Mutagenetix > Incidental Mutation

Incidental Mutation 'R8791:Rapgef6'

670953

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

068609-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R8791 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

54413673-54590111 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 54459295 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glutamic Acid at position 156 (D156E)

Ref Sequence

ENSEMBL: ENSMUSP00000104523 (fasta)

Gene Model

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

AlphaFold

Q5NCJ1

Predicted Effect

possibly damaging
Transcript: ENSMUST00000101206
AA Change: D156E

PolyPhen 2 Score 0.890 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000098766
Gene: ENSMUSG00000037533
AA Change: D156E

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: D156E

PolyPhen 2 Score 0.890 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000099804
Gene: ENSMUSG00000037533
AA Change: D156E

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

probably benign
Transcript: ENSMUST00000108895
AA Change: D156E

PolyPhen 2 Score 0.147 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000104523
Gene: ENSMUSG00000037533
AA Change: D156E

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

probably benign
Transcript: ENSMUST00000207429
AA Change: D156E

PolyPhen 2 Score 0.028 (Sensitivity: 0.95; Specificity: 0.81)

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.7%
20x: 99.1%

Validation Efficiency

100% (47/47)

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: 47 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4931422A03Rik	G	T	2: 103,823,022 (GRCm39)	T87K	possibly damaging	Het
Adar	G	A	3: 89,643,445 (GRCm39)	R442Q	probably benign	Het
Agtr1b	T	A	3: 20,370,280 (GRCm39)	S109C	probably damaging	Het
Akr1c6	T	A	13: 4,499,373 (GRCm39)	Y248N	probably benign	Het
Alpk2	A	T	18: 65,438,597 (GRCm39)	V932E	probably benign	Het
Apba3	T	A	10: 81,105,104 (GRCm39)	S126T	probably benign	Het
Brca2	T	A	5: 150,466,061 (GRCm39)	S1942T	possibly damaging	Het
Ccdc149	C	T	5: 52,596,552 (GRCm39)	C20Y	probably damaging	Het
Cd63	C	A	10: 128,748,071 (GRCm39)	N156K	probably benign	Het
Clvs1	A	G	4: 9,429,807 (GRCm39)	E270G	probably damaging	Het
Cplane1	A	G	15: 8,216,744 (GRCm39)	Y654C	probably damaging	Het
Dgki	A	T	6: 36,996,875 (GRCm39)	D574E	probably damaging	Het
Esrrb	A	G	12: 86,517,056 (GRCm39)	S63G	probably damaging	Het
Exoc1	C	T	5: 76,683,412 (GRCm39)	R46C	probably damaging	Het
Fcgr4	C	A	1: 170,847,477 (GRCm39)	A25D	probably damaging	Het
Fgf4	T	C	7: 144,415,408 (GRCm39)	V56A	probably benign	Het
Gfpt2	A	G	11: 49,714,043 (GRCm39)	I267V	probably benign	Het
Gm20939	A	C	17: 95,184,648 (GRCm39)	H432P	probably damaging	Het
Gpr179	A	T	11: 97,242,739 (GRCm39)	L35Q	probably damaging	Het
Idh1	CA	CAA	1: 65,204,347 (GRCm39)		probably null	Het
Ildr1	T	C	16: 36,528,762 (GRCm39)	I69T	probably damaging	Het
Lrfn1	A	G	7: 28,159,344 (GRCm39)	D421G	probably benign	Het
Mmp15	C	T	8: 96,096,288 (GRCm39)	Q360*	probably null	Het
Nfatc2	T	C	2: 168,378,214 (GRCm39)	K484E	probably damaging	Het
Nkpd1	G	C	7: 19,258,095 (GRCm39)	V625L	probably benign	Het
Nlrp4a	C	A	7: 26,143,561 (GRCm39)		probably benign	Het
Nme9	T	A	9: 99,350,301 (GRCm39)	I178N	probably damaging	Het
Nrp2	C	T	1: 62,788,356 (GRCm39)	T352I	probably damaging	Het
Ntrk1	T	C	3: 87,686,990 (GRCm39)	I723V	probably damaging	Het
Or5p50	C	T	7: 107,422,557 (GRCm39)	V40M	possibly damaging	Het
Pias3	C	A	3: 96,612,201 (GRCm39)	Q553K	probably benign	Het
Pnp2	T	G	14: 51,200,873 (GRCm39)	H119Q	probably benign	Het
Rint1	T	C	5: 24,005,594 (GRCm39)	V92A	probably damaging	Het
Rnf148	A	T	6: 23,654,993 (GRCm39)	M1K	probably null	Het
Rnh1	C	T	7: 140,742,346 (GRCm39)	R404H	probably benign	Het
Slc4a8	T	C	15: 100,705,134 (GRCm39)	V832A	possibly damaging	Het
Snx31	A	T	15: 36,537,678 (GRCm39)	C167S	probably benign	Het
Spart	A	G	3: 55,029,100 (GRCm39)	D297G	probably benign	Het
Spata13	C	T	14: 60,929,275 (GRCm39)	R278C	probably damaging	Het
Tmc1	T	C	19: 20,767,209 (GRCm39)	T716A	probably benign	Het
Tpi1	A	G	6: 124,789,483 (GRCm39)	V164A	probably damaging	Het
Trim17	A	G	11: 58,862,002 (GRCm39)	S345G	probably benign	Het
Vmn1r199	T	A	13: 22,567,687 (GRCm39)	L327Q	probably damaging	Het
Washc4	C	T	10: 83,386,748 (GRCm39)	T124I	probably benign	Het
Wdr76	C	T	2: 121,357,484 (GRCm39)	T180I	probably benign	Het
Zcchc8	T	C	5: 123,845,362 (GRCm39)	N333D	probably benign	Het
Zfp516	T	C	18: 82,975,460 (GRCm39)	S553P	probably damaging	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
R5701:Rapgef6	UTSW	11	54,567,220 (GRCm39)	missense	possibly damaging	0.76
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
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'- GACTTCATAGACTGTCTGAAAGATG -3'
(R):5'- AGTCGACTGCCTGAGTTCTC -3'

Sequencing Primer
(F):5'- CTGTCTGAAAGATGGAAAAACTGG -3'
(R):5'- TCCTAATTCAGTCACTACAAAGGC -3'

Posted On

2021-04-30