Mutagenetix > Incidental Mutation

Incidental Mutation 'R9086:Rabgef1'

690593

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

068905-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.853) question?

Stock #

R9086 (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 130240792 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Phenylalanine at position 304 (I304F)

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: I304F

PolyPhen 2 Score 0.049 (Sensitivity: 0.94; Specificity: 0.83)

SMART Domains

Protein: ENSMUSP00000026390
Gene: ENSMUSG00000025340
AA Change: I304F

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

probably benign
Transcript: ENSMUST00000119797
AA Change: I304F

PolyPhen 2 Score 0.049 (Sensitivity: 0.94; Specificity: 0.83)

SMART Domains

Protein: ENSMUSP00000114103
Gene: ENSMUSG00000025340
AA Change: I304F

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 benign
Transcript: ENSMUST00000143865

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

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.7%

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: 69 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca9	T	C	11: 109,992,879 (GRCm39)	E1595G	probably damaging	Het
Ank1	T	C	8: 23,589,636 (GRCm39)	V608A	probably damaging	Het
Arl14epl	T	C	18: 47,065,661 (GRCm39)	V142A	possibly damaging	Het
Atp8a1	T	C	5: 67,932,159 (GRCm39)	D210G		Het
Baz1b	T	C	5: 135,260,538 (GRCm39)	F1112L	probably damaging	Het
Cage1	T	A	13: 38,206,898 (GRCm39)	I316F	probably damaging	Het
Car2	A	C	3: 14,952,968 (GRCm39)	T37P	probably benign	Het
Catsper2	TAGGATGGCTTTTCTCAGGATAGCTTTTCTCAGGATGGCTTTTCTCAGGATAGCTTTTCTCAGGATGGCTTTTCTCAGGATAGCTTTTCT	TAGGATGGCTTTTCTCAGGATAGCTTTTCTCAGGATGGCTTTTCTCAGGATAGCTTTTCT	2: 121,228,053 (GRCm39)		probably benign	Het
Cntnap3	T	A	13: 64,929,573 (GRCm39)	D542V	probably damaging	Het
Coro1b	T	C	19: 4,202,525 (GRCm39)	Y338H	probably damaging	Het
Ctdspl2	G	A	2: 121,838,298 (GRCm39)		probably null	Het
Cyp2a12	T	C	7: 26,735,944 (GRCm39)	F451S	probably damaging	Het
Dpm2	T	C	2: 32,462,391 (GRCm39)	L59P	probably damaging	Het
Duoxa2	A	G	2: 122,131,821 (GRCm39)	Y170C	probably damaging	Het
Dus2	T	A	8: 106,742,573 (GRCm39)	Y34*	probably null	Het
Dzip3	A	G	16: 48,781,493 (GRCm39)	I266T	possibly damaging	Het
Ebf3	T	C	7: 136,800,994 (GRCm39)	T455A	possibly damaging	Het
Echdc2	C	T	4: 108,027,076 (GRCm39)	Q74*	probably null	Het
Efhc1	T	C	1: 21,025,592 (GRCm39)	Y33H	probably damaging	Het
Fam20a	A	T	11: 109,566,754 (GRCm39)	C378*	probably null	Het
Fbxo25	C	A	8: 13,989,621 (GRCm39)	P356Q	probably damaging	Het
Fig4	G	T	10: 41,161,399 (GRCm39)	T59K	possibly damaging	Het
Gbp10	T	A	5: 105,366,369 (GRCm39)	M512L	probably benign	Het
Gdf10	T	A	14: 33,654,221 (GRCm39)	Y243N	probably damaging	Het
Golga5	T	A	12: 102,458,476 (GRCm39)	S640T	probably benign	Het
H1f9	A	T	11: 94,859,083 (GRCm39)	K126M	possibly damaging	Het
Ints1	A	T	5: 139,743,947 (GRCm39)	H1540Q	probably benign	Het
Lipo3	A	T	19: 33,534,529 (GRCm39)	L310Q	probably benign	Het
Lrrk2	A	G	15: 91,640,051 (GRCm39)	K1532R	probably benign	Het
Ltc4s	T	C	11: 50,128,074 (GRCm39)	Y59C	probably damaging	Het
Macf1	T	A	4: 123,377,944 (GRCm39)	H1427L	probably damaging	Het
Mroh2b	A	G	15: 4,982,754 (GRCm39)		probably null	Het
Mthfd1l	A	T	10: 3,923,412 (GRCm39)	D53V	probably benign	Het
Muc4	C	A	16: 32,577,842 (GRCm39)	P303Q		Het
Nrxn1	A	G	17: 90,469,792 (GRCm39)	F1293S	probably damaging	Het
Nrxn2	G	A	19: 6,540,108 (GRCm39)	E803K	probably damaging	Het
Nup155	A	G	15: 8,177,830 (GRCm39)	D1071G	possibly damaging	Het
Or1l4b	T	A	2: 37,036,426 (GRCm39)	D67E	probably damaging	Het
Or2ag18	A	T	7: 106,405,126 (GRCm39)	I181N	probably benign	Het
Or2ak6	T	A	11: 58,592,955 (GRCm39)	S143T	possibly damaging	Het
Papln	A	G	12: 83,821,633 (GRCm39)	E287G	probably damaging	Het
Pex13	C	A	11: 23,615,760 (GRCm39)	G29C	probably damaging	Het
Phrf1	C	A	7: 140,839,412 (GRCm39)	T869K	unknown	Het
Pitrm1	A	G	13: 6,627,517 (GRCm39)	T912A	probably benign	Het
Pla2g4c	A	G	7: 13,071,692 (GRCm39)	K171E	probably benign	Het
Pnpla7	A	T	2: 24,929,709 (GRCm39)	T833S	probably damaging	Het
Por	G	T	5: 135,744,918 (GRCm39)		probably null	Het
Rab3ip	G	A	10: 116,775,310 (GRCm39)	S16L	probably damaging	Het
Rbbp8	T	C	18: 11,875,736 (GRCm39)	V883A	possibly damaging	Het
Rnase4	A	G	14: 51,342,429 (GRCm39)	D51G	possibly damaging	Het
Rnf13	A	C	3: 57,740,997 (GRCm39)	D291A	probably benign	Het
Rps6kb2	A	T	19: 4,209,270 (GRCm39)	I191N	probably damaging	Het
Scn1a	A	G	2: 66,181,358 (GRCm39)	L55S	probably benign	Het
Son	T	A	16: 91,467,418 (GRCm39)	F2260I	unknown	Het
Spata31h1	C	T	10: 82,124,577 (GRCm39)	S2811N	probably benign	Het
Ssr1	A	G	13: 38,167,449 (GRCm39)	I238T	probably benign	Het
Stk11ip	A	G	1: 75,506,818 (GRCm39)	E633G	possibly damaging	Het
Svs3a	A	G	2: 164,132,062 (GRCm39)	Y211C	probably benign	Het
Sytl1	T	A	4: 132,988,175 (GRCm39)	E60D	possibly damaging	Het
Tlcd5	C	T	9: 43,022,664 (GRCm39)	R230Q	probably benign	Het
Tlr1	T	C	5: 65,083,198 (GRCm39)	I460V	probably damaging	Het
Tmem64	T	C	4: 15,266,718 (GRCm39)	I256T	probably damaging	Het
Ttll5	G	A	12: 85,964,516 (GRCm39)	A553T	possibly damaging	Het
Ttll5	A	T	12: 86,071,107 (GRCm39)	T1327S	probably benign	Het
Upp2	T	A	2: 58,680,177 (GRCm39)	C334*	probably null	Het
Wdr74	C	A	19: 8,713,358 (GRCm39)	N24K	possibly damaging	Het
Zbtb42	G	A	12: 112,645,848 (GRCm39)	V8I	probably benign	Het
Zfp541	T	A	7: 15,824,329 (GRCm39)	L1078Q	probably damaging	Het
Zfr2	T	C	10: 81,076,029 (GRCm39)	V212A	probably 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
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
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
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'- AAGGAATTTGGGGCTAGCC -3'
(R):5'- CCAGGTTGGTGAAGTAGTAGC -3'

Sequencing Primer
(F):5'- GCCCTGGGCTATAAATATAAGCTC -3'
(R):5'- TGAAGTAGTAGCCATCCTCGC -3'

Posted On

2021-12-30