Mutagenetix > Incidental Mutation

Incidental Mutation 'R7253:Rapgef1'

564046

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

045314-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R7253 (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 29589733 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glutamic Acid to Glycine at position 258 (E258G)

Ref Sequence

ENSEMBL: ENSMUSP00000092703 (fasta)

Gene Model

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

AlphaFold

Q3UHC1

Predicted Effect

possibly damaging
Transcript: ENSMUST00000091146
AA Change: E220G

PolyPhen 2 Score 0.894 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000088680
Gene: ENSMUSG00000039844
AA Change: E220G

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: E258G

PolyPhen 2 Score 0.719 (Sensitivity: 0.86; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000092703
Gene: ENSMUSG00000039844
AA Change: E258G

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: E258G

PolyPhen 2 Score 0.990 (Sensitivity: 0.72; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000099936
Gene: ENSMUSG00000039844
AA Change: E258G

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

possibly damaging
Transcript: ENSMUST00000147755
AA Change: E220G

PolyPhen 2 Score 0.816 (Sensitivity: 0.84; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000121615
Gene: ENSMUSG00000039844
AA Change: E220G

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

0.0775

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.8%
20x: 99.4%

Validation Efficiency

99% (74/75)

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: 76 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700009N14Rik	A	G	4: 39,451,391 (GRCm39)	H199R	not run	Het
Ak9	A	G	10: 41,308,480 (GRCm39)	N1804S	unknown	Het
Akr1c21	C	A	13: 4,627,139 (GRCm39)	T147N	probably damaging	Het
Aldh1a2	A	G	9: 71,123,216 (GRCm39)	T30A	probably benign	Het
Alox15	T	C	11: 70,236,724 (GRCm39)	D447G	probably damaging	Het
Amigo2	T	C	15: 97,142,956 (GRCm39)	I489V	probably benign	Het
Ano9	A	T	7: 140,687,350 (GRCm39)	Y322N	probably damaging	Het
Arhgap40	G	T	2: 158,389,576 (GRCm39)	W583L	probably benign	Het
Atxn2	A	G	5: 121,916,084 (GRCm39)	E430G	probably damaging	Het
Brip1	T	C	11: 86,034,104 (GRCm39)	Y539C	possibly damaging	Het
C87436	T	A	6: 86,442,790 (GRCm39)	L454Q	probably damaging	Het
Casp4	T	G	9: 5,324,868 (GRCm39)	Y227D	probably benign	Het
Ccn6	T	G	10: 39,031,031 (GRCm39)	N164T	probably benign	Het
Chd4	T	A	6: 125,083,555 (GRCm39)		probably null	Het
Chrna10	A	G	7: 101,761,293 (GRCm39)	C433R	probably benign	Het
Cntln	A	T	4: 85,036,710 (GRCm39)	N214I	probably damaging	Het
Colec12	G	A	18: 9,848,922 (GRCm39)	V367I	probably damaging	Het
Cyp46a1	T	C	12: 108,318,255 (GRCm39)	I222T	probably benign	Het
Dagla	A	T	19: 10,239,945 (GRCm39)		probably null	Het
Dcaf7	C	A	11: 105,938,669 (GRCm39)		probably null	Het
Dclk2	C	T	3: 86,700,566 (GRCm39)	R638H	probably damaging	Het
E2f7	A	G	10: 110,602,164 (GRCm39)		probably null	Het
Fam184a	G	T	10: 53,574,901 (GRCm39)	T236K	probably benign	Het
Glyctk	T	C	9: 106,032,661 (GRCm39)	T451A	probably damaging	Het
Hectd4	A	G	5: 121,452,944 (GRCm39)	K484E	possibly damaging	Het
Hspbap1	G	T	16: 35,637,600 (GRCm39)	C243F	unknown	Het
Hspg2	A	C	4: 137,247,257 (GRCm39)	N1160T	probably benign	Het
Ighv5-8	C	T	12: 113,618,728 (GRCm39)	L48F	probably benign	Het
Jazf1	C	A	6: 52,754,637 (GRCm39)	E146D	probably benign	Het
Katnb1	C	T	8: 95,822,125 (GRCm39)	Q284*	probably null	Het
Kctd18	G	T	1: 58,001,115 (GRCm39)	Y213*	probably null	Het
Klk1b26	T	C	7: 43,664,213 (GRCm39)	S23P	possibly damaging	Het
Krt88	T	C	15: 101,348,392 (GRCm39)	L26P	probably damaging	Het
Lrrc8b	G	A	5: 105,629,522 (GRCm39)	V623I	probably benign	Het
Map3k4	T	A	17: 12,490,955 (GRCm39)	M159L	probably benign	Het
Mast3	C	A	8: 71,242,326 (GRCm39)		probably null	Het
Mier1	G	A	4: 102,996,544 (GRCm39)		probably null	Het
Mrpl46	T	C	7: 78,431,207 (GRCm39)	D117G	probably damaging	Het
Ms4a6b	A	G	19: 11,497,760 (GRCm39)	S20G	probably benign	Het
Mup10	A	T	4: 60,538,077 (GRCm39)	M4K	unknown	Het
Nlrp5	C	T	7: 23,116,816 (GRCm39)	A180V	possibly damaging	Het
Nlrx1	T	A	9: 44,176,001 (GRCm39)		probably null	Het
Odad3	T	C	9: 21,913,767 (GRCm39)	T2A	probably damaging	Het
Or2a52	T	C	6: 43,144,744 (GRCm39)	F251L	probably damaging	Het
Or2t45	T	C	11: 58,669,822 (GRCm39)	Y290H	probably damaging	Het
Or4c103	T	C	2: 88,513,969 (GRCm39)	T36A	possibly damaging	Het
Or51aa2	C	T	7: 103,187,995 (GRCm39)	A149T	probably benign	Het
Or5af2	T	A	11: 58,708,366 (GRCm39)	C177*	probably null	Het
Or5ak22	A	G	2: 85,229,983 (GRCm39)	I298T	probably benign	Het
Otud1	C	A	2: 19,663,742 (GRCm39)	D290E	probably damaging	Het
Pank4	A	G	4: 155,055,377 (GRCm39)	N249S	probably benign	Het
Pccb	G	T	9: 100,913,966 (GRCm39)	S84R	probably benign	Het
Pemt	A	T	11: 59,862,081 (GRCm39)	H194Q	possibly damaging	Het
Phtf2	A	G	5: 20,970,856 (GRCm39)	I634T	possibly damaging	Het
Pias2	T	G	18: 77,207,811 (GRCm39)	I232R	probably damaging	Het
Plce1	A	G	19: 38,686,952 (GRCm39)	E620G	probably damaging	Het
Pramel17	A	T	4: 101,692,725 (GRCm39)	V425E	probably benign	Het
Ptpn13	G	A	5: 103,713,150 (GRCm39)	E1758K	possibly damaging	Het
Ptprq	T	A	10: 107,444,134 (GRCm39)	Q1490L	probably benign	Het
Ptx3	G	T	3: 66,132,368 (GRCm39)	M296I	probably benign	Het
R3hdm2	C	T	10: 127,317,644 (GRCm39)	P464L	probably damaging	Het
Rgl2	T	C	17: 34,153,964 (GRCm39)	F457L	possibly damaging	Het
Rsf1	GGCGGCGGC	GGCGGCGGCCGCGGCGGC	7: 97,229,122 (GRCm39)		probably benign	Het
Senp8	T	C	9: 59,644,478 (GRCm39)	N226S	probably benign	Het
Six5	C	T	7: 18,828,901 (GRCm39)	R114C	probably damaging	Het
Slc10a1	T	C	12: 81,004,958 (GRCm39)	T195A	probably benign	Het
Slpi	G	T	2: 164,197,467 (GRCm39)	Q51K	probably benign	Het
Smarca4	T	C	9: 21,570,256 (GRCm39)	V753A	probably benign	Het
Tbc1d32	C	A	10: 56,074,537 (GRCm39)	M225I	probably benign	Het
Tent5a	C	A	9: 85,208,770 (GRCm39)	G18C	probably benign	Het
Tnfrsf21	G	A	17: 43,348,558 (GRCm39)	V57I	probably benign	Het
Trim44	G	T	2: 102,177,313 (GRCm39)	P336T	possibly damaging	Het
Txlnb	A	G	10: 17,703,633 (GRCm39)	I264V	probably damaging	Het
Xirp2	A	C	2: 67,343,826 (GRCm39)	E2022D	probably benign	Het
Zfp975	A	G	7: 42,311,036 (GRCm39)	*526R	probably null	Het
Zp1	A	G	19: 10,893,933 (GRCm39)	L424P	probably 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
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
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'- TTTAGAGCATCCTGGTAGCTGG -3'
(R):5'- CAGGCACAGTTATCCTTCAGC -3'

Sequencing Primer
(F):5'- CTGGTCAGTGATGAAACGCC -3'
(R):5'- GGCACAGTTATCCTTCAGCTCATTC -3'

Posted On

2019-06-26