Mutagenetix > Incidental Mutation

Incidental Mutation 'R9712:Arhgef40'

730276

Institutional Source

Beutler Lab

Gene Symbol

Arhgef40

Ensembl Gene

ENSMUSG00000004562

Gene Name

Rho guanine nucleotide exchange factor (GEF) 40

Synonyms

E130112L23Rik

MMRRC Submission

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.144) question?

Stock #

R9712 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

51984719-52006251 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 51988958 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Threonine at position 153 (I153T)

Ref Sequence

ENSEMBL: ENSMUSP00000091331 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000093813] [ENSMUST00000100639] [ENSMUST00000182061] [ENSMUST00000182193] [ENSMUST00000182338] [ENSMUST00000182649] [ENSMUST00000182760] [ENSMUST00000182905] [ENSMUST00000182909] [ENSMUST00000183208]

AlphaFold

Q3UPH7

Predicted Effect

probably damaging
Transcript: ENSMUST00000093813
AA Change: I153T

PolyPhen 2 Score 0.987 (Sensitivity: 0.73; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000091331
Gene: ENSMUSG00000004562
AA Change: I153T

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: I153T

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000098204
Gene: ENSMUSG00000004562
AA Change: I153T

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 damaging
Transcript: ENSMUST00000182061
AA Change: I153T

PolyPhen 2 Score 0.992 (Sensitivity: 0.70; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000138128
Gene: ENSMUSG00000004562
AA Change: I153T

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: ENSMUST00000182193

Predicted Effect

probably benign
Transcript: ENSMUST00000182338

SMART Domains

Protein: ENSMUSP00000138482
Gene: ENSMUSG00000004562

Domain	Start	End	E-Value	Type
low complexity region	72	85	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000182649

Predicted Effect

probably damaging
Transcript: ENSMUST00000182760
AA Change: I153T

PolyPhen 2 Score 0.984 (Sensitivity: 0.74; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000138125
Gene: ENSMUSG00000004562
AA Change: I153T

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: ENSMUST00000182905
AA Change: I153T

PolyPhen 2 Score 0.991 (Sensitivity: 0.71; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000138797
Gene: ENSMUSG00000004562
AA Change: I153T

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

probably damaging
Transcript: ENSMUST00000182909
AA Change: I153T

PolyPhen 2 Score 0.987 (Sensitivity: 0.73; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000138635
Gene: ENSMUSG00000004562
AA Change: I153T

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

unknown
Transcript: ENSMUST00000183208
AA Change: I153T

SMART Domains

Protein: ENSMUSP00000138354
Gene: ENSMUSG00000004562
AA Change: I153T

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

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.6%

Validation Efficiency

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: 84 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1810055G02Rik	A	T	19: 3,715,784	M20L	probably benign	Het
9430007A20Rik	C	T	4: 144,528,784	A258V	probably benign	Het
Abca8b	T	A	11: 109,942,337	D1241V	probably benign	Het
Adam20	G	A	8: 40,795,453	R200H	probably benign	Het
Adcy10	T	C	1: 165,513,112	F229L	probably damaging	Het
Adsl	A	T	15: 80,955,639	N126I	probably benign	Het
Ahnak	AGATCTC	A	19: 9,007,028		probably benign	Het
Ahnak	GATCTCTAT	GAT	19: 9,007,029		probably benign	Het
Aktip	G	A	8: 91,129,727	P41S	probably damaging	Het
Alkbh3	C	A	2: 93,980,973	R258L	probably damaging	Het
Arfgap3	A	G	15: 83,313,533	Y341H	probably benign	Het
Arhgef26	C	T	3: 62,423,613	L583F	probably damaging	Het
Atp1a1	T	C	3: 101,591,441	S179G	probably benign	Het
Bok	T	C	1: 93,686,507	S21P	probably damaging	Het
C130060K24Rik	A	G	6: 65,456,140	I315V	probably benign	Het
Ccdc136	A	G	6: 29,417,442	E754G	probably benign	Het
Cers3	A	G	7: 66,773,630	K108E	probably benign	Het
Cmya5	T	C	13: 93,065,373		probably null	Het
Col19a1	T	C	1: 24,328,067	E478G	possibly damaging	Het
Colec10	T	A	15: 54,459,784	S134R	possibly damaging	Het
Ctnnb1	A	T	9: 120,955,829	I514F	probably damaging	Het
Cux1	C	T	5: 136,309,819	E664K	probably benign	Het
Dars	T	C	1: 128,405,462	Q75R	probably benign	Het
Disp1	T	A	1: 183,135,815	S16C	probably damaging	Het
Dnah7a	A	T	1: 53,559,140	V1412E	probably benign	Het
Ect2l	C	T	10: 18,168,434	V226I	probably benign	Het
Ep400	T	A	5: 110,756,643	H30L	unknown	Het
Ephx4	A	G	5: 107,419,781	I202V	probably benign	Het
Exoc3	A	T	13: 74,192,908	F259Y	probably damaging	Het
Ezr	T	C	17: 6,752,995	E229G	probably damaging	Het
Fat1	A	T	8: 45,017,380	I1472L	probably benign	Het
Fsd1l	T	G	4: 53,679,972	D223E	probably benign	Het
Gata6	A	T	18: 11,059,064	D377V	possibly damaging	Het
Gm12185	A	T	11: 48,907,389	M759K	probably benign	Het
Gm21994	C	T	2: 150,254,576	R311Q	probably benign	Het
Gm9922	C	T	14: 101,729,457	A120T	unknown	Het
Hectd4	A	T	5: 121,310,681	Y364F	probably benign	Het
Hnrnph1	A	G	11: 50,385,869	S465G	unknown	Het
Ifi204	T	C	1: 173,749,358	Y559C	probably damaging	Het
Ift88	T	C	14: 57,481,396	S613P	probably damaging	Het
Kif21a	G	C	15: 90,985,325	A441G	probably damaging	Het
Kif21a	G	T	15: 90,995,512	T191K	probably benign	Het
Lrit1	T	A	14: 37,060,127	C252*	probably null	Het
Ncbp1	T	A	4: 46,144,837	D29E	probably benign	Het
Nlrp10	A	T	7: 108,925,528	D248E	probably damaging	Het
Nphp4	T	G	4: 152,547,064	V807G	probably benign	Het
Nsd1	T	C	13: 55,246,043	S589P	possibly damaging	Het
Oas1b	T	A	5: 120,814,485	N80K	probably damaging	Het
Olfr1055	G	A	2: 86,347,239	H176Y	probably benign	Het
Olfr1135	A	T	2: 87,671,761	I202N	probably benign	Het
Oprk1	T	A	1: 5,598,873	C181S	probably damaging	Het
Oprl1	T	A	2: 181,718,419	N89K	probably damaging	Het
Pdcd11	A	G	19: 47,129,302	K1697E	probably damaging	Het
Pdp1	G	A	4: 11,961,607	H254Y	probably benign	Het
Pds5b	A	T	5: 150,805,663	D1419V	possibly damaging	Het
Per1	G	T	11: 69,100,649	G3V	probably benign	Het
Pex16	C	A	2: 92,376,643	N55K	probably damaging	Het
Phldb2	C	A	16: 45,774,977	L862F	probably benign	Het
Pld5	T	A	1: 175,964,006	D478V	probably benign	Het
Pms2	T	C	5: 143,914,796	I177T	probably damaging	Het
Pou1f1	A	T	16: 65,529,872	E119D	probably benign	Het
Ppp2r1a	A	C	17: 20,958,796	E295A	probably damaging	Het
Rad51ap2	A	T	12: 11,457,592	N505I	possibly damaging	Het
Rasal3	A	C	17: 32,396,562	V434G	probably damaging	Het
Rasgrf2	C	T	13: 91,987,973	V6M		Het
Rwdd1	A	T	10: 34,001,156	D197E		Het
Scn11a	A	T	9: 119,790,010	C755*	probably null	Het
Skil	T	C	3: 31,116,860	S443P	probably benign	Het
Slc12a6	T	C	2: 112,356,472	C939R	probably damaging	Het
Slc25a36	A	G	9: 97,079,177	S269P	probably benign	Het
Srrm4	T	A	5: 116,482,393	H92L	unknown	Het
Styk1	CTCTTCATGATTTTCTT	CTCTT	6: 131,301,649		probably benign	Het
Tbc1d4	A	T	14: 101,507,410	V260E	probably benign	Het
Tbc1d8	T	C	1: 39,385,232	N593D	probably damaging	Het
Trex1	C	A	9: 109,058,737	R62L	probably damaging	Het
Trpm3	A	T	19: 22,715,352	D269V	possibly damaging	Het
Trpv4	G	T	5: 114,633,150	Y439*	probably null	Het
Ttn	G	A	2: 76,734,248	T28515I	probably damaging	Het
Ucn2	G	A	9: 108,986,503	G111D	probably damaging	Het
Uhrf2	A	G	19: 30,056,481	I212V	possibly damaging	Het
Usp24	T	A	4: 106,347,367	M261K	probably benign	Het
Vmn1r235	A	T	17: 21,261,698	D95V	probably benign	Het
Vwf	G	A	6: 125,624,573	R826Q		Het
Zfp28	T	C	7: 6,393,879	C438R	probably damaging	Het

Other mutations in Arhgef40

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00332:Arhgef40	APN	14	51988960	missense	probably damaging	1.00
IGL00848:Arhgef40	APN	14	51987427	missense	probably damaging	1.00
IGL00966:Arhgef40	APN	14	51991698	critical splice donor site	probably null
IGL01123:Arhgef40	APN	14	51994346	missense	probably damaging	0.99
IGL02110:Arhgef40	APN	14	51989405	missense	probably damaging	1.00
IGL02490:Arhgef40	APN	14	51989195	missense	probably damaging	0.99
IGL02505:Arhgef40	APN	14	52000863	missense	probably damaging	1.00
IGL02636:Arhgef40	APN	14	51997408	missense	probably damaging	1.00
R0200:Arhgef40	UTSW	14	51996974	missense	probably damaging	0.99
R0496:Arhgef40	UTSW	14	52004907	unclassified	probably benign
R0608:Arhgef40	UTSW	14	51996974	missense	probably damaging	0.99
R0826:Arhgef40	UTSW	14	52000993	missense	probably benign	0.05
R1126:Arhgef40	UTSW	14	51997126	missense	probably damaging	0.96
R1330:Arhgef40	UTSW	14	51990156	missense	probably benign	0.42
R1612:Arhgef40	UTSW	14	52004081	missense	probably damaging	1.00
R1794:Arhgef40	UTSW	14	51989930	missense	possibly damaging	0.94
R1844:Arhgef40	UTSW	14	51997623	missense	probably damaging	0.99
R2018:Arhgef40	UTSW	14	52003705	missense	probably damaging	1.00
R2064:Arhgef40	UTSW	14	51996183	missense	probably damaging	1.00
R2321:Arhgef40	UTSW	14	51994276	splice site	probably benign
R3877:Arhgef40	UTSW	14	52002285	missense	probably damaging	1.00
R4233:Arhgef40	UTSW	14	51990171	missense	possibly damaging	0.50
R4596:Arhgef40	UTSW	14	51987224	critical splice donor site	probably null
R4676:Arhgef40	UTSW	14	51990959	nonsense	probably null
R4703:Arhgef40	UTSW	14	52002310	missense	probably damaging	1.00
R4704:Arhgef40	UTSW	14	52002310	missense	probably damaging	1.00
R4719:Arhgef40	UTSW	14	52004938	unclassified	probably benign
R4915:Arhgef40	UTSW	14	51990099	missense	probably damaging	1.00
R4917:Arhgef40	UTSW	14	51990099	missense	probably damaging	1.00
R4918:Arhgef40	UTSW	14	51990099	missense	probably damaging	1.00
R5097:Arhgef40	UTSW	14	51989689	missense	probably damaging	1.00
R5183:Arhgef40	UTSW	14	52004099	missense	probably damaging	0.98
R5195:Arhgef40	UTSW	14	51989812	missense	possibly damaging	0.68
R5367:Arhgef40	UTSW	14	51989699	missense	probably damaging	0.99
R5381:Arhgef40	UTSW	14	51991849	missense	probably damaging	0.99
R5594:Arhgef40	UTSW	14	51996157	missense	probably damaging	1.00
R5632:Arhgef40	UTSW	14	51994338	missense	probably damaging	1.00
R5665:Arhgef40	UTSW	14	52000900	missense	possibly damaging	0.80
R5798:Arhgef40	UTSW	14	51997032	missense	probably damaging	1.00
R5820:Arhgef40	UTSW	14	51987496	missense	possibly damaging	0.76
R6229:Arhgef40	UTSW	14	51990090	missense	probably benign	0.06
R6451:Arhgef40	UTSW	14	52000999	missense	probably damaging	1.00
R6633:Arhgef40	UTSW	14	51997431	missense	probably damaging	1.00
R6642:Arhgef40	UTSW	14	51990962	unclassified	probably benign
R6675:Arhgef40	UTSW	14	51991641	missense	probably damaging	0.99
R6781:Arhgef40	UTSW	14	51997897	intron	probably benign
R6901:Arhgef40	UTSW	14	51997368	missense	probably damaging	1.00
R7852:Arhgef40	UTSW	14	51991797	missense	unknown
R7857:Arhgef40	UTSW	14	51988755	missense	probably damaging	0.97
R7914:Arhgef40	UTSW	14	51987575	missense	probably damaging	1.00
R8060:Arhgef40	UTSW	14	51984995	splice site	probably benign
R8144:Arhgef40	UTSW	14	51998175	missense	probably damaging	1.00
R8195:Arhgef40	UTSW	14	51988769	missense	probably damaging	1.00
R8432:Arhgef40	UTSW	14	51989400	missense	probably benign	0.00
R8738:Arhgef40	UTSW	14	52000957	missense	probably damaging	1.00
R8830:Arhgef40	UTSW	14	52003708	missense	probably damaging	1.00
R9038:Arhgef40	UTSW	14	51997615	missense	probably damaging	0.96
U24488:Arhgef40	UTSW	14	51998216	missense	probably benign	0.07
X0023:Arhgef40	UTSW	14	52003684	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- AGGCCCAGTATAGTGGATTCCTC -3'
(R):5'- TACCAAGTACCTCCTCAGGG -3'

Sequencing Primer
(F):5'- GCCACTCTGCTTGCATGAG -3'
(R):5'- TCCTCAGGGAGTGGAGAGCTG -3'

Posted On

2022-10-06