Incidental Mutation 'R3946:Trmt13'
ID 307696
Institutional Source Beutler Lab
Gene Symbol Trmt13
Ensembl Gene ENSMUSG00000033439
Gene Name tRNA methyltransferase 13
Synonyms A930028L21Rik, Ccdc76, 4631408H19Rik
MMRRC Submission 040827-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.151) question?
Stock # R3946 (G1)
Quality Score 225
Status Validated
Chromosome 3
Chromosomal Location 116374742-116408236 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 116375167 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Phenylalanine to Serine at position 447 (F447S)
Ref Sequence ENSEMBL: ENSMUSP00000047320 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000029573] [ENSMUST00000041524] [ENSMUST00000183638] [ENSMUST00000184963] [ENSMUST00000197190]
AlphaFold Q8BYH3
Predicted Effect probably benign
Transcript: ENSMUST00000029573
SMART Domains Protein: ENSMUSP00000029573
Gene: ENSMUSG00000027961

DomainStartEndE-ValueType
LRR 105 127 1.15e1 SMART
LRR_TYP 128 151 7.26e-3 SMART
LRR 175 197 6.58e0 SMART
LRR 198 220 1e1 SMART
LRR 221 243 7.16e0 SMART
LRR 244 267 6.58e0 SMART
Predicted Effect probably damaging
Transcript: ENSMUST00000041524
AA Change: F447S

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000047320
Gene: ENSMUSG00000033439
AA Change: F447S

DomainStartEndE-ValueType
Pfam:zf-TRM13_CCCH 17 45 7.2e-17 PFAM
Pfam:zf-U11-48K 56 80 3.4e-12 PFAM
Pfam:TRM13 165 469 7e-96 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000156161
Predicted Effect probably benign
Transcript: ENSMUST00000183638
SMART Domains Protein: ENSMUSP00000139223
Gene: ENSMUSG00000033439

DomainStartEndE-ValueType
Pfam:zf-TRM13_CCCH 16 46 1.4e-17 PFAM
Pfam:zf-U11-48K 55 81 1.2e-12 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000184963
SMART Domains Protein: ENSMUSP00000138868
Gene: ENSMUSG00000033439

DomainStartEndE-ValueType
Pfam:zf-TRM13_CCCH 16 46 2.9e-17 PFAM
Pfam:zf-U11-48K 55 81 2.3e-12 PFAM
Pfam:TRM13 165 285 3.4e-42 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000197190
SMART Domains Protein: ENSMUSP00000143637
Gene: ENSMUSG00000033439

DomainStartEndE-ValueType
Pfam:TRM13 116 179 5.2e-19 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000199439
Meta Mutation Damage Score 0.9095 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.0%
  • 20x: 94.1%
Validation Efficiency 98% (60/61)
Allele List at MGI
Other mutations in this stock
Total: 61 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abi2 A G 1: 60,492,913 (GRCm39) Q328R probably damaging Het
Agr3 C A 12: 35,997,512 (GRCm39) probably benign Het
Brca2 T A 5: 150,460,169 (GRCm39) S481R probably damaging Het
Cabin1 T G 10: 75,581,093 (GRCm39) Q411P probably damaging Het
Calr3 A G 8: 73,197,464 (GRCm39) Y22H probably damaging Het
Caprin1 T A 2: 103,627,111 (GRCm39) I59F probably damaging Het
Cdk5rap1 T C 2: 154,190,636 (GRCm39) T442A probably damaging Het
Chn2 T C 6: 54,246,411 (GRCm39) probably benign Het
Cic C A 7: 24,971,771 (GRCm39) R501S possibly damaging Het
Coch A G 12: 51,648,595 (GRCm39) probably null Het
Defa25 G A 8: 21,574,506 (GRCm39) V17I probably null Het
Dglucy T C 12: 100,804,959 (GRCm39) probably null Het
Dtx1 T G 5: 120,819,351 (GRCm39) T616P possibly damaging Het
Eef1g T C 19: 8,947,341 (GRCm39) L171P probably benign Het
Fam135a A G 1: 24,069,475 (GRCm39) S465P probably damaging Het
Gm14412 A T 2: 177,006,478 (GRCm39) C472* probably null Het
Gm7104 T C 12: 88,252,812 (GRCm39) noncoding transcript Het
Got2 A G 8: 96,614,858 (GRCm39) S26P probably benign Het
H2-M11 A G 17: 36,860,123 (GRCm39) I329M probably damaging Het
Hmcn2 T A 2: 31,272,406 (GRCm39) D1295E possibly damaging Het
Hoxd12 G T 2: 74,505,771 (GRCm39) R114L probably damaging Het
Ilkap A C 1: 91,314,972 (GRCm39) D124E probably damaging Het
Maco1 A G 4: 134,531,792 (GRCm39) Y626H probably damaging Het
Med6 T C 12: 81,628,625 (GRCm39) Y88C probably damaging Het
Mep1a A T 17: 43,785,932 (GRCm39) L719* probably null Het
Mmp23 T C 4: 155,736,480 (GRCm39) Y187C probably damaging Het
Myo1g A G 11: 6,470,760 (GRCm39) M32T possibly damaging Het
Ncstn T C 1: 171,895,061 (GRCm39) E614G probably benign Het
Nr2c2 C T 6: 92,140,119 (GRCm39) R464W probably damaging Het
Or4f15 G A 2: 111,813,642 (GRCm39) T259M possibly damaging Het
Otub2 T A 12: 103,359,085 (GRCm39) L58* probably null Het
Pcdhga12 G A 18: 37,900,682 (GRCm39) V505I probably benign Het
Pcdhga9 T A 18: 37,870,897 (GRCm39) V242D probably damaging Het
Pex1 C T 5: 3,676,084 (GRCm39) L891F probably damaging Het
Pgm2 C T 5: 64,269,404 (GRCm39) T497I probably benign Het
Pikfyve T C 1: 65,235,840 (GRCm39) F171L probably damaging Het
Pilrb1 T G 5: 137,855,654 (GRCm39) K79T probably benign Het
Pin1 C T 9: 20,566,660 (GRCm39) R21W probably damaging Het
Prxl2c T C 13: 64,456,912 (GRCm39) I104V probably damaging Het
Ptprq A G 10: 107,522,253 (GRCm39) probably benign Het
Rad17 G A 13: 100,759,371 (GRCm39) A552V possibly damaging Het
Rbbp8 A G 18: 11,851,925 (GRCm39) T249A probably benign Het
Rtkn A T 6: 83,112,957 (GRCm39) I10F probably benign Het
Scube2 T A 7: 109,456,797 (GRCm39) I103F possibly damaging Het
Sec23b A G 2: 144,423,893 (GRCm39) H514R probably benign Het
Serbp1 T A 6: 67,249,204 (GRCm39) D223E probably benign Het
Slc14a1 C A 18: 78,154,607 (GRCm39) V260L probably benign Het
Slc22a23 A G 13: 34,367,109 (GRCm39) I633T probably damaging Het
Stk19 A T 17: 35,043,723 (GRCm39) probably benign Het
Svs5 T C 2: 164,079,047 (GRCm39) M287V probably benign Het
Syne3 T A 12: 104,924,325 (GRCm39) Q358L probably damaging Het
Synj1 A G 16: 90,806,984 (GRCm39) F58L possibly damaging Het
Tg T C 15: 66,545,872 (GRCm39) V198A probably damaging Het
Tle4 A T 19: 14,574,752 (GRCm39) Y9N probably damaging Het
Tmx3 G A 18: 90,542,459 (GRCm39) A186T possibly damaging Het
Traf3 G A 12: 111,221,679 (GRCm39) S280N possibly damaging Het
Trp53bp1 T A 2: 121,059,107 (GRCm39) H918L probably damaging Het
Ush2a T G 1: 188,460,701 (GRCm39) V2654G probably benign Het
Vinac1 A G 2: 128,881,521 (GRCm39) L135P probably damaging Het
Vmn2r25 A G 6: 123,817,057 (GRCm39) Y175H probably damaging Het
Zfp335 T C 2: 164,734,109 (GRCm39) D1330G probably damaging Het
Other mutations in Trmt13
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00926:Trmt13 APN 3 116,383,884 (GRCm39) nonsense probably null
IGL01516:Trmt13 APN 3 116,383,459 (GRCm39) unclassified probably benign
IGL01732:Trmt13 APN 3 116,375,113 (GRCm39) missense probably damaging 1.00
IGL01783:Trmt13 APN 3 116,376,561 (GRCm39) nonsense probably null
IGL02470:Trmt13 APN 3 116,383,877 (GRCm39) critical splice donor site probably null
IGL02492:Trmt13 APN 3 116,376,192 (GRCm39) missense possibly damaging 0.53
IGL02531:Trmt13 APN 3 116,385,840 (GRCm39) critical splice donor site probably null
IGL03156:Trmt13 APN 3 116,379,451 (GRCm39) missense probably benign 0.00
R0394:Trmt13 UTSW 3 116,376,299 (GRCm39) missense probably damaging 1.00
R0446:Trmt13 UTSW 3 116,376,275 (GRCm39) missense probably damaging 1.00
R2211:Trmt13 UTSW 3 116,388,403 (GRCm39) missense probably benign 0.00
R2942:Trmt13 UTSW 3 116,379,421 (GRCm39) missense probably damaging 1.00
R3124:Trmt13 UTSW 3 116,383,893 (GRCm39) missense probably benign 0.00
R3945:Trmt13 UTSW 3 116,375,167 (GRCm39) missense probably damaging 1.00
R4255:Trmt13 UTSW 3 116,376,337 (GRCm39) nonsense probably null
R4520:Trmt13 UTSW 3 116,375,262 (GRCm39) splice site probably null
R4609:Trmt13 UTSW 3 116,388,476 (GRCm39) utr 5 prime probably benign
R4678:Trmt13 UTSW 3 116,383,404 (GRCm39) missense probably damaging 1.00
R4679:Trmt13 UTSW 3 116,383,404 (GRCm39) missense probably damaging 1.00
R4703:Trmt13 UTSW 3 116,388,247 (GRCm39) missense probably benign 0.00
R6526:Trmt13 UTSW 3 116,385,864 (GRCm39) missense probably damaging 1.00
R7064:Trmt13 UTSW 3 116,376,346 (GRCm39) missense probably damaging 1.00
R7079:Trmt13 UTSW 3 116,376,480 (GRCm39) missense probably benign 0.00
R7308:Trmt13 UTSW 3 116,388,388 (GRCm39) missense probably benign 0.09
R8347:Trmt13 UTSW 3 116,376,417 (GRCm39) missense probably benign 0.00
R8491:Trmt13 UTSW 3 116,376,228 (GRCm39) missense probably benign
R8544:Trmt13 UTSW 3 116,386,094 (GRCm39) splice site probably null
R9108:Trmt13 UTSW 3 116,375,129 (GRCm39) missense probably damaging 1.00
R9208:Trmt13 UTSW 3 116,376,356 (GRCm39) missense possibly damaging 0.95
R9492:Trmt13 UTSW 3 116,388,281 (GRCm39) missense probably benign 0.10
Predicted Primers PCR Primer
(F):5'- GAGCCCTGCTGAAAAGGAATAC -3'
(R):5'- GCTTCGTAAATGGCAGTGG -3'

Sequencing Primer
(F):5'- GAAGACAAACGTCACGTTC -3'
(R):5'- GTGGCCAAACTTGGTATG -3'
Posted On 2015-04-17