Incidental Mutation 'R3913:Tyw1'
ID 309499
Institutional Source Beutler Lab
Gene Symbol Tyw1
Ensembl Gene ENSMUSG00000056310
Gene Name tRNA-yW synthesizing protein 1 homolog (S. cerevisiae)
Synonyms Rsafd1
MMRRC Submission 040911-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R3913 (G1)
Quality Score 225
Status Validated
Chromosome 5
Chromosomal Location 130284460-130370404 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 130287876 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Aspartic acid at position 36 (V36D)
Ref Sequence ENSEMBL: ENSMUSP00000047318 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000026387] [ENSMUST00000040213] [ENSMUST00000044204] [ENSMUST00000100662] [ENSMUST00000125625] [ENSMUST00000139211] [ENSMUST00000147619]
AlphaFold Q8BJM7
Predicted Effect probably benign
Transcript: ENSMUST00000026387
SMART Domains Protein: ENSMUSP00000026387
Gene: ENSMUSG00000025337

DomainStartEndE-ValueType
Pfam:SBDS 14 101 1.2e-36 PFAM
Pfam:SBDS_C 107 225 2.1e-42 PFAM
Predicted Effect possibly damaging
Transcript: ENSMUST00000040213
AA Change: V36D

PolyPhen 2 Score 0.640 (Sensitivity: 0.87; Specificity: 0.91)
SMART Domains Protein: ENSMUSP00000037173
Gene: ENSMUSG00000056310
AA Change: V36D

DomainStartEndE-ValueType
transmembrane domain 20 39 N/A INTRINSIC
Pfam:Flavodoxin_1 73 224 1.6e-27 PFAM
low complexity region 276 288 N/A INTRINSIC
Pfam:Radical_SAM 399 581 1.1e-29 PFAM
Pfam:Wyosine_form 583 646 3.6e-29 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000044204
AA Change: V36D

PolyPhen 2 Score 0.977 (Sensitivity: 0.76; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000047318
Gene: ENSMUSG00000056310
AA Change: V36D

DomainStartEndE-ValueType
transmembrane domain 20 39 N/A INTRINSIC
Pfam:Flavodoxin_1 73 224 1.5e-27 PFAM
low complexity region 276 288 N/A INTRINSIC
transmembrane domain 375 397 N/A INTRINSIC
transmembrane domain 423 445 N/A INTRINSIC
Predicted Effect possibly damaging
Transcript: ENSMUST00000100662
AA Change: V36D

PolyPhen 2 Score 0.640 (Sensitivity: 0.87; Specificity: 0.91)
SMART Domains Protein: ENSMUSP00000098226
Gene: ENSMUSG00000056310
AA Change: V36D

DomainStartEndE-ValueType
transmembrane domain 20 39 N/A INTRINSIC
Pfam:Flavodoxin_1 73 224 4.9e-28 PFAM
low complexity region 276 288 N/A INTRINSIC
low complexity region 319 332 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000125625
SMART Domains Protein: ENSMUSP00000115494
Gene: ENSMUSG00000025337

DomainStartEndE-ValueType
Pfam:SBDS 3 66 2.1e-25 PFAM
Pfam:SBDS_C 69 173 9.9e-40 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000139211
Predicted Effect possibly damaging
Transcript: ENSMUST00000147619
AA Change: V13D

PolyPhen 2 Score 0.640 (Sensitivity: 0.87; Specificity: 0.91)
SMART Domains Protein: ENSMUSP00000123693
Gene: ENSMUSG00000056310
AA Change: V13D

DomainStartEndE-ValueType
Pfam:Flavodoxin_1 50 201 4.3e-28 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000173375
Predicted Effect noncoding transcript
Transcript: ENSMUST00000201598
Predicted Effect noncoding transcript
Transcript: ENSMUST00000200815
Meta Mutation Damage Score 0.6002 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.3%
  • 20x: 95.3%
Validation Efficiency 100% (59/59)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] Wybutosine (yW) is a hypermodified guanosine found in phenylalanine tRNA adjacent to the anticodon that stabilizes codon-anticodon interactions in the ribosome. In yeast, the homolog of this gene is essential for the synthesis of wybutosine. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2015]
Allele List at MGI
Other mutations in this stock
Total: 53 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adh7 T A 3: 137,927,541 (GRCm39) V29E probably damaging Het
Adra1d T A 2: 131,404,075 (GRCm39) D5V probably damaging Het
Arid1b A G 17: 5,392,532 (GRCm39) I2021V possibly damaging Het
Birc6 A T 17: 74,880,608 (GRCm39) R462* probably null Het
Cchcr1 T C 17: 35,836,233 (GRCm39) V341A probably damaging Het
Cimip3 AC A 17: 47,744,348 (GRCm39) probably benign Het
Crybg1 T C 10: 43,874,759 (GRCm39) D783G possibly damaging Het
Dcaf15 T C 8: 84,825,794 (GRCm39) Y271C probably damaging Het
Dcun1d2 A C 8: 13,331,082 (GRCm39) M16R probably damaging Het
Dnah17 C T 11: 117,971,675 (GRCm39) probably benign Het
Dnttip2 T C 3: 122,069,040 (GRCm39) V85A possibly damaging Het
Eprs1 G A 1: 185,111,939 (GRCm39) probably null Het
Exoc7 T C 11: 116,197,731 (GRCm39) D27G probably benign Het
Gdpd5 A G 7: 99,087,546 (GRCm39) D70G probably null Het
Glyr1 A G 16: 4,849,777 (GRCm39) F199L probably damaging Het
Golga4 T A 9: 118,368,039 (GRCm39) M414K probably damaging Het
Gpr132 C A 12: 112,816,640 (GRCm39) W62L probably benign Het
Gpr179 A T 11: 97,225,591 (GRCm39) V2188E probably benign Het
Ilf3 C T 9: 21,309,422 (GRCm39) A526V possibly damaging Het
Ints10 T A 8: 69,266,272 (GRCm39) S478T probably damaging Het
Kcnab2 A G 4: 152,479,689 (GRCm39) V187A probably damaging Het
Kcnj15 C T 16: 95,097,329 (GRCm39) T317I probably damaging Het
Kirrel1 C T 3: 86,996,458 (GRCm39) M380I probably null Het
Klhl30 T C 1: 91,287,166 (GRCm39) V484A possibly damaging Het
Krt90 G A 15: 101,471,218 (GRCm39) R15W probably damaging Het
Liph G T 16: 21,781,009 (GRCm39) probably benign Het
Lrrc7 G A 3: 157,997,589 (GRCm39) L158F probably damaging Het
Maml1 T C 11: 50,154,259 (GRCm39) T602A probably benign Het
Mast4 A G 13: 102,895,177 (GRCm39) L782P probably damaging Het
Mei4 A G 9: 81,772,316 (GRCm39) K43R probably benign Het
Mettl4 A G 17: 95,047,960 (GRCm39) V227A probably benign Het
Mst1r G A 9: 107,791,945 (GRCm39) R827Q probably benign Het
Olfm1 A G 2: 28,098,186 (GRCm39) T83A possibly damaging Het
Or1e30 G T 11: 73,678,522 (GRCm39) G253W probably damaging Het
Or5m10b T C 2: 85,699,115 (GRCm39) Y60H probably damaging Het
Parp4 A G 14: 56,857,975 (GRCm39) E869G probably damaging Het
Pate4 C A 9: 35,523,140 (GRCm39) M1I probably null Het
Patj A G 4: 98,457,338 (GRCm39) D1280G probably damaging Het
Ppargc1b T C 18: 61,444,447 (GRCm39) S255G probably damaging Het
Rev3l A G 10: 39,696,552 (GRCm39) I521M probably damaging Het
Rlim T C X: 103,006,267 (GRCm39) T545A probably benign Het
Robo2 A T 16: 73,831,893 (GRCm39) D262E probably damaging Het
Sec14l5 A G 16: 4,965,720 (GRCm39) probably benign Het
Sema4b A G 7: 79,870,222 (GRCm39) S467G probably benign Het
Setd2 C T 9: 110,380,114 (GRCm39) R1310C probably damaging Het
Sh3d19 T C 3: 85,992,083 (GRCm39) I37T probably damaging Het
Slc23a3 T A 1: 75,105,566 (GRCm39) I422F probably benign Het
Snap91 T C 9: 86,674,610 (GRCm39) T534A possibly damaging Het
Son A T 16: 91,456,999 (GRCm39) probably benign Het
Tnks A T 8: 35,340,228 (GRCm39) S463R probably damaging Het
Tubb3 A G 8: 124,147,748 (GRCm39) H227R possibly damaging Het
Vwa5a T C 9: 38,646,039 (GRCm39) I469T probably damaging Het
Zdhhc8 A G 16: 18,044,587 (GRCm39) L311P possibly damaging Het
Other mutations in Tyw1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL02329:Tyw1 APN 5 130,295,921 (GRCm39) missense probably benign 0.20
IGL02873:Tyw1 APN 5 130,364,171 (GRCm39) missense probably benign 0.00
IGL02879:Tyw1 APN 5 130,325,612 (GRCm39) missense probably damaging 1.00
IGL03080:Tyw1 APN 5 130,295,896 (GRCm39) missense probably damaging 1.00
IGL03291:Tyw1 APN 5 130,328,834 (GRCm39) missense probably damaging 1.00
IGL03297:Tyw1 APN 5 130,369,575 (GRCm39) missense probably damaging 1.00
remnant UTSW 5 130,291,762 (GRCm39) missense probably damaging 0.99
schimmel UTSW 5 130,298,065 (GRCm39) missense probably damaging 1.00
tyrone UTSW 5 130,325,520 (GRCm39) nonsense probably null
yang UTSW 5 130,287,876 (GRCm39) missense probably damaging 0.98
R1420:Tyw1 UTSW 5 130,303,586 (GRCm39) critical splice donor site probably null
R1650:Tyw1 UTSW 5 130,317,752 (GRCm39) missense possibly damaging 0.91
R1674:Tyw1 UTSW 5 130,298,169 (GRCm39) missense probably benign 0.01
R1789:Tyw1 UTSW 5 130,287,834 (GRCm39) missense probably damaging 0.99
R1996:Tyw1 UTSW 5 130,291,652 (GRCm39) splice site probably benign
R2421:Tyw1 UTSW 5 130,298,101 (GRCm39) missense probably damaging 1.00
R4412:Tyw1 UTSW 5 130,364,073 (GRCm39) splice site probably null
R4835:Tyw1 UTSW 5 130,305,899 (GRCm39) missense probably benign
R5058:Tyw1 UTSW 5 130,305,927 (GRCm39) missense probably benign 0.03
R5190:Tyw1 UTSW 5 130,296,756 (GRCm39) nonsense probably null
R5398:Tyw1 UTSW 5 130,305,998 (GRCm39) intron probably benign
R5459:Tyw1 UTSW 5 130,303,547 (GRCm39) missense probably damaging 1.00
R5597:Tyw1 UTSW 5 130,303,498 (GRCm39) missense probably benign 0.00
R5704:Tyw1 UTSW 5 130,310,863 (GRCm39) nonsense probably null
R5825:Tyw1 UTSW 5 130,296,929 (GRCm39) missense probably damaging 0.99
R5887:Tyw1 UTSW 5 130,354,540 (GRCm39) missense probably damaging 1.00
R6072:Tyw1 UTSW 5 130,296,752 (GRCm39) missense possibly damaging 0.92
R6349:Tyw1 UTSW 5 130,305,872 (GRCm39) missense possibly damaging 0.82
R6366:Tyw1 UTSW 5 130,310,792 (GRCm39) unclassified probably benign
R7012:Tyw1 UTSW 5 130,306,571 (GRCm39) splice site probably null
R7259:Tyw1 UTSW 5 130,296,713 (GRCm39) splice site probably null
R7328:Tyw1 UTSW 5 130,291,685 (GRCm39) missense probably benign 0.08
R7555:Tyw1 UTSW 5 130,303,547 (GRCm39) missense probably damaging 1.00
R8006:Tyw1 UTSW 5 130,296,913 (GRCm39) missense possibly damaging 0.87
R8171:Tyw1 UTSW 5 130,328,855 (GRCm39) missense probably benign 0.19
R8196:Tyw1 UTSW 5 130,328,862 (GRCm39) missense probably damaging 1.00
R8714:Tyw1 UTSW 5 130,298,065 (GRCm39) missense probably damaging 1.00
R8715:Tyw1 UTSW 5 130,298,065 (GRCm39) missense probably damaging 1.00
R8716:Tyw1 UTSW 5 130,298,065 (GRCm39) missense probably damaging 1.00
R8970:Tyw1 UTSW 5 130,298,065 (GRCm39) missense probably damaging 1.00
R8992:Tyw1 UTSW 5 130,298,065 (GRCm39) missense probably damaging 1.00
R9117:Tyw1 UTSW 5 130,298,065 (GRCm39) missense probably damaging 1.00
R9119:Tyw1 UTSW 5 130,298,065 (GRCm39) missense probably damaging 1.00
R9120:Tyw1 UTSW 5 130,298,065 (GRCm39) missense probably damaging 1.00
R9172:Tyw1 UTSW 5 130,325,520 (GRCm39) nonsense probably null
R9204:Tyw1 UTSW 5 130,298,065 (GRCm39) missense probably damaging 1.00
R9205:Tyw1 UTSW 5 130,298,065 (GRCm39) missense probably damaging 1.00
R9207:Tyw1 UTSW 5 130,298,065 (GRCm39) missense probably damaging 1.00
R9325:Tyw1 UTSW 5 130,291,762 (GRCm39) missense probably damaging 0.99
R9364:Tyw1 UTSW 5 130,298,065 (GRCm39) missense probably damaging 1.00
R9368:Tyw1 UTSW 5 130,298,065 (GRCm39) missense probably damaging 1.00
R9369:Tyw1 UTSW 5 130,298,065 (GRCm39) missense probably damaging 1.00
R9470:Tyw1 UTSW 5 130,298,065 (GRCm39) missense probably damaging 1.00
R9471:Tyw1 UTSW 5 130,298,065 (GRCm39) missense probably damaging 1.00
R9566:Tyw1 UTSW 5 130,298,065 (GRCm39) missense probably damaging 1.00
R9567:Tyw1 UTSW 5 130,298,065 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- ACAACATCAATGGGCATCTTTG -3'
(R):5'- CGAGCAAACGAACTGGTTC -3'

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