Incidental Mutation 'R5060:Rabgef1'
| ID |
386557 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Rabgef1
|
| Ensembl Gene |
ENSMUSG00000025340 |
| Gene Name |
RAB guanine nucleotide exchange factor (GEF) 1 |
| Synonyms |
Ras negative regulator Rabex-5 |
| MMRRC Submission |
042650-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.850)
|
| Stock # |
R5060 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
5 |
| Chromosomal Location |
130200644-130243178 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 130240844 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Tyrosine to Cysteine
at position 321
(Y321C)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000114103
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000026390]
[ENSMUST00000119027]
[ENSMUST00000119797]
[ENSMUST00000148264]
|
| AlphaFold |
Q9JM13 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000026390
AA Change: Y321C
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000026390
Gene: ENSMUSG00000025340
AA Change: Y321C
| Domain | Start | End | E-Value | Type |
|---|
|
ZnF_A20
|
16 |
40 |
1.5e-12 |
SMART |
|
low complexity region
|
56 |
80 |
N/A |
INTRINSIC |
|
low complexity region
|
82 |
106 |
N/A |
INTRINSIC |
|
VPS9
|
262 |
383 |
1.8e-29 |
SMART |
|
coiled coil region
|
411 |
445 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000119027
|
| SMART Domains |
Protein: ENSMUSP00000112537
Gene: ENSMUSG00000025340
| Domain | Start | End | E-Value | Type |
|---|
|
ZnF_A20
|
16 |
40 |
2.35e-10 |
SMART |
|
low complexity region
|
56 |
80 |
N/A |
INTRINSIC |
|
low complexity region
|
82 |
106 |
N/A |
INTRINSIC |
|
PDB:1TXU|A
|
132 |
221 |
7e-51 |
PDB |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000119542
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000119797
AA Change: Y321C
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000114103
Gene: ENSMUSG00000025340
AA Change: Y321C
| Domain | Start | End | E-Value | Type |
|---|
|
ZnF_A20
|
16 |
40 |
1.4e-12 |
SMART |
|
low complexity region
|
56 |
80 |
N/A |
INTRINSIC |
|
low complexity region
|
82 |
106 |
N/A |
INTRINSIC |
|
VPS9
|
262 |
383 |
1.8e-29 |
SMART |
|
coiled coil region
|
411 |
445 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000125937
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000143865
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000147493
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000202729
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000148264
|
| SMART Domains |
Protein: ENSMUSP00000119245
Gene: ENSMUSG00000025340
| Domain | Start | End | E-Value | Type |
|---|
|
ZnF_A20
|
16 |
40 |
2.35e-10 |
SMART |
|
low complexity region
|
56 |
80 |
N/A |
INTRINSIC |
|
low complexity region
|
82 |
106 |
N/A |
INTRINSIC |
|
PDB:1TXU|A
|
132 |
250 |
1e-72 |
PDB |
|
| Meta Mutation Damage Score |
0.6134 |
| Coding Region Coverage |
- 1x: 99.1%
- 3x: 98.4%
- 10x: 96.5%
- 20x: 92.9%
|
| Validation Efficiency |
98% (52/53) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] RABGEF1 forms a complex with rabaptin-5 (RABPT5; MIM 603616) that is required for endocytic membrane fusion, and it serves as a specific guanine nucleotide exchange factor (GEF) for RAB5 (RAB5A; MIM 179512) (Horiuchi et al., 1997 [PubMed 9323142]).[supplied by OMIM, Mar 2010]
PHENOTYPE: Nullizygous mutations can cause neonatal or postnatal lethality associated with severe skin inflammation, high mast cell numbers and serum levels of IgE and histamine, and enhanced mast cell degranulation and release of mediators and cytokines in response to high affinity IgE receptor aggregation. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 42 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| A530064D06Rik |
A |
T |
17: 48,474,107 (GRCm39) |
L17Q |
probably damaging |
Het |
| Abca6 |
A |
G |
11: 110,110,430 (GRCm39) |
V573A |
possibly damaging |
Het |
| Abcc9 |
A |
G |
6: 142,571,836 (GRCm39) |
|
probably benign |
Het |
| Actg1 |
A |
G |
11: 120,237,839 (GRCm39) |
S234P |
probably benign |
Het |
| Acvr2a |
A |
G |
2: 48,780,311 (GRCm39) |
D177G |
probably damaging |
Het |
| Adamts12 |
T |
C |
15: 11,300,054 (GRCm39) |
C914R |
probably damaging |
Het |
| Adprhl1 |
A |
G |
8: 13,298,621 (GRCm39) |
I103T |
possibly damaging |
Het |
| Als2cl |
C |
T |
9: 110,713,205 (GRCm39) |
L32F |
probably damaging |
Het |
| Ank2 |
T |
C |
3: 126,739,570 (GRCm39) |
|
probably benign |
Het |
| Ankrd52 |
T |
A |
10: 128,225,710 (GRCm39) |
S959R |
possibly damaging |
Het |
| Bnc2 |
C |
A |
4: 84,449,872 (GRCm39) |
A122S |
probably benign |
Het |
| Cert1 |
A |
T |
13: 96,739,663 (GRCm39) |
K226N |
probably benign |
Het |
| Cfap54 |
C |
T |
10: 92,875,013 (GRCm39) |
V443M |
probably damaging |
Het |
| Cilk1 |
C |
T |
9: 78,060,978 (GRCm39) |
T208I |
probably benign |
Het |
| Clca4b |
T |
A |
3: 144,617,267 (GRCm39) |
R794S |
probably damaging |
Het |
| Cyp2c65 |
T |
C |
19: 39,049,514 (GRCm39) |
L14P |
unknown |
Het |
| Ggt5 |
T |
C |
10: 75,440,608 (GRCm39) |
M243T |
probably benign |
Het |
| Gmds |
A |
G |
13: 32,124,482 (GRCm39) |
I292T |
probably benign |
Het |
| Gpcpd1 |
A |
T |
2: 132,386,355 (GRCm39) |
V341E |
probably damaging |
Het |
| Grm3 |
A |
G |
5: 9,620,167 (GRCm39) |
F359S |
probably damaging |
Het |
| Hcn1 |
A |
T |
13: 118,010,441 (GRCm39) |
K340* |
probably null |
Het |
| Heatr9 |
T |
C |
11: 83,403,258 (GRCm39) |
E427G |
probably benign |
Het |
| Kif26b |
G |
A |
1: 178,358,195 (GRCm39) |
G102D |
unknown |
Het |
| Mark3 |
T |
C |
12: 111,584,760 (GRCm39) |
F119L |
probably damaging |
Het |
| Melk |
T |
C |
4: 44,350,959 (GRCm39) |
V500A |
probably benign |
Het |
| Mrpl41 |
A |
G |
2: 24,864,295 (GRCm39) |
F126L |
probably damaging |
Het |
| Or10c1 |
C |
A |
17: 37,522,307 (GRCm39) |
A146S |
probably benign |
Het |
| Or6c3b |
C |
T |
10: 129,527,699 (GRCm39) |
M70I |
probably benign |
Het |
| Pax7 |
A |
T |
4: 139,506,928 (GRCm39) |
S372T |
probably benign |
Het |
| Pax7 |
A |
T |
4: 139,556,906 (GRCm39) |
I118N |
probably damaging |
Het |
| Plcl1 |
G |
T |
1: 55,735,671 (GRCm39) |
M337I |
possibly damaging |
Het |
| Poc1a |
G |
T |
9: 106,227,012 (GRCm39) |
|
probably benign |
Het |
| Rhobtb3 |
A |
C |
13: 76,061,389 (GRCm39) |
L252R |
probably benign |
Het |
| Rlf |
A |
G |
4: 121,004,063 (GRCm39) |
V1639A |
probably benign |
Het |
| Tff1 |
A |
G |
17: 31,381,682 (GRCm39) |
V65A |
probably damaging |
Het |
| Trpm4 |
G |
T |
7: 44,971,258 (GRCm39) |
D222E |
probably damaging |
Het |
| Ttn |
A |
T |
2: 76,643,741 (GRCm39) |
D13162E |
probably damaging |
Het |
| Unc5d |
A |
T |
8: 29,209,723 (GRCm39) |
S466T |
probably benign |
Het |
| Vmn1r73 |
A |
G |
7: 11,490,683 (GRCm39) |
Y167C |
probably damaging |
Het |
| Vwde |
C |
T |
6: 13,208,323 (GRCm39) |
|
probably null |
Het |
| Xpr1 |
T |
C |
1: 155,204,430 (GRCm39) |
|
probably null |
Het |
| Zbtb40 |
A |
G |
4: 136,728,604 (GRCm39) |
V413A |
possibly damaging |
Het |
|
| Other mutations in Rabgef1 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00432:Rabgef1
|
APN |
5 |
130,237,565 (GRCm39) |
nonsense |
probably null |
|
|
IGL00964:Rabgef1
|
APN |
5 |
130,219,863 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL01830:Rabgef1
|
APN |
5 |
130,240,907 (GRCm39) |
missense |
possibly damaging |
0.88 |
|
IGL02161:Rabgef1
|
APN |
5 |
130,235,940 (GRCm39) |
splice site |
probably benign |
|
|
IGL02231:Rabgef1
|
APN |
5 |
130,240,816 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02429:Rabgef1
|
APN |
5 |
130,239,329 (GRCm39) |
missense |
possibly damaging |
0.48 |
|
IGL02620:Rabgef1
|
APN |
5 |
130,219,863 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL03005:Rabgef1
|
APN |
5 |
130,237,638 (GRCm39) |
missense |
probably damaging |
1.00 |
|
LCD18:Rabgef1
|
UTSW |
5 |
130,187,586 (GRCm38) |
frame shift |
probably null |
|
|
R0227:Rabgef1
|
UTSW |
5 |
130,219,831 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1028:Rabgef1
|
UTSW |
5 |
130,241,703 (GRCm39) |
nonsense |
probably null |
|
|
R1838:Rabgef1
|
UTSW |
5 |
130,241,862 (GRCm39) |
missense |
probably benign |
0.01 |
|
R2027:Rabgef1
|
UTSW |
5 |
130,237,620 (GRCm39) |
missense |
possibly damaging |
0.69 |
|
R2074:Rabgef1
|
UTSW |
5 |
130,216,402 (GRCm39) |
missense |
probably benign |
0.21 |
|
R2079:Rabgef1
|
UTSW |
5 |
130,219,776 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R2355:Rabgef1
|
UTSW |
5 |
130,240,928 (GRCm39) |
missense |
probably benign |
0.29 |
|
R3625:Rabgef1
|
UTSW |
5 |
130,240,961 (GRCm39) |
critical splice donor site |
probably null |
|
|
R3892:Rabgef1
|
UTSW |
5 |
130,237,520 (GRCm39) |
splice site |
probably benign |
|
|
R5249:Rabgef1
|
UTSW |
5 |
130,241,841 (GRCm39) |
missense |
probably benign |
0.00 |
|
R6597:Rabgef1
|
UTSW |
5 |
130,219,885 (GRCm39) |
critical splice donor site |
probably null |
|
|
R7223:Rabgef1
|
UTSW |
5 |
130,219,801 (GRCm39) |
missense |
probably benign |
0.14 |
|
R7326:Rabgef1
|
UTSW |
5 |
130,216,192 (GRCm39) |
intron |
probably benign |
|
|
R8762:Rabgef1
|
UTSW |
5 |
130,237,557 (GRCm39) |
missense |
possibly damaging |
0.67 |
|
R9086:Rabgef1
|
UTSW |
5 |
130,240,792 (GRCm39) |
missense |
probably benign |
0.05 |
|
R9142:Rabgef1
|
UTSW |
5 |
130,237,554 (GRCm39) |
missense |
possibly damaging |
0.78 |
|
R9697:Rabgef1
|
UTSW |
5 |
130,241,781 (GRCm39) |
missense |
probably benign |
|
|
| Predicted Primers |
PCR Primer
(F):5'- CGGTGAGATACTTCTAAAGCCG -3'
(R):5'- TTCTCAGCAGACTGTGGTCC -3'
Sequencing Primer
(F):5'- GTGAGATACTTCTAAAGCCGTGTTC -3'
(R):5'- ACTCTGAGAGGCACGCATC -3'
|
| Posted On |
2016-06-06 |
Incidental Mutation