Mutagenetix > Incidental Mutation

Incidental Mutation 'R0047:Rapgef6'

15944

Institutional Source

Beutler Lab

Gene Symbol

Rapgef6

Ensembl Gene

ENSMUSG00000037533

Gene Name

Rap guanine nucleotide exchange factor (GEF) 6

Synonyms

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

MMRRC Submission

038341-MU

Accession Numbers

Genbank: NM_175258; MGI: 2384761

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R0047 (G1)

Quality Score

Status

Validated

Chromosome

Chromosomal Location

54522847-54699285 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 54546378 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Methionine to Lysine at position 49 (M49K)

Ref Sequence

ENSEMBL: ENSMUSP00000104523 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000101206] [ENSMUST00000102743] [ENSMUST00000108895] [ENSMUST00000207429]

AlphaFold

Q5NCJ1

Predicted Effect

probably benign
Transcript: ENSMUST00000101206
AA Change: M49K

PolyPhen 2 Score 0.298 (Sensitivity: 0.91; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000098766
Gene: ENSMUSG00000037533
AA Change: M49K

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

probably benign
Transcript: ENSMUST00000102743
AA Change: M49K

PolyPhen 2 Score 0.298 (Sensitivity: 0.91; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000099804
Gene: ENSMUSG00000037533
AA Change: M49K

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: ENSMUST00000108895
AA Change: M49K

PolyPhen 2 Score 0.653 (Sensitivity: 0.87; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000104523
Gene: ENSMUSG00000037533
AA Change: M49K

Domain	Start	End	E-Value	Type
internal_repeat_1	10	82	1.95e-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	526	1.03e-25	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000139360

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000155132

Predicted Effect

possibly damaging
Transcript: ENSMUST00000207429
AA Change: M49K

PolyPhen 2 Score 0.488 (Sensitivity: 0.88; Specificity: 0.90)

Meta Mutation Damage Score

0.4624

Coding Region Coverage

1x: 89.2%
3x: 86.3%
10x: 78.8%
20x: 65.9%

Validation Efficiency

95% (110/116)

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: 71 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1110002E22Rik	A	G	3: 138,066,264 (GRCm38)	T405A	probably damaging	Het
4932438A13Rik	T	A	3: 36,908,192 (GRCm38)	L481M	possibly damaging	Het
Acer1	A	T	17: 56,955,624 (GRCm38)	D175E	possibly damaging	Het
Adamts9	G	A	6: 92,905,306 (GRCm38)		probably benign	Het
Amigo3	T	C	9: 108,054,658 (GRCm38)	S427P	probably benign	Het
Arid4a	T	G	12: 71,075,419 (GRCm38)	L858W	probably damaging	Het
Bbox1	A	G	2: 110,268,302 (GRCm38)	F310S	probably damaging	Het
Bmper	T	A	9: 23,406,686 (GRCm38)	C534S	probably damaging	Het
Cacna1d	T	G	14: 30,346,790 (GRCm38)		probably benign	Het
Capn12	G	A	7: 28,890,387 (GRCm38)		probably null	Het
Chchd1	T	C	14: 20,704,163 (GRCm38)	S48P	possibly damaging	Het
Cnot7	A	G	8: 40,495,921 (GRCm38)		probably benign	Het
Cux1	T	C	5: 136,363,253 (GRCm38)		probably benign	Het
Cyp2b19	T	A	7: 26,766,826 (GRCm38)	D351E	probably benign	Het
Dctn1	G	T	6: 83,182,632 (GRCm38)	G31*	probably null	Het
Duox1	T	A	2: 122,346,641 (GRCm38)		probably benign	Het
Egflam	T	G	15: 7,253,430 (GRCm38)	E382A	possibly damaging	Het
Ext1	T	C	15: 53,345,146 (GRCm38)	N73S	probably benign	Het
Glg1	A	T	8: 111,165,582 (GRCm38)	M866K	probably damaging	Het
Gm3333	A	G	13: 62,274,471 (GRCm38)		noncoding transcript	Het
Golm1	T	A	13: 59,645,100 (GRCm38)	H197L	probably benign	Het
Gtse1	A	G	15: 85,862,378 (GRCm38)	K132E	probably damaging	Het
Gxylt2	A	T	6: 100,733,378 (GRCm38)		probably benign	Het
Hrc	T	A	7: 45,336,689 (GRCm38)	S421R	probably benign	Het
Ighg2c	T	A	12: 113,288,168 (GRCm38)		probably benign	Het
Ihh	A	G	1: 74,946,591 (GRCm38)	I245T	probably benign	Het
Ilf3	T	A	9: 21,388,714 (GRCm38)	M65K	possibly damaging	Het
Kif9	A	G	9: 110,485,038 (GRCm38)	I33V	probably benign	Het
Lama1	A	T	17: 67,795,186 (GRCm38)		probably benign	Het
Lamb1	T	C	12: 31,278,601 (GRCm38)	I188T	possibly damaging	Het
Lpp	T	A	16: 24,661,800 (GRCm38)		probably benign	Het
Mark2	A	C	19: 7,283,577 (GRCm38)		probably benign	Het
Mmp3	T	C	9: 7,451,910 (GRCm38)		probably benign	Het
Mthfd1l	T	A	10: 3,978,727 (GRCm38)		probably benign	Het
Mtr	A	T	13: 12,222,226 (GRCm38)	S569T	probably damaging	Het
Myh13	T	A	11: 67,367,237 (GRCm38)	S1752T	probably benign	Het
Myo5a	T	A	9: 75,156,207 (GRCm38)	L565H	probably damaging	Het
Numa1	A	G	7: 102,009,453 (GRCm38)	K296E	probably damaging	Het
Olfr1477	A	G	19: 13,502,589 (GRCm38)	E82G	probably benign	Het
Olfr201	C	T	16: 59,269,211 (GRCm38)	G152D	probably damaging	Het
Olfr613	A	T	7: 103,552,322 (GRCm38)	Y179F	probably damaging	Het
Pla2g2c	T	C	4: 138,743,590 (GRCm38)		probably benign	Het
Pnpla7	A	T	2: 25,011,606 (GRCm38)	E548V	probably damaging	Het
Ppm1m	C	A	9: 106,196,696 (GRCm38)	E273*	probably null	Het
Ppp2r1b	C	T	9: 50,861,573 (GRCm38)	R117*	probably null	Het
Psg-ps1	A	G	7: 17,677,881 (GRCm38)		noncoding transcript	Het
Rabgap1l	G	A	1: 160,231,789 (GRCm38)		probably benign	Het
Rnf219	T	A	14: 104,503,344 (GRCm38)		probably null	Het
Rtel1	T	G	2: 181,323,405 (GRCm38)	I146M	probably damaging	Het
Sdr9c7	A	T	10: 127,903,672 (GRCm38)	M219L	probably benign	Het
Serpinb1a	A	T	13: 32,850,276 (GRCm38)	L44Q	probably damaging	Het
Slc13a4	A	G	6: 35,287,362 (GRCm38)	I190T	possibly damaging	Het
Slc46a2	A	G	4: 59,914,392 (GRCm38)	L177P	probably damaging	Het
Slc47a2	C	T	11: 61,336,242 (GRCm38)	V167M	possibly damaging	Het
Snrnp200	C	T	2: 127,234,954 (GRCm38)		probably benign	Het
Snx13	C	A	12: 35,101,124 (GRCm38)		probably benign	Het
Snx25	C	T	8: 46,041,365 (GRCm38)	A828T	probably damaging	Het
Spic	A	G	10: 88,675,941 (GRCm38)	L151P	probably damaging	Het
Sptb	G	T	12: 76,622,950 (GRCm38)	Q535K	probably damaging	Het
Ssu2	G	A	6: 112,374,820 (GRCm38)	H315Y	probably damaging	Het
Stk32a	T	C	18: 43,313,378 (GRCm38)		probably benign	Het
Tcaf2	A	G	6: 42,629,613 (GRCm38)	I469T	probably benign	Het
Tln2	A	G	9: 67,240,672 (GRCm38)		probably benign	Het
Top2a	T	A	11: 98,997,856 (GRCm38)	I1260L	probably benign	Het
Treml1	C	A	17: 48,364,980 (GRCm38)	S91*	probably null	Het
Trmt11	T	C	10: 30,535,243 (GRCm38)	N418S	probably benign	Het
Ttf1	A	G	2: 29,084,655 (GRCm38)	Y801C	probably damaging	Het
Usp34	C	T	11: 23,464,403 (GRCm38)	A2782V	probably benign	Het
Vps4a	T	C	8: 107,036,701 (GRCm38)	L29P	probably damaging	Het
Wdfy3	A	G	5: 101,944,033 (GRCm38)	I480T	probably damaging	Het
Ywhag	A	T	5: 135,911,299 (GRCm38)	V147E	probably damaging	Het

Other mutations in Rapgef6

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00436:Rapgef6	APN	11	54,679,265 (GRCm38)	missense	probably benign	0.00
IGL00507:Rapgef6	APN	11	54,664,109 (GRCm38)	nonsense	probably null
IGL00809:Rapgef6	APN	11	54,649,300 (GRCm38)	missense	probably damaging	1.00
IGL00843:Rapgef6	APN	11	54,691,273 (GRCm38)	missense	probably benign	0.03
IGL00899:Rapgef6	APN	11	54,620,018 (GRCm38)	nonsense	probably null
IGL01372:Rapgef6	APN	11	54,668,611 (GRCm38)	splice site	probably benign
IGL01604:Rapgef6	APN	11	54,694,563 (GRCm38)	missense	probably damaging	0.99
IGL01935:Rapgef6	APN	11	54,610,842 (GRCm38)	missense	possibly damaging	0.78
IGL01991:Rapgef6	APN	11	54,552,869 (GRCm38)	missense	probably benign	0.37
IGL02243:Rapgef6	APN	11	54,676,400 (GRCm38)	missense	probably damaging	1.00
IGL02407:Rapgef6	APN	11	54,676,355 (GRCm38)	missense	possibly damaging	0.91
IGL02676:Rapgef6	APN	11	54,649,346 (GRCm38)	unclassified	probably benign
IGL02934:Rapgef6	APN	11	54,625,864 (GRCm38)	missense	probably damaging	1.00
IGL03076:Rapgef6	APN	11	54,625,967 (GRCm38)	missense	probably damaging	1.00
IGL03110:Rapgef6	APN	11	54,696,089 (GRCm38)	missense	probably damaging	0.97
IGL03256:Rapgef6	APN	11	54,657,429 (GRCm38)	missense	probably damaging	1.00
shocker	UTSW	11	54,620,016 (GRCm38)	missense	probably damaging	1.00
D4216:Rapgef6	UTSW	11	54,668,746 (GRCm38)	splice site	probably benign
PIT4305001:Rapgef6	UTSW	11	54,679,377 (GRCm38)	missense	probably damaging	1.00
PIT4366001:Rapgef6	UTSW	11	54,691,620 (GRCm38)	missense	probably damaging	0.98
R0047:Rapgef6	UTSW	11	54,546,378 (GRCm38)	missense	possibly damaging	0.65
R0125:Rapgef6	UTSW	11	54,625,875 (GRCm38)	nonsense	probably null
R0189:Rapgef6	UTSW	11	54,691,249 (GRCm38)	missense	probably benign
R0201:Rapgef6	UTSW	11	54,619,941 (GRCm38)	missense	probably damaging	1.00
R0505:Rapgef6	UTSW	11	54,625,963 (GRCm38)	missense	probably benign	0.00
R0524:Rapgef6	UTSW	11	54,690,284 (GRCm38)	missense	probably benign	0.32
R0853:Rapgef6	UTSW	11	54,668,677 (GRCm38)	missense	probably damaging	1.00
R1203:Rapgef6	UTSW	11	54,691,699 (GRCm38)	missense	probably benign	0.09
R1440:Rapgef6	UTSW	11	54,626,708 (GRCm38)	missense	probably damaging	1.00
R1453:Rapgef6	UTSW	11	54,639,727 (GRCm38)	splice site	probably null
R1530:Rapgef6	UTSW	11	54,661,183 (GRCm38)	missense	probably damaging	1.00
R1593:Rapgef6	UTSW	11	54,546,397 (GRCm38)	frame shift	probably null
R1620:Rapgef6	UTSW	11	54,626,594 (GRCm38)	missense	possibly damaging	0.88
R1628:Rapgef6	UTSW	11	54,546,397 (GRCm38)	frame shift	probably null
R1629:Rapgef6	UTSW	11	54,546,397 (GRCm38)	frame shift	probably null
R1630:Rapgef6	UTSW	11	54,546,397 (GRCm38)	frame shift	probably null
R1634:Rapgef6	UTSW	11	54,546,397 (GRCm38)	frame shift	probably null
R1640:Rapgef6	UTSW	11	54,657,405 (GRCm38)	missense	probably damaging	1.00
R1686:Rapgef6	UTSW	11	54,691,632 (GRCm38)	missense	possibly damaging	0.81
R1722:Rapgef6	UTSW	11	54,546,397 (GRCm38)	frame shift	probably null
R1743:Rapgef6	UTSW	11	54,676,284 (GRCm38)	missense	probably damaging	1.00
R1816:Rapgef6	UTSW	11	54,694,488 (GRCm38)	missense	probably benign
R1851:Rapgef6	UTSW	11	54,642,811 (GRCm38)	missense	probably benign	0.01
R1852:Rapgef6	UTSW	11	54,642,811 (GRCm38)	missense	probably benign	0.01
R1868:Rapgef6	UTSW	11	54,546,397 (GRCm38)	frame shift	probably null
R1888:Rapgef6	UTSW	11	54,660,828 (GRCm38)	missense	probably damaging	1.00
R1888:Rapgef6	UTSW	11	54,660,828 (GRCm38)	missense	probably damaging	1.00
R1942:Rapgef6	UTSW	11	54,657,263 (GRCm38)	missense	possibly damaging	0.95
R1943:Rapgef6	UTSW	11	54,657,263 (GRCm38)	missense	possibly damaging	0.95
R2031:Rapgef6	UTSW	11	54,552,858 (GRCm38)	missense	probably benign	0.30
R2087:Rapgef6	UTSW	11	54,631,249 (GRCm38)	missense	probably damaging	1.00
R2106:Rapgef6	UTSW	11	54,668,686 (GRCm38)	missense	probably benign	0.17
R2362:Rapgef6	UTSW	11	54,694,272 (GRCm38)	missense	probably damaging	1.00
R2484:Rapgef6	UTSW	11	54,642,756 (GRCm38)	missense	possibly damaging	0.48
R2566:Rapgef6	UTSW	11	54,687,711 (GRCm38)	missense	possibly damaging	0.66
R2872:Rapgef6	UTSW	11	54,661,175 (GRCm38)	missense	probably damaging	1.00
R2872:Rapgef6	UTSW	11	54,661,175 (GRCm38)	missense	probably damaging	1.00
R3744:Rapgef6	UTSW	11	54,625,934 (GRCm38)	missense	probably benign	0.40
R3848:Rapgef6	UTSW	11	54,691,308 (GRCm38)	missense	probably damaging	0.97
R4823:Rapgef6	UTSW	11	54,694,500 (GRCm38)	missense	probably benign	0.08
R4859:Rapgef6	UTSW	11	54,636,163 (GRCm38)	missense	probably benign
R4906:Rapgef6	UTSW	11	54,552,836 (GRCm38)	missense	probably damaging	1.00
R4911:Rapgef6	UTSW	11	54,622,317 (GRCm38)	missense	probably damaging	0.97
R4937:Rapgef6	UTSW	11	54,657,317 (GRCm38)	missense	probably damaging	1.00
R5033:Rapgef6	UTSW	11	54,691,381 (GRCm38)	missense	possibly damaging	0.92
R5249:Rapgef6	UTSW	11	54,523,117 (GRCm38)	missense	probably benign	0.19
R5304:Rapgef6	UTSW	11	54,657,374 (GRCm38)	missense	probably benign	0.01
R5656:Rapgef6	UTSW	11	54,636,136 (GRCm38)	missense	possibly damaging	0.95
R5701:Rapgef6	UTSW	11	54,676,394 (GRCm38)	missense	possibly damaging	0.76
R5758:Rapgef6	UTSW	11	54,668,644 (GRCm38)	missense	probably damaging	1.00
R5973:Rapgef6	UTSW	11	54,639,783 (GRCm38)	missense	probably damaging	1.00
R6177:Rapgef6	UTSW	11	54,620,016 (GRCm38)	missense	probably damaging	1.00
R6268:Rapgef6	UTSW	11	54,649,247 (GRCm38)	missense	probably damaging	1.00
R6287:Rapgef6	UTSW	11	54,626,338 (GRCm38)	splice site	probably null
R6293:Rapgef6	UTSW	11	54,634,781 (GRCm38)	missense	probably damaging	1.00
R6471:Rapgef6	UTSW	11	54,691,737 (GRCm38)	missense	probably damaging	0.99
R6863:Rapgef6	UTSW	11	54,546,380 (GRCm38)	missense	probably benign	0.00
R6950:Rapgef6	UTSW	11	54,676,380 (GRCm38)	missense	probably benign	0.09
R7144:Rapgef6	UTSW	11	54,657,365 (GRCm38)	missense	possibly damaging	0.78
R7171:Rapgef6	UTSW	11	54,676,363 (GRCm38)	missense	possibly damaging	0.94
R7199:Rapgef6	UTSW	11	54,546,426 (GRCm38)	missense	probably benign	0.00
R7291:Rapgef6	UTSW	11	54,691,239 (GRCm38)	missense	probably benign	0.05
R7436:Rapgef6	UTSW	11	54,610,921 (GRCm38)	critical splice donor site	probably null
R7498:Rapgef6	UTSW	11	54,620,004 (GRCm38)	missense	probably damaging	1.00
R7506:Rapgef6	UTSW	11	54,636,171 (GRCm38)	missense	probably benign	0.00
R7527:Rapgef6	UTSW	11	54,634,961 (GRCm38)	missense	unknown
R7646:Rapgef6	UTSW	11	54,625,954 (GRCm38)	missense	probably benign	0.00
R7655:Rapgef6	UTSW	11	54,694,453 (GRCm38)	missense	probably benign	0.10
R7656:Rapgef6	UTSW	11	54,694,453 (GRCm38)	missense	probably benign	0.10
R7687:Rapgef6	UTSW	11	54,661,075 (GRCm38)	missense	possibly damaging	0.93
R7768:Rapgef6	UTSW	11	54,626,588 (GRCm38)	missense	probably damaging	1.00
R7788:Rapgef6	UTSW	11	54,694,399 (GRCm38)	missense	probably damaging	1.00
R7890:Rapgef6	UTSW	11	54,626,723 (GRCm38)	missense	probably damaging	1.00
R8113:Rapgef6	UTSW	11	54,625,958 (GRCm38)	missense	probably benign	0.03
R8337:Rapgef6	UTSW	11	54,631,301 (GRCm38)	nonsense	probably null
R8393:Rapgef6	UTSW	11	54,687,661 (GRCm38)	missense	probably benign
R8465:Rapgef6	UTSW	11	54,691,482 (GRCm38)	missense	probably benign	0.00
R8492:Rapgef6	UTSW	11	54,690,237 (GRCm38)	missense	probably damaging	0.99
R8791:Rapgef6	UTSW	11	54,568,469 (GRCm38)	missense	probably benign	0.15
R8866:Rapgef6	UTSW	11	54,552,874 (GRCm38)	critical splice donor site	probably null
R8917:Rapgef6	UTSW	11	54,691,566 (GRCm38)	nonsense	probably null
R8921:Rapgef6	UTSW	11	54,679,239 (GRCm38)	missense	probably benign	0.09
R9031:Rapgef6	UTSW	11	54,687,841 (GRCm38)	missense	probably benign	0.00
R9093:Rapgef6	UTSW	11	54,597,086 (GRCm38)	nonsense	probably null
R9354:Rapgef6	UTSW	11	54,619,923 (GRCm38)	missense	possibly damaging	0.66
R9514:Rapgef6	UTSW	11	54,552,858 (GRCm38)	missense	probably benign	0.14
R9516:Rapgef6	UTSW	11	54,691,343 (GRCm38)	missense	probably damaging	1.00
R9739:Rapgef6	UTSW	11	54,622,363 (GRCm38)	missense	probably benign	0.03
R9789:Rapgef6	UTSW	11	54,649,271 (GRCm38)	missense	probably benign	0.03

Posted On

2013-01-08