Mutagenetix > Incidental Mutation

Incidental Mutation 'R6933:Rapgef2'

540150

Institutional Source

Beutler Lab

Gene Symbol

Rapgef2

Ensembl Gene

ENSMUSG00000062232

Gene Name

Rap guanine nucleotide exchange factor (GEF) 2

Synonyms

CNRasGEF, nRapGEP, 5830453M24Rik, RA-GEF-1, Pdzgef1

MMRRC Submission

045048-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R6933 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

78969823-79193824 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 78993266 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Asparagine at position 889 (Y889N)

Ref Sequence

ENSEMBL: ENSMUSP00000141542 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000118100] [ENSMUST00000118340] [ENSMUST00000195708]

AlphaFold

Q8CHG7

Predicted Effect

probably damaging
Transcript: ENSMUST00000118100
AA Change: Y741N

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

SMART Domains

Protein: ENSMUSP00000114119
Gene: ENSMUSG00000062232
AA Change: Y741N

Domain	Start	End	E-Value	Type
low complexity region	38	62	N/A	INTRINSIC
low complexity region	84	95	N/A	INTRINSIC
cNMP	135	253	2.48e-15	SMART
RasGEFN	267	380	1.3e-31	SMART
PDZ	395	467	1.28e-12	SMART
RA	606	692	7.59e-23	SMART
RasGEF	713	950	6.09e-100	SMART
low complexity region	1030	1046	N/A	INTRINSIC
low complexity region	1110	1124	N/A	INTRINSIC
low complexity region	1140	1161	N/A	INTRINSIC
low complexity region	1392	1405	N/A	INTRINSIC
low complexity region	1440	1455	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000118340
AA Change: Y739N

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

SMART Domains

Protein: ENSMUSP00000113778
Gene: ENSMUSG00000062232
AA Change: Y739N

Domain	Start	End	E-Value	Type
low complexity region	36	60	N/A	INTRINSIC
low complexity region	82	93	N/A	INTRINSIC
cNMP	133	251	2.48e-15	SMART
RasGEFN	265	378	1.3e-31	SMART
PDZ	393	465	1.28e-12	SMART
RA	604	690	7.59e-23	SMART
RasGEF	711	948	6.09e-100	SMART
low complexity region	1028	1044	N/A	INTRINSIC
low complexity region	1108	1122	N/A	INTRINSIC
low complexity region	1138	1159	N/A	INTRINSIC
low complexity region	1390	1403	N/A	INTRINSIC
low complexity region	1438	1453	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000195708
AA Change: Y889N

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

SMART Domains

Protein: ENSMUSP00000141542
Gene: ENSMUSG00000062232
AA Change: Y889N

Domain	Start	End	E-Value	Type
cNMP	24	131	3.9e-4	SMART
low complexity region	186	210	N/A	INTRINSIC
low complexity region	232	243	N/A	INTRINSIC
cNMP	283	401	1.2e-17	SMART
RasGEFN	415	528	6.4e-34	SMART
PDZ	543	615	6.4e-15	SMART
RA	754	840	4.8e-25	SMART
RasGEF	861	1098	3.8e-102	SMART
low complexity region	1178	1194	N/A	INTRINSIC
low complexity region	1258	1272	N/A	INTRINSIC
low complexity region	1288	1309	N/A	INTRINSIC
low complexity region	1540	1553	N/A	INTRINSIC
low complexity region	1588	1603	N/A	INTRINSIC

Meta Mutation Damage Score

0.9575

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.2%
20x: 97.7%

Validation Efficiency

93% (41/44)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] Members of the RAS (see HRAS; MIM 190020) subfamily of GTPases function in signal transduction as GTP/GDP-regulated switches that cycle between inactive GDP- and active GTP-bound states. Guanine nucleotide exchange factors (GEFs), such as RAPGEF2, serve as RAS activators by promoting acquisition of GTP to maintain the active GTP-bound state and are the key link between cell surface receptors and RAS activation (Rebhun et al., 2000 [PubMed 10934204]).[supplied by OMIM, Mar 2008]
PHENOTYPE: Homozygotes for a null allele die at mid-gestation exhibiting growth arrest and defects in vascular development, neural tube closure and embryo turning. Homozygotes for another null allele show yolk sac vascular defects, impaired cell physiology and heart, primitive gut, liver and brain formation. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 44 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Ank3	G	T	10: 69,740,042 (GRCm39)	K814N	probably damaging	Het
Anks1b	A	G	10: 89,905,352 (GRCm39)	H231R	probably damaging	Het
Anks6	A	G	4: 47,049,164 (GRCm39)	V247A	probably benign	Het
Antxrl	A	G	14: 33,797,728 (GRCm39)	N568D	possibly damaging	Het
Ccnl1	T	C	3: 65,855,373 (GRCm39)	T366A	probably benign	Het
Ccr2	T	G	9: 123,906,161 (GRCm39)	L147R	probably damaging	Het
Cdc40	A	G	10: 40,720,992 (GRCm39)	V318A	probably damaging	Het
Cfap61	T	A	2: 145,792,970 (GRCm39)		probably null	Het
Cfap97d2	CA	CAA	8: 13,784,865 (GRCm39)		probably null	Het
Clk3	A	T	9: 57,669,132 (GRCm39)	Y31N	probably damaging	Het
Cmya5	T	C	13: 93,231,644 (GRCm39)	Y1148C	probably benign	Het
Cntnap5b	T	C	1: 100,311,175 (GRCm39)	V927A	probably benign	Het
Dync1i1	A	C	6: 5,913,333 (GRCm39)	T217P	probably damaging	Het
Elovl4	A	G	9: 83,667,153 (GRCm39)	V68A	probably damaging	Het
Ep400	C	A	5: 110,813,728 (GRCm39)	K2890N	probably damaging	Het
Fam114a2	T	C	11: 57,374,897 (GRCm39)	I481V	probably benign	Het
Fam83e	A	G	7: 45,371,818 (GRCm39)	T72A	probably benign	Het
Fnip2	A	T	3: 79,425,418 (GRCm39)	M59K	probably benign	Het
Lrpprc	T	C	17: 85,030,131 (GRCm39)	K1089R	probably benign	Het
Mndal	T	A	1: 173,703,249 (GRCm39)	E52V	probably damaging	Het
Myom1	C	A	17: 71,359,666 (GRCm39)	T446K	probably damaging	Het
Nbea	A	T	3: 55,631,031 (GRCm39)	F2199I	possibly damaging	Het
Nr1h2	A	T	7: 44,199,437 (GRCm39)	L438Q	probably damaging	Het
Or52n2c	A	G	7: 104,574,330 (GRCm39)	C214R	probably benign	Het
Pet117	T	A	2: 144,211,019 (GRCm39)	V13E	possibly damaging	Het
Pnpla8	A	G	12: 44,330,210 (GRCm39)	E254G	probably benign	Het
Polr2a	T	C	11: 69,627,003 (GRCm39)	E1485G	probably damaging	Het
Polr2a	C	T	11: 69,630,293 (GRCm39)	R1258Q	probably benign	Het
Ptpn4	T	C	1: 119,700,878 (GRCm39)		probably benign	Het
Sbf1	G	A	15: 89,184,572 (GRCm39)	R1115C	probably damaging	Het
Sfpq	GCCGCCGCAGCAGCCTCCGCCGCAGCAGCC	GCCGCCGCAGCAGCC	4: 126,915,419 (GRCm39)		probably benign	Het
Shank2	A	T	7: 143,645,515 (GRCm39)	T366S	probably benign	Het
Slc22a23	T	C	13: 34,489,163 (GRCm39)	I241V	probably benign	Het
Sox11	G	T	12: 27,391,493 (GRCm39)	S305R	probably damaging	Het
Sox21	T	C	14: 118,472,725 (GRCm39)	H108R	possibly damaging	Het
Taok1	A	T	11: 77,446,479 (GRCm39)	S417T	probably benign	Het
Tg	C	T	15: 66,636,158 (GRCm39)	R582C	possibly damaging	Het
Traf3	T	C	12: 111,221,658 (GRCm39)	V273A	possibly damaging	Het
Tspyl3	T	C	2: 153,067,203 (GRCm39)	T12A	probably benign	Het
Vmn2r86	A	T	10: 130,282,126 (GRCm39)	I830N	probably damaging	Het
Vps26b	A	T	9: 26,926,613 (GRCm39)	F129I	possibly damaging	Het
Washc3	A	G	10: 88,037,714 (GRCm39)	N24S	probably damaging	Het
Xirp2	C	A	2: 67,345,201 (GRCm39)	Q2481K	probably benign	Het
Zfhx4	T	C	3: 5,478,047 (GRCm39)	V3554A	probably damaging	Het

Other mutations in Rapgef2

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00488:Rapgef2	APN	3	78,999,332 (GRCm39)	missense	possibly damaging	0.89
IGL01024:Rapgef2	APN	3	78,977,445 (GRCm39)	missense	probably benign	0.43
IGL01448:Rapgef2	APN	3	79,011,269 (GRCm39)	critical splice donor site	probably null
IGL01448:Rapgef2	APN	3	78,976,244 (GRCm39)	missense	probably benign
IGL01928:Rapgef2	APN	3	79,011,270 (GRCm39)	missense	probably damaging	1.00
IGL01973:Rapgef2	APN	3	78,999,116 (GRCm39)	splice site	probably null
IGL02015:Rapgef2	APN	3	78,999,371 (GRCm39)	splice site	probably benign
IGL02498:Rapgef2	APN	3	78,974,060 (GRCm39)	missense	probably damaging	0.97
IGL02631:Rapgef2	APN	3	78,990,533 (GRCm39)	missense	possibly damaging	0.77
IGL02835:Rapgef2	APN	3	79,000,293 (GRCm39)	splice site	probably benign
IGL02887:Rapgef2	APN	3	78,976,187 (GRCm39)	splice site	probably benign
IGL03030:Rapgef2	APN	3	78,981,614 (GRCm39)	critical splice donor site	probably null
IGL03035:Rapgef2	APN	3	79,001,731 (GRCm39)	missense	probably damaging	1.00
IGL03222:Rapgef2	APN	3	78,995,302 (GRCm39)	missense	probably damaging	1.00
IGL03227:Rapgef2	APN	3	78,999,920 (GRCm39)	splice site	probably benign
IGL03326:Rapgef2	APN	3	78,999,140 (GRCm39)	missense	probably damaging	0.96
IGL03335:Rapgef2	APN	3	79,006,492 (GRCm39)	missense	probably damaging	1.00
IGL03384:Rapgef2	APN	3	78,990,853 (GRCm39)	missense	probably damaging	1.00
Bulge	UTSW	3	78,986,439 (GRCm39)	missense	probably benign	0.01
Hai_phat	UTSW	3	78,993,266 (GRCm39)	missense	probably damaging	1.00
R0022:Rapgef2	UTSW	3	78,995,207 (GRCm39)	missense	probably damaging	1.00
R0022:Rapgef2	UTSW	3	78,995,207 (GRCm39)	missense	probably damaging	1.00
R0038:Rapgef2	UTSW	3	78,976,703 (GRCm39)	missense	probably benign	0.00
R0117:Rapgef2	UTSW	3	78,986,484 (GRCm39)	missense	probably benign	0.00
R0225:Rapgef2	UTSW	3	79,011,412 (GRCm39)	missense	probably damaging	0.99
R0723:Rapgef2	UTSW	3	78,986,481 (GRCm39)	missense	probably benign	0.20
R0788:Rapgef2	UTSW	3	79,006,502 (GRCm39)	missense	possibly damaging	0.59
R1311:Rapgef2	UTSW	3	78,990,854 (GRCm39)	missense	probably benign	0.12
R1374:Rapgef2	UTSW	3	78,995,275 (GRCm39)	missense	probably benign	0.08
R1507:Rapgef2	UTSW	3	78,988,600 (GRCm39)	splice site	probably benign
R1523:Rapgef2	UTSW	3	79,000,056 (GRCm39)	missense	probably damaging	1.00
R1753:Rapgef2	UTSW	3	78,996,098 (GRCm39)	missense	possibly damaging	0.65
R1759:Rapgef2	UTSW	3	78,974,038 (GRCm39)	missense	possibly damaging	0.89
R1766:Rapgef2	UTSW	3	79,000,010 (GRCm39)	missense	probably damaging	1.00
R2436:Rapgef2	UTSW	3	78,996,079 (GRCm39)	missense	possibly damaging	0.95
R3033:Rapgef2	UTSW	3	78,981,613 (GRCm39)	critical splice donor site	probably null
R3766:Rapgef2	UTSW	3	78,996,057 (GRCm39)	missense	probably benign	0.01
R4118:Rapgef2	UTSW	3	78,976,194 (GRCm39)	critical splice donor site	probably null
R4416:Rapgef2	UTSW	3	78,976,364 (GRCm39)	nonsense	probably null
R4722:Rapgef2	UTSW	3	78,976,480 (GRCm39)	missense	probably benign	0.00
R4743:Rapgef2	UTSW	3	79,080,375 (GRCm39)	missense	probably damaging	0.99
R4780:Rapgef2	UTSW	3	79,077,076 (GRCm39)	splice site	probably benign
R4825:Rapgef2	UTSW	3	78,990,534 (GRCm39)	missense	probably benign	0.03
R4861:Rapgef2	UTSW	3	78,981,743 (GRCm39)	missense	probably benign	0.01
R4861:Rapgef2	UTSW	3	78,981,743 (GRCm39)	missense	probably benign	0.01
R4900:Rapgef2	UTSW	3	78,981,670 (GRCm39)	missense	probably benign	0.02
R4943:Rapgef2	UTSW	3	78,971,854 (GRCm39)	missense	probably benign	0.00
R5291:Rapgef2	UTSW	3	78,977,366 (GRCm39)	missense	possibly damaging	0.64
R5369:Rapgef2	UTSW	3	78,976,739 (GRCm39)	missense	probably benign	0.00
R5413:Rapgef2	UTSW	3	78,995,173 (GRCm39)	missense	probably damaging	1.00
R5561:Rapgef2	UTSW	3	78,995,950 (GRCm39)	critical splice donor site	probably null
R5568:Rapgef2	UTSW	3	79,011,308 (GRCm39)	missense	probably damaging	1.00
R5642:Rapgef2	UTSW	3	79,002,157 (GRCm39)	missense	probably damaging	1.00
R5783:Rapgef2	UTSW	3	78,995,300 (GRCm39)	missense	probably benign	0.00
R6041:Rapgef2	UTSW	3	78,976,469 (GRCm39)	missense	probably benign	0.00
R6193:Rapgef2	UTSW	3	78,976,751 (GRCm39)	missense	possibly damaging	0.48
R6324:Rapgef2	UTSW	3	78,986,439 (GRCm39)	missense	probably benign	0.01
R6551:Rapgef2	UTSW	3	79,122,342 (GRCm39)	splice site	probably null
R6688:Rapgef2	UTSW	3	78,976,435 (GRCm39)	missense	probably benign	0.03
R6908:Rapgef2	UTSW	3	79,011,370 (GRCm39)	missense	probably benign	0.01
R6913:Rapgef2	UTSW	3	78,993,281 (GRCm39)	missense	probably damaging	1.00
R7086:Rapgef2	UTSW	3	78,993,353 (GRCm39)	missense	probably benign	0.08
R7106:Rapgef2	UTSW	3	78,973,915 (GRCm39)	missense	probably benign
R7228:Rapgef2	UTSW	3	78,976,525 (GRCm39)	missense	probably benign	0.03
R7242:Rapgef2	UTSW	3	78,995,210 (GRCm39)	nonsense	probably null
R7257:Rapgef2	UTSW	3	78,989,934 (GRCm39)	missense	probably damaging	0.99
R7322:Rapgef2	UTSW	3	79,053,130 (GRCm39)	start codon destroyed	probably null	0.02
R7443:Rapgef2	UTSW	3	78,988,531 (GRCm39)	missense	probably damaging	1.00
R7450:Rapgef2	UTSW	3	79,080,366 (GRCm39)	missense	probably benign	0.01
R7472:Rapgef2	UTSW	3	78,976,580 (GRCm39)	missense	probably benign	0.45
R7884:Rapgef2	UTSW	3	78,973,933 (GRCm39)	missense	possibly damaging	0.49
R7954:Rapgef2	UTSW	3	78,977,454 (GRCm39)	nonsense	probably null
R7957:Rapgef2	UTSW	3	79,122,276 (GRCm39)	missense	probably benign	0.27
R8071:Rapgef2	UTSW	3	79,000,343 (GRCm39)	missense	probably damaging	1.00
R8261:Rapgef2	UTSW	3	78,993,325 (GRCm39)	missense	probably benign	0.34
R8268:Rapgef2	UTSW	3	78,993,263 (GRCm39)	missense	probably benign	0.12
R8309:Rapgef2	UTSW	3	78,990,509 (GRCm39)	missense	possibly damaging	0.65
R8505:Rapgef2	UTSW	3	78,986,349 (GRCm39)	nonsense	probably null
R8783:Rapgef2	UTSW	3	79,005,651 (GRCm39)	missense	probably damaging	1.00
R8897:Rapgef2	UTSW	3	79,019,566 (GRCm39)	missense	probably damaging	1.00
R8965:Rapgef2	UTSW	3	78,999,851 (GRCm39)	missense	probably damaging	1.00
R9028:Rapgef2	UTSW	3	78,981,651 (GRCm39)	missense	probably damaging	1.00
R9284:Rapgef2	UTSW	3	79,000,010 (GRCm39)	missense	probably damaging	1.00
R9371:Rapgef2	UTSW	3	79,082,300 (GRCm39)	missense	probably damaging	1.00
R9479:Rapgef2	UTSW	3	79,019,495 (GRCm39)	missense	probably damaging	1.00
R9493:Rapgef2	UTSW	3	79,019,495 (GRCm39)	missense	probably damaging	1.00
R9494:Rapgef2	UTSW	3	79,019,495 (GRCm39)	missense	probably damaging	1.00
R9500:Rapgef2	UTSW	3	78,974,093 (GRCm39)	missense	probably benign
R9657:Rapgef2	UTSW	3	78,999,191 (GRCm39)	missense	probably damaging	0.99

Predicted Primers

PCR Primer
(F):5'- ACCTGATGATTGCAAACATGGAG -3'
(R):5'- TTGGCATCTGAAGAGCTTCTG -3'

Sequencing Primer
(F):5'- CATTCCCTGCAGTGCAAGGC -3'
(R):5'- ATCTGAAGAGCTTCTGTTTCTTTCAG -3'

Posted On

2018-11-06