Mutagenetix > Incidental Mutation

Incidental Mutation 'R8117:Rapgef3'

631302

Institutional Source

Beutler Lab

Gene Symbol

Rapgef3

Ensembl Gene

ENSMUSG00000022469

Gene Name

Rap guanine nucleotide exchange factor (GEF) 3

Synonyms

2310016P22Rik, 9330170P05Rik, Epac1

MMRRC Submission

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.197) question?

Stock #

R8117 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

97744770-97767972 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 97750866 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glutamic Acid at position 619 (D619E)

Ref Sequence

ENSEMBL: ENSMUSP00000116426 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000126854] [ENSMUST00000128775] [ENSMUST00000129223] [ENSMUST00000134885] [ENSMUST00000175894] [ENSMUST00000177352]

AlphaFold

Q8VCC8

Predicted Effect

probably benign
Transcript: ENSMUST00000126854
AA Change: D619E

PolyPhen 2 Score 0.014 (Sensitivity: 0.96; Specificity: 0.79)

SMART Domains

Protein: ENSMUSP00000116426
Gene: ENSMUSG00000022469
AA Change: D619E

Domain	Start	End	E-Value	Type
DEP	111	186	2.05e-25	SMART
low complexity region	197	208	N/A	INTRINSIC
low complexity region	230	241	N/A	INTRINSIC
cNMP	245	364	2.53e-12	SMART
RasGEFN	383	514	7.04e-10	SMART
Blast:RasGEF	547	644	6e-45	BLAST
RasGEF	661	926	7.98e-95	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000128775
AA Change: D619E

PolyPhen 2 Score 0.008 (Sensitivity: 0.96; Specificity: 0.76)

SMART Domains

Protein: ENSMUSP00000120126
Gene: ENSMUSG00000022469
AA Change: D619E

Domain	Start	End	E-Value	Type
DEP	111	186	2.05e-25	SMART
low complexity region	197	208	N/A	INTRINSIC
low complexity region	230	241	N/A	INTRINSIC
cNMP	245	364	2.53e-12	SMART
RasGEFN	383	514	7.04e-10	SMART
Blast:RasGEF	547	644	7e-45	BLAST
RasGEF	661	909	5.53e-80	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000129223
AA Change: D619E

PolyPhen 2 Score 0.015 (Sensitivity: 0.96; Specificity: 0.79)

SMART Domains

Protein: ENSMUSP00000118148
Gene: ENSMUSG00000022469
AA Change: D619E

Domain	Start	End	E-Value	Type
DEP	111	186	2.05e-25	SMART
low complexity region	197	208	N/A	INTRINSIC
low complexity region	230	241	N/A	INTRINSIC
cNMP	245	364	2.53e-12	SMART
RasGEFN	383	514	7.04e-10	SMART
Blast:RasGEF	547	644	6e-45	BLAST
RasGEF	661	918	2.11e-85	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000134885

SMART Domains

Protein: ENSMUSP00000135317
Gene: ENSMUSG00000022469

Domain	Start	End	E-Value	Type
RasGEF	1	216	2.91e-56	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000175894

Predicted Effect

probably benign
Transcript: ENSMUST00000177352
AA Change: D577E

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000135238
Gene: ENSMUSG00000022469
AA Change: D577E

Domain	Start	End	E-Value	Type
DEP	69	144	2.05e-25	SMART
low complexity region	155	166	N/A	INTRINSIC
low complexity region	188	199	N/A	INTRINSIC
cNMP	203	322	2.53e-12	SMART
RasGEFN	341	472	7.04e-10	SMART
Blast:RasGEF	505	602	3e-45	BLAST
RasGEF	619	884	7.98e-95	SMART

Coding Region Coverage

1x: 99.8%
3x: 99.5%
10x: 98.5%
20x: 94.4%

Validation Efficiency

99% (73/74)

MGI Phenotype

PHENOTYPE: Mice homozygous for a knock-out allele exhibit decreased induced neuron apoptosis. Mice homozygous for a different allele exhibit impaired glucose homeostasis with decreased insulin secretion, increased susceptibility to diet-induced obesity and streptozotocin-induced insulitis and hyperglycemia. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 71 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2010315B03Rik	T	C	9: 124,295,448	T14A		Het
2610008E11Rik	T	C	10: 79,094,455	N42D	probably benign	Het
Ankrd54	T	A	15: 79,055,441	M183L		Het
Apob	G	A	12: 8,006,435	G1639D	probably damaging	Het
B3gat2	A	G	1: 23,844,980	T283A	probably benign	Het
Bmpr2	T	G	1: 59,847,093	S296R	probably damaging	Het
Cand1	G	A	10: 119,206,816	T1123I	probably damaging	Het
Cc2d2a	T	C	5: 43,712,439	F943S	probably damaging	Het
Ccdc40	T	C	11: 119,253,385	I912T	probably benign	Het
Cdkn2d	G	A	9: 21,289,151	S108L	probably benign	Het
Cep295	G	A	9: 15,334,364	T932I	probably damaging	Het
Cntn5	A	G	9: 9,673,950	S716P	probably benign	Het
Col18a1	T	C	10: 77,059,974	E903G	probably benign	Het
Ctrc	T	A	4: 141,838,661	I229F	probably damaging	Het
Cyb561d2	C	T	9: 107,541,572	A18T	probably benign	Het
Dnajb4	T	A	3: 152,193,452	K46*	probably null	Het
Dsc2	C	T	18: 20,032,274	G881R	possibly damaging	Het
Dsg1c	C	T	18: 20,276,959	H495Y	probably benign	Het
Eif2b3	A	G	4: 117,022,217	D18G	probably damaging	Het
Enam	A	T	5: 88,503,526	I965L	probably benign	Het
Fhod3	T	A	18: 25,115,853	I1363K	probably damaging	Het
Fras1	A	G	5: 96,707,386	Y1918C	probably damaging	Het
Fsip2	T	A	2: 82,992,952	I6343N	possibly damaging	Het
Gm15922	G	A	7: 3,737,076	T340I	probably damaging	Het
Gm996	A	G	2: 25,579,234	F222L	probably benign	Het
Gpr45	G	C	1: 43,033,315	V373L	probably damaging	Het
Hdac2	G	T	10: 36,997,970	Q365H	probably damaging	Het
Hspa12b	A	G	2: 131,138,469	T103A	possibly damaging	Het
Ifrd1	A	T	12: 40,212,351	S287T	probably benign	Het
Igkv6-15	G	A	6: 70,406,638	P60S	possibly damaging	Het
Ippk	C	T	13: 49,446,342	P226S		Het
Kctd19	T	A	8: 105,395,437	D109V	unknown	Het
Matn4	G	A	2: 164,392,931	S540L	probably damaging	Het
Matn4	T	C	2: 164,399,762	K248E	probably benign	Het
Muc16	G	A	9: 18,508,910	Q97*	probably null	Het
Mup18	A	G	4: 61,674,001	C9R	unknown	Het
Myh1	A	G	11: 67,222,205	K1845R	probably damaging	Het
Mysm1	G	A	4: 94,960,390	R469*	probably null	Het
Naip1	T	C	13: 100,427,001	D552G	possibly damaging	Het
Nrcam	A	G	12: 44,571,588	D787G	probably benign	Het
Nrcam	G	A	12: 44,598,582	V1256I	probably damaging	Het
Obscn	G	T	11: 59,042,154	H4799N	possibly damaging	Het
Olfr1192-ps1	A	G	2: 88,652,385	K78E	probably damaging	Het
Olfr1366	T	C	13: 21,537,952	K3E	probably benign	Het
Olfr670	T	C	7: 104,960,149	I194M	probably damaging	Het
Olfr837	A	G	9: 19,137,057	I21M	probably benign	Het
Pcdhgb5	T	C	18: 37,733,249	F699S	probably damaging	Het
Phtf2	T	C	5: 20,802,040	E175G	probably benign	Het
Ppp2r5c	A	G	12: 110,551,085	H218R	possibly damaging	Het
Ptgs2	A	G	1: 150,104,034	R297G	probably damaging	Het
Ric1	G	A	19: 29,574,791	V321I	probably benign	Het
Ripor1	T	C	8: 105,617,473	V413A	probably damaging	Het
Rsf1	G	T	7: 97,639,257		probably null	Het
Sccpdh	A	G	1: 179,676,452	D122G	probably damaging	Het
Sec16a	A	T	2: 26,441,429	H191Q	probably benign	Het
Slco1a5	G	T	6: 142,262,692	N124K	probably damaging	Het
Snrnp200	A	G	2: 127,229,131	T1111A	probably benign	Het
Stard9	G	A	2: 120,704,430	G3723S	probably benign	Het
Tanc2	T	A	11: 105,835,162	V384E	probably damaging	Het
Tbrg1	A	G	9: 37,657,000	F49L	possibly damaging	Het
Tecta	A	G	9: 42,377,631	F546S	probably damaging	Het
Tmem132c	A	G	5: 127,360,112	R222G	probably benign	Het
Trub2	C	T	2: 29,778,727		probably null	Het
Tti1	G	T	2: 158,007,498	P607Q	probably damaging	Het
Vmn1r62	T	A	7: 5,675,727	F136I	possibly damaging	Het
Vmn2r111	T	A	17: 22,571,488	H179L	probably benign	Het
Wdfy4	A	T	14: 32,977,106	C2703*	probably null	Het
Wdfy4	G	A	14: 33,104,115	P1193L		Het
Wipf3	A	G	6: 54,483,831	K88R	probably benign	Het
Zfp641	C	T	15: 98,288,975	G256R	probably damaging	Het
Zfp993	T	A	4: 146,657,515	C99S	probably benign	Het

Other mutations in Rapgef3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01314:Rapgef3	APN	15	97748223	missense	probably damaging	1.00
IGL01339:Rapgef3	APN	15	97758059	missense	probably damaging	1.00
IGL01670:Rapgef3	APN	15	97749662	missense	probably benign	0.15
IGL01902:Rapgef3	APN	15	97750300	missense	probably benign	0.32
IGL02137:Rapgef3	APN	15	97750144	missense	probably benign	0.08
IGL02419:Rapgef3	APN	15	97750290	missense	probably benign	0.33
IGL02427:Rapgef3	APN	15	97747136	splice site	probably null
IGL02648:Rapgef3	APN	15	97758392	missense	probably damaging	1.00
IGL02834:Rapgef3	APN	15	97748265	missense	probably damaging	0.98
IGL03389:Rapgef3	APN	15	97749516	missense	probably damaging	1.00
IGL03055:Rapgef3	UTSW	15	97749489	splice site	probably benign
R0394:Rapgef3	UTSW	15	97757819	intron	probably benign
R0538:Rapgef3	UTSW	15	97757817	intron	probably benign
R0744:Rapgef3	UTSW	15	97761585	splice site	probably benign
R1288:Rapgef3	UTSW	15	97759342	missense	probably benign	0.31
R1512:Rapgef3	UTSW	15	97757501	missense	probably benign	0.24
R1676:Rapgef3	UTSW	15	97761182	missense	probably benign	0.35
R1745:Rapgef3	UTSW	15	97750178	missense	probably benign	0.22
R1928:Rapgef3	UTSW	15	97750033	missense	probably damaging	1.00
R2063:Rapgef3	UTSW	15	97766961	missense	probably damaging	1.00
R2067:Rapgef3	UTSW	15	97766961	missense	probably damaging	1.00
R2092:Rapgef3	UTSW	15	97760723	missense	probably damaging	1.00
R4358:Rapgef3	UTSW	15	97748648	missense	probably benign	0.05
R4624:Rapgef3	UTSW	15	97758929	missense	probably damaging	1.00
R4627:Rapgef3	UTSW	15	97758929	missense	probably damaging	1.00
R4727:Rapgef3	UTSW	15	97760600	missense	probably damaging	1.00
R4812:Rapgef3	UTSW	15	97753803	missense	probably benign	0.21
R4928:Rapgef3	UTSW	15	97757375	missense	probably damaging	1.00
R5161:Rapgef3	UTSW	15	97757725	missense	probably damaging	1.00
R5442:Rapgef3	UTSW	15	97758861	missense	probably damaging	0.99
R5652:Rapgef3	UTSW	15	97758437	missense	probably benign	0.00
R5837:Rapgef3	UTSW	15	97757342	splice site	probably benign
R6056:Rapgef3	UTSW	15	97758861	missense	probably damaging	0.99
R6167:Rapgef3	UTSW	15	97767411	unclassified	probably benign
R6694:Rapgef3	UTSW	15	97759984	missense	probably benign	0.03
R7039:Rapgef3	UTSW	15	97761568	missense	probably benign	0.01
R7154:Rapgef3	UTSW	15	97753877	missense	probably benign
R7380:Rapgef3	UTSW	15	97766791	missense	probably benign	0.00
R7655:Rapgef3	UTSW	15	97761209	missense	probably damaging	1.00
R7656:Rapgef3	UTSW	15	97761209	missense	probably damaging	1.00
R7754:Rapgef3	UTSW	15	97757746	missense	probably damaging	1.00
R7849:Rapgef3	UTSW	15	97758390	critical splice donor site	probably null
R8061:Rapgef3	UTSW	15	97761520	missense	probably benign
R8179:Rapgef3	UTSW	15	97760740	missense	probably benign	0.06
R8819:Rapgef3	UTSW	15	97748657	missense	probably benign	0.39
R8820:Rapgef3	UTSW	15	97748657	missense	probably benign	0.39
R8824:Rapgef3	UTSW	15	97766908	missense	probably benign	0.39
R9779:Rapgef3	UTSW	15	97745598	missense	probably damaging	0.99
R9781:Rapgef3	UTSW	15	97745598	missense	probably damaging	0.99
R9782:Rapgef3	UTSW	15	97745598	missense	probably damaging	0.99
RF024:Rapgef3	UTSW	15	97760740	missense	probably benign	0.06
X0011:Rapgef3	UTSW	15	97761473	critical splice donor site	probably null

Predicted Primers

PCR Primer
(F):5'- GCAAGCACGTTCCTCCATTC -3'
(R):5'- CTCGTCCATAAGTGACTAGTCTCAG -3'

Sequencing Primer
(F):5'- AGCACGTTCCTCCATTCTCTGTG -3'
(R):5'- CATAAGTGACTAGTCTCAGGTGCTG -3'

Posted On

2020-06-30