Mutagenetix > Incidental Mutation

Incidental Mutation 'R4627:Rapgef3'

348908

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

041892-MU

Accession Numbers

Essential gene?

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

Stock #

R4627 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

97744770-97767972 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

G to T at 97758929 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glutamic Acid at position 318 (D318E)

Ref Sequence

ENSEMBL: ENSMUSP00000118148 (fasta)

Gene Model

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

AlphaFold

Q8VCC8

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000123397

Predicted Effect

probably damaging
Transcript: ENSMUST00000126854
AA Change: D318E

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

SMART Domains

Protein: ENSMUSP00000116426
Gene: ENSMUSG00000022469
AA Change: D318E

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

possibly damaging
Transcript: ENSMUST00000128775
AA Change: D318E

PolyPhen 2 Score 0.832 (Sensitivity: 0.84; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000120126
Gene: ENSMUSG00000022469
AA Change: D318E

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: D318E

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

SMART Domains

Protein: ENSMUSP00000118148
Gene: ENSMUSG00000022469
AA Change: D318E

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

noncoding transcript
Transcript: ENSMUST00000153241

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000153464

Predicted Effect

probably benign
Transcript: ENSMUST00000175894

Predicted Effect

probably benign
Transcript: ENSMUST00000177352
AA Change: D276E

PolyPhen 2 Score 0.050 (Sensitivity: 0.94; Specificity: 0.83)

SMART Domains

Protein: ENSMUSP00000135238
Gene: ENSMUSG00000022469
AA Change: D276E

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

0.6467

Coding Region Coverage

1x: 99.3%
3x: 98.7%
10x: 97.3%
20x: 95.4%

Validation Efficiency

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: 92 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2010111I01Rik	T	C	13: 63,068,092 (GRCm38)	S393P	probably benign	Het
Adam6a	A	T	12: 113,544,949 (GRCm38)	D314V	probably benign	Het
Adamts18	C	T	8: 113,773,168 (GRCm38)	W371*	probably null	Het
Adamtsl2	T	A	2: 27,093,585 (GRCm38)	L331Q	probably damaging	Het
Akr1c13	G	T	13: 4,197,870 (GRCm38)	V214F	probably damaging	Het
Aldoart1	T	C	4: 72,852,443 (GRCm38)	T43A	probably benign	Het
Alkbh2	C	T	5: 114,124,226 (GRCm38)	E148K	probably damaging	Het
Ano7	T	C	1: 93,375,185 (GRCm38)	I15T	probably benign	Het
Aox3	A	T	1: 58,125,035 (GRCm38)	T155S	probably damaging	Het
Ap2a1	C	T	7: 44,904,419 (GRCm38)	V535M	probably damaging	Het
Apbb2	C	T	5: 66,400,076 (GRCm38)		probably null	Het
Astn1	C	A	1: 158,502,251 (GRCm38)	H225Q	possibly damaging	Het
Atm	A	G	9: 53,456,506 (GRCm38)	I2439T	possibly damaging	Het
Atp1b2	T	A	11: 69,601,334 (GRCm38)	I263F	probably damaging	Het
Ccdc184	A	T	15: 98,168,757 (GRCm38)	N148Y	probably benign	Het
Cdca7	TGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGA	TGAAGAAGAAGAAGAAGAAGAAGAAGAAGA	2: 72,481,861 (GRCm38)		probably benign	Het
Cep192	C	G	18: 67,812,369 (GRCm38)	P180R	probably benign	Het
Cfap46	A	T	7: 139,680,927 (GRCm38)	L85Q	probably damaging	Het
Cfap46	T	C	7: 139,657,281 (GRCm38)	Y571C	probably damaging	Het
Chchd6	G	A	6: 89,384,660 (GRCm38)	L226F	probably damaging	Het
Cnot6l	A	G	5: 96,077,211 (GRCm38)	V541A	probably benign	Het
Cobl	T	C	11: 12,251,093 (GRCm38)	E1214G	probably damaging	Het
Cpsf2	G	A	12: 101,989,895 (GRCm38)	R319Q	probably benign	Het
Csdc2	T	C	15: 81,949,123 (GRCm38)	V107A	probably benign	Het
Csmd1	A	G	8: 16,697,917 (GRCm38)	W273R	probably benign	Het
Diexf	T	C	1: 193,107,695 (GRCm38)	T719A	probably benign	Het
Dnah2	T	A	11: 69,465,376 (GRCm38)	N2156I	probably damaging	Het
Dsp	A	G	13: 38,168,641 (GRCm38)	Y165C	probably benign	Het
Exoc1	T	C	5: 76,542,228 (GRCm38)	V205A	probably benign	Het
Fam98c	T	C	7: 29,155,268 (GRCm38)	T49A	possibly damaging	Het
Fbln2	G	T	6: 91,259,767 (GRCm38)	V755L	probably damaging	Het
Fhad1	A	T	4: 141,896,468 (GRCm38)	V1371D	possibly damaging	Het
Folh1	A	T	7: 86,773,252 (GRCm38)	M59K	probably benign	Het
Foxf2	A	T	13: 31,626,888 (GRCm38)	H270L	probably benign	Het
Gm14401	G	A	2: 177,086,316 (GRCm38)	R65H	probably benign	Het
Gpn1	C	A	5: 31,498,393 (GRCm38)	Y592*	probably null	Het
Hmcn1	T	G	1: 150,595,894 (GRCm38)	D4903A	probably benign	Het
Hnf1a	T	C	5: 114,955,871 (GRCm38)	R220G	probably damaging	Het
Hoxd10	G	A	2: 74,692,292 (GRCm38)	A105T	probably benign	Het
Kcnd3	C	T	3: 105,658,766 (GRCm38)	A421V	probably damaging	Het
Kidins220	C	T	12: 25,057,042 (GRCm38)	T1498I	possibly damaging	Het
Klhl2	G	T	8: 64,758,191 (GRCm38)	Y274*	probably null	Het
Lmbrd1	A	G	1: 24,705,999 (GRCm38)	Y140C	probably damaging	Het
Mapk8ip3	G	A	17: 24,903,293 (GRCm38)	T706I	probably benign	Het
Mast4	A	C	13: 103,334,021 (GRCm38)	S58A	possibly damaging	Het
Mcm6	T	C	1: 128,351,548 (GRCm38)	D167G	probably benign	Het
Mmachc	A	T	4: 116,703,471 (GRCm38)	S276T	probably damaging	Het
Nfat5	A	T	8: 107,369,276 (GRCm38)	Q1289L	probably damaging	Het
Nlrc4	G	T	17: 74,446,628 (GRCm38)	F253L	probably damaging	Het
Nr1i3	C	A	1: 171,216,445 (GRCm38)	A112E	probably benign	Het
Olfr1367	T	C	13: 21,347,464 (GRCm38)	F179L	probably damaging	Het
Olfr45	T	A	7: 140,691,378 (GRCm38)	S158T	probably benign	Het
Olfr455	T	A	6: 42,538,441 (GRCm38)	T194S	possibly damaging	Het
Olfr853	G	T	9: 19,537,673 (GRCm38)	Q86K	possibly damaging	Het
Orc5	G	T	5: 22,548,005 (GRCm38)	F10L	probably benign	Het
Pde10a	A	C	17: 8,981,652 (GRCm38)	D779A	probably damaging	Het
Pde4b	T	C	4: 102,601,605 (GRCm38)	L486S	probably damaging	Het
Pex2	A	T	3: 5,561,281 (GRCm38)	I156N	probably damaging	Het
Phtf2	C	T	5: 20,773,740 (GRCm38)	R63Q	probably damaging	Het
Prag1	A	G	8: 36,103,292 (GRCm38)	Y343C	probably damaging	Het
Prdm16	A	T	4: 154,367,240 (GRCm38)	Y170N	probably damaging	Het
Prpf6	A	C	2: 181,601,474 (GRCm38)	K5T	probably damaging	Het
Ptpn1	A	G	2: 167,967,781 (GRCm38)	K103R	probably benign	Het
Ralgapa2	A	G	2: 146,361,453 (GRCm38)	S1159P	possibly damaging	Het
Ripk4	A	T	16: 97,744,026 (GRCm38)	S474T	probably damaging	Het
Rmi1	A	G	13: 58,409,136 (GRCm38)	R400G	probably benign	Het
Sec16a	A	G	2: 26,429,393 (GRCm38)	V1491A	probably damaging	Het
Sec16a	C	T	2: 26,431,068 (GRCm38)		probably null	Het
Setd7	G	T	3: 51,542,665 (GRCm38)	N113K	probably damaging	Het
Shank2	C	T	7: 144,411,424 (GRCm38)	T1502M	probably damaging	Het
Skor1	A	T	9: 63,145,476 (GRCm38)	C376S	probably damaging	Het
Slc12a3	A	T	8: 94,329,384 (GRCm38)	L49F	probably benign	Het
Slc35d3	C	T	10: 19,849,331 (GRCm38)	V260M	probably damaging	Het
Slc46a1	T	A	11: 78,466,889 (GRCm38)	V256E	probably benign	Het
Slc6a1	T	C	6: 114,308,106 (GRCm38)	S127P	probably benign	Het
Syngr4	A	G	7: 45,887,028 (GRCm38)	L190P	probably damaging	Het
Tagap	G	A	17: 7,926,941 (GRCm38)		probably null	Het
Tamm41	A	T	6: 115,035,002 (GRCm38)	N89K	probably benign	Het
Tbc1d31	T	A	15: 57,967,912 (GRCm38)	M922K	probably benign	Het
Tbk1	T	C	10: 121,568,080 (GRCm38)	N254S	possibly damaging	Het
Tfec	A	G	6: 16,840,479 (GRCm38)	S140P	probably damaging	Het
Tnrc18	T	C	5: 142,740,128 (GRCm38)	E1802G	unknown	Het
Tom1l2	C	T	11: 60,242,707 (GRCm38)		probably null	Het
Tonsl	T	G	15: 76,637,224 (GRCm38)	K323Q	probably damaging	Het
Tsnaxip1	A	T	8: 105,841,407 (GRCm38)	E268D	probably damaging	Het
Ttf1	C	A	2: 29,065,160 (GRCm38)	H179N	possibly damaging	Het
Ttn	T	C	2: 76,726,173 (GRCm38)	S30163G	probably damaging	Het
Ube2c	A	G	2: 164,772,173 (GRCm38)	N143S	possibly damaging	Het
Ugt1a10	G	A	1: 88,218,390 (GRCm38)	R519Q	probably damaging	Het
Vmn2r9	T	C	5: 108,847,597 (GRCm38)	Y395C	probably damaging	Het
Vwa8	G	A	14: 79,103,697 (GRCm38)		probably null	Het
Zfp9	A	G	6: 118,464,976 (GRCm38)	Y242H	probably 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
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
R4928:Rapgef3	UTSW	15	97,757,375 (GRCm38)	missense	probably damaging	1.00
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'- TGTTCTCTCACGCCAAACTG -3'
(R):5'- TGGACACTCCCTTTGATAGCC -3'

Sequencing Primer
(F):5'- GATCCCAAGTGTCCTTACAAATTC -3'
(R):5'- CCCTTTGATAGCCCCAAGG -3'

Posted On

2015-10-08