Incidental Mutation 'R4422:Arhgef9'
ID 327183
Institutional Source Beutler Lab
Gene Symbol Arhgef9
Ensembl Gene ENSMUSG00000025656
Gene Name CDC42 guanine nucleotide exchange factor 9
Synonyms collybistin, 9630036L12Rik
MMRRC Submission 041695-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.212) question?
Stock # R4422 (G1)
Quality Score 222
Status Validated
Chromosome X
Chromosomal Location 94092541-94240462 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to G at 94144670 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Leucine at position 131 (I131L)
Ref Sequence ENSEMBL: ENSMUSP00000142905 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000113873] [ENSMUST00000113876] [ENSMUST00000113878] [ENSMUST00000113882] [ENSMUST00000113883] [ENSMUST00000113884] [ENSMUST00000182562] [ENSMUST00000113885] [ENSMUST00000128565] [ENSMUST00000197206] [ENSMUST00000197364] [ENSMUST00000198753] [ENSMUST00000200628] [ENSMUST00000199920] [ENSMUST00000181987] [ENSMUST00000182001]
AlphaFold Q3UTH8
Predicted Effect probably benign
Transcript: ENSMUST00000113873
AA Change: I50L

PolyPhen 2 Score 0.105 (Sensitivity: 0.93; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000109505
Gene: ENSMUSG00000025656
AA Change: I50L

DomainStartEndE-ValueType
RhoGEF 5 184 1.63e-63 SMART
PH 217 325 5.41e-10 SMART
low complexity region 363 372 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000113876
AA Change: I131L

PolyPhen 2 Score 0.105 (Sensitivity: 0.93; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000109508
Gene: ENSMUSG00000025656
AA Change: I131L

DomainStartEndE-ValueType
SH3 1 45 6.5e-7 SMART
RhoGEF 86 265 1.63e-63 SMART
PH 298 406 5.41e-10 SMART
low complexity region 444 453 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000113878
AA Change: I152L

PolyPhen 2 Score 0.105 (Sensitivity: 0.93; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000109510
Gene: ENSMUSG00000025656
AA Change: I152L

DomainStartEndE-ValueType
SH3 11 66 2.11e-15 SMART
RhoGEF 107 286 1.63e-63 SMART
PH 319 427 5.41e-10 SMART
low complexity region 465 474 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000113882
AA Change: I152L

PolyPhen 2 Score 0.105 (Sensitivity: 0.93; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000109514
Gene: ENSMUSG00000025656
AA Change: I152L

DomainStartEndE-ValueType
SH3 11 66 2.11e-15 SMART
RhoGEF 107 286 1.63e-63 SMART
PH 319 427 5.41e-10 SMART
low complexity region 465 474 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000113883
AA Change: I152L

PolyPhen 2 Score 0.105 (Sensitivity: 0.93; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000109515
Gene: ENSMUSG00000025656
AA Change: I152L

DomainStartEndE-ValueType
SH3 11 66 2.11e-15 SMART
RhoGEF 107 286 1.63e-63 SMART
PH 319 427 5.41e-10 SMART
low complexity region 465 474 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000113884
AA Change: I159L

PolyPhen 2 Score 0.436 (Sensitivity: 0.89; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000109516
Gene: ENSMUSG00000025656
AA Change: I159L

DomainStartEndE-ValueType
SH3 18 73 2.11e-15 SMART
RhoGEF 114 293 1.63e-63 SMART
PH 326 434 5.41e-10 SMART
low complexity region 509 518 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000182562
AA Change: I50L

PolyPhen 2 Score 0.123 (Sensitivity: 0.93; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000138147
Gene: ENSMUSG00000025656
AA Change: I50L

DomainStartEndE-ValueType
Pfam:RhoGEF 5 54 6.4e-14 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000113885
AA Change: I152L

PolyPhen 2 Score 0.245 (Sensitivity: 0.91; Specificity: 0.88)
SMART Domains Protein: ENSMUSP00000109517
Gene: ENSMUSG00000025656
AA Change: I152L

DomainStartEndE-ValueType
SH3 11 66 2.11e-15 SMART
RhoGEF 107 286 1.63e-63 SMART
PH 319 427 5.41e-10 SMART
low complexity region 465 474 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000128565
AA Change: I99L

PolyPhen 2 Score 0.436 (Sensitivity: 0.89; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000138258
Gene: ENSMUSG00000025656
AA Change: I99L

DomainStartEndE-ValueType
RhoGEF 54 233 1.63e-63 SMART
PH 266 374 5.41e-10 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000197206
AA Change: I99L

PolyPhen 2 Score 0.436 (Sensitivity: 0.89; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000142769
Gene: ENSMUSG00000025656
AA Change: I99L

DomainStartEndE-ValueType
RhoGEF 54 233 1e-65 SMART
PH 266 374 2.4e-12 SMART
low complexity region 412 421 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000197364
AA Change: I159L

PolyPhen 2 Score 0.245 (Sensitivity: 0.91; Specificity: 0.88)
SMART Domains Protein: ENSMUSP00000142615
Gene: ENSMUSG00000025656
AA Change: I159L

DomainStartEndE-ValueType
SH3 18 73 1.3e-17 SMART
RhoGEF 114 293 1e-65 SMART
PH 326 434 2.4e-12 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000198753
AA Change: I92L

PolyPhen 2 Score 0.105 (Sensitivity: 0.93; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000142911
Gene: ENSMUSG00000025656
AA Change: I92L

DomainStartEndE-ValueType
RhoGEF 47 226 1e-65 SMART
Predicted Effect possibly damaging
Transcript: ENSMUST00000200628
AA Change: I131L

PolyPhen 2 Score 0.617 (Sensitivity: 0.87; Specificity: 0.91)
SMART Domains Protein: ENSMUSP00000142905
Gene: ENSMUSG00000025656
AA Change: I131L

DomainStartEndE-ValueType
SH3 1 45 4e-9 SMART
RhoGEF 86 220 4.2e-20 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000199920
AA Change: I131L

PolyPhen 2 Score 0.105 (Sensitivity: 0.93; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000143779
Gene: ENSMUSG00000025656
AA Change: I131L

DomainStartEndE-ValueType
SH3 1 45 6.5e-7 SMART
RhoGEF 86 265 1.63e-63 SMART
PH 298 406 5.41e-10 SMART
low complexity region 444 453 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000181987
AA Change: I159L

PolyPhen 2 Score 0.050 (Sensitivity: 0.94; Specificity: 0.83)
SMART Domains Protein: ENSMUSP00000138461
Gene: ENSMUSG00000025656
AA Change: I159L

DomainStartEndE-ValueType
SH3 18 73 2.11e-15 SMART
RhoGEF 114 293 1.63e-63 SMART
PH 326 434 5.41e-10 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000182001
AA Change: I131L

PolyPhen 2 Score 0.105 (Sensitivity: 0.93; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000138668
Gene: ENSMUSG00000025656
AA Change: I131L

DomainStartEndE-ValueType
SH3 1 45 6.5e-7 SMART
RhoGEF 86 265 1.63e-63 SMART
PH 298 406 5.41e-10 SMART
low complexity region 444 453 N/A INTRINSIC
Meta Mutation Damage Score 0.6685 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.3%
  • 20x: 95.3%
Validation Efficiency 96% (67/70)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is a Rho-like GTPase that switches between the active (GTP-bound) state and inactive (GDP-bound) state to regulate CDC42 and other genes. Defects in this gene are a cause of startle disease with epilepsy (STHEE), also known as hyperekplexia with epilepsy. Three transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Mar 2010]
PHENOTYPE: Male mice hemizygous for a null allele exhibit impaired spatial learning, increased anxiety-associated behaviors, and altered central nervous system synaptic transmission. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 63 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adamts13 T C 2: 26,895,412 (GRCm39) S1168P probably benign Het
Adgrf2 T C 17: 43,024,046 (GRCm39) M142V probably benign Het
Akna G T 4: 63,305,330 (GRCm39) Q479K possibly damaging Het
AW551984 A T 9: 39,511,373 (GRCm39) C111S probably null Het
Bak1 C A 17: 27,240,298 (GRCm39) G130W probably damaging Het
Bank1 T A 3: 135,788,972 (GRCm39) Q441L probably damaging Het
C030034I22Rik T C 17: 69,725,153 (GRCm39) noncoding transcript Het
Capns2 T A 8: 93,628,252 (GRCm39) I47N possibly damaging Het
Cct7 A G 6: 85,444,127 (GRCm39) R355G probably damaging Het
Cd19 C T 7: 126,012,578 (GRCm39) V272I probably benign Het
Cenpf A G 1: 189,390,547 (GRCm39) L1095S probably damaging Het
Cep44 G A 8: 56,991,652 (GRCm39) P317S probably benign Het
Chrm3 A T 13: 9,928,591 (GRCm39) Y148* probably null Het
Chrnb3 T C 8: 27,886,761 (GRCm39) V445A possibly damaging Het
Col4a4 T A 1: 82,467,559 (GRCm39) M852L unknown Het
Dhx29 T C 13: 113,083,781 (GRCm39) L612P probably damaging Het
Dlgap2 T C 8: 14,793,463 (GRCm39) probably null Het
Dnah17 T C 11: 117,972,799 (GRCm39) T2045A possibly damaging Het
Dync1li1 A G 9: 114,538,377 (GRCm39) T245A probably damaging Het
Epha4 T C 1: 77,488,354 (GRCm39) E42G probably damaging Het
Fam120b C A 17: 15,622,445 (GRCm39) T141K probably damaging Het
Fhod1 T C 8: 106,063,983 (GRCm39) probably benign Het
Gcnt2 T G 13: 41,014,001 (GRCm39) Y57* probably null Het
Gm5409 C T 6: 41,396,519 (GRCm39) noncoding transcript Het
Hip1r A G 5: 124,135,069 (GRCm39) K402E possibly damaging Het
Hlcs G A 16: 93,939,819 (GRCm39) P506L possibly damaging Het
Itih4 T A 14: 30,611,821 (GRCm39) F142I probably damaging Het
Krt78 T C 15: 101,856,375 (GRCm39) T479A probably benign Het
Lamb2 A G 9: 108,360,754 (GRCm39) D518G probably damaging Het
Ldlr G A 9: 21,649,248 (GRCm39) C341Y probably damaging Het
Lsr G T 7: 30,665,422 (GRCm39) N177K probably benign Het
Macf1 G A 4: 123,359,839 (GRCm39) S1815F probably damaging Het
Mms22l T C 4: 24,503,008 (GRCm39) S95P probably damaging Het
Mon2 A G 10: 122,878,887 (GRCm39) L218P probably damaging Het
Nlrp4f C T 13: 65,332,776 (GRCm39) probably null Het
Nrde2 G A 12: 100,112,286 (GRCm39) Q137* probably null Het
Or12e10 C A 2: 87,640,989 (GRCm39) T275K probably damaging Het
Or51l14 G T 7: 103,101,450 (GRCm39) R302L probably damaging Het
Or6z7 G T 7: 6,484,037 (GRCm39) Y39* probably null Het
Phf24 G A 4: 42,934,817 (GRCm39) C151Y probably damaging Het
Pik3r1 T G 13: 101,830,892 (GRCm39) N3T probably benign Het
Plcb2 T C 2: 118,542,484 (GRCm39) K821E probably benign Het
Ppat A G 5: 77,063,061 (GRCm39) W517R probably damaging Het
Prelid2 T C 18: 42,045,461 (GRCm39) T150A probably benign Het
Psg21 A G 7: 18,381,257 (GRCm39) S429P probably damaging Het
Reg4 T C 3: 98,140,360 (GRCm39) Y114H possibly damaging Het
Rsbn1l G T 5: 21,101,544 (GRCm39) H665Q probably damaging Het
Rspo2 T C 15: 43,033,150 (GRCm39) N24S probably benign Het
Ryr2 G T 13: 11,731,952 (GRCm39) C2329* probably null Het
Skint2 T A 4: 112,441,785 (GRCm39) probably benign Het
Spmap2l T C 5: 77,202,383 (GRCm39) I268T possibly damaging Het
Syvn1 C T 19: 6,099,951 (GRCm39) probably benign Het
Tmem53 T C 4: 117,123,149 (GRCm39) Y37H probably damaging Het
Tmem59l G A 8: 70,938,749 (GRCm39) R111W probably damaging Het
Tnks2 G A 19: 36,823,053 (GRCm39) V107I probably damaging Het
Tpcn1 T C 5: 120,680,583 (GRCm39) K549R probably damaging Het
Tubgcp4 T A 2: 121,019,882 (GRCm39) L404* probably null Het
Vmn2r86 T C 10: 130,288,845 (GRCm39) I219V possibly damaging Het
Vsig10 T C 5: 117,462,986 (GRCm39) S71P probably benign Het
Wnk1 T C 6: 119,930,856 (GRCm39) N896S probably benign Het
Zfp871 T A 17: 32,993,808 (GRCm39) S437C probably benign Het
Zfp871 C A 17: 32,993,807 (GRCm39) S456I probably benign Het
Zfp873 A G 10: 81,896,708 (GRCm39) T480A probably benign Het
Other mutations in Arhgef9
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00264:Arhgef9 APN X 94,125,237 (GRCm39) splice site probably null
IGL00690:Arhgef9 APN X 94,125,285 (GRCm39) missense probably damaging 1.00
IGL02536:Arhgef9 APN X 94,102,443 (GRCm39) missense probably damaging 1.00
IGL02863:Arhgef9 APN X 94,121,110 (GRCm39) missense probably damaging 1.00
R1820:Arhgef9 UTSW X 94,125,142 (GRCm39) missense probably damaging 1.00
R4423:Arhgef9 UTSW X 94,144,670 (GRCm39) missense possibly damaging 0.62
X0027:Arhgef9 UTSW X 94,098,605 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- CACTCACACACTCTTCCATGG -3'
(R):5'- ATCCCCTTATGAAAACTGAAAATGGG -3'

Sequencing Primer
(F):5'- ACACACTCTTCCATGGTTTCCTAGTG -3'
(R):5'- TCATGTGGGTCCTGAACAAC -3'
Posted On 2015-07-07