Mutagenetix > Incidental Mutation

Incidental Mutation 'R3877:Arhgef40'

276919

Institutional Source

Beutler Lab

Gene Symbol

Arhgef40

Ensembl Gene

ENSMUSG00000004562

Gene Name

Rho guanine nucleotide exchange factor 40

Synonyms

E130112L23Rik

MMRRC Submission

040904-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.172) question?

Stock #

R3877 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

52222176-52243708 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 52239742 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Alanine at position 1319 (T1319A)

Ref Sequence

ENSEMBL: ENSMUSP00000138635 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000067549] [ENSMUST00000093813] [ENSMUST00000100639] [ENSMUST00000166169] [ENSMUST00000182061] [ENSMUST00000182760] [ENSMUST00000182909] [ENSMUST00000183208] [ENSMUST00000182905] [ENSMUST00000228580] [ENSMUST00000226522]

AlphaFold

Q3UPH7

Predicted Effect

probably benign
Transcript: ENSMUST00000067549

SMART Domains

Protein: ENSMUSP00000068184
Gene: ENSMUSG00000049295

Domain	Start	End	E-Value	Type
low complexity region	30	47	N/A	INTRINSIC
ZnF_C2H2	61	83	6.23e-2	SMART
ZnF_C2H2	89	111	4.17e-3	SMART
low complexity region	113	146	N/A	INTRINSIC
ZnF_C2H2	167	190	3.07e-1	SMART
ZnF_C2H2	193	216	1.51e0	SMART
low complexity region	229	276	N/A	INTRINSIC
ZnF_C2H2	277	299	8.47e-4	SMART
ZnF_C2H2	305	327	1.38e-3	SMART
low complexity region	331	350	N/A	INTRINSIC
low complexity region	354	379	N/A	INTRINSIC
low complexity region	427	441	N/A	INTRINSIC
ZnF_C2H2	501	523	3.63e-3	SMART
ZnF_C2H2	529	551	1.58e-3	SMART
low complexity region	560	570	N/A	INTRINSIC
low complexity region	594	611	N/A	INTRINSIC
low complexity region	637	648	N/A	INTRINSIC
ZnF_C2H2	650	672	2.82e0	SMART
low complexity region	675	684	N/A	INTRINSIC
low complexity region	695	714	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000093813
AA Change: T1319A

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000091331
Gene: ENSMUSG00000004562
AA Change: T1319A

Domain	Start	End	E-Value	Type
low complexity region	201	223	N/A	INTRINSIC
low complexity region	306	320	N/A	INTRINSIC
low complexity region	332	345	N/A	INTRINSIC
low complexity region	351	395	N/A	INTRINSIC
low complexity region	451	472	N/A	INTRINSIC
low complexity region	550	564	N/A	INTRINSIC
low complexity region	581	606	N/A	INTRINSIC
low complexity region	773	792	N/A	INTRINSIC
low complexity region	885	914	N/A	INTRINSIC
low complexity region	958	996	N/A	INTRINSIC
Pfam:RhoGEF	1087	1246	6.1e-9	PFAM
PH	1264	1372	3.97e-8	SMART
low complexity region	1403	1424	N/A	INTRINSIC
low complexity region	1478	1491	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000100639
AA Change: T1319A

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000098204
Gene: ENSMUSG00000004562
AA Change: T1319A

Domain	Start	End	E-Value	Type
low complexity region	201	223	N/A	INTRINSIC
low complexity region	306	320	N/A	INTRINSIC
low complexity region	332	345	N/A	INTRINSIC
low complexity region	351	395	N/A	INTRINSIC
low complexity region	451	472	N/A	INTRINSIC
low complexity region	550	564	N/A	INTRINSIC
low complexity region	581	606	N/A	INTRINSIC
low complexity region	773	792	N/A	INTRINSIC
low complexity region	885	914	N/A	INTRINSIC
low complexity region	958	996	N/A	INTRINSIC
Pfam:RhoGEF	1087	1246	5.9e-9	PFAM
PH	1264	1372	3.97e-8	SMART
low complexity region	1430	1443	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000166169

SMART Domains

Protein: ENSMUSP00000126854
Gene: ENSMUSG00000049295

Domain	Start	End	E-Value	Type
low complexity region	30	47	N/A	INTRINSIC
ZnF_C2H2	61	83	6.23e-2	SMART
ZnF_C2H2	89	111	4.17e-3	SMART
low complexity region	113	146	N/A	INTRINSIC
ZnF_C2H2	167	190	3.07e-1	SMART
ZnF_C2H2	193	216	1.51e0	SMART
low complexity region	229	276	N/A	INTRINSIC
ZnF_C2H2	277	299	8.47e-4	SMART
ZnF_C2H2	305	327	1.38e-3	SMART
low complexity region	331	350	N/A	INTRINSIC
low complexity region	354	379	N/A	INTRINSIC
low complexity region	427	441	N/A	INTRINSIC
ZnF_C2H2	501	523	3.63e-3	SMART
ZnF_C2H2	529	551	1.58e-3	SMART
low complexity region	560	570	N/A	INTRINSIC
low complexity region	594	611	N/A	INTRINSIC
low complexity region	637	648	N/A	INTRINSIC
ZnF_C2H2	650	672	2.82e0	SMART
low complexity region	675	684	N/A	INTRINSIC
low complexity region	695	714	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000182061
AA Change: T1319A

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000138128
Gene: ENSMUSG00000004562
AA Change: T1319A

Domain	Start	End	E-Value	Type
low complexity region	201	223	N/A	INTRINSIC
low complexity region	306	320	N/A	INTRINSIC
low complexity region	332	345	N/A	INTRINSIC
low complexity region	351	395	N/A	INTRINSIC
low complexity region	451	472	N/A	INTRINSIC
low complexity region	550	564	N/A	INTRINSIC
low complexity region	581	606	N/A	INTRINSIC
low complexity region	773	792	N/A	INTRINSIC
low complexity region	885	914	N/A	INTRINSIC
low complexity region	958	996	N/A	INTRINSIC
Pfam:RhoGEF	1087	1247	3.7e-9	PFAM
PH	1264	1372	3.97e-8	SMART
low complexity region	1430	1443	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000182217

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000182504

Predicted Effect

possibly damaging
Transcript: ENSMUST00000182760
AA Change: T1328A

PolyPhen 2 Score 0.907 (Sensitivity: 0.81; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000138125
Gene: ENSMUSG00000004562
AA Change: T1328A

Domain	Start	End	E-Value	Type
low complexity region	201	223	N/A	INTRINSIC
low complexity region	306	320	N/A	INTRINSIC
low complexity region	332	345	N/A	INTRINSIC
low complexity region	351	395	N/A	INTRINSIC
low complexity region	451	472	N/A	INTRINSIC
low complexity region	550	564	N/A	INTRINSIC
low complexity region	581	606	N/A	INTRINSIC
low complexity region	782	801	N/A	INTRINSIC
low complexity region	894	923	N/A	INTRINSIC
low complexity region	967	1005	N/A	INTRINSIC
Pfam:RhoGEF	1096	1256	5.9e-9	PFAM
PH	1273	1381	3.97e-8	SMART
low complexity region	1412	1433	N/A	INTRINSIC
low complexity region	1487	1500	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000182909
AA Change: T1319A

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000138635
Gene: ENSMUSG00000004562
AA Change: T1319A

Domain	Start	End	E-Value	Type
low complexity region	201	223	N/A	INTRINSIC
low complexity region	306	320	N/A	INTRINSIC
low complexity region	332	345	N/A	INTRINSIC
low complexity region	351	395	N/A	INTRINSIC
low complexity region	451	472	N/A	INTRINSIC
low complexity region	550	564	N/A	INTRINSIC
low complexity region	581	606	N/A	INTRINSIC
low complexity region	773	792	N/A	INTRINSIC
low complexity region	885	914	N/A	INTRINSIC
low complexity region	958	996	N/A	INTRINSIC
Pfam:RhoGEF	1087	1247	3.9e-9	PFAM
PH	1264	1372	3.97e-8	SMART
low complexity region	1403	1424	N/A	INTRINSIC
low complexity region	1478	1491	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000183208

SMART Domains

Protein: ENSMUSP00000138354
Gene: ENSMUSG00000004562

Domain	Start	End	E-Value	Type
low complexity region	201	223	N/A	INTRINSIC
low complexity region	306	320	N/A	INTRINSIC
low complexity region	332	345	N/A	INTRINSIC
low complexity region	351	395	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000182905

SMART Domains

Protein: ENSMUSP00000138797
Gene: ENSMUSG00000004562

Domain	Start	End	E-Value	Type
low complexity region	201	223	N/A	INTRINSIC
low complexity region	306	320	N/A	INTRINSIC
low complexity region	332	345	N/A	INTRINSIC
low complexity region	351	395	N/A	INTRINSIC
low complexity region	451	472	N/A	INTRINSIC
low complexity region	550	564	N/A	INTRINSIC
low complexity region	581	606	N/A	INTRINSIC
low complexity region	773	792	N/A	INTRINSIC
low complexity region	885	914	N/A	INTRINSIC
low complexity region	958	996	N/A	INTRINSIC
SCOP:d1kz7a1	1073	1162	4e-7	SMART
Blast:RhoGEF	1087	1157	1e-8	BLAST

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000182644

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000182931

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000183213

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000182777

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000183022

Predicted Effect

probably benign
Transcript: ENSMUST00000228580

Predicted Effect

probably benign
Transcript: ENSMUST00000182667

Predicted Effect

probably benign
Transcript: ENSMUST00000182828

Predicted Effect

probably benign
Transcript: ENSMUST00000226522

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000226474

Meta Mutation Damage Score

0.2276

Coding Region Coverage

1x: 99.2%
3x: 98.7%
10x: 97.6%
20x: 96.2%

Validation Efficiency

100% (49/49)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein similar to guanosine nucleotide exchange factors for Rho GTPases. The encoded protein contains in its C-terminus a GEF domain involved in exchange activity and a pleckstrin homology domain. Alternatively spliced transcripts that encode different proteins have been described. [provided by RefSeq, Mar 2014]

Allele List at MGI

Other mutations in this stock

Total: 48 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adam20	G	A	8: 41,249,671 (GRCm39)	V594I	possibly damaging	Het
Adgb	A	T	10: 10,318,227 (GRCm39)		probably null	Het
Adgrb3	A	C	1: 25,150,906 (GRCm39)	L1109R	probably damaging	Het
Angptl4	G	A	17: 33,996,008 (GRCm39)	P323S	possibly damaging	Het
Arhgap21	A	T	2: 20,864,717 (GRCm39)	M1197K	probably damaging	Het
C4bp	A	G	1: 130,575,764 (GRCm39)		probably null	Het
Cd200r1	T	C	16: 44,610,374 (GRCm39)	S161P	possibly damaging	Het
Ckap5	A	G	2: 91,445,495 (GRCm39)	K1711E	possibly damaging	Het
Cldn19	T	C	4: 119,114,094 (GRCm39)	S79P	possibly damaging	Het
Cplane1	T	C	15: 8,251,427 (GRCm39)	S1900P	probably benign	Het
Dnah17	T	G	11: 117,915,533 (GRCm39)	N4334T	probably damaging	Het
Dpm2	G	A	2: 32,462,412 (GRCm39)		probably null	Het
Eef1a2	A	T	2: 180,794,626 (GRCm39)	V191E	probably damaging	Het
Gmds	G	A	13: 32,411,248 (GRCm39)	T62I	probably damaging	Het
Hyal5	A	T	6: 24,876,630 (GRCm39)	I168F	probably damaging	Het
Idh3a	T	C	9: 54,499,679 (GRCm39)	V31A	probably benign	Het
Inf2	C	A	12: 112,577,264 (GRCm39)	A1036E	unknown	Het
Kcnd3	C	T	3: 105,566,082 (GRCm39)	A421V	probably damaging	Het
Kidins220	T	A	12: 25,051,564 (GRCm39)		probably benign	Het
Kirrel1	C	T	3: 86,996,458 (GRCm39)	M380I	probably null	Het
Lrp1b	A	G	2: 41,335,206 (GRCm39)	C779R	probably damaging	Het
Lrp2	A	G	2: 69,289,816 (GRCm39)		probably null	Het
Lrp2	G	A	2: 69,379,391 (GRCm39)	T107M	probably damaging	Het
Lrpap1	T	C	5: 35,255,547 (GRCm39)	E184G	probably benign	Het
Mapre1	C	T	2: 153,588,201 (GRCm39)	T8M	possibly damaging	Het
Mms19	G	A	19: 41,954,695 (GRCm39)	Q75*	probably null	Het
Mtcl1	T	C	17: 66,649,949 (GRCm39)	I1390V	probably damaging	Het
Muc5b	A	G	7: 141,411,289 (GRCm39)	S1412G	unknown	Het
Myh4	A	T	11: 67,148,009 (GRCm39)	Q1686L	probably benign	Het
Or1e25	A	T	11: 73,493,979 (GRCm39)	D191V	probably damaging	Het
Or9s13	A	T	1: 92,547,805 (GRCm39)	D59V	probably damaging	Het
Rcvrn	A	T	11: 67,590,802 (GRCm39)	I129F	probably damaging	Het
Reg3b	T	A	6: 78,348,216 (GRCm39)	M10K	possibly damaging	Het
Rimbp2	T	A	5: 128,850,529 (GRCm39)	E918V	probably damaging	Het
Rpl5	A	G	5: 108,051,667 (GRCm39)	T154A	probably benign	Het
Sall4	A	C	2: 168,598,162 (GRCm39)	L195R	probably damaging	Het
Sh3gl2	T	C	4: 85,297,618 (GRCm39)	S199P	possibly damaging	Het
Shank1	G	T	7: 43,994,416 (GRCm39)	R859L	unknown	Het
Thsd7b	A	G	1: 130,117,919 (GRCm39)	E1445G	possibly damaging	Het
Tnfaip6	A	G	2: 51,942,339 (GRCm39)	E216G	probably benign	Het
Tram1	T	C	1: 13,639,827 (GRCm39)	T307A	probably benign	Het
Trpv5	A	G	6: 41,637,277 (GRCm39)	V354A	probably benign	Het
Tyro3	A	G	2: 119,643,774 (GRCm39)	E745G	probably damaging	Het
Vmn1r68	A	T	7: 10,261,408 (GRCm39)	I230N	probably damaging	Het
Vmn2r28	A	T	7: 5,491,357 (GRCm39)	W297R	probably damaging	Het
Vrk3	A	T	7: 44,412,460 (GRCm39)		probably null	Het
Zfhx4	T	C	3: 5,465,845 (GRCm39)	V2001A	probably benign	Het
Zfp512b	AG	AGG	2: 181,230,556 (GRCm39)		probably null	Het

Other mutations in Arhgef40

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00332:Arhgef40	APN	14	52,226,417 (GRCm39)	missense	probably damaging	1.00
IGL00848:Arhgef40	APN	14	52,224,884 (GRCm39)	missense	probably damaging	1.00
IGL00966:Arhgef40	APN	14	52,229,155 (GRCm39)	critical splice donor site	probably null
IGL01123:Arhgef40	APN	14	52,231,803 (GRCm39)	missense	probably damaging	0.99
IGL02110:Arhgef40	APN	14	52,226,862 (GRCm39)	missense	probably damaging	1.00
IGL02490:Arhgef40	APN	14	52,226,652 (GRCm39)	missense	probably damaging	0.99
IGL02505:Arhgef40	APN	14	52,238,320 (GRCm39)	missense	probably damaging	1.00
IGL02636:Arhgef40	APN	14	52,234,865 (GRCm39)	missense	probably damaging	1.00
R0200:Arhgef40	UTSW	14	52,234,431 (GRCm39)	missense	probably damaging	0.99
R0496:Arhgef40	UTSW	14	52,242,364 (GRCm39)	unclassified	probably benign
R0608:Arhgef40	UTSW	14	52,234,431 (GRCm39)	missense	probably damaging	0.99
R0826:Arhgef40	UTSW	14	52,238,450 (GRCm39)	missense	probably benign	0.05
R1126:Arhgef40	UTSW	14	52,234,583 (GRCm39)	missense	probably damaging	0.96
R1330:Arhgef40	UTSW	14	52,227,613 (GRCm39)	missense	probably benign	0.42
R1612:Arhgef40	UTSW	14	52,241,538 (GRCm39)	missense	probably damaging	1.00
R1794:Arhgef40	UTSW	14	52,227,387 (GRCm39)	missense	possibly damaging	0.94
R1844:Arhgef40	UTSW	14	52,235,080 (GRCm39)	missense	probably damaging	0.99
R2018:Arhgef40	UTSW	14	52,241,162 (GRCm39)	missense	probably damaging	1.00
R2064:Arhgef40	UTSW	14	52,233,640 (GRCm39)	missense	probably damaging	1.00
R2321:Arhgef40	UTSW	14	52,231,733 (GRCm39)	splice site	probably benign
R4233:Arhgef40	UTSW	14	52,227,628 (GRCm39)	missense	possibly damaging	0.50
R4596:Arhgef40	UTSW	14	52,224,681 (GRCm39)	critical splice donor site	probably null
R4676:Arhgef40	UTSW	14	52,228,416 (GRCm39)	nonsense	probably null
R4703:Arhgef40	UTSW	14	52,239,767 (GRCm39)	missense	probably damaging	1.00
R4704:Arhgef40	UTSW	14	52,239,767 (GRCm39)	missense	probably damaging	1.00
R4719:Arhgef40	UTSW	14	52,242,395 (GRCm39)	unclassified	probably benign
R4915:Arhgef40	UTSW	14	52,227,556 (GRCm39)	missense	probably damaging	1.00
R4917:Arhgef40	UTSW	14	52,227,556 (GRCm39)	missense	probably damaging	1.00
R4918:Arhgef40	UTSW	14	52,227,556 (GRCm39)	missense	probably damaging	1.00
R5097:Arhgef40	UTSW	14	52,227,146 (GRCm39)	missense	probably damaging	1.00
R5183:Arhgef40	UTSW	14	52,241,556 (GRCm39)	missense	probably damaging	0.98
R5195:Arhgef40	UTSW	14	52,227,269 (GRCm39)	missense	possibly damaging	0.68
R5367:Arhgef40	UTSW	14	52,227,156 (GRCm39)	missense	probably damaging	0.99
R5381:Arhgef40	UTSW	14	52,229,306 (GRCm39)	missense	probably damaging	0.99
R5594:Arhgef40	UTSW	14	52,233,614 (GRCm39)	missense	probably damaging	1.00
R5632:Arhgef40	UTSW	14	52,231,795 (GRCm39)	missense	probably damaging	1.00
R5665:Arhgef40	UTSW	14	52,238,357 (GRCm39)	missense	possibly damaging	0.80
R5798:Arhgef40	UTSW	14	52,234,489 (GRCm39)	missense	probably damaging	1.00
R5820:Arhgef40	UTSW	14	52,224,953 (GRCm39)	missense	possibly damaging	0.76
R6229:Arhgef40	UTSW	14	52,227,547 (GRCm39)	missense	probably benign	0.06
R6451:Arhgef40	UTSW	14	52,238,456 (GRCm39)	missense	probably damaging	1.00
R6633:Arhgef40	UTSW	14	52,234,888 (GRCm39)	missense	probably damaging	1.00
R6642:Arhgef40	UTSW	14	52,228,419 (GRCm39)	unclassified	probably benign
R6675:Arhgef40	UTSW	14	52,229,098 (GRCm39)	missense	probably damaging	0.99
R6781:Arhgef40	UTSW	14	52,235,354 (GRCm39)	intron	probably benign
R6901:Arhgef40	UTSW	14	52,234,825 (GRCm39)	missense	probably damaging	1.00
R7852:Arhgef40	UTSW	14	52,229,254 (GRCm39)	missense	unknown
R7857:Arhgef40	UTSW	14	52,226,212 (GRCm39)	missense	probably damaging	0.97
R7914:Arhgef40	UTSW	14	52,225,032 (GRCm39)	missense	probably damaging	1.00
R8060:Arhgef40	UTSW	14	52,222,452 (GRCm39)	splice site	probably benign
R8144:Arhgef40	UTSW	14	52,235,632 (GRCm39)	missense	probably damaging	1.00
R8195:Arhgef40	UTSW	14	52,226,226 (GRCm39)	missense	probably damaging	1.00
R8432:Arhgef40	UTSW	14	52,226,857 (GRCm39)	missense	probably benign	0.00
R8738:Arhgef40	UTSW	14	52,238,414 (GRCm39)	missense	probably damaging	1.00
R8830:Arhgef40	UTSW	14	52,241,165 (GRCm39)	missense	probably damaging	1.00
R9038:Arhgef40	UTSW	14	52,235,072 (GRCm39)	missense	probably damaging	0.96
R9712:Arhgef40	UTSW	14	52,226,415 (GRCm39)	missense	probably damaging	0.99
U24488:Arhgef40	UTSW	14	52,235,673 (GRCm39)	missense	probably benign	0.07
X0023:Arhgef40	UTSW	14	52,241,141 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- CGTCTCTGAGTGAGCCTTAC -3'
(R):5'- TTCCAAGCAGAACATCCCTG -3'

Sequencing Primer
(F):5'- CTGAGTGAGCCTTACTTTCCC -3'
(R):5'- AGAACATCCCTGTGGCCTG -3'

Posted On

2015-04-06