Mutagenetix > Incidental Mutation

Incidental Mutation 'R6145:Rapgef1'

488789

Institutional Source

Beutler Lab

Gene Symbol

Rapgef1

Ensembl Gene

ENSMUSG00000039844

Gene Name

Rap guanine nucleotide exchange factor (GEF) 1

Synonyms

Grf2, 4932418O06Rik, C3G

MMRRC Submission

044292-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R6145 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

29619720-29740978 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 29736666 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Cysteine at position 993 (Y993C)

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: Y1125C

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

SMART Domains

Protein: ENSMUSP00000088680
Gene: ENSMUSG00000039844
AA Change: Y1125C

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 damaging
Transcript: ENSMUST00000095087
AA Change: Y1131C

PolyPhen 2 Score 0.979 (Sensitivity: 0.75; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000092703
Gene: ENSMUSG00000039844
AA Change: Y1131C

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: Y993C

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

SMART Domains

Protein: ENSMUSP00000099936
Gene: ENSMUSG00000039844
AA Change: Y993C

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: Y549C

SMART Domains

Protein: ENSMUSP00000117631
Gene: ENSMUSG00000039844
AA Change: Y549C

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: 99.5%
10x: 98.0%
20x: 95.0%

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: 77 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2810459M11Rik	T	A	1: 86,052,942 (GRCm38)		probably null	Het
Abca8b	A	G	11: 109,973,808 (GRCm38)	V316A	probably benign	Het
Acad10	A	T	5: 121,622,033 (GRCm38)	V999D	probably damaging	Het
Acot8	A	G	2: 164,803,065 (GRCm38)	V66A	probably benign	Het
Ankrd11	T	C	8: 122,892,661 (GRCm38)	H1484R	probably damaging	Het
Anxa6	A	G	11: 54,994,904 (GRCm38)	F405S	probably damaging	Het
Asmt	G	A	X: 170,674,663 (GRCm38)	V101I	probably damaging	Het
Atp1a2	C	T	1: 172,287,238 (GRCm38)	V327I	probably damaging	Het
Brdt	A	G	5: 107,377,999 (GRCm38)	E906G	possibly damaging	Het
Cacna1g	A	T	11: 94,462,261 (GRCm38)	C313S	probably damaging	Het
Camk2d	T	C	3: 126,805,858 (GRCm38)	I329T	probably benign	Het
Cavin4	A	T	4: 48,663,794 (GRCm38)	H58L	probably damaging	Het
Ccdc78	C	A	17: 25,789,065 (GRCm38)	P317T	probably benign	Het
Cdc16	T	G	8: 13,767,573 (GRCm38)	Y295D	possibly damaging	Het
Cdyl2	T	A	8: 116,594,978 (GRCm38)	N270I	probably damaging	Het
Cfap221	T	A	1: 119,984,816 (GRCm38)	I114F	possibly damaging	Het
Dmxl1	A	G	18: 49,912,766 (GRCm38)	E2414G	possibly damaging	Het
Dnaaf9	T	C	2: 130,778,473 (GRCm38)	I247V	probably benign	Het
Dnah1	C	A	14: 31,300,970 (GRCm38)	R1070L	probably benign	Het
Dnah14	T	C	1: 181,666,417 (GRCm38)	S1713P	probably benign	Het
Dock10	C	A	1: 80,575,904 (GRCm38)	G602*	probably null	Het
Ep400	A	T	5: 110,756,703 (GRCm38)	V10D	possibly damaging	Het
Epas1	T	C	17: 86,829,429 (GRCm38)	C807R	probably benign	Het
Esrrb	C	T	12: 86,505,899 (GRCm38)	P200L	probably benign	Het
Fbxw26	T	C	9: 109,732,623 (GRCm38)	I168V	probably benign	Het
Fsip2	A	T	2: 82,993,768 (GRCm38)	H6615L	possibly damaging	Het
Galk2	A	T	2: 125,946,842 (GRCm38)	Q272L	possibly damaging	Het
Gas7	A	C	11: 67,629,612 (GRCm38)	T43P	probably damaging	Het
Gm5134	A	T	10: 75,995,839 (GRCm38)	I371F	probably damaging	Het
Gpr31b	C	T	17: 13,051,379 (GRCm38)	R301Q	possibly damaging	Het
Grk1	T	A	8: 13,405,765 (GRCm38)	Y216*	probably null	Het
Grm5	T	A	7: 88,026,601 (GRCm38)	M441K	probably damaging	Het
Heatr6	A	G	11: 83,766,136 (GRCm38)	E408G	probably damaging	Het
Hoxc9	G	T	15: 102,983,959 (GRCm38)	K201N	probably damaging	Het
Igsf10	T	A	3: 59,331,656 (GRCm38)	Y368F	possibly damaging	Het
Il2ra	A	T	2: 11,680,246 (GRCm38)	D131V	probably damaging	Het
Imp4	A	G	1: 34,440,096 (GRCm38)	E19G	probably benign	Het
Kcnk18	T	C	19: 59,235,607 (GRCm38)	*395Q	probably null	Het
Kdm6b	A	T	11: 69,405,026 (GRCm38)	L805Q	unknown	Het
Lgr4	T	A	2: 110,007,243 (GRCm38)	L427*	probably null	Het
Myt1l	G	A	12: 29,832,381 (GRCm38)	S525N	unknown	Het
Nasp	G	A	4: 116,611,077 (GRCm38)	T237I	probably benign	Het
Nell2	G	T	15: 95,473,561 (GRCm38)	Q98K	probably damaging	Het
Nfasc	C	T	1: 132,634,717 (GRCm38)	G107R	probably damaging	Het
Nsun4	A	G	4: 116,040,206 (GRCm38)	S203P	probably damaging	Het
Or1m1	T	G	9: 18,755,569 (GRCm38)	D22A	probably benign	Het
Or7g35	T	C	9: 19,584,888 (GRCm38)	V117A	probably benign	Het
Otogl	G	A	10: 107,777,117 (GRCm38)		silent	Het
Pde10a	T	C	17: 8,929,117 (GRCm38)	V366A	probably damaging	Het
Pdxk	T	A	10: 78,443,791 (GRCm38)	D250V	probably benign	Het
Pih1d1	T	A	7: 45,159,044 (GRCm38)	I179N	probably damaging	Het
Plaa	T	A	4: 94,583,992 (GRCm38)	I294F	probably damaging	Het
Pmel	C	A	10: 128,715,935 (GRCm38)	P213T	probably damaging	Het
Pom121l2	A	T	13: 21,982,302 (GRCm38)	R248*	probably null	Het
Pou2f1	T	C	1: 165,875,433 (GRCm38)		probably benign	Het
Ppm1j	G	A	3: 104,781,379 (GRCm38)	R98H	probably damaging	Het
Prkdc	C	T	16: 15,772,073 (GRCm38)	P2600L	probably damaging	Het
Prom1	T	C	5: 44,029,649 (GRCm38)	N422S	probably benign	Het
Pspn	C	T	17: 56,999,467 (GRCm38)	C154Y	probably damaging	Het
Ptdss1	T	C	13: 66,972,637 (GRCm38)		probably null	Het
Scrn2	A	C	11: 97,032,853 (GRCm38)	T219P	probably benign	Het
Sec23ip	T	G	7: 128,778,484 (GRCm38)	S874R	probably damaging	Het
Septin4	G	A	11: 87,585,246 (GRCm38)		probably null	Het
Slc15a3	C	T	19: 10,857,251 (GRCm38)	L499F	probably damaging	Het
Spaca9	G	A	2: 28,693,781 (GRCm38)	R64W	probably damaging	Het
Sra1	A	G	18: 36,667,575 (GRCm38)	M193T	probably damaging	Het
Srsf4	G	T	4: 131,900,294 (GRCm38)		probably benign	Het
Syne1	T	C	10: 5,052,750 (GRCm38)	D8055G	probably damaging	Het
Syne4	T	A	7: 30,316,563 (GRCm38)		probably null	Het
Tbc1d24	C	A	17: 24,208,229 (GRCm38)	G253V	probably damaging	Het
Tbck	T	A	3: 132,732,215 (GRCm38)	I467N	probably damaging	Het
Tln1	T	A	4: 43,538,030 (GRCm38)	M1857L	possibly damaging	Het
Ttll2	T	C	17: 7,351,632 (GRCm38)	R299G	probably benign	Het
Ugt2b36	T	G	5: 87,066,213 (GRCm38)	E524A	probably benign	Het
Vmn2r124	C	T	17: 18,062,851 (GRCm38)	T269I	probably benign	Het
Vmn2r4	A	G	3: 64,406,943 (GRCm38)	F206L	probably benign	Het
Zfp346	A	G	13: 55,115,574 (GRCm38)	K156R	probably damaging	Het

Other mutations in Rapgef1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00156:Rapgef1	APN	2	29,722,269 (GRCm38)	missense	probably benign
IGL00917:Rapgef1	APN	2	29,702,523 (GRCm38)	missense	probably benign	0.00
IGL02618:Rapgef1	APN	2	29,737,943 (GRCm38)	missense	probably damaging	1.00
IGL02642:Rapgef1	APN	2	29,700,860 (GRCm38)	splice site	probably benign
IGL02974:Rapgef1	APN	2	29,710,216 (GRCm38)	missense	possibly damaging	0.64
R0034:Rapgef1	UTSW	2	29,724,768 (GRCm38)	splice site	probably benign
R0034:Rapgef1	UTSW	2	29,724,768 (GRCm38)	splice site	probably benign
R0241:Rapgef1	UTSW	2	29,702,670 (GRCm38)	missense	possibly damaging	0.53
R0241:Rapgef1	UTSW	2	29,702,670 (GRCm38)	missense	possibly damaging	0.53
R0279:Rapgef1	UTSW	2	29,726,227 (GRCm38)	missense	probably damaging	1.00
R0432:Rapgef1	UTSW	2	29,679,816 (GRCm38)	missense	possibly damaging	0.86
R1817:Rapgef1	UTSW	2	29,686,256 (GRCm38)	missense	probably damaging	1.00
R1837:Rapgef1	UTSW	2	29,737,426 (GRCm38)	missense	probably damaging	1.00
R1970:Rapgef1	UTSW	2	29,733,711 (GRCm38)	missense	probably damaging	1.00
R1980:Rapgef1	UTSW	2	29,722,227 (GRCm38)	missense	probably benign
R2076:Rapgef1	UTSW	2	29,702,508 (GRCm38)	missense	probably benign	0.00
R2363:Rapgef1	UTSW	2	29,736,596 (GRCm38)	missense	possibly damaging	0.63
R3016:Rapgef1	UTSW	2	29,707,393 (GRCm38)	missense	probably damaging	1.00
R3053:Rapgef1	UTSW	2	29,724,856 (GRCm38)	missense	probably damaging	1.00
R3777:Rapgef1	UTSW	2	29,719,689 (GRCm38)	missense	possibly damaging	0.67
R3980:Rapgef1	UTSW	2	29,719,650 (GRCm38)	missense	probably benign	0.33
R4491:Rapgef1	UTSW	2	29,719,656 (GRCm38)	missense	possibly damaging	0.93
R4524:Rapgef1	UTSW	2	29,679,246 (GRCm38)	missense	probably benign	0.00
R4732:Rapgef1	UTSW	2	29,689,160 (GRCm38)	missense	probably damaging	1.00
R4733:Rapgef1	UTSW	2	29,689,160 (GRCm38)	missense	probably damaging	1.00
R5391:Rapgef1	UTSW	2	29,737,965 (GRCm38)	missense	probably damaging	1.00
R5395:Rapgef1	UTSW	2	29,737,965 (GRCm38)	missense	probably damaging	1.00
R5611:Rapgef1	UTSW	2	29,702,436 (GRCm38)	missense	probably damaging	0.96
R6062:Rapgef1	UTSW	2	29,700,732 (GRCm38)	missense	probably damaging	0.96
R6580:Rapgef1	UTSW	2	29,730,609 (GRCm38)	missense	possibly damaging	0.95
R6892:Rapgef1	UTSW	2	29,699,840 (GRCm38)	critical splice donor site	probably null
R6897:Rapgef1	UTSW	2	29,702,502 (GRCm38)	missense	probably damaging	1.00
R6957:Rapgef1	UTSW	2	29,733,698 (GRCm38)	missense	possibly damaging	0.62
R7039:Rapgef1	UTSW	2	29,726,214 (GRCm38)	missense	probably damaging	0.97
R7149:Rapgef1	UTSW	2	29,720,700 (GRCm38)	missense	probably damaging	0.98
R7253:Rapgef1	UTSW	2	29,699,721 (GRCm38)	missense	possibly damaging	0.72
R7315:Rapgef1	UTSW	2	29,734,492 (GRCm38)	missense	probably damaging	0.98
R7956:Rapgef1	UTSW	2	29,699,015 (GRCm38)	missense	probably benign	0.03
R8161:Rapgef1	UTSW	2	29,679,198 (GRCm38)	missense	probably benign	0.08
R8162:Rapgef1	UTSW	2	29,735,999 (GRCm38)	missense	probably damaging	0.99
R8372:Rapgef1	UTSW	2	29,710,231 (GRCm38)	missense	probably damaging	0.99
R8373:Rapgef1	UTSW	2	29,710,231 (GRCm38)	missense	probably damaging	0.99
R8485:Rapgef1	UTSW	2	29,710,174 (GRCm38)	missense	probably damaging	1.00
R8838:Rapgef1	UTSW	2	29,737,446 (GRCm38)	missense	possibly damaging	0.77
R9484:Rapgef1	UTSW	2	29,735,809 (GRCm38)	missense	possibly damaging	0.95
R9521:Rapgef1	UTSW	2	29,734,279 (GRCm38)	missense	probably benign	0.16
RF005:Rapgef1	UTSW	2	29,707,195 (GRCm38)	splice site	probably null

Predicted Primers

PCR Primer
(F):5'- CACTATTAGCAGGCGTCCAC -3'
(R):5'- AATGCCAAACTGTTAACTGAGC -3'

Sequencing Primer
(F):5'- CCACAGGGCTTTCGTTGGTATC -3'
(R):5'- GCCTTTGCAGAACACTTGG -3'

Posted On

2017-10-10