Mutagenetix > Incidental Mutation

Incidental Mutation 'R6056:Rapgef3'

484434

Institutional Source

Beutler Lab

Gene Symbol

Rapgef3

Ensembl Gene

ENSMUSG00000022469

Gene Name

Rap guanine nucleotide exchange factor (GEF) 3

Synonyms

Epac1, 9330170P05Rik, 2310016P22Rik

MMRRC Submission

044223-MU

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.267) question?

Stock #

R6056 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

97642651-97665853 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 97656742 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glycine at position 299 (D299G)

Ref Sequence

ENSEMBL: ENSMUSP00000135238 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000126854] [ENSMUST00000128775] [ENSMUST00000129223] [ENSMUST00000134371] [ENSMUST00000134885] [ENSMUST00000177352] [ENSMUST00000175894] [ENSMUST00000149419] [ENSMUST00000146620]

AlphaFold

Q8VCC8

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000123397

Predicted Effect

probably damaging
Transcript: ENSMUST00000126854
AA Change: D341G

PolyPhen 2 Score 0.978 (Sensitivity: 0.76; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000116426
Gene: ENSMUSG00000022469
AA Change: D341G

Domain	Start	End	E-Value	Type
DEP	111	186	2.05e-25	SMART
low complexity region	197	208	N/A	INTRINSIC
low complexity region	230	241	N/A	INTRINSIC
cNMP	245	364	2.53e-12	SMART
RasGEFN	383	514	7.04e-10	SMART
Blast:RasGEF	547	644	6e-45	BLAST
RasGEF	661	926	7.98e-95	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000128775
AA Change: D341G

PolyPhen 2 Score 0.985 (Sensitivity: 0.74; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000120126
Gene: ENSMUSG00000022469
AA Change: D341G

Domain	Start	End	E-Value	Type
DEP	111	186	2.05e-25	SMART
low complexity region	197	208	N/A	INTRINSIC
low complexity region	230	241	N/A	INTRINSIC
cNMP	245	364	2.53e-12	SMART
RasGEFN	383	514	7.04e-10	SMART
Blast:RasGEF	547	644	7e-45	BLAST
RasGEF	661	909	5.53e-80	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000129223
AA Change: D341G

PolyPhen 2 Score 0.978 (Sensitivity: 0.76; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000118148
Gene: ENSMUSG00000022469
AA Change: D341G

Domain	Start	End	E-Value	Type
DEP	111	186	2.05e-25	SMART
low complexity region	197	208	N/A	INTRINSIC
low complexity region	230	241	N/A	INTRINSIC
cNMP	245	364	2.53e-12	SMART
RasGEFN	383	514	7.04e-10	SMART
Blast:RasGEF	547	644	6e-45	BLAST
RasGEF	661	918	2.11e-85	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000134371

SMART Domains

Protein: ENSMUSP00000122746
Gene: ENSMUSG00000022469

Domain	Start	End	E-Value	Type
Blast:cNMP	1	24	9e-8	BLAST
PDB:3CF6\|E	1	67	5e-12	PDB
Blast:RasGEFN	36	67	2e-15	BLAST

Predicted Effect

probably benign
Transcript: ENSMUST00000134885

SMART Domains

Protein: ENSMUSP00000135317
Gene: ENSMUSG00000022469

Domain	Start	End	E-Value	Type
RasGEF	1	216	2.91e-56	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000142196

Predicted Effect

probably damaging
Transcript: ENSMUST00000177352
AA Change: D299G

PolyPhen 2 Score 0.992 (Sensitivity: 0.70; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000135238
Gene: ENSMUSG00000022469
AA Change: D299G

Domain	Start	End	E-Value	Type
DEP	69	144	2.05e-25	SMART
low complexity region	155	166	N/A	INTRINSIC
low complexity region	188	199	N/A	INTRINSIC
cNMP	203	322	2.53e-12	SMART
RasGEFN	341	472	7.04e-10	SMART
Blast:RasGEF	505	602	3e-45	BLAST
RasGEF	619	884	7.98e-95	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000146214

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000153241

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000153464

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000149373

Predicted Effect

probably benign
Transcript: ENSMUST00000175894

Predicted Effect

probably benign
Transcript: ENSMUST00000149419

Predicted Effect

probably benign
Transcript: ENSMUST00000146620

SMART Domains

Protein: ENSMUSP00000116673
Gene: ENSMUSG00000022469

Domain	Start	End	E-Value	Type
DEP	69	144	2.05e-25	SMART

Meta Mutation Damage Score

0.6097

Coding Region Coverage

1x: 99.9%
3x: 99.7%
10x: 98.4%
20x: 95.4%

Validation Efficiency

96% (99/103)

MGI Phenotype

PHENOTYPE: Mice homozygous for a knock-out allele exhibit decreased induced neuron apoptosis. Mice homozygous for a different allele exhibit impaired glucose homeostasis with decreased insulin secretion, increased susceptibility to diet-induced obesity and streptozotocin-induced insulitis and hyperglycemia. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 101 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2310002L09Rik	A	T	4: 73,861,115 (GRCm39)	W162R	probably benign	Het
4930438A08Rik	C	A	11: 58,184,464 (GRCm39)	P394H	probably damaging	Het
Aggf1	C	T	13: 95,508,123 (GRCm39)	C81Y	probably benign	Het
Agxt2	A	T	15: 10,378,963 (GRCm39)	D188V	probably damaging	Het
Angpt2	T	C	8: 18,748,132 (GRCm39)	K376R	probably benign	Het
Anxa5	A	G	3: 36,504,840 (GRCm39)	S241P	probably damaging	Het
Aox3	A	T	1: 58,209,018 (GRCm39)	K850N	probably damaging	Het
Arid5a	T	C	1: 36,358,473 (GRCm39)	M415T	probably benign	Het
Aspa	T	A	11: 73,199,578 (GRCm39)	N233I	probably damaging	Het
Atp4b	C	T	8: 13,438,782 (GRCm39)	R198Q	probably damaging	Het
Atp8b2	A	T	3: 89,853,528 (GRCm39)	V719E	possibly damaging	Het
Bltp2	C	A	11: 78,162,210 (GRCm39)	L691I	possibly damaging	Het
Cacna1s	T	G	1: 136,033,574 (GRCm39)	V1017G	probably damaging	Het
Chrna4	G	T	2: 180,671,235 (GRCm39)	Q174K	probably damaging	Het
Chrnb1	A	T	11: 69,677,765 (GRCm39)	V329D	probably damaging	Het
Chst14	T	C	2: 118,758,214 (GRCm39)	L336P	probably damaging	Het
Clec2e	T	C	6: 129,077,772 (GRCm39)	D22G	probably benign	Het
Csrnp2	A	C	15: 100,380,263 (GRCm39)	S343A	probably benign	Het
Dapl1	C	A	2: 59,315,057 (GRCm39)	A2E	probably damaging	Het
Dlec1	G	T	9: 118,950,991 (GRCm39)	R519L	probably damaging	Het
Dmgdh	T	A	13: 93,845,251 (GRCm39)	F415I	possibly damaging	Het
Dmgdh	T	C	13: 93,888,834 (GRCm39)	V824A	probably damaging	Het
Dnah11	T	G	12: 117,892,191 (GRCm39)	T3661P	probably benign	Het
Dnah3	A	G	7: 119,629,254 (GRCm39)	F1434L	probably damaging	Het
Dnajc11	C	A	4: 152,062,583 (GRCm39)		probably benign	Het
Dot1l	A	G	10: 80,621,929 (GRCm39)	E527G	probably damaging	Het
Drc7	T	C	8: 95,801,679 (GRCm39)	L680P	probably damaging	Het
Dysf	T	C	6: 84,083,844 (GRCm39)	Y742H	probably benign	Het
Ece1	A	G	4: 137,688,958 (GRCm39)	Y665C	probably damaging	Het
Emc1	A	G	4: 139,081,533 (GRCm39)	K54E	possibly damaging	Het
Enoph1	C	T	5: 100,215,760 (GRCm39)	T247M	probably damaging	Het
Exoc2	T	C	13: 31,084,812 (GRCm39)	K383R	probably benign	Het
Fam227b	A	T	2: 125,962,972 (GRCm39)	H181Q	probably damaging	Het
Fsip2	A	T	2: 82,816,017 (GRCm39)	M3917L	probably benign	Het
Gtf3a	T	A	5: 146,892,338 (GRCm39)		probably benign	Het
Hgfac	T	A	5: 35,198,973 (GRCm39)	C11*	probably null	Het
Hmcn1	C	A	1: 150,539,660 (GRCm39)	A2944S	probably damaging	Het
Hps5	T	A	7: 46,416,521 (GRCm39)	Y947F	probably benign	Het
Ighv2-5	A	T	12: 113,649,120 (GRCm39)	I111K	probably benign	Het
Inpp5e	A	T	2: 26,297,860 (GRCm39)	L247*	probably null	Het
Kbtbd11	T	C	8: 15,077,577 (GRCm39)	S59P	probably benign	Het
Kctd19	G	A	8: 106,123,082 (GRCm39)	H111Y	probably damaging	Het
Kif1a	T	C	1: 92,952,370 (GRCm39)	D1303G	probably damaging	Het
Kif7	A	G	7: 79,363,842 (GRCm39)	V22A	possibly damaging	Het
Lrit3	A	T	3: 129,583,004 (GRCm39)	C328S	probably damaging	Het
Lrrc37a	G	T	11: 103,388,484 (GRCm39)	Q2314K	unknown	Het
LTO1	G	T	7: 144,469,023 (GRCm39)	V17L	possibly damaging	Het
Lurap1	G	T	4: 115,994,599 (GRCm39)	P211T	possibly damaging	Het
Mbd2	T	A	18: 70,713,874 (GRCm39)	N5K	possibly damaging	Het
Mbtps1	A	C	8: 120,242,341 (GRCm39)	L894V	probably benign	Het
Mefv	G	A	16: 3,525,906 (GRCm39)	S787F	possibly damaging	Het
Miip	T	A	4: 147,946,792 (GRCm39)	I289F	probably damaging	Het
Mogat2	T	A	7: 98,872,720 (GRCm39)	I155F	possibly damaging	Het
Mpp3	C	A	11: 101,902,515 (GRCm39)		probably null	Het
Mrrf	A	G	2: 36,067,233 (GRCm39)	K220E	probably damaging	Het
Mtmr6	C	T	14: 60,535,619 (GRCm39)	P485L	probably damaging	Het
Mtor	G	A	4: 148,621,892 (GRCm39)	R1896K	probably benign	Het
Myh3	C	T	11: 66,978,371 (GRCm39)	P453S	probably benign	Het
Nebl	A	G	2: 17,455,045 (GRCm39)	V112A	probably benign	Het
Nmnat2	G	A	1: 152,950,480 (GRCm39)	W55*	probably null	Het
Nprl3	A	G	11: 32,217,432 (GRCm39)	S37P	probably damaging	Het
Or4a73	T	C	2: 89,421,445 (GRCm39)	N5D	possibly damaging	Het
Pcdhga4	T	G	18: 37,819,383 (GRCm39)	S311A	probably benign	Het
Pcdhgb6	T	C	18: 37,876,165 (GRCm39)	V291A	probably benign	Het
Peg10	GAT	GATCAT	6: 4,756,449 (GRCm39)		probably benign	Het
Peg3	T	C	7: 6,712,570 (GRCm39)	E884G	probably damaging	Het
Pgpep1	G	A	8: 71,105,101 (GRCm39)	T53M	probably damaging	Het
Phf12	A	G	11: 77,900,341 (GRCm39)	T146A	probably benign	Het
Polr3k	C	G	2: 181,506,281 (GRCm39)	N10K	probably damaging	Het
Prickle4	C	A	17: 48,001,135 (GRCm39)	G144C	probably damaging	Het
Ptpn6	T	C	6: 124,709,398 (GRCm39)	Y25C	probably damaging	Het
Rad1	A	G	15: 10,488,160 (GRCm39)	I95V	probably damaging	Het
Rad23b	A	G	4: 55,382,540 (GRCm39)	T248A	probably benign	Het
Rcc2	T	G	4: 140,444,335 (GRCm39)	V342G	possibly damaging	Het
Rgs3	G	T	4: 62,544,143 (GRCm39)	R136L	probably damaging	Het
Scube2	A	T	7: 109,432,220 (GRCm39)	C399*	probably null	Het
Serpinb3d	T	C	1: 107,007,452 (GRCm39)	Y178C	probably damaging	Het
Slc1a7	A	G	4: 107,869,458 (GRCm39)	T508A	probably benign	Het
Slc29a4	C	T	5: 142,705,832 (GRCm39)	R439C	probably damaging	Het
Sntg2	A	G	12: 30,362,560 (GRCm39)	I62T	probably benign	Het
Sowaha	G	A	11: 53,369,914 (GRCm39)	P274L	probably damaging	Het
Sptan1	A	G	2: 29,886,794 (GRCm39)	N869S	probably benign	Het
Stx18	C	A	5: 38,263,908 (GRCm39)	A64D	probably damaging	Het
Stxbp5	A	G	10: 9,646,430 (GRCm39)	V94A	probably benign	Het
Sult1a1	T	A	7: 126,275,624 (GRCm39)		probably null	Het
Susd1	G	T	4: 59,379,687 (GRCm39)	H313Q	possibly damaging	Het
Tdrd9	A	T	12: 111,951,475 (GRCm39)	K88N	probably damaging	Het
Tlr5	A	C	1: 182,801,603 (GRCm39)	R302S	possibly damaging	Het
Tnr	C	T	1: 159,714,479 (GRCm39)	T786I	probably damaging	Het
Tprg1l	A	G	4: 154,244,552 (GRCm39)	S148P	probably damaging	Het
Trpc4ap	T	A	2: 155,512,994 (GRCm39)	N127I	probably damaging	Het
Tulp2	T	A	7: 45,139,797 (GRCm39)		probably null	Het
Uggt2	C	T	14: 119,273,381 (GRCm39)		probably null	Het
Ulk4	T	A	9: 121,102,021 (GRCm39)	Y19F	probably damaging	Het
Upf1	T	C	8: 70,785,687 (GRCm39)	Y1053C	probably damaging	Het
Vars2	A	T	17: 35,976,680 (GRCm39)	H223Q	probably benign	Het
Vmn2r106	T	A	17: 20,487,806 (GRCm39)		probably null	Het
Ythdc2	T	A	18: 44,973,277 (GRCm39)	F305I	probably damaging	Het
Zfp281	T	C	1: 136,553,178 (GRCm39)	F52S	possibly damaging	Het
Zfp292	A	T	4: 34,809,784 (GRCm39)	C1087S	probably damaging	Het
Zfp335	A	T	2: 164,737,018 (GRCm39)		probably null	Het

Other mutations in Rapgef3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01314:Rapgef3	APN	15	97,646,104 (GRCm39)	missense	probably damaging	1.00
IGL01339:Rapgef3	APN	15	97,655,940 (GRCm39)	missense	probably damaging	1.00
IGL01670:Rapgef3	APN	15	97,647,543 (GRCm39)	missense	probably benign	0.15
IGL01902:Rapgef3	APN	15	97,648,181 (GRCm39)	missense	probably benign	0.32
IGL02137:Rapgef3	APN	15	97,648,025 (GRCm39)	missense	probably benign	0.08
IGL02419:Rapgef3	APN	15	97,648,171 (GRCm39)	missense	probably benign	0.33
IGL02427:Rapgef3	APN	15	97,645,017 (GRCm39)	splice site	probably null
IGL02648:Rapgef3	APN	15	97,656,273 (GRCm39)	missense	probably damaging	1.00
IGL02834:Rapgef3	APN	15	97,646,146 (GRCm39)	missense	probably damaging	0.98
IGL03389:Rapgef3	APN	15	97,647,397 (GRCm39)	missense	probably damaging	1.00
IGL03055:Rapgef3	UTSW	15	97,647,370 (GRCm39)	splice site	probably benign
R0394:Rapgef3	UTSW	15	97,655,700 (GRCm39)	intron	probably benign
R0538:Rapgef3	UTSW	15	97,655,698 (GRCm39)	intron	probably benign
R0744:Rapgef3	UTSW	15	97,659,466 (GRCm39)	splice site	probably benign
R1288:Rapgef3	UTSW	15	97,657,223 (GRCm39)	missense	probably benign	0.31
R1512:Rapgef3	UTSW	15	97,655,382 (GRCm39)	missense	probably benign	0.24
R1676:Rapgef3	UTSW	15	97,659,063 (GRCm39)	missense	probably benign	0.35
R1745:Rapgef3	UTSW	15	97,648,059 (GRCm39)	missense	probably benign	0.22
R1928:Rapgef3	UTSW	15	97,647,914 (GRCm39)	missense	probably damaging	1.00
R2063:Rapgef3	UTSW	15	97,664,842 (GRCm39)	missense	probably damaging	1.00
R2067:Rapgef3	UTSW	15	97,664,842 (GRCm39)	missense	probably damaging	1.00
R2092:Rapgef3	UTSW	15	97,658,604 (GRCm39)	missense	probably damaging	1.00
R4358:Rapgef3	UTSW	15	97,646,529 (GRCm39)	missense	probably benign	0.05
R4624:Rapgef3	UTSW	15	97,656,810 (GRCm39)	missense	probably damaging	1.00
R4627:Rapgef3	UTSW	15	97,656,810 (GRCm39)	missense	probably damaging	1.00
R4727:Rapgef3	UTSW	15	97,658,481 (GRCm39)	missense	probably damaging	1.00
R4812:Rapgef3	UTSW	15	97,651,684 (GRCm39)	missense	probably benign	0.21
R4928:Rapgef3	UTSW	15	97,655,256 (GRCm39)	missense	probably damaging	1.00
R5161:Rapgef3	UTSW	15	97,655,606 (GRCm39)	missense	probably damaging	1.00
R5442:Rapgef3	UTSW	15	97,656,742 (GRCm39)	missense	probably damaging	0.99
R5652:Rapgef3	UTSW	15	97,656,318 (GRCm39)	missense	probably benign	0.00
R5837:Rapgef3	UTSW	15	97,655,223 (GRCm39)	splice site	probably benign
R6167:Rapgef3	UTSW	15	97,665,292 (GRCm39)	unclassified	probably benign
R6694:Rapgef3	UTSW	15	97,657,865 (GRCm39)	missense	probably benign	0.03
R7039:Rapgef3	UTSW	15	97,659,449 (GRCm39)	missense	probably benign	0.01
R7154:Rapgef3	UTSW	15	97,651,758 (GRCm39)	missense	probably benign
R7380:Rapgef3	UTSW	15	97,664,672 (GRCm39)	missense	probably benign	0.00
R7655:Rapgef3	UTSW	15	97,659,090 (GRCm39)	missense	probably damaging	1.00
R7656:Rapgef3	UTSW	15	97,659,090 (GRCm39)	missense	probably damaging	1.00
R7754:Rapgef3	UTSW	15	97,655,627 (GRCm39)	missense	probably damaging	1.00
R7849:Rapgef3	UTSW	15	97,656,271 (GRCm39)	critical splice donor site	probably null
R8061:Rapgef3	UTSW	15	97,659,401 (GRCm39)	missense	probably benign
R8117:Rapgef3	UTSW	15	97,648,747 (GRCm39)	missense	probably benign	0.01
R8179:Rapgef3	UTSW	15	97,658,621 (GRCm39)	missense	probably benign	0.06
R8819:Rapgef3	UTSW	15	97,646,538 (GRCm39)	missense	probably benign	0.39
R8820:Rapgef3	UTSW	15	97,646,538 (GRCm39)	missense	probably benign	0.39
R8824:Rapgef3	UTSW	15	97,664,789 (GRCm39)	missense	probably benign	0.39
R9779:Rapgef3	UTSW	15	97,643,479 (GRCm39)	missense	probably damaging	0.99
R9781:Rapgef3	UTSW	15	97,643,479 (GRCm39)	missense	probably damaging	0.99
R9782:Rapgef3	UTSW	15	97,643,479 (GRCm39)	missense	probably damaging	0.99
RF024:Rapgef3	UTSW	15	97,658,621 (GRCm39)	missense	probably benign	0.06
X0011:Rapgef3	UTSW	15	97,659,354 (GRCm39)	critical splice donor site	probably null

Predicted Primers

PCR Primer
(F):5'- TCCAGATCCACCTGCATCAG -3'
(R):5'- AGTCTGTCCCTCCTACCAAG -3'

Posted On

2017-07-14