Mutagenetix > Incidental Mutation

Incidental Mutation 'R4928:Rapgef3'

381046

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

042529-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.186) question?

Stock #

R4928 (G1)

Quality Score

114

Status

Validated

Chromosome

Chromosomal Location

97744770-97767972 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 97757375 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glycine at position 486 (D486G)

Ref Sequence

ENSEMBL: ENSMUSP00000120126 (fasta)

Gene Model

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

AlphaFold

Q8VCC8

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000123397

Predicted Effect

probably damaging
Transcript: ENSMUST00000126854
AA Change: D486G

PolyPhen 2 Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000116426
Gene: ENSMUSG00000022469
AA Change: D486G

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: D486G

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000120126
Gene: ENSMUSG00000022469
AA Change: D486G

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: D486G

PolyPhen 2 Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000118148
Gene: ENSMUSG00000022469
AA Change: D486G

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

noncoding transcript
Transcript: ENSMUST00000146214

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000149373

Predicted Effect

probably benign
Transcript: ENSMUST00000149419

Predicted Effect

probably damaging
Transcript: ENSMUST00000177352
AA Change: D444G

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000135238
Gene: ENSMUSG00000022469
AA Change: D444G

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: ENSMUST00000153241

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000153464

Predicted Effect

probably benign
Transcript: ENSMUST00000175894

Meta Mutation Damage Score

0.6787

Coding Region Coverage

1x: 99.1%
3x: 98.3%
10x: 96.3%
20x: 92.5%

Validation Efficiency

98% (123/126)

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: 110 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
A530021J07Rik	G	T	7: 83,155,878 (GRCm38)		noncoding transcript	Het
Aasdh	T	A	5: 76,896,688 (GRCm38)	K118N	possibly damaging	Het
Abca14	A	T	7: 120,324,580 (GRCm38)	N1620I	possibly damaging	Het
Acap1	A	T	11: 69,885,815 (GRCm38)	S149T	possibly damaging	Het
Adgre1	T	A	17: 57,444,064 (GRCm38)	Y579*	probably null	Het
AI314180	A	G	4: 58,827,073 (GRCm38)	V1020A	probably damaging	Het
Aifm3	T	C	16: 17,500,432 (GRCm38)		probably benign	Het
Aldh16a1	A	G	7: 45,141,961 (GRCm38)	W107R	probably damaging	Het
Amer2	A	T	14: 60,379,445 (GRCm38)	H363L	possibly damaging	Het
Arhgap10	A	G	8: 77,426,328 (GRCm38)		probably null	Het
Arhgef6	A	T	X: 57,234,878 (GRCm38)	D742E	probably damaging	Het
Astn2	A	T	4: 65,729,407 (GRCm38)	N731K	probably damaging	Het
Atp1a2	T	C	1: 172,278,387 (GRCm38)	T904A	possibly damaging	Het
Atr	C	T	9: 95,907,299 (GRCm38)	R1503W	probably damaging	Het
Cdh3	G	T	8: 106,536,610 (GRCm38)	R97L	probably benign	Het
Chst2	C	T	9: 95,406,006 (GRCm38)	V96I	probably benign	Het
Cit	T	A	5: 115,985,797 (GRCm38)	N1464K	probably benign	Het
Col17a1	A	T	19: 47,670,458 (GRCm38)		probably null	Het
Col4a3	G	A	1: 82,710,977 (GRCm38)		probably benign	Het
Copz1	T	A	15: 103,291,330 (GRCm38)	S57R	probably damaging	Het
Cpped1	A	T	16: 11,828,279 (GRCm38)	F227Y	probably damaging	Het
Cyp2j12	A	T	4: 96,102,151 (GRCm38)		probably null	Het
Dctn1	T	A	6: 83,189,207 (GRCm38)	I195N	possibly damaging	Het
Dhrs7b	A	G	11: 60,851,925 (GRCm38)	I148V	probably benign	Het
Dnah17	T	C	11: 118,027,433 (GRCm38)	D4096G	probably damaging	Het
Dnajc13	T	C	9: 104,233,638 (GRCm38)	N145D	possibly damaging	Het
Ercc6l2	T	C	13: 63,894,813 (GRCm38)		probably benign	Het
Fads6	T	G	11: 115,296,561 (GRCm38)	I103L	probably benign	Het
Fam189a1	G	T	7: 64,759,368 (GRCm38)	S426*	probably null	Het
Fat4	T	G	3: 39,010,465 (GRCm38)	Y4857D	probably damaging	Het
Fbxl14	T	A	6: 119,480,710 (GRCm38)	L284Q	probably damaging	Het
Fkbp9	T	C	6: 56,849,670 (GRCm38)	V85A	possibly damaging	Het
Galnt13	T	A	2: 54,516,565 (GRCm38)	V9E	probably damaging	Het
Gm14412	A	T	2: 177,314,580 (GRCm38)	S507R	probably benign	Het
Gm15142	T	A	X: 154,638,419 (GRCm38)		noncoding transcript	Het
Gm4787	T	C	12: 81,378,838 (GRCm38)	E182G	probably benign	Het
Gm6811	C	A	17: 21,094,631 (GRCm38)		noncoding transcript	Het
Gm9791	A	T	3: 34,005,069 (GRCm38)		noncoding transcript	Het
Hoxb7	A	T	11: 96,289,510 (GRCm38)		probably null	Het
Ift122	T	A	6: 115,915,858 (GRCm38)		probably benign	Het
Krt28	C	T	11: 99,374,632 (GRCm38)	V70I	probably benign	Het
Lig1	T	C	7: 13,298,738 (GRCm38)	S459P	probably damaging	Het
Lrfn3	C	T	7: 30,360,623 (GRCm38)	R59H	possibly damaging	Het
Mavs	T	C	2: 131,246,743 (GRCm38)	V489A	probably benign	Het
Mcm8	C	T	2: 132,839,479 (GRCm38)	P625L	probably benign	Het
Megf10	G	T	18: 57,240,673 (GRCm38)	R181L	probably benign	Het
Mgrn1	G	A	16: 4,927,862 (GRCm38)	G440D	probably benign	Het
Mllt3	T	C	4: 87,782,405 (GRCm38)		probably null	Het
Muc5ac	T	A	7: 141,817,902 (GRCm38)	Y2613*	probably null	Het
Myh14	C	T	7: 44,635,502 (GRCm38)	G662S	probably benign	Het
Myod1	T	A	7: 46,377,050 (GRCm38)	N126K	probably damaging	Het
Nae1	A	T	8: 104,516,142 (GRCm38)	H439Q	possibly damaging	Het
Narf	T	A	11: 121,244,939 (GRCm38)	V136E	possibly damaging	Het
Ncapd3	T	A	9: 27,071,735 (GRCm38)	C926*	probably null	Het
Ndufv2	C	A	17: 66,092,658 (GRCm38)		probably null	Het
Neb	T	C	2: 52,212,975 (GRCm38)	S449G	possibly damaging	Het
Nek10	C	T	14: 14,930,577 (GRCm38)	P698L	probably damaging	Het
Nox3	T	A	17: 3,635,275 (GRCm38)	E566V	probably null	Het
Oas1a	C	T	5: 120,905,724 (GRCm38)	R115H	probably benign	Het
Olfr1076	T	A	2: 86,509,125 (GRCm38)	L222H	probably damaging	Het
Olfr1130	C	A	2: 87,608,143 (GRCm38)	L252I	probably benign	Het
Olfr1152	A	G	2: 87,868,230 (GRCm38)	M80V	probably benign	Het
Olfr65	A	G	7: 103,906,672 (GRCm38)	T78A	probably damaging	Het
Pbld2	A	G	10: 63,047,999 (GRCm38)	H142R	probably damaging	Het
Pcdha4	C	T	18: 36,954,816 (GRCm38)	T684M	probably benign	Het
Phc3	G	T	3: 30,950,919 (GRCm38)	T175N	probably damaging	Het
Pigs	G	T	11: 78,329,002 (GRCm38)	V68L	probably damaging	Het
Pik3c2g	T	A	6: 139,967,802 (GRCm38)	D857E	possibly damaging	Het
Pitpnm3	G	A	11: 72,063,172 (GRCm38)	P550S	probably damaging	Het
Pla2g15	G	A	8: 106,163,218 (GRCm38)	W374*	probably null	Het
Ptpn14	G	A	1: 189,822,642 (GRCm38)	C133Y	probably damaging	Het
Ptpn20	A	G	14: 33,614,489 (GRCm38)	N95S	probably benign	Het
Ptrh2	G	T	11: 86,690,036 (GRCm38)	V160F	probably damaging	Het
Rev3l	T	G	10: 39,823,985 (GRCm38)	S1493A	probably benign	Het
Rgs9	T	A	11: 109,225,744 (GRCm38)	D411V	probably benign	Het
Rgsl1	A	T	1: 153,793,768 (GRCm38)	Y291N	probably damaging	Het
Rprd2	A	G	3: 95,764,537 (GRCm38)	Y1185H	probably damaging	Het
Rpusd3	A	G	6: 113,416,206 (GRCm38)		probably benign	Het
Scnn1a	T	C	6: 125,322,173 (GRCm38)	I72T	probably damaging	Het
Sdk1	A	T	5: 141,857,003 (GRCm38)		probably benign	Het
Sfmbt2	T	C	2: 10,445,745 (GRCm38)	L277P	probably benign	Het
Sgf29	A	G	7: 126,664,982 (GRCm38)	E73G	probably damaging	Het
Slc12a6	T	A	2: 112,352,961 (GRCm38)	F764L	probably damaging	Het
Slc4a2	T	C	5: 24,435,342 (GRCm38)		probably null	Het
Slc9a3	T	G	13: 74,157,719 (GRCm38)	V285G	probably damaging	Het
Slc9c1	A	G	16: 45,575,409 (GRCm38)	T608A	probably benign	Het
Slfnl1	C	T	4: 120,535,685 (GRCm38)	R325C	probably damaging	Het
Smarcad1	T	A	6: 65,074,914 (GRCm38)	F344I	probably benign	Het
Snrnp70	A	T	7: 45,377,281 (GRCm38)		probably null	Het
Sod2	C	T	17: 13,008,186 (GRCm38)	T9M	probably benign	Het
Spag5	T	A	11: 78,314,373 (GRCm38)	S633T	probably damaging	Het
Spta1	A	T	1: 174,191,056 (GRCm38)	I531L	probably benign	Het
Stra8	A	G	6: 34,933,156 (GRCm38)	E60G	probably benign	Het
Sult2a3	T	A	7: 14,111,557 (GRCm38)	I126F	probably benign	Het
Syt1	T	C	10: 108,504,512 (GRCm38)	H315R	possibly damaging	Het
Tanc2	T	C	11: 105,867,762 (GRCm38)	L783P	probably damaging	Het
Thbs2	C	T	17: 14,678,900 (GRCm38)	C646Y	probably damaging	Het
Ticam2	T	A	18: 46,560,922 (GRCm38)	K33*	probably null	Het
Trim17	T	C	11: 58,954,301 (GRCm38)		probably benign	Het
Tsr1	G	A	11: 74,907,879 (GRCm38)	M691I	probably benign	Het
Ttn	T	A	2: 76,762,419 (GRCm38)	I20790F	probably damaging	Het
Tubb2b	A	T	13: 34,128,185 (GRCm38)	Y208*	probably null	Het
Ubr1	T	A	2: 120,914,938 (GRCm38)	I890F	probably damaging	Het
Usp54	T	C	14: 20,562,192 (GRCm38)	E852G	probably damaging	Het
Vmn2r78	T	C	7: 86,954,627 (GRCm38)	V671A	probably damaging	Het
Wipi1	T	C	11: 109,579,649 (GRCm38)	K315E	probably benign	Het
Xrn2	T	C	2: 147,051,718 (GRCm38)	V735A	possibly damaging	Het
Zdbf2	T	A	1: 63,308,814 (GRCm38)	D2117E	possibly damaging	Het
Zfp287	A	T	11: 62,714,136 (GRCm38)	C648*	probably null	Het
Zfp369	A	G	13: 65,296,800 (GRCm38)	T586A	possibly damaging	Het

Other mutations in Rapgef3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01314:Rapgef3	APN	15	97,748,223 (GRCm38)	missense	probably damaging	1.00
IGL01339:Rapgef3	APN	15	97,758,059 (GRCm38)	missense	probably damaging	1.00
IGL01670:Rapgef3	APN	15	97,749,662 (GRCm38)	missense	probably benign	0.15
IGL01902:Rapgef3	APN	15	97,750,300 (GRCm38)	missense	probably benign	0.32
IGL02137:Rapgef3	APN	15	97,750,144 (GRCm38)	missense	probably benign	0.08
IGL02419:Rapgef3	APN	15	97,750,290 (GRCm38)	missense	probably benign	0.33
IGL02427:Rapgef3	APN	15	97,747,136 (GRCm38)	splice site	probably null
IGL02648:Rapgef3	APN	15	97,758,392 (GRCm38)	missense	probably damaging	1.00
IGL02834:Rapgef3	APN	15	97,748,265 (GRCm38)	missense	probably damaging	0.98
IGL03389:Rapgef3	APN	15	97,749,516 (GRCm38)	missense	probably damaging	1.00
IGL03055:Rapgef3	UTSW	15	97,749,489 (GRCm38)	splice site	probably benign
R0394:Rapgef3	UTSW	15	97,757,819 (GRCm38)	intron	probably benign
R0538:Rapgef3	UTSW	15	97,757,817 (GRCm38)	intron	probably benign
R0744:Rapgef3	UTSW	15	97,761,585 (GRCm38)	splice site	probably benign
R1288:Rapgef3	UTSW	15	97,759,342 (GRCm38)	missense	probably benign	0.31
R1512:Rapgef3	UTSW	15	97,757,501 (GRCm38)	missense	probably benign	0.24
R1676:Rapgef3	UTSW	15	97,761,182 (GRCm38)	missense	probably benign	0.35
R1745:Rapgef3	UTSW	15	97,750,178 (GRCm38)	missense	probably benign	0.22
R1928:Rapgef3	UTSW	15	97,750,033 (GRCm38)	missense	probably damaging	1.00
R2063:Rapgef3	UTSW	15	97,766,961 (GRCm38)	missense	probably damaging	1.00
R2067:Rapgef3	UTSW	15	97,766,961 (GRCm38)	missense	probably damaging	1.00
R2092:Rapgef3	UTSW	15	97,760,723 (GRCm38)	missense	probably damaging	1.00
R4358:Rapgef3	UTSW	15	97,748,648 (GRCm38)	missense	probably benign	0.05
R4624:Rapgef3	UTSW	15	97,758,929 (GRCm38)	missense	probably damaging	1.00
R4627:Rapgef3	UTSW	15	97,758,929 (GRCm38)	missense	probably damaging	1.00
R4727:Rapgef3	UTSW	15	97,760,600 (GRCm38)	missense	probably damaging	1.00
R4812:Rapgef3	UTSW	15	97,753,803 (GRCm38)	missense	probably benign	0.21
R5161:Rapgef3	UTSW	15	97,757,725 (GRCm38)	missense	probably damaging	1.00
R5442:Rapgef3	UTSW	15	97,758,861 (GRCm38)	missense	probably damaging	0.99
R5652:Rapgef3	UTSW	15	97,758,437 (GRCm38)	missense	probably benign	0.00
R5837:Rapgef3	UTSW	15	97,757,342 (GRCm38)	splice site	probably benign
R6056:Rapgef3	UTSW	15	97,758,861 (GRCm38)	missense	probably damaging	0.99
R6167:Rapgef3	UTSW	15	97,767,411 (GRCm38)	unclassified	probably benign
R6694:Rapgef3	UTSW	15	97,759,984 (GRCm38)	missense	probably benign	0.03
R7039:Rapgef3	UTSW	15	97,761,568 (GRCm38)	missense	probably benign	0.01
R7154:Rapgef3	UTSW	15	97,753,877 (GRCm38)	missense	probably benign
R7380:Rapgef3	UTSW	15	97,766,791 (GRCm38)	missense	probably benign	0.00
R7655:Rapgef3	UTSW	15	97,761,209 (GRCm38)	missense	probably damaging	1.00
R7656:Rapgef3	UTSW	15	97,761,209 (GRCm38)	missense	probably damaging	1.00
R7754:Rapgef3	UTSW	15	97,757,746 (GRCm38)	missense	probably damaging	1.00
R7849:Rapgef3	UTSW	15	97,758,390 (GRCm38)	critical splice donor site	probably null
R8061:Rapgef3	UTSW	15	97,761,520 (GRCm38)	missense	probably benign
R8117:Rapgef3	UTSW	15	97,750,866 (GRCm38)	missense	probably benign	0.01
R8179:Rapgef3	UTSW	15	97,760,740 (GRCm38)	missense	probably benign	0.06
R8819:Rapgef3	UTSW	15	97,748,657 (GRCm38)	missense	probably benign	0.39
R8820:Rapgef3	UTSW	15	97,748,657 (GRCm38)	missense	probably benign	0.39
R8824:Rapgef3	UTSW	15	97,766,908 (GRCm38)	missense	probably benign	0.39
R9779:Rapgef3	UTSW	15	97,745,598 (GRCm38)	missense	probably damaging	0.99
R9781:Rapgef3	UTSW	15	97,745,598 (GRCm38)	missense	probably damaging	0.99
R9782:Rapgef3	UTSW	15	97,745,598 (GRCm38)	missense	probably damaging	0.99
RF024:Rapgef3	UTSW	15	97,760,740 (GRCm38)	missense	probably benign	0.06
X0011:Rapgef3	UTSW	15	97,761,473 (GRCm38)	critical splice donor site	probably null

Predicted Primers

PCR Primer
(F):5'- CTGTTCCCTCAGCAAGTTGC -3'
(R):5'- AGGAATCTCAAAGTGGCCGC -3'

Sequencing Primer
(F):5'- CAAGTTGCTAAGTCGGGCATCTC -3'
(R):5'- AGCAGTCGGGTCCTGTATGAC -3'

Posted On

2016-04-15