Mutagenetix > Incidental Mutation

Incidental Mutation 'R4358:Rapgef3'

324676

Institutional Source

Beutler Lab

Gene Symbol

Rapgef3

Ensembl Gene

ENSMUSG00000022469

Gene Name

Rap guanine nucleotide exchange factor (GEF) 3

Synonyms

2310016P22Rik, 9330170P05Rik, Epac1

MMRRC Submission

041110-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.197) question?

Stock #

R4358 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

97744770-97767972 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 97748648 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 794 (V794A)

Ref Sequence

ENSEMBL: ENSMUSP00000118148 (fasta)

Gene Model

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

AlphaFold

Q8VCC8

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000123397

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000125002

Predicted Effect

probably benign
Transcript: ENSMUST00000126854
AA Change: V802A

PolyPhen 2 Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)

SMART Domains

Protein: ENSMUSP00000116426
Gene: ENSMUSG00000022469
AA Change: V802A

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 benign
Transcript: ENSMUST00000128775
AA Change: V785A

PolyPhen 2 Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)

SMART Domains

Protein: ENSMUSP00000120126
Gene: ENSMUSG00000022469
AA Change: V785A

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 benign
Transcript: ENSMUST00000129223
AA Change: V794A

PolyPhen 2 Score 0.053 (Sensitivity: 0.94; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000118148
Gene: ENSMUSG00000022469
AA Change: V794A

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: ENSMUST00000134885
AA Change: V92A

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

SMART Domains

Protein: ENSMUSP00000135317
Gene: ENSMUSG00000022469
AA Change: V92A

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000146214

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000155810

Predicted Effect

probably benign
Transcript: ENSMUST00000175894

Predicted Effect

probably benign
Transcript: ENSMUST00000177352
AA Change: V760A

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

SMART Domains

Protein: ENSMUSP00000135238
Gene: ENSMUSG00000022469
AA Change: V760A

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

Meta Mutation Damage Score

0.0604

Coding Region Coverage

1x: 99.3%
3x: 98.7%
10x: 97.5%
20x: 95.8%

Validation Efficiency

98% (48/49)

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: 41 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Alpk1	C	T	3: 127,729,373	V7M	probably damaging	Het
Birc6	T	A	17: 74,619,668		probably null	Het
Chil3	G	A	3: 106,160,499	Q117*	probably null	Het
Daglb	T	C	5: 143,473,134		probably benign	Het
Dnah11	G	A	12: 118,125,843	R1163*	probably null	Het
Ftsj3	G	A	11: 106,253,676	A134V	probably benign	Het
G530012D18Rik	G	C	1: 85,577,202		probably benign	Het
Gfod2	T	C	8: 105,717,545	N122S	possibly damaging	Het
Golga4	A	G	9: 118,551,878	E507G	probably benign	Het
Ids	C	A	X: 70,346,344	G506C	probably damaging	Het
Ifna15	G	T	4: 88,557,842	T135N	probably benign	Het
Igsf9b	G	A	9: 27,309,478	V47I	possibly damaging	Het
Kif24	A	G	4: 41,413,827		probably null	Het
L3hypdh	A	T	12: 72,077,424	D247E	probably damaging	Het
Lama2	A	T	10: 26,984,493	N2999K	probably damaging	Het
Lpcat2	C	A	8: 92,873,106	P234Q	probably benign	Het
Lrp10	C	T	14: 54,468,366	R338C	probably damaging	Het
Mcm9	A	C	10: 53,537,653	C444G	probably benign	Het
Mecom	G	A	3: 29,979,785	Q246*	probably null	Het
Mib1	A	G	18: 10,751,844	N242S	probably benign	Het
Olfr13	T	A	6: 43,174,226	M80K	probably damaging	Het
Olfr943	G	A	9: 39,184,568	C127Y	probably damaging	Het
P3h4	A	G	11: 100,413,626	F263S	probably damaging	Het
Pcsk1	T	C	13: 75,112,719	S354P	possibly damaging	Het
Pms2	T	A	5: 143,925,926	F617Y	probably damaging	Het
Prps2	T	A	X: 167,363,549	K176*	probably null	Het
Psmd13	G	T	7: 140,889,505		probably benign	Het
Pygl	G	A	12: 70,195,690	S573L	probably damaging	Het
Rasgrf2	C	A	13: 91,890,677	D1017Y	probably damaging	Het
Rb1cc1	A	G	1: 6,245,637	D555G	probably damaging	Het
Rptor	G	T	11: 119,671,345	E111D	probably damaging	Het
Sall4	T	C	2: 168,755,480	E480G	probably benign	Het
Scn4a	G	A	11: 106,348,857		probably null	Het
Scn8a	G	A	15: 100,940,133	A94T	probably benign	Het
Slc26a6	T	A	9: 108,861,783	C636S	probably benign	Het
Slc38a11	T	C	2: 65,358,116	K103R	probably benign	Het
Sned1	T	C	1: 93,274,659	L675P	probably benign	Het
Spsb1	T	C	4: 149,906,775	H112R	probably damaging	Het
Tmem132d	G	A	5: 127,984,341	T399M	possibly damaging	Het
Zfp939	A	G	7: 39,473,720		noncoding transcript	Het
Zfp951	T	C	5: 104,814,675	K342E	probably damaging	Het

Other mutations in Rapgef3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01314:Rapgef3	APN	15	97748223	missense	probably damaging	1.00
IGL01339:Rapgef3	APN	15	97758059	missense	probably damaging	1.00
IGL01670:Rapgef3	APN	15	97749662	missense	probably benign	0.15
IGL01902:Rapgef3	APN	15	97750300	missense	probably benign	0.32
IGL02137:Rapgef3	APN	15	97750144	missense	probably benign	0.08
IGL02419:Rapgef3	APN	15	97750290	missense	probably benign	0.33
IGL02427:Rapgef3	APN	15	97747136	splice site	probably null
IGL02648:Rapgef3	APN	15	97758392	missense	probably damaging	1.00
IGL02834:Rapgef3	APN	15	97748265	missense	probably damaging	0.98
IGL03389:Rapgef3	APN	15	97749516	missense	probably damaging	1.00
IGL03055:Rapgef3	UTSW	15	97749489	splice site	probably benign
R0394:Rapgef3	UTSW	15	97757819	intron	probably benign
R0538:Rapgef3	UTSW	15	97757817	intron	probably benign
R0744:Rapgef3	UTSW	15	97761585	splice site	probably benign
R1288:Rapgef3	UTSW	15	97759342	missense	probably benign	0.31
R1512:Rapgef3	UTSW	15	97757501	missense	probably benign	0.24
R1676:Rapgef3	UTSW	15	97761182	missense	probably benign	0.35
R1745:Rapgef3	UTSW	15	97750178	missense	probably benign	0.22
R1928:Rapgef3	UTSW	15	97750033	missense	probably damaging	1.00
R2063:Rapgef3	UTSW	15	97766961	missense	probably damaging	1.00
R2067:Rapgef3	UTSW	15	97766961	missense	probably damaging	1.00
R2092:Rapgef3	UTSW	15	97760723	missense	probably damaging	1.00
R4624:Rapgef3	UTSW	15	97758929	missense	probably damaging	1.00
R4627:Rapgef3	UTSW	15	97758929	missense	probably damaging	1.00
R4727:Rapgef3	UTSW	15	97760600	missense	probably damaging	1.00
R4812:Rapgef3	UTSW	15	97753803	missense	probably benign	0.21
R4928:Rapgef3	UTSW	15	97757375	missense	probably damaging	1.00
R5161:Rapgef3	UTSW	15	97757725	missense	probably damaging	1.00
R5442:Rapgef3	UTSW	15	97758861	missense	probably damaging	0.99
R5652:Rapgef3	UTSW	15	97758437	missense	probably benign	0.00
R5837:Rapgef3	UTSW	15	97757342	splice site	probably benign
R6056:Rapgef3	UTSW	15	97758861	missense	probably damaging	0.99
R6167:Rapgef3	UTSW	15	97767411	unclassified	probably benign
R6694:Rapgef3	UTSW	15	97759984	missense	probably benign	0.03
R7039:Rapgef3	UTSW	15	97761568	missense	probably benign	0.01
R7154:Rapgef3	UTSW	15	97753877	missense	probably benign
R7380:Rapgef3	UTSW	15	97766791	missense	probably benign	0.00
R7655:Rapgef3	UTSW	15	97761209	missense	probably damaging	1.00
R7656:Rapgef3	UTSW	15	97761209	missense	probably damaging	1.00
R7754:Rapgef3	UTSW	15	97757746	missense	probably damaging	1.00
R7849:Rapgef3	UTSW	15	97758390	critical splice donor site	probably null
R8061:Rapgef3	UTSW	15	97761520	missense	probably benign
R8117:Rapgef3	UTSW	15	97750866	missense	probably benign	0.01
R8179:Rapgef3	UTSW	15	97760740	missense	probably benign	0.06
R8819:Rapgef3	UTSW	15	97748657	missense	probably benign	0.39
R8820:Rapgef3	UTSW	15	97748657	missense	probably benign	0.39
R8824:Rapgef3	UTSW	15	97766908	missense	probably benign	0.39
R9779:Rapgef3	UTSW	15	97745598	missense	probably damaging	0.99
R9781:Rapgef3	UTSW	15	97745598	missense	probably damaging	0.99
R9782:Rapgef3	UTSW	15	97745598	missense	probably damaging	0.99
RF024:Rapgef3	UTSW	15	97760740	missense	probably benign	0.06
X0011:Rapgef3	UTSW	15	97761473	critical splice donor site	probably null

Predicted Primers

PCR Primer
(F):5'- TGGTATCTCCTGGGGTATCTACC -3'
(R):5'- ACTTAGAAAGCCAGGCCTCAG -3'

Sequencing Primer
(F):5'- GGTATCTACCACAGCCTCGG -3'
(R):5'- CCAGGCCTCAGTGCTGTTTG -3'

Posted On

2015-06-24