Mutagenetix > Incidental Mutation

Incidental Mutation 'R1837:Rapgef1'

205364

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

039864-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R1837 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

29509732-29630376 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 29627438 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Methionine at position 1027 (I1027M)

Ref Sequence

ENSEMBL: ENSMUSP00000099936 (fasta)

Gene Model

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

AlphaFold

Q3UHC1

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000051212

Predicted Effect

probably damaging
Transcript: ENSMUST00000091146
AA Change: I1159M

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

SMART Domains

Protein: ENSMUSP00000088680
Gene: ENSMUSG00000039844
AA Change: I1159M

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

possibly damaging
Transcript: ENSMUST00000095087
AA Change: I1165M

PolyPhen 2 Score 0.891 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000092703
Gene: ENSMUSG00000039844
AA Change: I1165M

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: I1027M

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

SMART Domains

Protein: ENSMUSP00000099936
Gene: ENSMUSG00000039844
AA Change: I1027M

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

noncoding transcript
Transcript: ENSMUST00000123953

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000137719

Predicted Effect

unknown
Transcript: ENSMUST00000147488
AA Change: I583M

SMART Domains

Protein: ENSMUSP00000117631
Gene: ENSMUSG00000039844
AA Change: I583M

Domain	Start	End	E-Value	Type
low complexity region	12	22	N/A	INTRINSIC
low complexity region	54	65	N/A	INTRINSIC
low complexity region	135	146	N/A	INTRINSIC
RasGEFN	253	395	8.04e-37	SMART
RasGEF	402	631	5.85e-102	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000147755

SMART Domains

Protein: ENSMUSP00000121615
Gene: ENSMUSG00000039844

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

0.6467

Coding Region Coverage

1x: 97.4%
3x: 96.8%
10x: 94.9%
20x: 91.6%

Validation Efficiency

99% (86/87)

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: 85 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Actl10	G	T	2: 154,394,962 (GRCm39)	G305W	probably damaging	Het
Actr3b	A	T	5: 26,030,157 (GRCm39)	T74S	probably benign	Het
Add2	A	G	6: 86,095,540 (GRCm39)	E652G	probably damaging	Het
Alg9	T	A	9: 50,717,615 (GRCm39)	V83D	probably damaging	Het
Atp13a2	T	A	4: 140,721,643 (GRCm39)	Y244*	probably null	Het
BB014433	C	G	8: 15,092,629 (GRCm39)	V75L	unknown	Het
Bcr	A	G	10: 75,003,932 (GRCm39)		probably benign	Het
Begain	G	A	12: 109,001,249 (GRCm39)		probably benign	Het
Bzw1	A	G	1: 58,439,277 (GRCm39)	K67E	probably damaging	Het
Ccdc141	T	C	2: 76,842,009 (GRCm39)	E1474G	probably benign	Het
Cdc73	T	A	1: 143,543,395 (GRCm39)	T314S	possibly damaging	Het
Cfap206	T	C	4: 34,728,813 (GRCm39)	T31A	probably damaging	Het
Cfap58	G	A	19: 48,017,578 (GRCm39)	E813K	probably damaging	Het
Clstn2	C	A	9: 97,465,593 (GRCm39)	A133S	probably benign	Het
Col14a1	A	T	15: 55,245,891 (GRCm39)	D465V	unknown	Het
Col2a1	C	T	15: 97,894,522 (GRCm39)		probably benign	Het
Dab2	A	G	15: 6,365,957 (GRCm39)		probably benign	Het
Eme1	T	C	11: 94,536,787 (GRCm39)	D464G	probably benign	Het
Eml6	T	C	11: 29,699,802 (GRCm39)		probably null	Het
Ern1	C	A	11: 106,349,783 (GRCm39)	L44F	probably damaging	Het
Fam111a	T	A	19: 12,564,816 (GRCm39)	S188R	probably benign	Het
Fam151b	A	T	13: 92,610,639 (GRCm39)		probably benign	Het
Fmo6	T	C	1: 162,750,379 (GRCm39)	N226D	probably benign	Het
Ggt1	A	G	10: 75,415,128 (GRCm39)	D214G	probably benign	Het
Gm14226	A	G	2: 154,866,930 (GRCm39)	I296V	probably benign	Het
Gm9915	A	T	1: 42,269,847 (GRCm39)		noncoding transcript	Het
Heatr5b	T	C	17: 79,128,180 (GRCm39)	D485G	possibly damaging	Het
Helz2	A	T	2: 180,871,082 (GRCm39)	I2785N	probably damaging	Het
Htt	C	T	5: 34,976,367 (GRCm39)	T723M	probably benign	Het
Hydin	C	A	8: 111,296,257 (GRCm39)	H3595Q	probably benign	Het
Il6ra	T	C	3: 89,797,579 (GRCm39)	D96G	probably benign	Het
Kif5a	G	A	10: 127,072,684 (GRCm39)	Q702*	probably null	Het
Klhdc7a	G	T	4: 139,694,381 (GRCm39)	P189T	probably benign	Het
Krt7	A	G	15: 101,317,463 (GRCm39)	D252G	probably benign	Het
Lad1	C	A	1: 135,757,444 (GRCm39)	D394E	probably benign	Het
Lhx8	A	T	3: 154,033,692 (GRCm39)	C38S	possibly damaging	Het
Lta4h	C	T	10: 93,305,037 (GRCm39)	T280M	probably damaging	Het
Magi2	A	T	5: 20,670,825 (GRCm39)	T163S	probably damaging	Het
Med1	G	T	11: 98,060,238 (GRCm39)	D230E	probably damaging	Het
Mmp1b	A	T	9: 7,386,409 (GRCm39)	F171I	probably damaging	Het
Mprip	T	C	11: 59,657,571 (GRCm39)	V801A	probably damaging	Het
Mtrf1	A	G	14: 79,639,273 (GRCm39)	E135G	possibly damaging	Het
Muc5ac	T	A	7: 141,360,823 (GRCm39)	M1378K	probably benign	Het
Myo3a	A	T	2: 22,467,604 (GRCm39)	Q286L	possibly damaging	Het
Ndor1	C	T	2: 25,138,408 (GRCm39)	G391R	probably damaging	Het
Nefl	C	T	14: 68,324,075 (GRCm39)	R438C	probably damaging	Het
Nlrp3	G	A	11: 59,439,742 (GRCm39)	V440I	probably benign	Het
Notch3	A	T	17: 32,343,296 (GRCm39)	L1959Q	probably damaging	Het
Noto	A	G	6: 85,401,159 (GRCm39)	T63A	probably benign	Het
Oc90	G	A	15: 65,761,529 (GRCm39)	T163M	probably damaging	Het
Or1l4	T	A	2: 37,092,114 (GRCm39)	M287K	probably benign	Het
Or4c114	A	T	2: 88,905,176 (GRCm39)	Y86*	probably null	Het
Or5an10	A	G	19: 12,275,740 (GRCm39)	V252A	probably damaging	Het
Pdpr	C	A	8: 111,861,366 (GRCm39)	P787T	probably damaging	Het
Phlda1	A	G	10: 111,343,092 (GRCm39)	Q276R	probably benign	Het
Ptpn21	T	G	12: 98,699,885 (GRCm39)	K10Q	probably damaging	Het
Ptprb	A	G	10: 116,177,531 (GRCm39)	E1364G	probably benign	Het
Rabep1	T	A	11: 70,795,484 (GRCm39)	W237R	probably damaging	Het
Rai1	A	T	11: 60,080,224 (GRCm39)	K1429N	probably damaging	Het
Rit1	C	G	3: 88,636,477 (GRCm39)	T127S	probably damaging	Het
Rpap1	A	C	2: 119,600,366 (GRCm39)		probably null	Het
Senp7	T	A	16: 55,978,879 (GRCm39)	C471S	probably benign	Het
Slc16a14	A	G	1: 84,890,120 (GRCm39)	V395A	probably benign	Het
Slc45a1	C	T	4: 150,722,916 (GRCm39)	G323S	probably benign	Het
Syne2	A	T	12: 76,014,434 (GRCm39)	E3208D	probably damaging	Het
Tap1	C	T	17: 34,407,083 (GRCm39)	A77V	possibly damaging	Het
Ticam1	T	C	17: 56,577,799 (GRCm39)	E432G	possibly damaging	Het
Tmem192	C	A	8: 65,416,992 (GRCm39)		probably benign	Het
Trub1	T	C	19: 57,441,461 (GRCm39)	V28A	probably benign	Het
Ttc21b	A	T	2: 66,028,106 (GRCm39)	L1121H	probably benign	Het
Ttc38	A	G	15: 85,735,764 (GRCm39)	D290G	probably damaging	Het
Ulk1	C	T	5: 110,937,247 (GRCm39)	G683D	probably damaging	Het
Vmn1r122	A	T	7: 20,867,291 (GRCm39)	F255I	probably benign	Het
Vmn2r68	T	A	7: 84,882,886 (GRCm39)	I289F	probably damaging	Het
Vps39	A	T	2: 120,155,878 (GRCm39)	L514H	probably damaging	Het
Wdr48	T	G	9: 119,734,482 (GRCm39)	S134A	probably damaging	Het
Yap1	A	T	9: 7,962,350 (GRCm39)	Y139N	probably damaging	Het
Ylpm1	T	C	12: 85,076,107 (GRCm39)	V486A	possibly damaging	Het
Zbtb38	T	C	9: 96,569,048 (GRCm39)	T679A	probably benign	Het
Zfp292	A	G	4: 34,810,264 (GRCm39)	S927P	probably damaging	Het
Zfp324	C	T	7: 12,704,156 (GRCm39)	T115I	probably benign	Het
Zfp523	T	A	17: 28,413,967 (GRCm39)	I34N	probably damaging	Het
Zfp945	A	T	17: 23,070,247 (GRCm39)	C551S	probably damaging	Het
Zfp958	A	G	8: 4,678,590 (GRCm39)	H205R	probably damaging	Het
Zfp974	G	A	7: 27,609,781 (GRCm39)	P648L	possibly damaging	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
R1817:Rapgef1	UTSW	2	29,576,268 (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'- ATCAGGTCCTGGTGGCAAAG -3'
(R):5'- GGATTGACAGCCTCCTTGTG -3'

Sequencing Primer
(F):5'- GCAAAGCCAGCACATAGC -3'
(R):5'- CAGACCAGGAATTGAGCCCTTTATG -3'

Posted On

2014-06-23