Mutagenetix > Incidental Mutation

Incidental Mutation 'R7223:Rabgef1'

561932

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

045295-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.850) question?

Stock #

R7223 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

130200644-130243178 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 130219801 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glutamic Acid to Valine at position 88 (E88V)

Ref Sequence

ENSEMBL: ENSMUSP00000026390 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000026390] [ENSMUST00000119027] [ENSMUST00000119797] [ENSMUST00000148264]

AlphaFold

Q9JM13

Predicted Effect

probably benign
Transcript: ENSMUST00000026390
AA Change: E88V

PolyPhen 2 Score 0.141 (Sensitivity: 0.92; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000026390
Gene: ENSMUSG00000025340
AA Change: E88V

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
AA Change: E88V

PolyPhen 2 Score 0.373 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000112537
Gene: ENSMUSG00000025340
AA Change: E88V

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

probably benign
Transcript: ENSMUST00000119797
AA Change: E88V

PolyPhen 2 Score 0.141 (Sensitivity: 0.92; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000114103
Gene: ENSMUSG00000025340
AA Change: E88V

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

probably damaging
Transcript: ENSMUST00000148264
AA Change: E88V

PolyPhen 2 Score 0.957 (Sensitivity: 0.78; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000119245
Gene: ENSMUSG00000025340
AA Change: E88V

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

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.8%

Validation Efficiency

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: 82 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcb11	A	T	2: 69,104,487 (GRCm39)	V733E	probably benign	Het
Adam34	A	T	8: 44,105,041 (GRCm39)	N201K	probably benign	Het
Aldh3b2	A	C	19: 4,029,592 (GRCm39)	S322R	probably damaging	Het
Anpep	A	T	7: 79,475,058 (GRCm39)	L914Q	probably damaging	Het
Arhgap30	T	C	1: 171,235,139 (GRCm39)	F535S	probably damaging	Het
Baiap3	G	A	17: 25,462,814 (GRCm39)	R1075C	probably benign	Het
Baz2a	G	T	10: 127,948,475 (GRCm39)	G252V	probably damaging	Het
Brinp3	T	A	1: 146,776,812 (GRCm39)	S420T	possibly damaging	Het
Carmil3	T	C	14: 55,733,695 (GRCm39)	F359S	possibly damaging	Het
Ccdc124	A	T	8: 71,321,170 (GRCm39)	L190Q	probably damaging	Het
Ccr6	T	C	17: 8,474,972 (GRCm39)	V59A	probably damaging	Het
Ccr8	T	A	9: 119,923,683 (GRCm39)	I266N	probably damaging	Het
Cdh23	T	A	10: 60,167,596 (GRCm39)	E1798V	probably damaging	Het
Cdk5rap2	T	C	4: 70,153,684 (GRCm39)	N1713S	probably benign	Het
Cep19	T	A	16: 31,922,833 (GRCm39)	I33N	probably damaging	Het
Cers3	A	T	7: 66,433,163 (GRCm39)	Y196F	probably damaging	Het
Cidea	T	C	18: 67,499,491 (GRCm39)	I126T	probably damaging	Het
Copg2	A	T	6: 30,789,689 (GRCm39)	Y546*	probably null	Het
Cul3	A	T	1: 80,264,717 (GRCm39)	V261E	probably benign	Het
Cyp2g1	A	T	7: 26,514,057 (GRCm39)	D221V	probably damaging	Het
Cyp8b1	G	A	9: 121,744,163 (GRCm39)	H390Y	probably damaging	Het
Daam1	T	C	12: 72,035,717 (GRCm39)	F971L	probably damaging	Het
Dnajc24	G	A	2: 105,832,311 (GRCm39)	S24L	possibly damaging	Het
Dpysl3	T	C	18: 43,571,107 (GRCm39)	S56G	probably benign	Het
Esp1	A	G	17: 41,041,972 (GRCm39)	D88G	probably benign	Het
Fam171b	A	G	2: 83,708,574 (GRCm39)	T359A	probably damaging	Het
Fam186b	T	C	15: 99,177,718 (GRCm39)	E536G	possibly damaging	Het
Fbxo3	T	C	2: 103,873,357 (GRCm39)	V156A	possibly damaging	Het
Gls2	C	A	10: 128,035,063 (GRCm39)	H65Q	probably benign	Het
Gp2	A	G	7: 119,050,721 (GRCm39)		probably null	Het
Gpcpd1	T	A	2: 132,375,976 (GRCm39)	K435I	probably benign	Het
Gpx6	T	A	13: 21,501,840 (GRCm39)		probably null	Het
Hps3	A	T	3: 20,084,583 (GRCm39)	S202T	probably benign	Het
Htr1d	T	A	4: 136,170,812 (GRCm39)	L347H	probably damaging	Het
Igfals	T	C	17: 25,100,208 (GRCm39)	L433P	probably damaging	Het
Ilvbl	C	T	10: 78,419,530 (GRCm39)	H537Y	probably benign	Het
Iqgap2	A	T	13: 95,765,480 (GRCm39)	M1530K	probably damaging	Het
Jarid2	A	G	13: 45,049,798 (GRCm39)	T247A	possibly damaging	Het
L3hypdh	C	T	12: 72,120,783 (GRCm39)	V323I	possibly damaging	Het
Lama3	C	T	18: 12,715,665 (GRCm39)	T1707I	possibly damaging	Het
Map6	G	T	7: 98,917,232 (GRCm39)	A2S	probably damaging	Het
Mfap3	T	A	11: 57,421,066 (GRCm39)	I349K	probably benign	Het
Mybl2	A	G	2: 162,914,625 (GRCm39)	T248A	probably benign	Het
N6amt1	A	G	16: 87,159,548 (GRCm39)	*151W	probably null	Het
Nhlrc1	A	G	13: 47,167,684 (GRCm39)	V191A	probably benign	Het
Nkx2-5	T	C	17: 27,058,594 (GRCm39)	E120G	possibly damaging	Het
Or2y10	T	A	11: 49,454,925 (GRCm39)	M59K	probably damaging	Het
Or52r1b	C	A	7: 102,690,839 (GRCm39)	T46N	possibly damaging	Het
Or8b41	T	C	9: 38,055,049 (GRCm39)	V201A	probably benign	Het
Or8k28	T	A	2: 86,286,211 (GRCm39)	I135F	possibly damaging	Het
Pcdha8	T	G	18: 37,126,201 (GRCm39)	L228V	probably benign	Het
Pcsk2	A	G	2: 143,532,253 (GRCm39)	T134A	possibly damaging	Het
Phldb3	G	A	7: 24,324,078 (GRCm39)	R484Q	probably benign	Het
Pipox	A	G	11: 77,772,012 (GRCm39)	S371P	probably damaging	Het
Plekhg1	T	C	10: 3,823,343 (GRCm39)	S159P		Het
Psme4	C	T	11: 30,824,226 (GRCm39)	P1737S	probably benign	Het
Pygm	G	A	19: 6,438,893 (GRCm39)	D328N	probably benign	Het
Rims2	G	T	15: 39,300,428 (GRCm39)	R245L	probably benign	Het
Slc38a4	T	C	15: 96,908,226 (GRCm39)	I172V	probably damaging	Het
Slc4a10	T	A	2: 62,099,009 (GRCm39)	Y586N	probably damaging	Het
Snap91	C	T	9: 86,761,610 (GRCm39)		probably benign	Het
Sorcs1	C	T	19: 50,178,480 (GRCm39)	V881I	probably benign	Het
Spef2	A	T	15: 9,601,726 (GRCm39)	V1512E	unknown	Het
Sufu	T	C	19: 46,441,716 (GRCm39)	I292T	possibly damaging	Het
Tet1	T	C	10: 62,649,450 (GRCm39)	N87D	possibly damaging	Het
Tmem108	T	C	9: 103,376,733 (GRCm39)	T239A	not run	Het
Tmem121	A	T	12: 113,152,114 (GRCm39)	K111*	probably null	Het
Tpp2	T	A	1: 44,008,048 (GRCm39)	D417E	probably damaging	Het
Tpr	G	A	1: 150,315,007 (GRCm39)	E2025K	possibly damaging	Het
Trappc3	C	T	4: 126,168,945 (GRCm39)	A145V	possibly damaging	Het
Ttn	T	C	2: 76,721,325 (GRCm39)	D6754G	probably null	Het
Unc13c	T	A	9: 73,536,473 (GRCm39)	M1627L	probably benign	Het
Ush2a	A	G	1: 188,542,414 (GRCm39)	I3327V	probably benign	Het
Vmn1r74	C	T	7: 11,580,894 (GRCm39)	Q65*	probably null	Het
Wdr18	G	A	10: 79,796,202 (GRCm39)	R69H	probably damaging	Het
Zbed5	G	T	5: 129,929,279 (GRCm39)	D132Y	probably damaging	Het
Zfp644	A	T	5: 106,785,448 (GRCm39)	Y366*	probably null	Het
Zfyve26	T	C	12: 79,292,945 (GRCm39)	N2068S	probably damaging	Het
Zic2	T	C	14: 122,713,503 (GRCm39)	F139S	probably damaging	Het
Zmynd11	T	C	13: 9,760,198 (GRCm39)	Q141R	probably benign	Het
Zrsr2-ps1	A	G	11: 22,923,388 (GRCm39)	E54G	probably benign	Het
Zscan10	G	A	17: 23,828,456 (GRCm39)	D333N	probably benign	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
R5060:Rabgef1	UTSW	5	130,240,844 (GRCm39)	missense	probably damaging	1.00
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
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'- TGAGATCTCAGACCCACTTGG -3'
(R):5'- TCTCTTGGGCTTACAGAAGTGAGAG -3'

Sequencing Primer
(F):5'- AGAGGACCCAGATCATTC -3'
(R):5'- CTTACAGAAGTGAGAGGCTGAGC -3'

Posted On

2019-06-26