Mutagenetix > Incidental Mutation

Incidental Mutation 'R9484:Rapgef1'

716416

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

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R9484 (G1)

Quality Score

108.008

Status

Not validated

Chromosome

Chromosomal Location

29509732-29630376 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 29625821 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Proline at position 1042 (S1042P)

Ref Sequence

ENSEMBL: ENSMUSP00000092703 (fasta)

Gene Model

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

AlphaFold

Q3UHC1

Predicted Effect

probably damaging
Transcript: ENSMUST00000091146
AA Change: S1036P

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000088680
Gene: ENSMUSG00000039844
AA Change: S1036P

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: S1042P

PolyPhen 2 Score 0.946 (Sensitivity: 0.80; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000092703
Gene: ENSMUSG00000039844
AA Change: S1042P

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: S904P

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000099936
Gene: ENSMUSG00000039844
AA Change: S904P

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

SMART Domains

Protein: ENSMUSP00000117631
Gene: ENSMUSG00000039844
AA Change: S460P

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

Coding Region Coverage

1x: 99.9%
3x: 99.8%
10x: 99.2%
20x: 97.1%

Validation Efficiency

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: 83 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acads	A	T	5: 115,250,845 (GRCm39)	C151S	probably damaging	Het
Actr8	T	C	14: 29,708,301 (GRCm39)	I193T	probably benign	Het
Btbd2	T	C	10: 80,480,103 (GRCm39)	N419S	probably benign	Het
Cacna2d1	T	A	5: 16,561,831 (GRCm39)	W821R	probably damaging	Het
Cadps2	T	C	6: 23,626,646 (GRCm39)	Y214C	probably benign	Het
Calu	T	A	6: 29,366,162 (GRCm39)	L180Q	probably damaging	Het
Corin	C	T	5: 72,497,280 (GRCm39)	V615I	probably damaging	Het
Cyp8b1	A	T	9: 121,744,983 (GRCm39)	D116E	probably benign	Het
D630036H23Rik	C	A	12: 36,431,711 (GRCm39)	A96S	unknown	Het
Ddx24	A	T	12: 103,377,555 (GRCm39)	Y717N	probably damaging	Het
Dmap1	G	T	4: 117,533,308 (GRCm39)	Q249K	probably benign	Het
Dnah10	T	A	5: 124,900,508 (GRCm39)	W3922R	probably damaging	Het
Dnah14	T	C	1: 181,517,773 (GRCm39)	F2036L	probably benign	Het
Dnah14	T	C	1: 181,625,311 (GRCm39)	I4064T	probably benign	Het
Dock9	A	C	14: 121,818,844 (GRCm39)	V1546G	probably damaging	Het
Eif1ad4	A	T	12: 87,862,249 (GRCm39)	Q37L	possibly damaging	Het
Eif3a	A	T	19: 60,755,006 (GRCm39)	S1059T	unknown	Het
Ep300	A	G	15: 81,521,026 (GRCm39)	E1262G	unknown	Het
Evl	T	A	12: 108,652,716 (GRCm39)	I387N	probably damaging	Het
Fat2	A	C	11: 55,200,752 (GRCm39)	V774G	probably damaging	Het
Fez1	T	A	9: 36,755,093 (GRCm39)	Y31N	probably benign	Het
Fkbp10	A	G	11: 100,313,960 (GRCm39)	I435V	probably damaging	Het
Flnb	A	G	14: 7,929,004 (GRCm38)	D1911G	probably benign	Het
Fnbp1	T	C	2: 30,973,038 (GRCm39)	Y154C	probably benign	Het
Fndc10	T	C	4: 155,779,496 (GRCm39)	I180T	possibly damaging	Het
Frmd4a	G	A	2: 4,609,026 (GRCm39)	V965I	possibly damaging	Het
Gabrr2	A	G	4: 33,071,352 (GRCm39)	H64R	possibly damaging	Het
Glis3	T	C	19: 28,508,403 (GRCm39)	D527G	probably damaging	Het
H2-Ob	T	A	17: 34,459,989 (GRCm39)	F33L	probably damaging	Het
Hbb-bh1	C	T	7: 103,492,239 (GRCm39)	E27K	probably benign	Het
Ifnb1	T	A	4: 88,440,915 (GRCm39)	T33S	probably benign	Het
Igkv4-80	T	A	6: 68,993,766 (GRCm39)	T42S	probably damaging	Het
Irs2	C	T	8: 11,057,334 (GRCm39)	G366D	probably damaging	Het
Kcnk2	CAAA	CAA	1: 188,988,891 (GRCm39)		probably null	Het
Krtap5-3	T	A	7: 141,756,068 (GRCm39)	C302S	unknown	Het
Lgi1	A	G	19: 38,294,757 (GRCm39)	K510E	probably benign	Het
Lgi2	T	A	5: 52,695,936 (GRCm39)	D341V	probably benign	Het
Lin7c	T	C	2: 109,724,813 (GRCm39)	I14T	probably benign	Het
Lrrc19	A	T	4: 94,531,573 (GRCm39)	M13K	probably benign	Het
Lrrc69	T	C	4: 14,666,012 (GRCm39)	I315M	probably benign	Het
Mtcl3	G	A	10: 29,072,969 (GRCm39)	D754N	probably damaging	Het
Myo5c	A	T	9: 75,204,770 (GRCm39)	D1541V	probably damaging	Het
Mypn	T	G	10: 63,003,019 (GRCm39)	M373L	probably benign	Het
Nckipsd	C	A	9: 108,689,837 (GRCm39)	H333N	probably damaging	Het
Nrg2	A	T	18: 36,157,401 (GRCm39)	L428Q	probably null	Het
Or13a20	T	C	7: 140,231,904 (GRCm39)	L4S	probably benign	Het
Or2b28	C	A	13: 21,531,587 (GRCm39)	T163K	probably damaging	Het
Or5an11	T	C	19: 12,245,735 (GRCm39)	I47T	possibly damaging	Het
Otogl	T	A	10: 107,657,894 (GRCm39)		probably null	Het
Otogl	C	T	10: 107,737,156 (GRCm39)	G86D	probably damaging	Het
Papln	A	T	12: 83,838,618 (GRCm39)	Q1249L	probably benign	Het
Plxna2	G	T	1: 194,327,202 (GRCm39)	G379C	probably damaging	Het
Pofut2	T	C	10: 77,095,260 (GRCm39)	I35T	probably benign	Het
Pros1	A	G	16: 62,744,887 (GRCm39)	T501A	possibly damaging	Het
Rps6kb1	C	T	11: 86,408,443 (GRCm39)	E185K	probably damaging	Het
Slc13a2	A	T	11: 78,294,233 (GRCm39)	L216Q	probably damaging	Het
Slc22a14	T	C	9: 119,009,615 (GRCm39)	Y160C	probably damaging	Het
Slc22a4	T	A	11: 53,879,773 (GRCm39)	I429F	possibly damaging	Het
Slc26a3	A	G	12: 31,511,785 (GRCm39)	K457E	probably damaging	Het
Slc47a2	T	C	11: 61,227,060 (GRCm39)	I169M	possibly damaging	Het
Slco1a1	C	T	6: 141,854,672 (GRCm39)	V660I	probably benign	Het
Smyd1	A	G	6: 71,202,450 (GRCm39)	Y252H	probably damaging	Het
Spp2	A	T	1: 88,334,695 (GRCm39)		probably benign	Het
Stra8	T	A	6: 34,911,121 (GRCm39)	W250R	probably damaging	Het
Syne1	A	C	10: 5,170,359 (GRCm39)	L5183R	probably damaging	Het
Tdrd9	T	C	12: 112,012,684 (GRCm39)	S1203P	probably damaging	Het
Th	C	A	7: 142,453,620 (GRCm39)	E27*	probably null	Het
Thada	C	A	17: 84,736,619 (GRCm39)	L887F	probably damaging	Het
Timm23	T	C	14: 31,902,586 (GRCm39)	T186A	probably benign	Het
Tmem132b	A	T	5: 125,860,420 (GRCm39)	E555V	probably damaging	Het
Tnik	A	T	3: 28,649,093 (GRCm39)	Q457L	unknown	Het
Uba7	C	A	9: 107,861,037 (GRCm39)	H942Q	probably benign	Het
Upf2	T	C	2: 5,966,078 (GRCm39)	S233P	unknown	Het
Urm1	T	A	2: 29,732,760 (GRCm39)	N72K	probably damaging	Het
Usp10	T	C	8: 120,675,504 (GRCm39)	S508P	possibly damaging	Het
Usp37	G	A	1: 74,499,081 (GRCm39)	P632S	probably damaging	Het
Wdr77	T	A	3: 105,872,404 (GRCm39)	N209K	probably benign	Het
Zbtb24	C	T	10: 41,327,429 (GRCm39)	T105M	probably benign	Het
Zfp341	T	A	2: 154,485,763 (GRCm39)	I671N	probably damaging	Het
Zfp414	A	G	17: 33,848,984 (GRCm39)	T73A	probably benign	Het
Zfp574	A	T	7: 24,781,404 (GRCm39)	I809F	possibly damaging	Het
Zfp62	T	C	11: 49,108,108 (GRCm39)	I733T	probably damaging	Het
Zfp719	A	G	7: 43,239,581 (GRCm39)	I390V	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
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
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'- TGAAAGATGCTCCAGTCCCC -3'
(R):5'- AAGTTGTTGAGCTTGCGCAG -3'

Sequencing Primer
(F):5'- GAACTGTCTGGACCCTAGAATATAG -3'
(R):5'- AGCTTGCGCAGGTGCTG -3'

Posted On

2022-07-18