Mutagenetix > Incidental Mutation

Incidental Mutation 'R7956:Rapgef1'

649798

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

046000-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R7956 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

29509732-29630376 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 29589027 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Valine at position 223 (I223V)

Ref Sequence

ENSEMBL: ENSMUSP00000092703 (fasta)

Gene Model

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

AlphaFold

Q3UHC1

Predicted Effect

probably benign
Transcript: ENSMUST00000091146
AA Change: I185V

PolyPhen 2 Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)

SMART Domains

Protein: ENSMUSP00000088680
Gene: ENSMUSG00000039844
AA Change: I185V

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: I223V

PolyPhen 2 Score 0.029 (Sensitivity: 0.95; Specificity: 0.82)

SMART Domains

Protein: ENSMUSP00000092703
Gene: ENSMUSG00000039844
AA Change: I223V

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 benign
Transcript: ENSMUST00000102872
AA Change: I223V

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

SMART Domains

Protein: ENSMUSP00000099936
Gene: ENSMUSG00000039844
AA Change: I223V

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 benign
Transcript: ENSMUST00000147488

SMART Domains

Protein: ENSMUSP00000117631
Gene: ENSMUSG00000039844

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
AA Change: I185V

PolyPhen 2 Score 0.049 (Sensitivity: 0.94; Specificity: 0.83)

SMART Domains

Protein: ENSMUSP00000121615
Gene: ENSMUSG00000039844
AA Change: I185V

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

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.7%
20x: 99.1%

Validation Efficiency

100% (78/78)

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: 84 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
5031439G07Rik	T	C	15: 84,834,963 (GRCm39)	S332G	possibly damaging	Het
Acaca	A	T	11: 84,211,406 (GRCm39)	N1573Y	probably damaging	Het
Arhgef33	A	G	17: 80,662,477 (GRCm39)	K220R	possibly damaging	Het
Arsj	A	T	3: 126,232,151 (GRCm39)	D299V	probably damaging	Het
Asic3	A	C	5: 24,621,975 (GRCm39)	I412L	possibly damaging	Het
AU018091	A	T	7: 3,211,095 (GRCm39)	L278Q	probably benign	Het
Baat	A	T	4: 49,490,117 (GRCm39)	F322L	probably damaging	Het
Bap1	A	G	14: 30,977,525 (GRCm39)	Q280R	probably benign	Het
Bet1	T	C	6: 4,079,965 (GRCm39)	E66G	probably benign	Het
Brpf1	T	C	6: 113,297,493 (GRCm39)	S1000P	probably benign	Het
Ccdc78	A	T	17: 26,006,091 (GRCm39)	E86D	possibly damaging	Het
Ccdc88a	T	G	11: 29,413,892 (GRCm39)	L810R	probably damaging	Het
Cd209f	T	C	8: 4,154,859 (GRCm39)	T80A	probably benign	Het
Chrna7	T	G	7: 62,753,541 (GRCm39)	K326T	possibly damaging	Het
Cldn15	T	C	5: 137,003,504 (GRCm39)	S169P	probably damaging	Het
Cmklr2	T	C	1: 63,222,665 (GRCm39)	N190S	probably damaging	Het
Corin	A	G	5: 72,579,530 (GRCm39)	S281P	probably damaging	Het
Coro1a	A	G	7: 126,300,727 (GRCm39)	V200A	probably benign	Het
Crebrf	C	G	17: 26,961,631 (GRCm39)	P243A	probably benign	Het
Cxxc1	T	G	18: 74,352,054 (GRCm39)		probably null	Het
Dera	C	T	6: 137,813,826 (GRCm39)	T282M	probably benign	Het
Dnah12	A	T	14: 26,430,427 (GRCm39)	D345V	probably damaging	Het
Dop1b	T	C	16: 93,567,916 (GRCm39)		probably null	Het
Dst	T	A	1: 34,264,699 (GRCm39)	V2623E	probably damaging	Het
Dysf	T	C	6: 83,985,978 (GRCm39)	F28L	probably benign	Het
Eogt	C	A	6: 97,120,926 (GRCm39)	V96F	probably benign	Het
Exoc1	A	T	5: 76,705,704 (GRCm39)	T464S	probably benign	Het
Fam234a	A	G	17: 26,435,551 (GRCm39)	Y278H	probably damaging	Het
Gatd3a	T	C	10: 77,999,405 (GRCm39)		probably null	Het
Gne	T	A	4: 44,044,962 (GRCm39)	I391L	probably benign	Het
Gpr22	G	T	12: 31,759,219 (GRCm39)	T301K	possibly damaging	Het
Gria1	A	G	11: 57,080,626 (GRCm39)	D203G	possibly damaging	Het
Grin2c	T	C	11: 115,140,974 (GRCm39)	E1048G	probably benign	Het
Hcn4	A	G	9: 58,751,456 (GRCm39)	T361A	unknown	Het
Herc2	T	C	7: 55,763,148 (GRCm39)	S918P	probably damaging	Het
Hr	A	G	14: 70,797,327 (GRCm39)	E520G	probably benign	Het
Idi1	T	G	13: 8,937,996 (GRCm39)	S147R	possibly damaging	Het
Irf9	G	A	14: 55,846,481 (GRCm39)	G464E	probably benign	Het
Kif16b	T	C	2: 142,704,390 (GRCm39)	Y63C	probably benign	Het
Klhl31	A	T	9: 77,557,903 (GRCm39)	E206D	probably benign	Het
Lrch3	A	G	16: 32,806,377 (GRCm39)	M454V	probably null	Het
Lrp1b	A	C	2: 41,172,161 (GRCm39)		probably null	Het
Lyst	A	G	13: 13,815,788 (GRCm39)	D1224G	possibly damaging	Het
Maf1	T	A	15: 76,236,696 (GRCm39)	F9L	probably benign	Het
Mllt10	T	A	2: 18,175,068 (GRCm39)	I542N	probably benign	Het
Mrpl19	T	C	6: 81,940,962 (GRCm39)	N143S	probably benign	Het
Myo5c	A	G	9: 75,159,845 (GRCm39)	N291S	probably benign	Het
Myocd	G	T	11: 65,160,494 (GRCm39)	L11M	possibly damaging	Het
Or2ag2	G	A	7: 106,485,178 (GRCm39)	T282I	possibly damaging	Het
Or5ac20	C	A	16: 59,104,856 (GRCm39)	M1I	probably null	Het
Or5an10	A	C	19: 12,275,666 (GRCm39)	F277V	probably damaging	Het
Otogl	T	C	10: 107,713,887 (GRCm39)	I511V	possibly damaging	Het
Phf19	T	C	2: 34,796,567 (GRCm39)	Y121C	possibly damaging	Het
Pik3c2a	T	C	7: 115,949,350 (GRCm39)	T1346A	probably benign	Het
Pira1	C	G	7: 3,740,319 (GRCm39)	A301P	probably damaging	Het
Polr2b	A	G	5: 77,468,092 (GRCm39)	T131A	probably benign	Het
Pom121	T	C	5: 135,412,815 (GRCm39)	T456A	unknown	Het
Pom121l2	T	C	13: 22,167,316 (GRCm39)	L529S	probably damaging	Het
Prss34	A	G	17: 25,518,553 (GRCm39)	I214V	probably benign	Het
Prss42	A	G	9: 110,628,402 (GRCm39)	Y182C	probably damaging	Het
Rbbp6	C	T	7: 122,600,561 (GRCm39)	P1523S	unknown	Het
Ripk1	T	G	13: 34,193,666 (GRCm39)	N9K	probably benign	Het
Six4	A	G	12: 73,150,535 (GRCm39)	L670S	possibly damaging	Het
Skint6	C	T	4: 112,703,894 (GRCm39)	D994N	possibly damaging	Het
Slc18a1	T	C	8: 69,491,466 (GRCm39)	D516G	probably benign	Het
Slc35g3	A	T	11: 69,651,623 (GRCm39)	Y121N	probably damaging	Het
Slc41a1	T	G	1: 131,771,766 (GRCm39)	S393R	possibly damaging	Het
Smg7	T	C	1: 152,719,953 (GRCm39)	H818R	probably benign	Het
Sorl1	A	G	9: 41,900,655 (GRCm39)	Y1686H	probably damaging	Het
Stab1	G	T	14: 30,881,981 (GRCm39)	T521K	probably benign	Het
Stard9	T	A	2: 120,535,852 (GRCm39)	Y4036*	probably null	Het
Tek	T	G	4: 94,687,580 (GRCm39)		probably null	Het
Tex35	C	T	1: 156,927,742 (GRCm39)	D143N	probably damaging	Het
Tgm1	T	A	14: 55,946,352 (GRCm39)	H428L	probably benign	Het
Tigd3	G	A	19: 5,942,594 (GRCm39)	P179S	possibly damaging	Het
Tnip3	T	A	6: 65,591,779 (GRCm39)		probably null	Het
Ttc1	A	G	11: 43,627,240 (GRCm39)		probably null	Het
Utp20	C	T	10: 88,618,476 (GRCm39)	E1175K	probably benign	Het
Vmn1r151	A	T	7: 22,199,085 (GRCm39)	S7T	possibly damaging	Het
Vmn1r34	T	A	6: 66,614,777 (GRCm39)		probably benign	Het
Vmn2r74	A	T	7: 85,605,166 (GRCm39)	M494K	probably benign	Het
Vps26c	T	C	16: 94,302,505 (GRCm39)	N234D	probably damaging	Het
Vsig10l	T	C	7: 43,117,494 (GRCm39)	S594P	probably benign	Het
Zfp937	A	G	2: 150,081,076 (GRCm39)	S369G	probably benign	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
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
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'- GCAGTTGAAACTTTGCAGTATGC -3'
(R):5'- ACAGCACTCTGAAGCTTAGTG -3'

Sequencing Primer
(F):5'- AGTATGCTGCTATGGTATTTTTAGAG -3'
(R):5'- ACTTACCACTGCAAAGGGGGC -3'

Posted On

2020-09-15