Mutagenetix > Incidental Mutation

Incidental Mutation 'R5732:Rpgr'

451517

Institutional Source

Beutler Lab

Gene Symbol

Rpgr

Ensembl Gene

ENSMUSG00000031174

Gene Name

retinitis pigmentosa GTPase regulator

Synonyms

Rp3h, Rd9

MMRRC Submission

043347-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R5732 (G1)

Quality Score

222

Status

Not validated

Chromosome

Chromosomal Location

10024455-10083034 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 10032511 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Proline to Leucine at position 857 (P857L)

Ref Sequence

ENSEMBL: ENSMUSP00000111194 (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: P857L

PolyPhen 2 Score 0.116 (Sensitivity: 0.93; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000037358
Gene: ENSMUSG00000031174
AA Change: P857L

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: P564L

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

SMART Domains

Protein: ENSMUSP00000072229
Gene: ENSMUSG00000031174
AA Change: P564L

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: P564L

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000073106
Gene: ENSMUSG00000031174
AA Change: P564L

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: P857L

PolyPhen 2 Score 0.116 (Sensitivity: 0.93; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000111194
Gene: ENSMUSG00000031174
AA Change: P857L

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: P564L

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

SMART Domains

Protein: ENSMUSP00000111195
Gene: ENSMUSG00000031174
AA Change: P564L

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: P469L

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000111196
Gene: ENSMUSG00000031174
AA Change: P469L

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

Meta Mutation Damage Score

0.0898

Coding Region Coverage

1x: 99.0%
3x: 98.3%
10x: 96.8%
20x: 94.5%

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: 46 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acaa1b	T	A	9: 118,977,462 (GRCm39)	M407L	possibly damaging	Het
Acsf2	T	C	11: 94,460,768 (GRCm39)		probably benign	Het
Apob	A	G	12: 8,060,353 (GRCm39)	D2945G	probably benign	Het
Atg2a	T	C	19: 6,307,490 (GRCm39)	Y1475H	probably damaging	Het
Capn5	A	G	7: 97,778,593 (GRCm39)	L342P	possibly damaging	Het
Ccdc152	A	G	15: 3,321,860 (GRCm39)		probably null	Het
Ccdc7b	A	G	8: 129,799,195 (GRCm39)	M91V	possibly damaging	Het
Cd3g	T	C	9: 44,884,929 (GRCm39)	E105G	possibly damaging	Het
Cdadc1	A	G	14: 59,834,360 (GRCm39)	L44P	probably damaging	Het
Cdh23	A	G	10: 60,167,096 (GRCm39)	V1852A	possibly damaging	Het
Cdx2	T	C	5: 147,238,833 (GRCm39)	Q252R	possibly damaging	Het
Cps1	A	T	1: 67,196,923 (GRCm39)	I325F	probably benign	Het
Dctn1	G	A	6: 83,174,931 (GRCm39)		probably null	Het
Dcun1d3	T	C	7: 119,457,256 (GRCm39)	K152R	probably benign	Het
Dhx35	G	A	2: 158,673,705 (GRCm39)	V379M	probably damaging	Het
Fam171a2	T	C	11: 102,330,807 (GRCm39)	E224G	possibly damaging	Het
Flt1	G	T	5: 147,571,293 (GRCm39)	Y671*	probably null	Het
Fndc3b	T	C	3: 27,515,922 (GRCm39)	Y628C	probably damaging	Het
Foxj3	A	T	4: 119,443,008 (GRCm39)	D144V	probably damaging	Het
Gp2	A	G	7: 119,048,331 (GRCm39)	V429A	probably damaging	Het
Hydin	T	A	8: 111,178,690 (GRCm39)	I1095N	probably benign	Het
Kat2a	A	G	11: 100,599,066 (GRCm39)	F571S	probably damaging	Het
Kcnq1	C	A	7: 142,702,493 (GRCm39)		probably benign	Het
Letm2	A	C	8: 26,077,341 (GRCm39)	S250A	possibly damaging	Het
Llgl1	T	C	11: 60,600,286 (GRCm39)	V545A	probably benign	Het
Lrfn3	T	C	7: 30,059,031 (GRCm39)	D398G	probably benign	Het
Lrig1	G	T	6: 94,676,520 (GRCm39)	C49*	probably null	Het
Mug1	A	G	6: 121,855,452 (GRCm39)	I929V	probably benign	Het
Naaa	G	A	5: 92,411,314 (GRCm39)	T291I	probably damaging	Het
Ndufaf1	G	A	2: 119,490,521 (GRCm39)	Q180*	probably null	Het
Nr3c1	A	T	18: 39,548,752 (GRCm39)	H741Q	probably damaging	Het
Nsun5	T	C	5: 135,400,204 (GRCm39)	L109P	probably damaging	Het
Pacsin3	A	G	2: 91,090,605 (GRCm39)	E18G	probably damaging	Het
Siglec1	G	A	2: 130,916,188 (GRCm39)	T1254M	probably benign	Het
Slc35a4	A	T	18: 36,815,394 (GRCm39)	T75S	probably benign	Het
Slc52a2	T	C	15: 76,425,274 (GRCm39)	I434T	probably benign	Het
Slco2a1	C	T	9: 102,927,455 (GRCm39)	T116I	probably damaging	Het
Snrpd2	T	C	7: 18,886,538 (GRCm39)		probably null	Het
Tbc1d32	T	A	10: 55,964,489 (GRCm39)	L903F	probably damaging	Het
Tex10	G	T	4: 48,460,046 (GRCm39)	T435K	probably damaging	Het
Tmem266	T	C	9: 55,288,120 (GRCm39)	S66P	probably damaging	Het
Top2b	A	T	14: 16,400,106 (GRCm38)	E581D	possibly damaging	Het
Uggt1	A	T	1: 36,200,852 (GRCm39)		probably null	Het
Wdr47	T	A	3: 108,540,472 (GRCm39)	Y622*	probably null	Het
Zfp644	A	T	5: 106,784,989 (GRCm39)	H519Q	probably damaging	Het
Zfp687	T	C	3: 94,918,528 (GRCm39)	M415V	possibly damaging	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
R4598:Rpgr	UTSW	X	10,062,255 (GRCm39)	missense	probably benign	0.00
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'- CAGGACATAACCTTGTCGCG -3'
(R):5'- CTGATGCAGTATCTTCATGTTCAG -3'

Sequencing Primer
(F):5'- GGACATAACCTTGTCGCGATACC -3'
(R):5'- GCAGTATCTTCATGTTCAGCATAGGC -3'

Posted On

2017-01-03