Incidental Mutation 'RF005:Rapgef1'
| ID |
628432 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Rapgef1
|
| Ensembl Gene |
ENSMUSG00000039844 |
| Gene Name |
Rap guanine nucleotide exchange factor (GEF) 1 |
| Synonyms |
C3G, Grf2, 4932418O06Rik |
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
RF005 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
2 |
| Chromosomal Location |
29509732-29630376 bp(+) (GRCm39) |
| Type of Mutation |
splice site |
| DNA Base Change (assembly) |
C to A
at 29597207 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000091146]
[ENSMUST00000095087]
[ENSMUST00000102872]
[ENSMUST00000147755]
|
| AlphaFold |
Q3UHC1 |
| Predicted Effect |
probably null
Transcript: ENSMUST00000091146
|
| SMART Domains |
Protein: ENSMUSP00000088680
Gene: ENSMUSG00000039844
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
191 |
206 |
N/A |
INTRINSIC |
|
low complexity region
|
309 |
324 |
N/A |
INTRINSIC |
|
low complexity region
|
468 |
478 |
N/A |
INTRINSIC |
|
low complexity region
|
510 |
521 |
N/A |
INTRINSIC |
|
low complexity region
|
592 |
603 |
N/A |
INTRINSIC |
|
low complexity region
|
664 |
682 |
N/A |
INTRINSIC |
|
low complexity region
|
689 |
700 |
N/A |
INTRINSIC |
|
low complexity region
|
727 |
741 |
N/A |
INTRINSIC |
|
RasGEFN
|
828 |
970 |
8.04e-37 |
SMART |
|
RasGEF
|
977 |
1206 |
5.85e-102 |
SMART |
|
| Predicted Effect |
probably null
Transcript: ENSMUST00000095087
|
| SMART Domains |
Protein: ENSMUSP00000092703
Gene: ENSMUSG00000039844
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
229 |
244 |
N/A |
INTRINSIC |
|
low complexity region
|
347 |
362 |
N/A |
INTRINSIC |
|
low complexity region
|
506 |
516 |
N/A |
INTRINSIC |
|
low complexity region
|
548 |
559 |
N/A |
INTRINSIC |
|
low complexity region
|
630 |
641 |
N/A |
INTRINSIC |
|
low complexity region
|
702 |
720 |
N/A |
INTRINSIC |
|
low complexity region
|
727 |
738 |
N/A |
INTRINSIC |
|
RasGEFN
|
834 |
976 |
8.04e-37 |
SMART |
|
RasGEF
|
983 |
1212 |
5.85e-102 |
SMART |
|
| Predicted Effect |
probably null
Transcript: ENSMUST00000102872
|
| SMART Domains |
Protein: ENSMUSP00000099936
Gene: ENSMUSG00000039844
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
229 |
244 |
N/A |
INTRINSIC |
|
low complexity region
|
347 |
362 |
N/A |
INTRINSIC |
|
low complexity region
|
506 |
516 |
N/A |
INTRINSIC |
|
low complexity region
|
548 |
559 |
N/A |
INTRINSIC |
|
RasGEFN
|
696 |
838 |
8.04e-37 |
SMART |
|
RasGEF
|
845 |
1074 |
5.85e-102 |
SMART |
|
| Predicted Effect |
probably null
Transcript: ENSMUST00000147488
|
| SMART Domains |
Protein: ENSMUSP00000117631
Gene: ENSMUSG00000039844
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
12 |
22 |
N/A |
INTRINSIC |
|
low complexity region
|
54 |
65 |
N/A |
INTRINSIC |
|
low complexity region
|
135 |
146 |
N/A |
INTRINSIC |
|
RasGEFN
|
253 |
395 |
8.04e-37 |
SMART |
|
RasGEF
|
402 |
631 |
5.85e-102 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000147755
|
| SMART Domains |
Protein: ENSMUSP00000121615
Gene: ENSMUSG00000039844
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
191 |
206 |
N/A |
INTRINSIC |
|
low complexity region
|
309 |
324 |
N/A |
INTRINSIC |
|
low complexity region
|
468 |
478 |
N/A |
INTRINSIC |
|
low complexity region
|
510 |
521 |
N/A |
INTRINSIC |
|
low complexity region
|
591 |
602 |
N/A |
INTRINSIC |
|
low complexity region
|
663 |
681 |
N/A |
INTRINSIC |
|
| Meta Mutation Damage Score |
0.9755 |
| Coding Region Coverage |
- 1x: 99.8%
- 3x: 99.7%
- 10x: 99.4%
- 20x: 98.6%
|
| Validation Efficiency |
94% (65/69) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a human guanine nucleotide exchange factor. It transduces signals from CRK by binding the SH3 domain of CRK, and activating several members of the Ras family of GTPases. This signaling cascade that may be involved in apoptosis, integrin-mediated signal transduction, and cell transformation. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some variants has not been determined. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for a null allele die before E7.5. Mice homozygous for a hypomorphic gene trap allele show embryonic lethality during organogenesis, altered neuroepithelium morphology, vascular maturation defects, hemorrhage, and reduced cell migration and adhesion. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 61 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 5430401F13Rik |
AGAAAGGAAAAGGTGGCCAG |
AGAAAGGAAAAGGTGGCCAGCAAAAACAGAAAGGAAAAGGTGGCCAG |
6: 131,529,847 (GRCm39) |
|
probably benign |
Het |
| A030005L19Rik |
CTGCTG |
CTGCTGTGGATGCTG |
1: 82,891,306 (GRCm39) |
|
probably benign |
Het |
| Abca1 |
G |
T |
4: 53,049,125 (GRCm39) |
T1651N |
probably damaging |
Het |
| Adamtsl3 |
A |
G |
7: 82,261,603 (GRCm39) |
T40A |
|
Het |
| Adgra3 |
A |
T |
5: 50,170,729 (GRCm39) |
|
probably null |
Het |
| Apcs |
A |
T |
1: 172,721,809 (GRCm39) |
M179K |
probably damaging |
Het |
| Baiap2 |
G |
A |
11: 119,887,355 (GRCm39) |
E217K |
possibly damaging |
Het |
| Bltp3a |
A |
T |
17: 28,104,505 (GRCm39) |
D517V |
probably damaging |
Het |
| Ccdc69 |
A |
G |
11: 54,951,349 (GRCm39) |
L24P |
probably damaging |
Het |
| Cdh16 |
T |
G |
8: 105,343,684 (GRCm39) |
N604T |
probably damaging |
Het |
| Cfb |
C |
T |
17: 35,077,022 (GRCm39) |
V538I |
possibly damaging |
Het |
| Col6a3 |
A |
G |
1: 90,738,984 (GRCm39) |
S1022P |
probably benign |
Het |
| Cpeb1 |
A |
G |
7: 81,011,554 (GRCm39) |
L129S |
possibly damaging |
Het |
| Crybg1 |
A |
G |
10: 43,880,741 (GRCm39) |
V149A |
probably benign |
Het |
| Cyp4f16 |
C |
A |
17: 32,764,169 (GRCm39) |
|
probably null |
Het |
| Dlg5 |
G |
A |
14: 24,208,561 (GRCm39) |
Q882* |
probably null |
Het |
| Fsip2 |
T |
A |
2: 82,822,876 (GRCm39) |
I6203K |
probably benign |
Het |
| Gabre |
CCGGCT |
CCGGCTACGGCT |
X: 71,313,651 (GRCm39) |
|
probably null |
Het |
| Gprc5d |
A |
T |
6: 135,093,517 (GRCm39) |
L130Q |
probably damaging |
Het |
| H13 |
G |
A |
2: 152,511,589 (GRCm39) |
E30K |
probably damaging |
Het |
| Hmcn1 |
T |
A |
1: 150,510,897 (GRCm39) |
K3609* |
probably null |
Het |
| Hsdl2 |
GCTGCAG |
GCTGCAGCAGCAGCCACATCTGCAG |
4: 59,610,652 (GRCm39) |
|
probably benign |
Het |
| Kl |
A |
C |
5: 150,876,885 (GRCm39) |
Y235S |
probably benign |
Het |
| Map6d1 |
G |
A |
16: 20,059,750 (GRCm39) |
T105I |
probably benign |
Het |
| Mast4 |
GGTGGTGGTGG |
GGTGGTGGTGGTGGTGG |
13: 102,872,815 (GRCm39) |
|
probably benign |
Het |
| Mbd1 |
TGTCTGCATCTGCGTCTTCGTCTGCATCTGCATCTGCGTCTTCGTCTGCATCTGCATCTGC |
TATCTGCATCTGCGTCTTCGTCTGCATCTGCATCTGC |
18: 74,406,644 (GRCm39) |
|
probably benign |
Het |
| Mms22l |
A |
G |
4: 24,517,207 (GRCm39) |
I363V |
probably benign |
Het |
| Myo7a |
T |
C |
7: 97,742,824 (GRCm39) |
I391V |
probably benign |
Het |
| Nab2 |
A |
T |
10: 127,500,233 (GRCm39) |
D286E |
probably benign |
Het |
| Nrxn1 |
G |
A |
17: 90,670,304 (GRCm39) |
R1144C |
probably damaging |
Het |
| Or51q1 |
A |
G |
7: 103,628,768 (GRCm39) |
D123G |
probably damaging |
Het |
| Or52j3 |
T |
C |
7: 102,835,898 (GRCm39) |
I30T |
possibly damaging |
Het |
| Or5al5 |
T |
C |
2: 85,961,414 (GRCm39) |
M198V |
probably benign |
Het |
| Pan2 |
G |
A |
10: 128,151,404 (GRCm39) |
E842K |
probably benign |
Het |
| Pate11 |
T |
C |
9: 36,386,970 (GRCm39) |
S13P |
possibly damaging |
Het |
| Polr1has |
CACCACCACCACCACCACCAC |
CACCACCACCACCACCACCACAACCACCACCACCACCACCAC |
17: 37,275,940 (GRCm39) |
|
probably benign |
Het |
| Prex2 |
A |
C |
1: 11,255,390 (GRCm39) |
D1145A |
possibly damaging |
Het |
| Prop1 |
A |
C |
11: 50,841,957 (GRCm39) |
Y150D |
possibly damaging |
Het |
| Prp2 |
AGGCCCACAGCAGCGACCCCCTCAAGGCCCACCACCACCAGGTGGCCCACAGCCGAGACCCCCTCAAGGCCCACCACC |
AGGCCCACAGCCGAGACCCCCTCAAGGCCCACCACC |
6: 132,577,464 (GRCm39) |
|
probably benign |
Het |
| Psip1 |
T |
C |
4: 83,378,735 (GRCm39) |
I353M |
probably damaging |
Het |
| Rgl1 |
G |
A |
1: 152,397,114 (GRCm39) |
S684L |
probably benign |
Het |
| Sbf2 |
T |
A |
7: 109,916,215 (GRCm39) |
D1552V |
probably damaging |
Het |
| Scpppq1 |
A |
C |
5: 104,222,725 (GRCm39) |
|
probably null |
Het |
| Serpinh1 |
C |
T |
7: 98,995,410 (GRCm39) |
V391M |
probably damaging |
Het |
| Slc35e4 |
A |
T |
11: 3,857,960 (GRCm39) |
L215Q |
possibly damaging |
Het |
| Tbl3 |
TCTT |
TCTTCTT |
17: 24,921,515 (GRCm39) |
|
probably benign |
Het |
| Tex15 |
T |
A |
8: 34,066,705 (GRCm39) |
M2045K |
probably benign |
Het |
| Tmprss15 |
T |
C |
16: 78,750,689 (GRCm39) |
*1070W |
probably null |
Het |
| Trav15-2-dv6-2 |
GAA |
GAACAA |
14: 53,887,211 (GRCm39) |
|
probably benign |
Het |
| Trav15-2-dv6-2 |
GGGAG |
GGGAGGAG |
14: 53,887,207 (GRCm39) |
|
probably benign |
Het |
| Trav15-2-dv6-2 |
GGAG |
GGAGGAG |
14: 53,887,208 (GRCm39) |
|
probably benign |
Het |
| Trim33 |
GCCCCGGCCCCCG |
GCCCCG |
3: 103,187,528 (GRCm39) |
|
probably null |
Het |
| Triobp |
GACAA |
GACAACCCCAGGACTCCCTGTGCCCAACGGAACAA |
15: 78,851,261 (GRCm39) |
|
probably benign |
Het |
| Tub |
C |
A |
7: 108,621,846 (GRCm39) |
Q95K |
probably benign |
Het |
| Usp9y |
T |
A |
Y: 1,435,046 (GRCm39) |
Q261L |
probably benign |
Het |
| Utp20 |
A |
T |
10: 88,661,319 (GRCm39) |
D29E |
probably damaging |
Het |
| Vill |
G |
A |
9: 118,889,507 (GRCm39) |
V148M |
probably damaging |
Het |
| Vmn2r120 |
C |
T |
17: 57,828,991 (GRCm39) |
E535K |
possibly damaging |
Het |
| Zfp451 |
A |
T |
1: 33,815,873 (GRCm39) |
Y692* |
probably null |
Het |
| Zfp599 |
A |
C |
9: 22,165,180 (GRCm39) |
V65G |
probably benign |
Het |
| Zfp808 |
T |
C |
13: 62,319,113 (GRCm39) |
V114A |
probably benign |
Het |
|
| Other mutations in Rapgef1 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00156:Rapgef1
|
APN |
2 |
29,612,281 (GRCm39) |
missense |
probably benign |
|
|
IGL00917:Rapgef1
|
APN |
2 |
29,592,535 (GRCm39) |
missense |
probably benign |
0.00 |
|
IGL02618:Rapgef1
|
APN |
2 |
29,627,955 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02642:Rapgef1
|
APN |
2 |
29,590,872 (GRCm39) |
splice site |
probably benign |
|
|
IGL02974:Rapgef1
|
APN |
2 |
29,600,228 (GRCm39) |
missense |
possibly damaging |
0.64 |
|
R0034:Rapgef1
|
UTSW |
2 |
29,614,780 (GRCm39) |
splice site |
probably benign |
|
|
R0034:Rapgef1
|
UTSW |
2 |
29,614,780 (GRCm39) |
splice site |
probably benign |
|
|
R0241:Rapgef1
|
UTSW |
2 |
29,592,682 (GRCm39) |
missense |
possibly damaging |
0.53 |
|
R0241:Rapgef1
|
UTSW |
2 |
29,592,682 (GRCm39) |
missense |
possibly damaging |
0.53 |
|
R0279:Rapgef1
|
UTSW |
2 |
29,616,239 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0432:Rapgef1
|
UTSW |
2 |
29,569,828 (GRCm39) |
missense |
possibly damaging |
0.86 |
|
R1817:Rapgef1
|
UTSW |
2 |
29,576,268 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1837:Rapgef1
|
UTSW |
2 |
29,627,438 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1970:Rapgef1
|
UTSW |
2 |
29,623,723 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1980:Rapgef1
|
UTSW |
2 |
29,612,239 (GRCm39) |
missense |
probably benign |
|
|
R2076:Rapgef1
|
UTSW |
2 |
29,592,520 (GRCm39) |
missense |
probably benign |
0.00 |
|
R2363:Rapgef1
|
UTSW |
2 |
29,626,608 (GRCm39) |
missense |
possibly damaging |
0.63 |
|
R3016:Rapgef1
|
UTSW |
2 |
29,597,405 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R3053:Rapgef1
|
UTSW |
2 |
29,614,868 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R3777:Rapgef1
|
UTSW |
2 |
29,609,701 (GRCm39) |
missense |
possibly damaging |
0.67 |
|
R3980:Rapgef1
|
UTSW |
2 |
29,609,662 (GRCm39) |
missense |
probably benign |
0.33 |
|
R4491:Rapgef1
|
UTSW |
2 |
29,609,668 (GRCm39) |
missense |
possibly damaging |
0.93 |
|
R4524:Rapgef1
|
UTSW |
2 |
29,569,258 (GRCm39) |
missense |
probably benign |
0.00 |
|
R4732:Rapgef1
|
UTSW |
2 |
29,579,172 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4733:Rapgef1
|
UTSW |
2 |
29,579,172 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5391:Rapgef1
|
UTSW |
2 |
29,627,977 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5395:Rapgef1
|
UTSW |
2 |
29,627,977 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5611:Rapgef1
|
UTSW |
2 |
29,592,448 (GRCm39) |
missense |
probably damaging |
0.96 |
|
R6062:Rapgef1
|
UTSW |
2 |
29,590,744 (GRCm39) |
missense |
probably damaging |
0.96 |
|
R6145:Rapgef1
|
UTSW |
2 |
29,626,678 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6580:Rapgef1
|
UTSW |
2 |
29,620,621 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
R6892:Rapgef1
|
UTSW |
2 |
29,589,852 (GRCm39) |
critical splice donor site |
probably null |
|
|
R6897:Rapgef1
|
UTSW |
2 |
29,592,514 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6957:Rapgef1
|
UTSW |
2 |
29,623,710 (GRCm39) |
missense |
possibly damaging |
0.62 |
|
R7039:Rapgef1
|
UTSW |
2 |
29,616,226 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R7149:Rapgef1
|
UTSW |
2 |
29,610,712 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R7253:Rapgef1
|
UTSW |
2 |
29,589,733 (GRCm39) |
missense |
possibly damaging |
0.72 |
|
R7315:Rapgef1
|
UTSW |
2 |
29,624,504 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R7956:Rapgef1
|
UTSW |
2 |
29,589,027 (GRCm39) |
missense |
probably benign |
0.03 |
|
R8161:Rapgef1
|
UTSW |
2 |
29,569,210 (GRCm39) |
missense |
probably benign |
0.08 |
|
R8162:Rapgef1
|
UTSW |
2 |
29,626,011 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R8372:Rapgef1
|
UTSW |
2 |
29,600,243 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R8373:Rapgef1
|
UTSW |
2 |
29,600,243 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R8485:Rapgef1
|
UTSW |
2 |
29,600,186 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8838:Rapgef1
|
UTSW |
2 |
29,627,458 (GRCm39) |
missense |
possibly damaging |
0.77 |
|
R9484:Rapgef1
|
UTSW |
2 |
29,625,821 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
R9521:Rapgef1
|
UTSW |
2 |
29,624,291 (GRCm39) |
missense |
probably benign |
0.16 |
|
| Predicted Primers |
PCR Primer
(F):5'- GACAGTCATCACGTCCAGAG -3'
(R):5'- CAGATGGGGAACTGCTTACC -3'
Sequencing Primer
(F):5'- GAGCCCACCATGCACTG -3'
(R):5'- GCTTACCAGCTGCCGTTG -3'
|
| Posted On |
2020-04-07 |
Incidental Mutation