Incidental Mutation 'R5279:Tyw3'
ID 404094
Institutional Source Beutler Lab
Gene Symbol Tyw3
Ensembl Gene ENSMUSG00000047583
Gene Name tRNA-yW synthesizing protein 3 homolog (S. cerevisiae)
Synonyms 5230400J09Rik
MMRRC Submission 042839-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.076) question?
Stock # R5279 (G1)
Quality Score 225
Status Validated
Chromosome 3
Chromosomal Location 154282157-154302750 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 154300108 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Cysteine to Arginine at position 80 (C80R)
Ref Sequence ENSEMBL: ENSMUSP00000057828 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000029850] [ENSMUST00000052774] [ENSMUST00000122976] [ENSMUST00000135723] [ENSMUST00000140644] [ENSMUST00000144764] [ENSMUST00000170461] [ENSMUST00000194876] [ENSMUST00000192462] [ENSMUST00000155232] [ENSMUST00000184537] [ENSMUST00000155385]
AlphaFold Q8BSA9
Predicted Effect probably benign
Transcript: ENSMUST00000029850
SMART Domains Protein: ENSMUSP00000029850
Gene: ENSMUSG00000028199

DomainStartEndE-ValueType
Pfam:ADH_N 35 131 3.3e-14 PFAM
Pfam:ADH_zinc_N 160 290 1.3e-30 PFAM
Pfam:ADH_zinc_N_2 192 329 1.7e-20 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000052774
AA Change: C80R

PolyPhen 2 Score 0.988 (Sensitivity: 0.73; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000057828
Gene: ENSMUSG00000047583
AA Change: C80R

DomainStartEndE-ValueType
Pfam:TYW3 9 194 8.1e-61 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000122976
AA Change: C103R

PolyPhen 2 Score 0.975 (Sensitivity: 0.76; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000114437
Gene: ENSMUSG00000047583
AA Change: C103R

DomainStartEndE-ValueType
Pfam:TYW3 31 149 4.4e-35 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000135723
SMART Domains Protein: ENSMUSP00000143311
Gene: ENSMUSG00000028199

DomainStartEndE-ValueType
PDB:1YB5|B 1 38 5e-17 PDB
SCOP:d1qora1 9 38 9e-5 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000140644
SMART Domains Protein: ENSMUSP00000115146
Gene: ENSMUSG00000028199

DomainStartEndE-ValueType
Pfam:ADH_N 35 98 1.5e-16 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000144764
SMART Domains Protein: ENSMUSP00000121269
Gene: ENSMUSG00000028199

DomainStartEndE-ValueType
Pfam:ADH_N 35 132 2.6e-17 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000170461
AA Change: C80R

PolyPhen 2 Score 0.964 (Sensitivity: 0.78; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000131461
Gene: ENSMUSG00000047583
AA Change: C80R

DomainStartEndE-ValueType
Pfam:TYW3 8 144 8.1e-45 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000148680
Predicted Effect probably benign
Transcript: ENSMUST00000194876
SMART Domains Protein: ENSMUSP00000142101
Gene: ENSMUSG00000028199

DomainStartEndE-ValueType
Pfam:ADH_N 35 139 2.2e-14 PFAM
Pfam:ADH_zinc_N 160 290 1.4e-27 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000192462
SMART Domains Protein: ENSMUSP00000142105
Gene: ENSMUSG00000028199

DomainStartEndE-ValueType
Pfam:ADH_N 35 131 2.8e-16 PFAM
Pfam:ADH_zinc_N 160 290 1.8e-29 PFAM
Pfam:ADH_zinc_N_2 192 329 4.3e-17 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000155232
SMART Domains Protein: ENSMUSP00000118449
Gene: ENSMUSG00000028199

DomainStartEndE-ValueType
Pfam:ADH_N 35 135 3.5e-17 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000184537
SMART Domains Protein: ENSMUSP00000139387
Gene: ENSMUSG00000028199

DomainStartEndE-ValueType
Pfam:ADH_N 35 180 4.7e-17 PFAM
Pfam:ADH_zinc_N 160 218 5.4e-13 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000155385
SMART Domains Protein: ENSMUSP00000122619
Gene: ENSMUSG00000028199

DomainStartEndE-ValueType
Pfam:ADH_N 35 130 2.1e-17 PFAM
Meta Mutation Damage Score 0.7391 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.7%
  • 10x: 97.3%
  • 20x: 95.4%
Validation Efficiency 99% (73/74)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] Wybutosine (yW) is a hypermodified guanosine at the 3-prime position adjacent to the anticodon of phenylalanine tRNA that stabilizes codon-anticodon interactions during decoding on the ribosome. TYW3 is the human homolog of a yeast gene essential for yW synthesis (Noma and Suzuki, 2006).[supplied by OMIM, Mar 2008]
Allele List at MGI
Other mutations in this stock
Total: 69 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca17 C A 17: 24,508,388 (GRCm39) G1049V probably damaging Het
Afdn G A 17: 14,109,214 (GRCm39) R1579H probably damaging Het
Ankrd28 T A 14: 31,456,963 (GRCm39) N386Y probably damaging Het
Atf7ip T A 6: 136,580,377 (GRCm39) Y1100* probably null Het
Atp9b T A 18: 80,956,073 (GRCm39) E3V probably damaging Het
AW554918 T G 18: 25,308,488 (GRCm39) D60E possibly damaging Het
Baz2b G T 2: 59,762,496 (GRCm39) Q927K probably damaging Het
Birc6 A G 17: 74,957,042 (GRCm39) R3659G probably damaging Het
C8a T G 4: 104,703,185 (GRCm39) N291H probably damaging Het
Calcoco1 G A 15: 102,619,420 (GRCm39) L390F probably damaging Het
Carmil3 A G 14: 55,739,028 (GRCm39) D894G probably damaging Het
Cdc20 A G 4: 118,290,711 (GRCm39) Y430H probably damaging Het
Cdc6 A T 11: 98,803,088 (GRCm39) I316F probably damaging Het
Ceacam23 T A 7: 17,607,214 (GRCm39) noncoding transcript Het
Cenpu T A 8: 47,031,945 (GRCm39) probably null Het
Csmd2 T A 4: 128,350,707 (GRCm39) V1592D probably benign Het
Csmd3 G T 15: 48,655,340 (GRCm39) probably null Het
Dnah7c T C 1: 46,558,429 (GRCm39) F512L probably benign Het
Fam136a T A 6: 86,343,686 (GRCm39) L61Q probably damaging Het
Fpgs A C 2: 32,582,779 (GRCm39) probably benign Het
Fzd4 G A 7: 89,056,881 (GRCm39) M309I probably benign Het
Gad2 A G 2: 22,563,969 (GRCm39) T391A probably benign Het
Gm11563 A T 11: 99,549,539 (GRCm39) S72T unknown Het
Gon4l A G 3: 88,794,944 (GRCm39) I716V probably benign Het
Itga9 T C 9: 118,457,273 (GRCm39) V128A probably damaging Het
Kat6a CGCAGCAGCAGCAGCAGCA CGCAGCAGCAGCA 8: 23,429,664 (GRCm39) probably benign Het
Lrrc9 T A 12: 72,542,368 (GRCm39) D1063E possibly damaging Het
Lyst T A 13: 13,823,387 (GRCm39) L1453* probably null Het
Mcm3ap T C 10: 76,343,373 (GRCm39) V1755A probably damaging Het
Mrc1 T C 2: 14,314,869 (GRCm39) S985P probably damaging Het
Mst1 A C 9: 107,959,414 (GRCm39) K233N probably damaging Het
Nr2c2ap G A 8: 70,584,653 (GRCm39) D42N probably damaging Het
Ntn1 A G 11: 68,276,538 (GRCm39) S137P probably benign Het
Pard3 T C 8: 128,186,867 (GRCm39) probably null Het
Pcdh15 T A 10: 74,430,015 (GRCm39) D1210E probably damaging Het
Pcdhga5 T C 18: 37,827,774 (GRCm39) L74P probably benign Het
Pcsk5 T C 19: 17,573,022 (GRCm39) probably null Het
Pdia3 T C 2: 121,244,484 (GRCm39) probably benign Het
Pikfyve A T 1: 65,235,858 (GRCm39) R177* probably null Het
Pklr A G 3: 89,050,566 (GRCm39) E409G probably damaging Het
Plod2 T C 9: 92,463,376 (GRCm39) Y154H probably damaging Het
Psmc3 T A 2: 90,884,667 (GRCm39) D6E probably benign Het
Ptpru T A 4: 131,547,334 (GRCm39) N205I possibly damaging Het
Rbm6 T C 9: 107,655,213 (GRCm39) E1006G probably benign Het
Rgl2 T C 17: 34,154,922 (GRCm39) V642A probably benign Het
Rnf8 T A 17: 29,845,680 (GRCm39) H104Q possibly damaging Het
Robo4 CGG CG 9: 37,322,786 (GRCm39) probably null Het
Rpa1 T C 11: 75,204,170 (GRCm39) N269S probably damaging Het
Sdk2 A G 11: 113,757,857 (GRCm39) M519T probably benign Het
Snx30 A G 4: 59,885,070 (GRCm39) S237G probably benign Het
Spx A G 6: 142,359,766 (GRCm39) N36S probably damaging Het
Stard7 T C 2: 127,137,416 (GRCm39) Y289H probably damaging Het
Sugp2 T C 8: 70,709,757 (GRCm39) probably benign Het
Susd4 C T 1: 182,715,043 (GRCm39) T288I probably damaging Het
Tceanc2 T A 4: 107,034,826 (GRCm39) probably null Het
Tm4sf4 T G 3: 57,341,159 (GRCm39) V97G probably benign Het
Tmtc1 C T 6: 148,256,629 (GRCm39) probably benign Het
Trappc11 C T 8: 47,958,339 (GRCm39) probably benign Het
Triobp G T 15: 78,878,591 (GRCm39) V398F possibly damaging Het
Ttll9 T A 2: 152,804,464 (GRCm39) S2T possibly damaging Het
Ttn T C 2: 76,731,320 (GRCm39) probably benign Het
Usp24 T C 4: 106,242,621 (GRCm39) V1177A possibly damaging Het
Vmn1r65 A G 7: 6,011,754 (GRCm39) V160A probably damaging Het
Vmn2r104 T A 17: 20,262,146 (GRCm39) H328L probably benign Het
Vmn2r65 A C 7: 84,589,849 (GRCm39) I689S probably damaging Het
Wrn A G 8: 33,731,129 (GRCm39) Y1068H probably damaging Het
Xpo4 C A 14: 57,850,866 (GRCm39) S346I probably benign Het
Zc3h3 T A 15: 75,711,439 (GRCm39) T341S probably benign Het
Zxdc T C 6: 90,347,419 (GRCm39) M260T possibly damaging Het
Other mutations in Tyw3
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL02444:Tyw3 APN 3 154,302,626 (GRCm39) missense probably damaging 0.98
IGL03226:Tyw3 APN 3 154,293,187 (GRCm39) missense possibly damaging 0.82
R0211:Tyw3 UTSW 3 154,293,132 (GRCm39) missense probably damaging 1.00
R0211:Tyw3 UTSW 3 154,293,132 (GRCm39) missense probably damaging 1.00
R1348:Tyw3 UTSW 3 154,299,451 (GRCm39) missense possibly damaging 0.47
R1443:Tyw3 UTSW 3 154,293,160 (GRCm39) missense probably benign 0.01
R1538:Tyw3 UTSW 3 154,302,506 (GRCm39) missense probably damaging 0.98
R4289:Tyw3 UTSW 3 154,302,645 (GRCm39) missense probably damaging 1.00
R6090:Tyw3 UTSW 3 154,302,704 (GRCm39) missense probably benign 0.01
R6982:Tyw3 UTSW 3 154,285,867 (GRCm39) missense probably benign 0.01
R7079:Tyw3 UTSW 3 154,299,426 (GRCm39) missense probably benign 0.04
R7080:Tyw3 UTSW 3 154,299,426 (GRCm39) missense probably benign 0.04
R7090:Tyw3 UTSW 3 154,299,426 (GRCm39) missense probably benign 0.04
R9774:Tyw3 UTSW 3 154,302,584 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- GCAGAGTGAAGTCCCTTCTTC -3'
(R):5'- CCATCTGAGCCCTAAGTTACTTG -3'

Sequencing Primer
(F):5'- atttgaacccagTGAGCC -3'
(R):5'- CTGAGCCCTAAGTTACTTGAATTG -3'
Posted On 2016-07-22