39)	I279F	probably damaging	Het
Pou4f1	T	C	14: 104,703,165 (GRCm39)	*422W	probably null	Het
Ptpn14	C	T	1: 189,582,728 (GRCm39)	P525L	probably benign	Het
Pyroxd2	C	A	19: 42,728,831 (GRCm39)	G190C	probably damaging	Het
Sptbn5	T	C	2: 119,887,691 (GRCm39)		noncoding transcript	Het
Tbc1d5	A	T	17: 51,270,772 (GRCm39)	F153Y	probably damaging	Het
Thop1	G	A	10: 80,916,278 (GRCm39)	G429S	probably damaging	Het
Trim30d	T	A	7: 104,132,736 (GRCm39)	I184L	probably benign	Het
Ubr5	T	C	15: 37,997,983 (GRCm39)	S1727G	probably benign	Het
Vezf1	T	C	11: 87,966,999 (GRCm39)	F77L	probably benign	Het
Vmn2r12	C	T	5: 109,238,370 (GRCm39)	A457T	probably benign	Het
Xirp1	A	T	9: 119,848,406 (GRCm39)	M159K	probably benign	Het
Zkscan17	C	T	11: 59,394,263 (GRCm39)	A113T	probably damaging	Het
Zyg11a	T	A	4: 108,067,391 (GRCm39)	N40Y	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
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
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'- TCAGGCTCCTTGCATATGAGC -3'
(R):5'- CGAGATGGTTCGGATGTCACTG -3'

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

Posted On

2015-04-17