Mutagenetix > Incidental Mutation

Incidental Mutation 'R5701:Rapgef6'

450902

Institutional Source

Beutler Lab

Gene Symbol

Rapgef6

Ensembl Gene

ENSMUSG00000037533

Gene Name

Rap guanine nucleotide exchange factor (GEF) 6

Synonyms

PDZ-GEF2, C030018K18Rik, Pdzgef2, RA-GEF-2

MMRRC Submission

043181-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R5701 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

54413673-54590111 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 54567220 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tryptophan to Arginine at position 857 (W857R)

Ref Sequence

ENSEMBL: ENSMUSP00000104522 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000094536] [ENSMUST00000101206] [ENSMUST00000102743] [ENSMUST00000108894] [ENSMUST00000207429]

AlphaFold

Q5NCJ1

Predicted Effect

probably benign
Transcript: ENSMUST00000094536
AA Change: W849R

PolyPhen 2 Score 0.201 (Sensitivity: 0.92; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000092114
Gene: ENSMUSG00000037533
AA Change: W849R

Domain	Start	End	E-Value	Type
cNMP	1	113	6.64e-7	SMART
RasGEFN	127	240	4.35e-33	SMART
PDZ	255	327	8.86e-16	SMART
low complexity region	409	420	N/A	INTRINSIC
RA	464	550	1.47e-20	SMART
RasGEF	571	853	3.88e-84	SMART
low complexity region	944	957	N/A	INTRINSIC
low complexity region	972	989	N/A	INTRINSIC
low complexity region	1016	1061	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000101206
AA Change: W1142R

PolyPhen 2 Score 0.598 (Sensitivity: 0.87; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000098766
Gene: ENSMUSG00000037533
AA Change: W1142R

Domain	Start	End	E-Value	Type
internal_repeat_1	10	82	1.45e-5	PROSPERO
low complexity region	187	205	N/A	INTRINSIC
low complexity region	231	239	N/A	INTRINSIC
cNMP	280	398	4.8e-13	SMART
RasGEFN	412	525	4.35e-33	SMART
PDZ	540	612	8.86e-16	SMART
low complexity region	694	705	N/A	INTRINSIC
RA	749	835	1.47e-20	SMART
RasGEF	856	1095	5.35e-87	SMART
low complexity region	1237	1250	N/A	INTRINSIC
low complexity region	1270	1293	N/A	INTRINSIC
low complexity region	1345	1364	N/A	INTRINSIC
low complexity region	1368	1380	N/A	INTRINSIC
low complexity region	1444	1452	N/A	INTRINSIC
low complexity region	1555	1568	N/A	INTRINSIC
low complexity region	1591	1604	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000102743
AA Change: W1134R

PolyPhen 2 Score 0.598 (Sensitivity: 0.87; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000099804
Gene: ENSMUSG00000037533
AA Change: W1134R

Domain	Start	End	E-Value	Type
internal_repeat_1	10	82	1.42e-5	PROSPERO
low complexity region	187	205	N/A	INTRINSIC
low complexity region	231	239	N/A	INTRINSIC
cNMP	280	398	4.8e-13	SMART
RasGEFN	412	525	4.35e-33	SMART
PDZ	540	612	8.86e-16	SMART
low complexity region	694	705	N/A	INTRINSIC
RA	749	835	1.47e-20	SMART
RasGEF	856	1138	3.88e-84	SMART
low complexity region	1229	1242	N/A	INTRINSIC
low complexity region	1262	1285	N/A	INTRINSIC
low complexity region	1337	1356	N/A	INTRINSIC
low complexity region	1360	1372	N/A	INTRINSIC
low complexity region	1436	1444	N/A	INTRINSIC
low complexity region	1547	1560	N/A	INTRINSIC
low complexity region	1583	1596	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000108894
AA Change: W857R

PolyPhen 2 Score 0.763 (Sensitivity: 0.85; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000104522
Gene: ENSMUSG00000037533
AA Change: W857R

Domain	Start	End	E-Value	Type
cNMP	1	113	6.64e-7	SMART
RasGEFN	127	240	4.35e-33	SMART
PDZ	255	327	8.86e-16	SMART
low complexity region	409	420	N/A	INTRINSIC
RA	464	550	1.47e-20	SMART
RasGEF	571	810	5.35e-87	SMART
low complexity region	952	965	N/A	INTRINSIC
low complexity region	980	997	N/A	INTRINSIC
low complexity region	1024	1069	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000207429
AA Change: W1139R

PolyPhen 2 Score 0.102 (Sensitivity: 0.93; Specificity: 0.86)

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 97.1%
20x: 94.9%

Validation Efficiency

MGI Phenotype

PHENOTYPE: Mice homozygous for a null allele exhibit an inlarged spleen, increased IgE and IgG levels and altered cytokine production. [provided by MGI curators]

Allele List at MGI

All alleles(16) : Targeted, knock-out(1) Targeted, other(2) Gene trapped(13)

Other mutations in this stock

Total: 43 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Armc8	A	G	9: 99,378,202 (GRCm39)		probably null	Het
Asxl1	A	G	2: 153,241,409 (GRCm39)	E653G	probably damaging	Het
AW551984	G	A	9: 39,504,118 (GRCm39)	A616V	probably benign	Het
Birc6	T	C	17: 75,004,420 (GRCm39)	M4763T	possibly damaging	Het
Bltp1	T	A	3: 36,975,509 (GRCm39)	M727K	probably benign	Het
Cand2	T	G	6: 115,774,893 (GRCm39)	F1034V	probably damaging	Het
Ccdc80	T	C	16: 44,936,741 (GRCm39)	V722A	possibly damaging	Het
Cd109	CATTTATTTATTTATTTATTTATTTATTTATTTAT	CATTTATTTATTTATTTATTTATTTATTTATTTATTTAT	9: 78,619,782 (GRCm39)		probably benign	Het
Chrnd	G	A	1: 87,125,380 (GRCm39)	V340I	possibly damaging	Het
Clip1	T	C	5: 123,751,366 (GRCm39)		probably benign	Het
Csmd3	T	C	15: 47,513,617 (GRCm39)	E1920G	probably damaging	Het
Csmd3	A	T	15: 48,403,729 (GRCm39)	F194I	probably damaging	Het
D930048N14Rik	T	A	11: 51,544,556 (GRCm39)		probably null	Het
Defa28	T	C	8: 22,073,863 (GRCm39)	Y89H	probably benign	Het
Dnah1	C	T	14: 30,996,001 (GRCm39)	G2705E	probably damaging	Het
Eci2	A	T	13: 35,174,250 (GRCm39)	S104T	possibly damaging	Het
Ep300	T	C	15: 81,485,696 (GRCm39)	S228P	unknown	Het
Gabrb2	T	A	11: 42,378,201 (GRCm39)	M139K	probably damaging	Het
Gbp4	T	A	5: 105,266,265 (GRCm39)	N592I	possibly damaging	Het
Gpr158	C	T	2: 21,751,520 (GRCm39)	R480C	probably damaging	Het
Gps1	A	G	11: 120,676,008 (GRCm39)	D71G	probably benign	Het
Hoxc9	T	C	15: 102,890,313 (GRCm39)	Y77H	possibly damaging	Het
Il9r	T	A	11: 32,143,263 (GRCm39)	Y231F	probably benign	Het
Klhl1	A	G	14: 96,438,816 (GRCm39)	M494T	probably benign	Het
Kmt2c	A	G	5: 25,519,015 (GRCm39)	V2365A	probably benign	Het
Kri1	T	A	9: 21,192,425 (GRCm39)	K241M	possibly damaging	Het
Macf1	A	T	4: 123,397,018 (GRCm39)	C928S	probably damaging	Het
Mcm2	T	C	6: 88,870,073 (GRCm39)	D32G	probably damaging	Het
Mex3d	T	C	10: 80,217,379 (GRCm39)	T613A	probably benign	Het
Mptx2	G	A	1: 173,102,414 (GRCm39)	L92F	probably benign	Het
Myh9	T	C	15: 77,675,964 (GRCm39)	I241V	probably benign	Het
Myo6	C	T	9: 80,165,809 (GRCm39)	T398I	probably damaging	Het
Nckap1l	G	A	15: 103,381,195 (GRCm39)	A366T	probably benign	Het
Or5m11	A	G	2: 85,782,168 (GRCm39)	T254A	possibly damaging	Het
Plscr5	A	T	9: 92,087,564 (GRCm39)	K178*	probably null	Het
Raxos1	G	A	18: 66,071,059 (GRCm39)		probably benign	Het
Rnf145	G	A	11: 44,422,120 (GRCm39)	V68M	possibly damaging	Het
Slc66a2	T	A	18: 80,315,693 (GRCm39)	D118E	possibly damaging	Het
Synpo2	C	G	3: 122,873,879 (GRCm39)	G1029A	probably damaging	Het
Tbc1d5	TTGCTGCTGCTGCTGCTGCTGGTGCTGCTGCTGCTG	TTGCTGCTGCTGCTGCTGGTGCTGCTGCTGCTG	17: 51,106,983 (GRCm39)		probably benign	Het
Vmn2r14	T	C	5: 109,367,816 (GRCm39)	Y392C	probably damaging	Het
Vmn2r55	A	G	7: 12,404,492 (GRCm39)	F304L	probably benign	Het
Zfp316	C	T	5: 143,240,132 (GRCm39)	G629D	probably benign	Het

Other mutations in Rapgef6

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00436:Rapgef6	APN	11	54,570,091 (GRCm39)	missense	probably benign	0.00
IGL00507:Rapgef6	APN	11	54,554,935 (GRCm39)	nonsense	probably null
IGL00809:Rapgef6	APN	11	54,540,126 (GRCm39)	missense	probably damaging	1.00
IGL00843:Rapgef6	APN	11	54,582,099 (GRCm39)	missense	probably benign	0.03
IGL00899:Rapgef6	APN	11	54,510,844 (GRCm39)	nonsense	probably null
IGL01372:Rapgef6	APN	11	54,559,437 (GRCm39)	splice site	probably benign
IGL01604:Rapgef6	APN	11	54,585,389 (GRCm39)	missense	probably damaging	0.99
IGL01935:Rapgef6	APN	11	54,501,668 (GRCm39)	missense	possibly damaging	0.78
IGL01991:Rapgef6	APN	11	54,443,695 (GRCm39)	missense	probably benign	0.37
IGL02243:Rapgef6	APN	11	54,567,226 (GRCm39)	missense	probably damaging	1.00
IGL02407:Rapgef6	APN	11	54,567,181 (GRCm39)	missense	possibly damaging	0.91
IGL02676:Rapgef6	APN	11	54,540,172 (GRCm39)	unclassified	probably benign
IGL02934:Rapgef6	APN	11	54,516,690 (GRCm39)	missense	probably damaging	1.00
IGL03076:Rapgef6	APN	11	54,516,793 (GRCm39)	missense	probably damaging	1.00
IGL03110:Rapgef6	APN	11	54,586,915 (GRCm39)	missense	probably damaging	0.97
IGL03256:Rapgef6	APN	11	54,548,255 (GRCm39)	missense	probably damaging	1.00
shocker	UTSW	11	54,510,842 (GRCm39)	missense	probably damaging	1.00
D4216:Rapgef6	UTSW	11	54,559,572 (GRCm39)	splice site	probably benign
PIT4305001:Rapgef6	UTSW	11	54,570,203 (GRCm39)	missense	probably damaging	1.00
PIT4366001:Rapgef6	UTSW	11	54,582,446 (GRCm39)	missense	probably damaging	0.98
R0047:Rapgef6	UTSW	11	54,437,204 (GRCm39)	missense	possibly damaging	0.65
R0047:Rapgef6	UTSW	11	54,437,204 (GRCm39)	missense	possibly damaging	0.65
R0125:Rapgef6	UTSW	11	54,516,701 (GRCm39)	nonsense	probably null
R0189:Rapgef6	UTSW	11	54,582,075 (GRCm39)	missense	probably benign
R0201:Rapgef6	UTSW	11	54,510,767 (GRCm39)	missense	probably damaging	1.00
R0505:Rapgef6	UTSW	11	54,516,789 (GRCm39)	missense	probably benign	0.00
R0524:Rapgef6	UTSW	11	54,581,110 (GRCm39)	missense	probably benign	0.32
R0853:Rapgef6	UTSW	11	54,559,503 (GRCm39)	missense	probably damaging	1.00
R1203:Rapgef6	UTSW	11	54,582,525 (GRCm39)	missense	probably benign	0.09
R1440:Rapgef6	UTSW	11	54,517,534 (GRCm39)	missense	probably damaging	1.00
R1453:Rapgef6	UTSW	11	54,530,553 (GRCm39)	splice site	probably null
R1530:Rapgef6	UTSW	11	54,552,009 (GRCm39)	missense	probably damaging	1.00
R1593:Rapgef6	UTSW	11	54,437,223 (GRCm39)	frame shift	probably null
R1620:Rapgef6	UTSW	11	54,517,420 (GRCm39)	missense	possibly damaging	0.88
R1628:Rapgef6	UTSW	11	54,437,223 (GRCm39)	frame shift	probably null
R1629:Rapgef6	UTSW	11	54,437,223 (GRCm39)	frame shift	probably null
R1630:Rapgef6	UTSW	11	54,437,223 (GRCm39)	frame shift	probably null
R1634:Rapgef6	UTSW	11	54,437,223 (GRCm39)	frame shift	probably null
R1640:Rapgef6	UTSW	11	54,548,231 (GRCm39)	missense	probably damaging	1.00
R1686:Rapgef6	UTSW	11	54,582,458 (GRCm39)	missense	possibly damaging	0.81
R1722:Rapgef6	UTSW	11	54,437,223 (GRCm39)	frame shift	probably null
R1743:Rapgef6	UTSW	11	54,567,110 (GRCm39)	missense	probably damaging	1.00
R1816:Rapgef6	UTSW	11	54,585,314 (GRCm39)	missense	probably benign
R1851:Rapgef6	UTSW	11	54,533,637 (GRCm39)	missense	probably benign	0.01
R1852:Rapgef6	UTSW	11	54,533,637 (GRCm39)	missense	probably benign	0.01
R1868:Rapgef6	UTSW	11	54,437,223 (GRCm39)	frame shift	probably null
R1888:Rapgef6	UTSW	11	54,551,654 (GRCm39)	missense	probably damaging	1.00
R1888:Rapgef6	UTSW	11	54,551,654 (GRCm39)	missense	probably damaging	1.00
R1942:Rapgef6	UTSW	11	54,548,089 (GRCm39)	missense	possibly damaging	0.95
R1943:Rapgef6	UTSW	11	54,548,089 (GRCm39)	missense	possibly damaging	0.95
R2031:Rapgef6	UTSW	11	54,443,684 (GRCm39)	missense	probably benign	0.30
R2087:Rapgef6	UTSW	11	54,522,075 (GRCm39)	missense	probably damaging	1.00
R2106:Rapgef6	UTSW	11	54,559,512 (GRCm39)	missense	probably benign	0.17
R2362:Rapgef6	UTSW	11	54,585,098 (GRCm39)	missense	probably damaging	1.00
R2484:Rapgef6	UTSW	11	54,533,582 (GRCm39)	missense	possibly damaging	0.48
R2566:Rapgef6	UTSW	11	54,578,537 (GRCm39)	missense	possibly damaging	0.66
R2872:Rapgef6	UTSW	11	54,552,001 (GRCm39)	missense	probably damaging	1.00
R2872:Rapgef6	UTSW	11	54,552,001 (GRCm39)	missense	probably damaging	1.00
R3744:Rapgef6	UTSW	11	54,516,760 (GRCm39)	missense	probably benign	0.40
R3848:Rapgef6	UTSW	11	54,582,134 (GRCm39)	missense	probably damaging	0.97
R4823:Rapgef6	UTSW	11	54,585,326 (GRCm39)	missense	probably benign	0.08
R4859:Rapgef6	UTSW	11	54,526,989 (GRCm39)	missense	probably benign
R4906:Rapgef6	UTSW	11	54,443,662 (GRCm39)	missense	probably damaging	1.00
R4911:Rapgef6	UTSW	11	54,513,143 (GRCm39)	missense	probably damaging	0.97
R4937:Rapgef6	UTSW	11	54,548,143 (GRCm39)	missense	probably damaging	1.00
R5033:Rapgef6	UTSW	11	54,582,207 (GRCm39)	missense	possibly damaging	0.92
R5249:Rapgef6	UTSW	11	54,413,943 (GRCm39)	missense	probably benign	0.19
R5304:Rapgef6	UTSW	11	54,548,200 (GRCm39)	missense	probably benign	0.01
R5656:Rapgef6	UTSW	11	54,526,962 (GRCm39)	missense	possibly damaging	0.95
R5758:Rapgef6	UTSW	11	54,559,470 (GRCm39)	missense	probably damaging	1.00
R5973:Rapgef6	UTSW	11	54,530,609 (GRCm39)	missense	probably damaging	1.00
R6177:Rapgef6	UTSW	11	54,510,842 (GRCm39)	missense	probably damaging	1.00
R6268:Rapgef6	UTSW	11	54,540,073 (GRCm39)	missense	probably damaging	1.00
R6287:Rapgef6	UTSW	11	54,517,164 (GRCm39)	splice site	probably null
R6293:Rapgef6	UTSW	11	54,525,607 (GRCm39)	missense	probably damaging	1.00
R6471:Rapgef6	UTSW	11	54,582,563 (GRCm39)	missense	probably damaging	0.99
R6863:Rapgef6	UTSW	11	54,437,206 (GRCm39)	missense	probably benign	0.00
R6950:Rapgef6	UTSW	11	54,567,206 (GRCm39)	missense	probably benign	0.09
R7144:Rapgef6	UTSW	11	54,548,191 (GRCm39)	missense	possibly damaging	0.78
R7171:Rapgef6	UTSW	11	54,567,189 (GRCm39)	missense	possibly damaging	0.94
R7199:Rapgef6	UTSW	11	54,437,252 (GRCm39)	missense	probably benign	0.00
R7291:Rapgef6	UTSW	11	54,582,065 (GRCm39)	missense	probably benign	0.05
R7436:Rapgef6	UTSW	11	54,501,747 (GRCm39)	critical splice donor site	probably null
R7498:Rapgef6	UTSW	11	54,510,830 (GRCm39)	missense	probably damaging	1.00
R7506:Rapgef6	UTSW	11	54,526,997 (GRCm39)	missense	probably benign	0.00
R7527:Rapgef6	UTSW	11	54,525,787 (GRCm39)	missense	unknown
R7646:Rapgef6	UTSW	11	54,516,780 (GRCm39)	missense	probably benign	0.00
R7655:Rapgef6	UTSW	11	54,585,279 (GRCm39)	missense	probably benign	0.10
R7656:Rapgef6	UTSW	11	54,585,279 (GRCm39)	missense	probably benign	0.10
R7687:Rapgef6	UTSW	11	54,551,901 (GRCm39)	missense	possibly damaging	0.93
R7768:Rapgef6	UTSW	11	54,517,414 (GRCm39)	missense	probably damaging	1.00
R7788:Rapgef6	UTSW	11	54,585,225 (GRCm39)	missense	probably damaging	1.00
R7890:Rapgef6	UTSW	11	54,517,549 (GRCm39)	missense	probably damaging	1.00
R8113:Rapgef6	UTSW	11	54,516,784 (GRCm39)	missense	probably benign	0.03
R8337:Rapgef6	UTSW	11	54,522,127 (GRCm39)	nonsense	probably null
R8393:Rapgef6	UTSW	11	54,578,487 (GRCm39)	missense	probably benign
R8465:Rapgef6	UTSW	11	54,582,308 (GRCm39)	missense	probably benign	0.00
R8492:Rapgef6	UTSW	11	54,581,063 (GRCm39)	missense	probably damaging	0.99
R8791:Rapgef6	UTSW	11	54,459,295 (GRCm39)	missense	probably benign	0.15
R8866:Rapgef6	UTSW	11	54,443,700 (GRCm39)	critical splice donor site	probably null
R8917:Rapgef6	UTSW	11	54,582,392 (GRCm39)	nonsense	probably null
R8921:Rapgef6	UTSW	11	54,570,065 (GRCm39)	missense	probably benign	0.09
R9031:Rapgef6	UTSW	11	54,578,667 (GRCm39)	missense	probably benign	0.00
R9093:Rapgef6	UTSW	11	54,487,912 (GRCm39)	nonsense	probably null
R9354:Rapgef6	UTSW	11	54,510,749 (GRCm39)	missense	possibly damaging	0.66
R9514:Rapgef6	UTSW	11	54,443,684 (GRCm39)	missense	probably benign	0.14
R9516:Rapgef6	UTSW	11	54,582,169 (GRCm39)	missense	probably damaging	1.00
R9739:Rapgef6	UTSW	11	54,513,189 (GRCm39)	missense	probably benign	0.03
R9789:Rapgef6	UTSW	11	54,540,097 (GRCm39)	missense	probably benign	0.03

Predicted Primers

PCR Primer
(F):5'- ATCTTTACAGGCTCTCATTGCAG -3'
(R):5'- GCTGCATGGGACTCAGTATC -3'

Sequencing Primer
(F):5'- CTTACAGGTCATTGAGTCAAGGC -3'
(R):5'- CATGGGACTCAGTATCTCATGAGC -3'

Posted On

2017-01-03