Mutagenetix > Incidental Mutation

Incidental Mutation 'R1817:Rapgef1'

204470

Institutional Source

Beutler Lab

Gene Symbol

Rapgef1

Ensembl Gene

ENSMUSG00000039844

Gene Name

Rap guanine nucleotide exchange factor (GEF) 1

Synonyms

C3G, Grf2, 4932418O06Rik

MMRRC Submission

039845-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R1817 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

29509732-29630376 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 29576268 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 117 (V117A)

Ref Sequence

ENSEMBL: ENSMUSP00000088680 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000091146] [ENSMUST00000095087] [ENSMUST00000102872] [ENSMUST00000147755]

AlphaFold

Q3UHC1

Predicted Effect

probably damaging
Transcript: ENSMUST00000091146
AA Change: V117A

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

SMART Domains

Protein: ENSMUSP00000088680
Gene: ENSMUSG00000039844
AA Change: V117A

Domain	Start	End	E-Value	Type
low complexity region	191	206	N/A	INTRINSIC
low complexity region	309	324	N/A	INTRINSIC
low complexity region	468	478	N/A	INTRINSIC
low complexity region	510	521	N/A	INTRINSIC
low complexity region	592	603	N/A	INTRINSIC
low complexity region	664	682	N/A	INTRINSIC
low complexity region	689	700	N/A	INTRINSIC
low complexity region	727	741	N/A	INTRINSIC
RasGEFN	828	970	8.04e-37	SMART
RasGEF	977	1206	5.85e-102	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000095087
AA Change: V155A

PolyPhen 2 Score 0.326 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000092703
Gene: ENSMUSG00000039844
AA Change: V155A

Domain	Start	End	E-Value	Type
low complexity region	229	244	N/A	INTRINSIC
low complexity region	347	362	N/A	INTRINSIC
low complexity region	506	516	N/A	INTRINSIC
low complexity region	548	559	N/A	INTRINSIC
low complexity region	630	641	N/A	INTRINSIC
low complexity region	702	720	N/A	INTRINSIC
low complexity region	727	738	N/A	INTRINSIC
RasGEFN	834	976	8.04e-37	SMART
RasGEF	983	1212	5.85e-102	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000102872
AA Change: V155A

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000099936
Gene: ENSMUSG00000039844
AA Change: V155A

Domain	Start	End	E-Value	Type
low complexity region	229	244	N/A	INTRINSIC
low complexity region	347	362	N/A	INTRINSIC
low complexity region	506	516	N/A	INTRINSIC
low complexity region	548	559	N/A	INTRINSIC
RasGEFN	696	838	8.04e-37	SMART
RasGEF	845	1074	5.85e-102	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000147755
AA Change: V117A

PolyPhen 2 Score 0.993 (Sensitivity: 0.70; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000121615
Gene: ENSMUSG00000039844
AA Change: V117A

Domain	Start	End	E-Value	Type
low complexity region	191	206	N/A	INTRINSIC
low complexity region	309	324	N/A	INTRINSIC
low complexity region	468	478	N/A	INTRINSIC
low complexity region	510	521	N/A	INTRINSIC
low complexity region	591	602	N/A	INTRINSIC
low complexity region	663	681	N/A	INTRINSIC

Meta Mutation Damage Score

0.3130

Coding Region Coverage

1x: 97.4%
3x: 96.9%
10x: 95.2%
20x: 91.9%

Validation Efficiency

95% (90/95)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a human guanine nucleotide exchange factor. It transduces signals from CRK by binding the SH3 domain of CRK, and activating several members of the Ras family of GTPases. This signaling cascade that may be involved in apoptosis, integrin-mediated signal transduction, and cell transformation. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some variants has not been determined. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for a null allele die before E7.5. Mice homozygous for a hypomorphic gene trap allele show embryonic lethality during organogenesis, altered neuroepithelium morphology, vascular maturation defects, hemorrhage, and reduced cell migration and adhesion. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 88 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca6	A	T	11: 110,110,144 (GRCm39)	S600T	probably benign	Het
Acly	T	A	11: 100,386,717 (GRCm39)	Q615L	probably benign	Het
Adgrf1	C	A	17: 43,620,924 (GRCm39)	T387K	probably benign	Het
Afg3l1	G	T	8: 124,228,670 (GRCm39)	K745N	probably damaging	Het
Armc8	T	C	9: 99,418,312 (GRCm39)	T39A	possibly damaging	Het
Atm	C	A	9: 53,403,533 (GRCm39)		probably benign	Het
Babam2	A	G	5: 32,214,890 (GRCm39)	T324A	probably damaging	Het
Btd	C	A	14: 31,384,246 (GRCm39)	D77E	possibly damaging	Het
Cadm1	T	A	9: 47,740,668 (GRCm39)		probably benign	Het
Card11	A	T	5: 140,871,315 (GRCm39)	D729E	probably benign	Het
Ccni	G	T	5: 93,335,967 (GRCm39)	T144K	possibly damaging	Het
Ceacam23	C	T	7: 17,607,255 (GRCm39)		noncoding transcript	Het
Cecr2	A	G	6: 120,708,228 (GRCm39)	T77A	probably damaging	Het
Cgas	A	G	9: 78,341,593 (GRCm39)		probably null	Het
Cpsf7	T	C	19: 10,512,803 (GRCm39)	F296L	possibly damaging	Het
Cyfip1	C	A	7: 55,523,196 (GRCm39)	N70K	possibly damaging	Het
Cyp4a12b	A	G	4: 115,271,259 (GRCm39)		probably benign	Het
Ddx20	A	T	3: 105,585,896 (GRCm39)	Y816*	probably null	Het
Ddx59	A	G	1: 136,360,245 (GRCm39)	I420V	probably damaging	Het
Dgat1	T	A	15: 76,386,703 (GRCm39)	M445L	probably damaging	Het
Dnah5	T	A	15: 28,246,546 (GRCm39)	L628*	probably null	Het
Dnah7a	A	C	1: 53,598,307 (GRCm39)	D1409E	probably benign	Het
Dnmt1	T	C	9: 20,838,422 (GRCm39)	T215A	probably benign	Het
Dsg4	C	T	18: 20,604,302 (GRCm39)	T923M	probably damaging	Het
Enox1	A	G	14: 77,852,915 (GRCm39)	I394V	possibly damaging	Het
Esrp2	A	T	8: 106,861,250 (GRCm39)	M183K	probably damaging	Het
Fam171a1	C	T	2: 3,179,410 (GRCm39)	P79S	probably benign	Het
Fga	A	G	3: 82,939,082 (GRCm39)	T486A	probably benign	Het
Fkbp10	G	T	11: 100,306,715 (GRCm39)	A36S	probably benign	Het
Fnip1	A	G	11: 54,393,279 (GRCm39)	T572A	probably benign	Het
Fxn	A	C	19: 24,257,765 (GRCm39)		probably null	Het
Gaa	C	T	11: 119,175,324 (GRCm39)	Q901*	probably null	Het
Gabrg1	A	G	5: 70,911,594 (GRCm39)	M344T	probably benign	Het
Galnt7	C	T	8: 57,991,212 (GRCm39)	V433M	probably damaging	Het
Gin1	A	G	1: 97,712,951 (GRCm39)		probably null	Het
Hydin	A	C	8: 111,259,459 (GRCm39)	D2477A	probably benign	Het
Igsf6	T	C	7: 120,670,031 (GRCm39)	Y37C	probably damaging	Het
Il18rap	A	G	1: 40,570,687 (GRCm39)	I210V	probably benign	Het
Kif3a	T	C	11: 53,489,561 (GRCm39)	Y138H	probably damaging	Het
Klra17	A	G	6: 129,845,681 (GRCm39)		probably null	Het
Lcorl	A	T	5: 45,952,688 (GRCm39)	I55N	probably damaging	Het
Lrrc49	A	G	9: 60,510,059 (GRCm39)	S398P	possibly damaging	Het
Ltv1	A	G	10: 13,055,018 (GRCm39)	L384S	probably damaging	Het
Mageb3	A	T	2: 121,784,918 (GRCm39)	Y261*	probably null	Het
Mical3	T	G	6: 121,019,196 (GRCm39)	T9P	probably benign	Het
Myrip	C	T	9: 120,217,228 (GRCm39)	S49L	probably damaging	Het
Nrap	T	C	19: 56,372,487 (GRCm39)		probably benign	Het
Or2m12	T	C	16: 19,104,627 (GRCm39)	N289D	probably damaging	Het
Or4k5	A	G	14: 50,385,728 (GRCm39)	V201A	probably benign	Het
Otoa	A	T	7: 120,759,753 (GRCm39)		probably benign	Het
Pals2	T	G	6: 50,140,411 (GRCm39)	F144V	probably benign	Het
Parp11	T	A	6: 127,467,008 (GRCm39)	I133N	probably damaging	Het
Pcnx1	A	G	12: 81,965,416 (GRCm39)	T528A	probably benign	Het
Pde4c	A	G	8: 71,179,638 (GRCm39)	H63R	probably benign	Het
Pdpk1	T	C	17: 24,329,878 (GRCm39)	K53E	probably damaging	Het
Pdzd7	A	T	19: 45,024,615 (GRCm39)	M468K	probably damaging	Het
Perm1	C	A	4: 156,303,061 (GRCm39)	P535Q	possibly damaging	Het
Pgap1	C	A	1: 54,575,128 (GRCm39)	A265S	probably benign	Het
Pik3c2a	A	T	7: 115,975,747 (GRCm39)		probably null	Het
Plxnd1	T	C	6: 115,957,562 (GRCm39)	T491A	possibly damaging	Het
Pms1	A	T	1: 53,246,128 (GRCm39)	D470E	probably benign	Het
Prf1	C	A	10: 61,138,762 (GRCm39)	T240N	probably damaging	Het
Prune2	A	G	19: 17,099,445 (GRCm39)	T1650A	probably benign	Het
Ptprf	A	G	4: 118,080,462 (GRCm39)	L1264P	probably benign	Het
Ptprs	A	G	17: 56,726,527 (GRCm39)	S948P	probably damaging	Het
Rnf123	A	G	9: 107,940,125 (GRCm39)	V756A	probably benign	Het
Sez6l2	A	G	7: 126,566,291 (GRCm39)	E741G	probably damaging	Het
Shc3	A	T	13: 51,626,888 (GRCm39)	I125K	possibly damaging	Het
Smr3a	A	T	5: 88,155,917 (GRCm39)		probably benign	Het
Spef2	C	T	15: 9,584,194 (GRCm39)	E1624K	probably damaging	Het
St6gal1	A	T	16: 23,140,083 (GRCm39)	K85*	probably null	Het
Taf1b	T	G	12: 24,597,121 (GRCm39)	D353E	possibly damaging	Het
Tcp10b	C	T	17: 13,286,590 (GRCm39)	P180S	possibly damaging	Het
Tlr9	A	T	9: 106,102,142 (GRCm39)	M478L	probably benign	Het
Tpr	A	T	1: 150,295,654 (GRCm39)	E892D	probably damaging	Het
Trio	C	T	15: 27,742,581 (GRCm39)	W22*	probably null	Het
Usp14	A	G	18: 10,024,673 (GRCm39)	V8A	probably damaging	Het
Vmn2r19	A	T	6: 123,307,011 (GRCm39)	K506N	possibly damaging	Het
Vmn2r45	T	A	7: 8,475,372 (GRCm39)	N552I	probably damaging	Het
Vmn2r56	A	T	7: 12,449,542 (GRCm39)	M232K	probably benign	Het
Vps13b	T	A	15: 35,910,788 (GRCm39)	F3517L	possibly damaging	Het
Yif1a	C	T	19: 5,142,333 (GRCm39)	R247*	probably null	Het
Zbtb5	A	G	4: 44,993,767 (GRCm39)	V539A	probably benign	Het
Zfp180	G	A	7: 23,804,652 (GRCm39)	R357Q	probably damaging	Het
Zfp536	A	G	7: 37,268,042 (GRCm39)	L458P	probably damaging	Het
Zfp646	G	A	7: 127,482,292 (GRCm39)	G1490S	probably benign	Het
Zfp970	C	T	2: 177,167,976 (GRCm39)	H517Y	probably damaging	Het
Zranb3	A	T	1: 127,945,293 (GRCm39)		probably null	Het

Other mutations in Rapgef1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00156:Rapgef1	APN	2	29,612,281 (GRCm39)	missense	probably benign
IGL00917:Rapgef1	APN	2	29,592,535 (GRCm39)	missense	probably benign	0.00
IGL02618:Rapgef1	APN	2	29,627,955 (GRCm39)	missense	probably damaging	1.00
IGL02642:Rapgef1	APN	2	29,590,872 (GRCm39)	splice site	probably benign
IGL02974:Rapgef1	APN	2	29,600,228 (GRCm39)	missense	possibly damaging	0.64
R0034:Rapgef1	UTSW	2	29,614,780 (GRCm39)	splice site	probably benign
R0034:Rapgef1	UTSW	2	29,614,780 (GRCm39)	splice site	probably benign
R0241:Rapgef1	UTSW	2	29,592,682 (GRCm39)	missense	possibly damaging	0.53
R0241:Rapgef1	UTSW	2	29,592,682 (GRCm39)	missense	possibly damaging	0.53
R0279:Rapgef1	UTSW	2	29,616,239 (GRCm39)	missense	probably damaging	1.00
R0432:Rapgef1	UTSW	2	29,569,828 (GRCm39)	missense	possibly damaging	0.86
R1837:Rapgef1	UTSW	2	29,627,438 (GRCm39)	missense	probably damaging	1.00
R1970:Rapgef1	UTSW	2	29,623,723 (GRCm39)	missense	probably damaging	1.00
R1980:Rapgef1	UTSW	2	29,612,239 (GRCm39)	missense	probably benign
R2076:Rapgef1	UTSW	2	29,592,520 (GRCm39)	missense	probably benign	0.00
R2363:Rapgef1	UTSW	2	29,626,608 (GRCm39)	missense	possibly damaging	0.63
R3016:Rapgef1	UTSW	2	29,597,405 (GRCm39)	missense	probably damaging	1.00
R3053:Rapgef1	UTSW	2	29,614,868 (GRCm39)	missense	probably damaging	1.00
R3777:Rapgef1	UTSW	2	29,609,701 (GRCm39)	missense	possibly damaging	0.67
R3980:Rapgef1	UTSW	2	29,609,662 (GRCm39)	missense	probably benign	0.33
R4491:Rapgef1	UTSW	2	29,609,668 (GRCm39)	missense	possibly damaging	0.93
R4524:Rapgef1	UTSW	2	29,569,258 (GRCm39)	missense	probably benign	0.00
R4732:Rapgef1	UTSW	2	29,579,172 (GRCm39)	missense	probably damaging	1.00
R4733:Rapgef1	UTSW	2	29,579,172 (GRCm39)	missense	probably damaging	1.00
R5391:Rapgef1	UTSW	2	29,627,977 (GRCm39)	missense	probably damaging	1.00
R5395:Rapgef1	UTSW	2	29,627,977 (GRCm39)	missense	probably damaging	1.00
R5611:Rapgef1	UTSW	2	29,592,448 (GRCm39)	missense	probably damaging	0.96
R6062:Rapgef1	UTSW	2	29,590,744 (GRCm39)	missense	probably damaging	0.96
R6145:Rapgef1	UTSW	2	29,626,678 (GRCm39)	missense	probably damaging	1.00
R6580:Rapgef1	UTSW	2	29,620,621 (GRCm39)	missense	possibly damaging	0.95
R6892:Rapgef1	UTSW	2	29,589,852 (GRCm39)	critical splice donor site	probably null
R6897:Rapgef1	UTSW	2	29,592,514 (GRCm39)	missense	probably damaging	1.00
R6957:Rapgef1	UTSW	2	29,623,710 (GRCm39)	missense	possibly damaging	0.62
R7039:Rapgef1	UTSW	2	29,616,226 (GRCm39)	missense	probably damaging	0.97
R7149:Rapgef1	UTSW	2	29,610,712 (GRCm39)	missense	probably damaging	0.98
R7253:Rapgef1	UTSW	2	29,589,733 (GRCm39)	missense	possibly damaging	0.72
R7315:Rapgef1	UTSW	2	29,624,504 (GRCm39)	missense	probably damaging	0.98
R7956:Rapgef1	UTSW	2	29,589,027 (GRCm39)	missense	probably benign	0.03
R8161:Rapgef1	UTSW	2	29,569,210 (GRCm39)	missense	probably benign	0.08
R8162:Rapgef1	UTSW	2	29,626,011 (GRCm39)	missense	probably damaging	0.99
R8372:Rapgef1	UTSW	2	29,600,243 (GRCm39)	missense	probably damaging	0.99
R8373:Rapgef1	UTSW	2	29,600,243 (GRCm39)	missense	probably damaging	0.99
R8485:Rapgef1	UTSW	2	29,600,186 (GRCm39)	missense	probably damaging	1.00
R8838:Rapgef1	UTSW	2	29,627,458 (GRCm39)	missense	possibly damaging	0.77
R9484:Rapgef1	UTSW	2	29,625,821 (GRCm39)	missense	possibly damaging	0.95
R9521:Rapgef1	UTSW	2	29,624,291 (GRCm39)	missense	probably benign	0.16
RF005:Rapgef1	UTSW	2	29,597,207 (GRCm39)	splice site	probably null

Predicted Primers

PCR Primer
(F):5'- ACATGGCATTCCCTTTCAGAAC -3'
(R):5'- TGATCACAGGATAAAGCCACAG -3'

Sequencing Primer
(F):5'- TTCAGAACCTGTGCTGGC -3'
(R):5'- CATCTGCTAGGAGTTGGCCAG -3'

Posted On

2014-06-23