Mutagenetix > Incidental Mutation

Incidental Mutation 'R4598:Rpgr'

345400

Institutional Source

Beutler Lab

Gene Symbol

Rpgr

Ensembl Gene

ENSMUSG00000031174

Gene Name

retinitis pigmentosa GTPase regulator

Synonyms

Rp3h, Rd9

MMRRC Submission

041814-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R4598 (G1)

Quality Score

222

Status

Not validated

Chromosome

Chromosomal Location

10024455-10083034 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 10062255 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Proline at position 343 (S343P)

Ref Sequence

ENSEMBL: ENSMUSP00000111196 (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: S438P

PolyPhen 2 Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)

SMART Domains

Protein: ENSMUSP00000037358
Gene: ENSMUSG00000031174
AA Change: S438P

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
AA Change: S438P

PolyPhen 2 Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)

SMART Domains

Protein: ENSMUSP00000072229
Gene: ENSMUSG00000031174
AA Change: S438P

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
AA Change: S438P

PolyPhen 2 Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)

SMART Domains

Protein: ENSMUSP00000073106
Gene: ENSMUSG00000031174
AA Change: S438P

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: S438P

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000111194
Gene: ENSMUSG00000031174
AA Change: S438P

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
AA Change: S438P

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000111195
Gene: ENSMUSG00000031174
AA Change: S438P

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
AA Change: S343P

PolyPhen 2 Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)

SMART Domains

Protein: ENSMUSP00000111196
Gene: ENSMUSG00000031174
AA Change: S343P

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

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.2%
20x: 95.1%

Validation Efficiency

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: 67 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
A830018L16Rik	G	A	1: 11,818,188 (GRCm39)		probably null	Het
Abca14	T	C	7: 119,854,626 (GRCm39)	V930A	probably benign	Het
Abcb7	A	C	X: 103,366,988 (GRCm39)	D135E	probably benign	Het
Ace	T	A	11: 105,872,585 (GRCm39)		probably null	Het
Acnat1	T	C	4: 49,450,781 (GRCm39)	D110G	probably benign	Het
Ak9	C	T	10: 41,259,907 (GRCm39)	P862S	probably damaging	Het
Atp1a3	A	G	7: 24,678,766 (GRCm39)	S972P	probably damaging	Het
Bmf	C	A	2: 118,379,609 (GRCm39)	A56S	probably benign	Het
C6	T	C	15: 4,792,852 (GRCm39)	L319P	possibly damaging	Het
Cab39	A	G	1: 85,776,050 (GRCm39)	Y249C	probably damaging	Het
Cdc14b	T	C	13: 64,395,088 (GRCm39)	T69A	probably benign	Het
Cep162	A	G	9: 87,085,848 (GRCm39)	Y1159H	possibly damaging	Het
Chrna7	A	G	7: 62,753,538 (GRCm39)	M327T	probably damaging	Het
Clca3a2	A	T	3: 144,511,444 (GRCm39)	N41K	probably damaging	Het
Clock	T	C	5: 76,383,657 (GRCm39)	M499V	probably benign	Het
Col5a3	A	G	9: 20,685,855 (GRCm39)		probably null	Het
Coq6	T	C	12: 84,408,913 (GRCm39)	V30A	probably benign	Het
Cyp3a57	A	G	5: 145,327,227 (GRCm39)	I473V	probably benign	Het
D430041D05Rik	A	T	2: 104,038,528 (GRCm39)	V1547D	probably damaging	Het
Dhx9	TCC	TC	1: 153,342,797 (GRCm39)		probably null	Het
Dock2	T	A	11: 34,189,536 (GRCm39)	Y1545F	probably damaging	Het
Eif4e3	T	A	6: 99,617,671 (GRCm39)	I67L	probably benign	Het
Epor	A	G	9: 21,873,155 (GRCm39)	S86P	probably benign	Het
Esp31	T	A	17: 38,952,012 (GRCm39)		probably null	Het
Esrp2	A	G	8: 106,859,343 (GRCm39)	M498T	probably damaging	Het
F5	T	C	1: 164,032,366 (GRCm39)	I1771T	probably benign	Het
Fancd2	C	A	6: 113,562,438 (GRCm39)	H1259Q	probably benign	Het
Gale	C	A	4: 135,695,148 (GRCm39)	S341*	probably null	Het
Ints12	T	A	3: 132,804,214 (GRCm39)	I67N	probably benign	Het
Kat2b	A	G	17: 53,977,826 (GRCm39)	Y791C	probably benign	Het
Kazn	A	G	4: 141,937,403 (GRCm39)	V108A	possibly damaging	Het
Kcnma1	T	C	14: 23,853,228 (GRCm39)	T109A	probably damaging	Het
Med13	T	C	11: 86,169,392 (GRCm39)	T1955A	probably damaging	Het
Megf10	G	A	18: 57,322,675 (GRCm39)		probably null	Het
Megf10	A	T	18: 57,420,884 (GRCm39)	S841C	probably damaging	Het
Mep1a	A	G	17: 43,802,469 (GRCm39)		probably null	Het
Mrap2	A	T	9: 87,064,842 (GRCm39)	E194D	probably damaging	Het
Msh2	A	G	17: 88,016,006 (GRCm39)	K546R	probably damaging	Het
Ndc80	T	C	17: 71,828,063 (GRCm39)	D88G	probably damaging	Het
Nrip1	A	G	16: 76,089,968 (GRCm39)	F530L	probably damaging	Het
Or2y10	T	C	11: 49,455,545 (GRCm39)	S266P	probably damaging	Het
Or52e7	A	C	7: 104,685,280 (GRCm39)	I292L	probably benign	Het
Or6c216	T	C	10: 129,678,864 (GRCm39)	T16A	possibly damaging	Het
Or9i16	A	T	19: 13,865,381 (GRCm39)	H64Q	probably damaging	Het
Oxtr	C	T	6: 112,466,713 (GRCm39)	G16R	probably benign	Het
Pdgfrb	A	T	18: 61,201,829 (GRCm39)	K464N	probably benign	Het
Pja2	A	T	17: 64,620,025 (GRCm39)	M1K	probably null	Het
Pkhd1	A	T	1: 20,573,280 (GRCm39)	N1875K	probably damaging	Het
Pogz	T	C	3: 94,787,491 (GRCm39)	S1360P	possibly damaging	Het
Proc	A	T	18: 32,256,512 (GRCm39)	L385Q	probably damaging	Het
Ptprm	A	G	17: 67,402,492 (GRCm39)	I132T	probably benign	Het
Rsu1	T	C	2: 13,174,815 (GRCm39)	Y225C	probably damaging	Het
Scyl1	A	G	19: 5,820,481 (GRCm39)	S118P	probably damaging	Het
Sec61a1	T	C	6: 88,483,131 (GRCm39)	N414D	probably benign	Het
Secisbp2l	C	T	2: 125,582,657 (GRCm39)	G933D	possibly damaging	Het
Sema7a	A	G	9: 57,860,834 (GRCm39)	D65G	probably benign	Het
Slc25a45	A	G	19: 5,934,464 (GRCm39)	Y144C	probably damaging	Het
Slc26a6	A	G	9: 108,733,579 (GRCm39)	Y103C	probably damaging	Het
Stat3	C	T	11: 100,794,500 (GRCm39)	D270N	probably damaging	Het
Taar8b	T	C	10: 23,967,736 (GRCm39)	S153G	probably benign	Het
Top1	A	G	2: 160,562,885 (GRCm39)	E697G	possibly damaging	Het
Trappc11	G	A	8: 47,966,801 (GRCm39)	T470I	probably damaging	Het
Ttc7b	G	A	12: 100,466,376 (GRCm39)	R79C	probably damaging	Het
Usp29	A	G	7: 6,965,479 (GRCm39)	T441A	probably benign	Het
Vmn2r110	A	T	17: 20,804,029 (GRCm39)	L182*	probably null	Het
Zgrf1	T	C	3: 127,394,679 (GRCm39)	I1345T	probably benign	Het
Zscan25	G	T	5: 145,227,815 (GRCm39)	R493L	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
R3434:Rpgr	UTSW	X	10,042,841 (GRCm39)	missense	probably benign	0.05
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'- ATCTTGAAAGACCCTCCTTTGAC -3'
(R):5'- GCTTCTAAGAAAATGTCTTGGTGC -3'

Sequencing Primer
(F):5'- GAAAGACCCTCCTTTGACTTAAAAAG -3'
(R):5'- GCTAATCTGGTAAGTGTTAGCCC -3'

Posted On

2015-09-25