Mutagenetix > Incidental Mutation

Incidental Mutation 'R3434:Rpgr'

266374

Institutional Source

Beutler Lab

Gene Symbol

Rpgr

Ensembl Gene

ENSMUSG00000031174

Gene Name

retinitis pigmentosa GTPase regulator

Synonyms

Rp3h, Rd9

MMRRC Submission

040652-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R3434 (G1)

Quality Score

222

Status

Validated

Chromosome

Chromosomal Location

10024455-10083034 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 10042841 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Proline at position 656 (S656P)

Ref Sequence

ENSEMBL: ENSMUSP00000037358 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000044598] [ENSMUST00000072393] [ENSMUST00000073392] [ENSMUST00000115532] [ENSMUST00000115533] [ENSMUST00000115534]

AlphaFold

no structure available at present

Predicted Effect

probably benign
Transcript: ENSMUST00000044598
AA Change: S656P

PolyPhen 2 Score 0.045 (Sensitivity: 0.94; Specificity: 0.83)

SMART Domains

Protein: ENSMUSP00000037358
Gene: ENSMUSG00000031174
AA Change: S656P

Domain	Start	End	E-Value	Type
Pfam:RCC1	91	140	2.4e-12	PFAM
Pfam:RCC1	143	193	2.1e-7	PFAM
Pfam:RCC1_2	180	209	4.5e-11	PFAM
Pfam:RCC1	196	243	2.2e-12	PFAM
Pfam:RCC1	246	296	6.3e-13	PFAM
Pfam:RCC1	300	348	9.9e-13	PFAM
Pfam:RCC1	352	402	2.5e-9	PFAM
low complexity region	433	460	N/A	INTRINSIC
low complexity region	754	766	N/A	INTRINSIC
low complexity region	820	829	N/A	INTRINSIC
low complexity region	879	897	N/A	INTRINSIC
low complexity region	913	924	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000072393

SMART Domains

Protein: ENSMUSP00000072229
Gene: ENSMUSG00000031174

Domain	Start	End	E-Value	Type
Pfam:RCC1_2	76	104	3e-8	PFAM
Pfam:RCC1	91	140	3.1e-13	PFAM
Pfam:RCC1	143	193	7.5e-9	PFAM
Pfam:RCC1_2	180	209	1.5e-11	PFAM
Pfam:RCC1	196	243	2.6e-13	PFAM
Pfam:RCC1	246	296	4.4e-13	PFAM
Pfam:RCC1	300	348	1.7e-12	PFAM
Pfam:RCC1	352	402	1.3e-9	PFAM
low complexity region	433	460	N/A	INTRINSIC
low complexity region	586	604	N/A	INTRINSIC
low complexity region	620	631	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000073392

SMART Domains

Protein: ENSMUSP00000073106
Gene: ENSMUSG00000031174

Domain	Start	End	E-Value	Type
Pfam:RCC1_2	76	104	3.3e-8	PFAM
Pfam:RCC1	91	140	3.5e-13	PFAM
Pfam:RCC1	143	193	8.4e-9	PFAM
Pfam:RCC1_2	180	209	1.7e-11	PFAM
Pfam:RCC1	196	243	3e-13	PFAM
Pfam:RCC1	246	296	4.9e-13	PFAM
Pfam:RCC1	300	348	1.9e-12	PFAM
Pfam:RCC1	352	402	1.5e-9	PFAM
low complexity region	433	460	N/A	INTRINSIC
low complexity region	586	604	N/A	INTRINSIC
low complexity region	620	631	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000115532
AA Change: S656P

PolyPhen 2 Score 0.008 (Sensitivity: 0.96; Specificity: 0.76)

SMART Domains

Protein: ENSMUSP00000111194
Gene: ENSMUSG00000031174
AA Change: S656P

Domain	Start	End	E-Value	Type
Pfam:RCC1_2	76	104	1.1e-7	PFAM
Pfam:RCC1	91	140	1.3e-12	PFAM
Pfam:RCC1	143	193	3.1e-8	PFAM
Pfam:RCC1_2	180	209	5.5e-11	PFAM
Pfam:RCC1	196	243	1.1e-12	PFAM
Pfam:RCC1	246	296	1.8e-12	PFAM
Pfam:RCC1	300	348	6.8e-12	PFAM
Pfam:RCC1	352	402	5.4e-9	PFAM
low complexity region	433	460	N/A	INTRINSIC
low complexity region	754	766	N/A	INTRINSIC
low complexity region	820	829	N/A	INTRINSIC
low complexity region	879	897	N/A	INTRINSIC
low complexity region	913	924	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000115533

SMART Domains

Protein: ENSMUSP00000111195
Gene: ENSMUSG00000031174

Domain	Start	End	E-Value	Type
Pfam:RCC1_2	76	104	7.1e-8	PFAM
Pfam:RCC1	91	140	8.4e-13	PFAM
Pfam:RCC1	143	193	2e-8	PFAM
Pfam:RCC1_2	180	209	3.7e-11	PFAM
Pfam:RCC1	196	243	7.1e-13	PFAM
Pfam:RCC1	246	296	1.2e-12	PFAM
Pfam:RCC1	300	348	4.4e-12	PFAM
Pfam:RCC1	352	402	3.5e-9	PFAM
low complexity region	433	460	N/A	INTRINSIC
low complexity region	586	604	N/A	INTRINSIC
low complexity region	620	631	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000115534

SMART Domains

Protein: ENSMUSP00000111196
Gene: ENSMUSG00000031174

Domain	Start	End	E-Value	Type
Pfam:RCC1	1	45	9.6e-11	PFAM
Pfam:RCC1	48	98	3.2e-8	PFAM
Pfam:RCC1_2	85	114	6.1e-11	PFAM
Pfam:RCC1	101	148	1.1e-12	PFAM
Pfam:RCC1	151	201	1.9e-12	PFAM
Pfam:RCC1	205	253	7.1e-12	PFAM
Pfam:RCC1	257	307	5.6e-9	PFAM
low complexity region	338	365	N/A	INTRINSIC
low complexity region	491	509	N/A	INTRINSIC
low complexity region	525	536	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000155734

Meta Mutation Damage Score

0.0898

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 97.0%
20x: 94.3%

Validation Efficiency

98% (54/55)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein with a series of six RCC1-like domains (RLDs), characteristic of the highly conserved guanine nucleotide exchange factors. The encoded protein is found in the Golgi body and interacts with RPGRIP1. This protein localizes to the outer segment of rod photoreceptors and is essential for their viability. Mutations in this gene have been associated with X-linked retinitis pigmentosa (XLRP). Multiple alternatively spliced transcript variants that encode different isoforms of this gene have been reported, but the full-length natures of only some have been determined. [provided by RefSeq, Dec 2008]
PHENOTYPE: Homo- and hemizygotes for an X-linked, targeted, null mutation exhibit ectopic placement of cone opsins, reduced levels of rhodopsin in rod cells, and partial degeneration of both cone and rod photoreceptors by 2-6 months of age. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 50 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca17	G	A	17: 24,508,511 (GRCm39)	A1008V	probably damaging	Het
Adora3	A	G	3: 105,812,231 (GRCm39)	K39R	probably benign	Het
Ankib1	A	G	5: 3,742,760 (GRCm39)	V1085A	probably damaging	Het
Atp7a	G	A	X: 105,138,463 (GRCm39)	R563K	probably benign	Het
Azin1	T	C	15: 38,493,820 (GRCm39)	I268V	probably benign	Het
Carm1	T	C	9: 21,480,769 (GRCm39)	F81S	probably damaging	Het
Ccnjl	A	G	11: 43,470,688 (GRCm39)	Y152C	probably damaging	Het
Chrna3	T	A	9: 54,931,610 (GRCm39)	I61F	possibly damaging	Het
Clca3a2	G	A	3: 144,514,522 (GRCm39)		probably benign	Het
Clstn2	T	A	9: 97,336,768 (GRCm39)	D903V	probably benign	Het
Dpysl3	C	T	18: 43,494,126 (GRCm39)	V70I	probably benign	Het
Drg2	A	T	11: 60,352,218 (GRCm39)	K180*	probably null	Het
Dync2h1	A	C	9: 7,011,236 (GRCm39)	H3659Q	probably benign	Het
Dysf	A	T	6: 84,047,870 (GRCm39)	Y349F	probably benign	Het
Epb41l4b	T	C	4: 57,040,865 (GRCm39)	N533D	probably benign	Het
Fam47e	T	A	5: 92,733,221 (GRCm39)	V152D	probably damaging	Het
Fasn	G	A	11: 120,713,599 (GRCm39)	A24V	probably damaging	Het
Fhl4	T	C	10: 84,934,308 (GRCm39)	T158A	probably benign	Het
Fnbp1l	C	T	3: 122,339,955 (GRCm39)	R499Q	probably damaging	Het
Hdlbp	A	T	1: 93,355,883 (GRCm39)	M358K	probably benign	Het
Ift74	A	G	4: 94,510,089 (GRCm39)		probably null	Het
Lhx4	A	G	1: 155,578,147 (GRCm39)	Y332H	probably damaging	Het
Mast2	A	T	4: 116,165,292 (GRCm39)	S1314T	probably benign	Het
Mast4	A	G	13: 102,923,887 (GRCm39)	I508T	probably damaging	Het
Mdn1	T	C	4: 32,733,726 (GRCm39)		probably null	Het
Mrps23	A	G	11: 88,100,940 (GRCm39)	K44E	probably damaging	Het
Mslnl	G	A	17: 25,961,908 (GRCm39)	V128M	probably damaging	Het
Mup6	G	T	4: 60,004,116 (GRCm39)		probably null	Het
Notch3	A	T	17: 32,377,592 (GRCm39)	D161E	possibly damaging	Het
Or2ag13	A	T	7: 106,472,976 (GRCm39)	Y159N	probably benign	Het
Or4a67	T	C	2: 88,598,413 (GRCm39)	D82G	probably damaging	Het
Or5w11	T	C	2: 87,459,418 (GRCm39)	F204L	probably benign	Het
P2rx4	T	A	5: 122,863,133 (GRCm39)	I202K	probably damaging	Het
Phykpl	A	G	11: 51,489,482 (GRCm39)	T363A	probably benign	Het
Pitpnm1	G	A	19: 4,162,234 (GRCm39)	A1047T	probably damaging	Het
Ppat	A	G	5: 77,065,912 (GRCm39)	I402T	probably damaging	Het
Rsbn1l	T	C	5: 21,110,928 (GRCm39)		probably benign	Het
Sacs	A	G	14: 61,449,752 (GRCm39)	K3933E	probably damaging	Het
Scn7a	T	C	2: 66,505,847 (GRCm39)	I1681V	probably benign	Het
Sel1l3	T	C	5: 53,274,432 (GRCm39)	D1016G	probably benign	Het
Sf3a3	C	A	4: 124,618,870 (GRCm39)	T277N	possibly damaging	Het
Slc35a5	A	G	16: 44,964,396 (GRCm39)	I279T	probably benign	Het
Slc39a10	T	C	1: 46,874,877 (GRCm39)	T142A	probably benign	Het
Tle3	T	A	9: 61,321,376 (GRCm39)		probably null	Het
Tmem117	T	C	15: 94,992,573 (GRCm39)	I411T	probably damaging	Het
Ttn	T	C	2: 76,698,721 (GRCm39)	T5A	possibly damaging	Het
Tubgcp3	T	C	8: 12,708,381 (GRCm39)		probably null	Het
Ush2a	C	T	1: 188,465,955 (GRCm39)	P2841L	probably damaging	Het
Vmn1r209	A	T	13: 22,990,267 (GRCm39)	M141K	probably benign	Het
Vmn2r91	A	T	17: 18,330,370 (GRCm39)		probably benign	Het

Other mutations in Rpgr

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00840:Rpgr	APN	X	10,074,948 (GRCm39)	missense	possibly damaging	0.63
IGL02394:Rpgr	APN	X	10,032,456 (GRCm39)	missense	probably benign	0.30
IGL02401:Rpgr	APN	X	10,024,956 (GRCm39)	missense	possibly damaging	0.78
R4598:Rpgr	UTSW	X	10,062,255 (GRCm39)	missense	probably benign	0.00
R5732:Rpgr	UTSW	X	10,032,511 (GRCm39)	missense	probably benign	0.12
R5734:Rpgr	UTSW	X	10,032,511 (GRCm39)	missense	probably benign	0.12
Z1177:Rpgr	UTSW	X	10,024,943 (GRCm39)	missense	probably benign	0.23

Predicted Primers

PCR Primer
(F):5'- AAAGGTCATATTCTGCTCACTGC -3'
(R):5'- CACCGTGCACTGAAAATGAG -3'

Sequencing Primer
(F):5'- AGGTCATATTCTGCTCACTGCTTCTC -3'
(R):5'- CACCGTGCACTGAAAATGAGGATAG -3'

Posted On

2015-02-18