Incidental Mutation 'R5488:Rab40c'
ID 430488
Institutional Source Beutler Lab
Gene Symbol Rab40c
Ensembl Gene ENSMUSG00000025730
Gene Name Rab40C, member RAS oncogene family
Synonyms RAR3
MMRRC Submission 043049-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.182) question?
Stock # R5488 (G1)
Quality Score 225
Status Validated
Chromosome 17
Chromosomal Location 26101088-26138688 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to A at 26109643 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Isoleucine at position 78 (T78I)
Ref Sequence ENSEMBL: ENSMUSP00000130093 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000026826] [ENSMUST00000163356] [ENSMUST00000164738] [ENSMUST00000164982] [ENSMUST00000166146] [ENSMUST00000167018] [ENSMUST00000167626] [ENSMUST00000179998]
AlphaFold Q8VHQ4
Predicted Effect probably benign
Transcript: ENSMUST00000026826
AA Change: T78I

PolyPhen 2 Score 0.064 (Sensitivity: 0.94; Specificity: 0.84)
SMART Domains Protein: ENSMUSP00000026826
Gene: ENSMUSG00000025730
AA Change: T78I

DomainStartEndE-ValueType
RAB 15 177 9.2e-77 SMART
SOCS 183 226 1.6e-18 SMART
SOCS_box 189 225 7.2e-10 SMART
low complexity region 238 262 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000163356
SMART Domains Protein: ENSMUSP00000130209
Gene: ENSMUSG00000025731

DomainStartEndE-ValueType
Pfam:DUF938 1 172 1.6e-74 PFAM
Pfam:Methyltransf_25 31 133 9e-8 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000164738
AA Change: T78I

PolyPhen 2 Score 0.981 (Sensitivity: 0.75; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000130093
Gene: ENSMUSG00000025730
AA Change: T78I

DomainStartEndE-ValueType
Pfam:Arf 5 110 5.2e-7 PFAM
Pfam:Miro 16 111 4.2e-12 PFAM
Pfam:Ras 16 111 2.6e-25 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000164982
AA Change: T78I

PolyPhen 2 Score 0.960 (Sensitivity: 0.78; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000127868
Gene: ENSMUSG00000025730
AA Change: T78I

DomainStartEndE-ValueType
RAB 15 158 5.56e-54 SMART
SOCS 164 207 2.56e-16 SMART
SOCS_box 170 206 9.29e-6 SMART
low complexity region 219 243 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000166146
SMART Domains Protein: ENSMUSP00000132355
Gene: ENSMUSG00000025730

DomainStartEndE-ValueType
SCOP:d3raba_ 10 43 3e-9 SMART
Blast:RAB 15 49 1e-15 BLAST
Predicted Effect noncoding transcript
Transcript: ENSMUST00000166619
Predicted Effect probably benign
Transcript: ENSMUST00000167018
AA Change: T78I

PolyPhen 2 Score 0.064 (Sensitivity: 0.94; Specificity: 0.84)
SMART Domains Protein: ENSMUSP00000131055
Gene: ENSMUSG00000025730
AA Change: T78I

DomainStartEndE-ValueType
RAB 15 177 1.88e-74 SMART
SOCS 183 226 2.56e-16 SMART
SOCS_box 189 225 9.29e-6 SMART
low complexity region 238 262 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000167626
AA Change: T78I

PolyPhen 2 Score 0.064 (Sensitivity: 0.94; Specificity: 0.84)
SMART Domains Protein: ENSMUSP00000127546
Gene: ENSMUSG00000025730
AA Change: T78I

DomainStartEndE-ValueType
RAB 15 177 9.2e-77 SMART
SOCS 183 226 1.6e-18 SMART
SOCS_box 189 225 7.2e-10 SMART
low complexity region 238 262 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000172168
Predicted Effect probably benign
Transcript: ENSMUST00000179998
AA Change: T78I

PolyPhen 2 Score 0.064 (Sensitivity: 0.94; Specificity: 0.84)
SMART Domains Protein: ENSMUSP00000136612
Gene: ENSMUSG00000025730
AA Change: T78I

DomainStartEndE-ValueType
RAB 15 177 9.4e-77 SMART
SOCS 183 226 1.7e-18 SMART
SOCS_box 189 225 7.3e-10 SMART
low complexity region 238 262 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000180868
Meta Mutation Damage Score 0.8696 question?
Coding Region Coverage
  • 1x: 98.2%
  • 3x: 97.2%
  • 10x: 95.1%
  • 20x: 90.5%
Validation Efficiency 97% (58/60)
Allele List at MGI
Other mutations in this stock
Total: 52 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca14 T A 7: 119,851,473 (GRCm39) V817D probably damaging Het
Abca5 A G 11: 110,183,009 (GRCm39) V1016A probably benign Het
Ano2 G T 6: 126,016,216 (GRCm39) M916I possibly damaging Het
Aqr T C 2: 113,963,554 (GRCm39) N632S probably damaging Het
Cd48 G A 1: 171,523,273 (GRCm39) V39I possibly damaging Het
Cdcp3 A G 7: 130,848,324 (GRCm39) D710G probably damaging Het
Cdk17 A G 10: 93,068,274 (GRCm39) T344A probably damaging Het
Chd8 A T 14: 52,450,505 (GRCm39) probably benign Het
Col4a1 A T 8: 11,362,550 (GRCm39) probably benign Het
Col9a3 G A 2: 180,258,318 (GRCm39) R579H probably damaging Het
Cripto G A 9: 110,772,265 (GRCm39) R44C probably benign Het
Cyp2c69 T G 19: 39,839,603 (GRCm39) Q340P probably null Het
D630003M21Rik T A 2: 158,058,941 (GRCm39) T320S probably benign Het
D630045J12Rik A T 6: 38,173,782 (GRCm39) S129T possibly damaging Het
Eif4a3l1 C G 6: 136,306,555 (GRCm39) R339G probably damaging Het
Fam13a A T 6: 59,001,303 (GRCm39) L8Q probably null Het
Fam83b T C 9: 76,452,881 (GRCm39) N62S probably benign Het
Foxred1 A T 9: 35,121,266 (GRCm39) V94E probably damaging Het
Gprc5a T C 6: 135,055,868 (GRCm39) V105A probably damaging Het
Gvin3 T A 7: 106,200,797 (GRCm39) noncoding transcript Het
Itga2 A T 13: 114,979,971 (GRCm39) W1077R probably damaging Het
Kat6b A G 14: 21,719,332 (GRCm39) D1228G probably damaging Het
Kctd3 A G 1: 188,713,563 (GRCm39) Y391H probably damaging Het
Kdelr2 T A 5: 143,389,784 (GRCm39) I23N probably damaging Het
Kmt2a A T 9: 44,752,335 (GRCm39) probably benign Het
Lao1 A G 4: 118,824,566 (GRCm39) E216G probably damaging Het
Mark4 G T 7: 19,163,532 (GRCm39) probably null Het
Mcm10 A G 2: 4,996,929 (GRCm39) W851R probably damaging Het
Mettl21e T C 1: 44,257,276 (GRCm39) Y14C probably benign Het
Miga1 CACAACAACAACAACAACA CACAACAACAACAACA 3: 152,039,083 (GRCm39) probably benign Het
Mmp20 A G 9: 7,643,958 (GRCm39) probably null Het
Nlrp5 A T 7: 23,117,359 (GRCm39) D361V probably benign Het
Nrip3 T C 7: 109,361,045 (GRCm39) T210A probably damaging Het
Or12d2 T C 17: 37,624,559 (GRCm39) T239A probably damaging Het
Or52s1b T C 7: 102,822,658 (GRCm39) Y62C probably damaging Het
Pcdh10 G A 3: 45,335,803 (GRCm39) G706S probably damaging Het
Pdzd2 G A 15: 12,382,762 (GRCm39) P1197L probably benign Het
Pfkfb3 T C 2: 11,489,480 (GRCm39) S273G probably benign Het
Pkn3 T C 2: 29,978,596 (GRCm39) probably null Het
Rec8 A T 14: 55,860,283 (GRCm39) Q291L probably benign Het
Robo4 CGG CG 9: 37,322,786 (GRCm39) probably null Het
Sart3 A G 5: 113,909,441 (GRCm39) W86R probably damaging Het
Slc6a11 A G 6: 114,220,855 (GRCm39) D462G probably damaging Het
Syne2 A G 12: 75,934,946 (GRCm39) T143A probably benign Het
Tardbp A G 4: 148,703,097 (GRCm39) F289S probably benign Het
Tdpoz1 T A 3: 93,577,974 (GRCm39) Y270F possibly damaging Het
Tmem117 ACCC ACC 15: 94,992,698 (GRCm39) probably null Het
Trim43a A T 9: 88,464,229 (GRCm39) I47F probably damaging Het
Vim A T 2: 13,580,392 (GRCm39) T202S probably benign Het
Vps13b A T 15: 35,770,688 (GRCm39) I2044L probably benign Het
Wdr5 T G 2: 27,415,165 (GRCm39) D192E probably damaging Het
Zmym2 A G 14: 57,193,712 (GRCm39) K1176E possibly damaging Het
Other mutations in Rab40c
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00500:Rab40c APN 17 26,104,059 (GRCm39) missense probably damaging 1.00
IGL01793:Rab40c APN 17 26,103,596 (GRCm39) missense probably damaging 1.00
IGL01936:Rab40c APN 17 26,103,644 (GRCm39) missense probably damaging 0.99
R0089:Rab40c UTSW 17 26,104,122 (GRCm39) missense probably damaging 1.00
R0456:Rab40c UTSW 17 26,103,631 (GRCm39) missense possibly damaging 0.68
R0837:Rab40c UTSW 17 26,103,667 (GRCm39) missense probably damaging 1.00
R1547:Rab40c UTSW 17 26,102,724 (GRCm39) missense probably damaging 1.00
R5955:Rab40c UTSW 17 26,103,631 (GRCm39) missense probably damaging 0.98
R7047:Rab40c UTSW 17 26,138,458 (GRCm39) missense probably damaging 0.98
R8923:Rab40c UTSW 17 26,102,664 (GRCm39) missense probably benign 0.01
R8951:Rab40c UTSW 17 26,138,407 (GRCm39) missense probably damaging 1.00
X0028:Rab40c UTSW 17 26,109,682 (GRCm39) splice site probably null
Predicted Primers PCR Primer
(F):5'- CGATGTCCAGATGTCAAAATACTTCAG -3'
(R):5'- AGCCTCCTCCAATTTTACTCATAACAG -3'

Sequencing Primer
(F):5'- ATGTAGCTCAGCCGTTGAAC -3'
(R):5'- CCTTTAATACCAGTGCTTAGGAGGC -3'
Posted On 2016-10-05