Mutagenetix > Incidental Mutation

Incidental Mutation 'IGL02394:Rpgr'

293923

Institutional Source

Australian Phenomics Network (link to record)

Gene Symbol

Rpgr

Ensembl Gene

ENSMUSG00000031174

Gene Name

retinitis pigmentosa GTPase regulator

Synonyms

Rp3h, Rd9

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

IGL02394

Quality Score

Status

Chromosome

Chromosomal Location

10024455-10083034 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to C at 10032456 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Arginine at position 582 (S582R)

Ref Sequence

ENSEMBL: ENSMUSP00000072229 (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: S875R

PolyPhen 2 Score 0.092 (Sensitivity: 0.93; Specificity: 0.85)

SMART Domains

Protein: ENSMUSP00000037358
Gene: ENSMUSG00000031174
AA Change: S875R

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: S582R

PolyPhen 2 Score 0.296 (Sensitivity: 0.91; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000072229
Gene: ENSMUSG00000031174
AA Change: S582R

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: S582R

PolyPhen 2 Score 0.017 (Sensitivity: 0.95; Specificity: 0.80)

SMART Domains

Protein: ENSMUSP00000073106
Gene: ENSMUSG00000031174
AA Change: S582R

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: S875R

PolyPhen 2 Score 0.092 (Sensitivity: 0.93; Specificity: 0.85)

SMART Domains

Protein: ENSMUSP00000111194
Gene: ENSMUSG00000031174
AA Change: S875R

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: S582R

PolyPhen 2 Score 0.068 (Sensitivity: 0.94; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000111195
Gene: ENSMUSG00000031174
AA Change: S582R

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: S487R

PolyPhen 2 Score 0.068 (Sensitivity: 0.94; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000111196
Gene: ENSMUSG00000031174
AA Change: S487R

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

Coding Region Coverage

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: 39 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Akt3	G	A	1: 176,886,985 (GRCm39)	T288M	probably damaging	Het
Baat	A	T	4: 49,489,812 (GRCm39)		probably benign	Het
Bclaf3	A	G	X: 158,338,485 (GRCm39)	Y444C	probably damaging	Het
Bcs1l	A	G	1: 74,629,459 (GRCm39)	T166A	probably damaging	Het
Cep135	C	T	5: 76,779,318 (GRCm39)	T776I	probably benign	Het
Clasrp	A	G	7: 19,337,179 (GRCm39)	L12P	probably damaging	Het
Csgalnact1	C	A	8: 68,854,144 (GRCm39)	G219V	probably damaging	Het
Cyp4f15	A	G	17: 32,911,609 (GRCm39)	I164V	possibly damaging	Het
Eps15	T	A	4: 109,170,162 (GRCm39)	L155M	probably damaging	Het
Fbxl20	G	A	11: 98,004,082 (GRCm39)	R69W	probably damaging	Het
Galnt9	A	G	5: 110,763,365 (GRCm39)	M457V	probably damaging	Het
Gemin2	T	A	12: 59,060,842 (GRCm39)		probably null	Het
Gm20521	T	A	14: 55,135,499 (GRCm39)	Y175N	probably damaging	Het
Gm3298	T	A	14: 5,018,778 (GRCm38)	C178S	probably benign	Het
Gpr37l1	T	C	1: 135,094,746 (GRCm39)	N166S	probably damaging	Het
Gpr45	A	G	1: 43,069,272 (GRCm39)		probably benign	Het
Gpr75	T	C	11: 30,842,190 (GRCm39)	I365T	possibly damaging	Het
Gsdmc2	T	C	15: 63,707,729 (GRCm39)	R22G	probably damaging	Het
Il23r	T	C	6: 67,443,256 (GRCm39)		probably benign	Het
Itgam	A	T	7: 127,684,114 (GRCm39)	T340S	probably benign	Het
Klk1b24	A	G	7: 43,841,294 (GRCm39)	D209G	possibly damaging	Het
Med13l	A	C	5: 118,886,898 (GRCm39)	T1600P	probably benign	Het
Muc16	G	T	9: 18,409,996 (GRCm39)	H137Q	probably damaging	Het
Nin	T	C	12: 70,090,805 (GRCm39)	E870G	probably damaging	Het
Or12k7	A	G	2: 36,958,497 (GRCm39)	Y60C	probably damaging	Het
Or5b120	A	G	19: 13,480,228 (GRCm39)	N174D	probably damaging	Het
Or6c215	A	T	10: 129,638,182 (GRCm39)	F71I	possibly damaging	Het
Pkhd1	T	C	1: 20,269,710 (GRCm39)	K3278R	possibly damaging	Het
Prlr	A	G	15: 10,328,664 (GRCm39)	N380D	probably benign	Het
Rph3a	T	C	5: 121,084,411 (GRCm39)		probably null	Het
Setd5	A	G	6: 113,087,859 (GRCm39)	H140R	probably benign	Het
Stoml3	C	A	3: 53,405,540 (GRCm39)		probably benign	Het
Teddm1a	A	C	1: 153,767,545 (GRCm39)	D3A	probably benign	Het
Tmem207	A	G	16: 26,335,586 (GRCm39)		probably benign	Het
Triml1	T	A	8: 43,591,629 (GRCm39)	Q243L	possibly damaging	Het
Usp5	G	A	6: 124,799,672 (GRCm39)	T274M	probably damaging	Het
Vav2	A	G	2: 27,187,671 (GRCm39)		probably benign	Het
Wdr5b	A	G	16: 35,862,633 (GRCm39)	N251D	probably damaging	Het
Wnk2	C	A	13: 49,235,375 (GRCm39)		probably null	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
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
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

Posted On

2015-04-16