Incidental Mutation 'R8003:Ybx3'
ID 616452
Institutional Source Beutler Lab
Gene Symbol Ybx3
Ensembl Gene ENSMUSG00000030189
Gene Name Y box protein 3
Synonyms dbpA, MSY4, MSY3, Dpba, Yb2, oxyR, Csda
MMRRC Submission 046043-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R8003 (G1)
Quality Score 225.009
Status Validated
Chromosome 6
Chromosomal Location 131341821-131365413 bp(-) (GRCm39)
Type of Mutation nonsense
DNA Base Change (assembly) A to T at 131345400 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Tyrosine to Stop codon at position 324 (Y324*)
Ref Sequence ENSEMBL: ENSMUSP00000032309 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000032309] [ENSMUST00000087865]
AlphaFold Q9JKB3
Predicted Effect probably null
Transcript: ENSMUST00000032309
AA Change: Y324*
SMART Domains Protein: ENSMUSP00000032309
Gene: ENSMUSG00000030189
AA Change: Y324*

DomainStartEndE-ValueType
low complexity region 3 13 N/A INTRINSIC
low complexity region 14 71 N/A INTRINSIC
CSP 84 152 8.65e-24 SMART
low complexity region 166 182 N/A INTRINSIC
low complexity region 186 198 N/A INTRINSIC
low complexity region 212 232 N/A INTRINSIC
low complexity region 278 293 N/A INTRINSIC
low complexity region 315 329 N/A INTRINSIC
Predicted Effect probably null
Transcript: ENSMUST00000087865
AA Change: Y255*
SMART Domains Protein: ENSMUSP00000085172
Gene: ENSMUSG00000030189
AA Change: Y255*

DomainStartEndE-ValueType
low complexity region 3 13 N/A INTRINSIC
low complexity region 14 71 N/A INTRINSIC
CSP 84 152 8.65e-24 SMART
low complexity region 166 182 N/A INTRINSIC
low complexity region 209 224 N/A INTRINSIC
low complexity region 246 260 N/A INTRINSIC
Meta Mutation Damage Score 0.9756 question?
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 100.0%
  • 10x: 99.7%
  • 20x: 99.2%
Validation Efficiency 100% (51/51)
MGI Phenotype PHENOTYPE: Half of mice homozygous for a knock-out allele exhibit male infertility associated with smaller testes and reduced sperm production, partly due to increased spermatocyte apoptosis during mid to late spermatogenesis and progressive seminiferous tubule degeneration. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 52 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adcy4 A G 14: 56,019,092 (GRCm39) V155A probably benign Het
Arfgef2 A G 2: 166,695,208 (GRCm39) Y527C probably damaging Het
Brca1 C T 11: 101,415,303 (GRCm39) G944R probably benign Het
C2cd2 A G 16: 97,687,286 (GRCm39) probably null Het
Cass4 T C 2: 172,269,879 (GRCm39) F654L unknown Het
Ccdc178 A T 18: 21,977,944 (GRCm39) probably null Het
Cct4 T C 11: 22,946,040 (GRCm39) probably null Het
Cish T C 9: 107,174,227 (GRCm39) V5A possibly damaging Het
Col5a1 G A 2: 27,848,340 (GRCm39) probably benign Het
Col6a3 G T 1: 90,703,455 (GRCm39) N3037K unknown Het
Csmd2 T A 4: 128,432,980 (GRCm39) C3012* probably null Het
Dclk2 T C 3: 86,700,608 (GRCm39) probably null Het
Dhx38 A T 8: 110,282,772 (GRCm39) D631E probably damaging Het
Eif2ak2 C A 17: 79,183,652 (GRCm39) A66S probably damaging Het
Ephx2 A G 14: 66,361,782 (GRCm39) probably null Het
Fbxw10 T G 11: 62,748,587 (GRCm39) C405G possibly damaging Het
Galnt13 G T 2: 54,950,497 (GRCm39) G393* probably null Het
Gm5591 G T 7: 38,219,183 (GRCm39) H563Q probably damaging Het
Gtf3c5 A G 2: 28,459,373 (GRCm39) I394T probably benign Het
Hectd4 G A 5: 121,477,581 (GRCm39) A2835T possibly damaging Het
Herc2 A G 7: 55,818,652 (GRCm39) D2781G possibly damaging Het
Kmt2b G T 7: 30,268,802 (GRCm39) H2642Q probably damaging Het
Lars1 A T 18: 42,354,684 (GRCm39) D754E probably damaging Het
Lrpprc A C 17: 85,059,745 (GRCm39) S690A probably benign Het
Map3k6 A G 4: 132,976,193 (GRCm39) T805A probably benign Het
Mthfd1l T G 10: 3,934,147 (GRCm39) S160A probably benign Het
Mtmr6 G A 14: 60,519,544 (GRCm39) probably null Het
Mybpc2 A T 7: 44,158,488 (GRCm39) M698K probably damaging Het
Myh8 T A 11: 67,190,586 (GRCm39) L1304M probably damaging Het
Mylip T A 13: 45,557,947 (GRCm39) V117E probably benign Het
Npc1l1 T C 11: 6,165,129 (GRCm39) Q1061R probably benign Het
Or12e13 A G 2: 87,664,081 (GRCm39) R233G probably benign Het
Or5d37 A T 2: 87,923,589 (GRCm39) Y230* probably null Het
Pkd2l2 G A 18: 34,561,232 (GRCm39) M413I probably damaging Het
Plch2 C T 4: 155,138,980 (GRCm39) G19D unknown Het
Pramel17 T C 4: 101,693,130 (GRCm39) K290R probably benign Het
Psg22 A C 7: 18,458,350 (GRCm39) Y347S probably damaging Het
Ptpre C A 7: 135,270,765 (GRCm39) Q314K probably damaging Het
Rgs6 T C 12: 83,032,144 (GRCm39) S54P probably damaging Het
Sbds C A 5: 130,279,726 (GRCm39) V130F possibly damaging Het
Slc1a7 G A 4: 107,869,473 (GRCm39) V513M probably benign Het
Slc24a2 A T 4: 87,094,552 (GRCm39) D322E probably benign Het
Slc45a4 G T 15: 73,457,162 (GRCm39) Y585* probably null Het
Slc7a4 A C 16: 17,392,315 (GRCm39) V373G possibly damaging Het
Sulf1 G A 1: 12,908,825 (GRCm39) V613M probably damaging Het
Syt1 T C 10: 108,472,434 (GRCm39) D150G probably damaging Het
Tnpo3 C A 6: 29,551,900 (GRCm39) V888F probably benign Het
Trim9 T C 12: 70,393,608 (GRCm39) H112R probably benign Het
Vmn2r80 T C 10: 78,984,711 (GRCm39) I21T probably benign Het
Wdr41 C A 13: 95,149,654 (GRCm39) A286E possibly damaging Het
Wnt8b T A 19: 44,500,396 (GRCm39) C328S probably damaging Het
Zmynd15 T A 11: 70,351,767 (GRCm39) H124Q probably benign Het
Other mutations in Ybx3
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL02135:Ybx3 APN 6 131,357,892 (GRCm39) missense probably damaging 1.00
IGL02203:Ybx3 APN 6 131,345,371 (GRCm39) missense probably benign 0.01
PIT1430001:Ybx3 UTSW 6 131,356,422 (GRCm39) missense probably damaging 1.00
R2869:Ybx3 UTSW 6 131,347,376 (GRCm39) missense probably damaging 1.00
R2869:Ybx3 UTSW 6 131,347,376 (GRCm39) missense probably damaging 1.00
R2870:Ybx3 UTSW 6 131,347,376 (GRCm39) missense probably damaging 1.00
R2870:Ybx3 UTSW 6 131,347,376 (GRCm39) missense probably damaging 1.00
R2873:Ybx3 UTSW 6 131,347,376 (GRCm39) missense probably damaging 1.00
R4654:Ybx3 UTSW 6 131,347,290 (GRCm39) missense probably damaging 0.99
R5878:Ybx3 UTSW 6 131,344,726 (GRCm39) critical splice donor site probably null
R5881:Ybx3 UTSW 6 131,345,451 (GRCm39) missense possibly damaging 0.71
R7796:Ybx3 UTSW 6 131,345,479 (GRCm39) missense probably damaging 0.98
R7833:Ybx3 UTSW 6 131,344,826 (GRCm39) missense possibly damaging 0.83
R7986:Ybx3 UTSW 6 131,356,362 (GRCm39) nonsense probably null
R8043:Ybx3 UTSW 6 131,361,469 (GRCm39) missense probably benign 0.13
R9802:Ybx3 UTSW 6 131,345,426 (GRCm39) missense probably benign 0.01
X0024:Ybx3 UTSW 6 131,357,867 (GRCm39) missense possibly damaging 0.88
Predicted Primers PCR Primer
(F):5'- AGCCTAAGTAAGCAATGTTGTGC -3'
(R):5'- ATGCCCTTGAGTACTCCTGC -3'

Sequencing Primer
(F):5'- CTTGATTAAGTGTCCAGTTTCACACG -3'
(R):5'- GAGTACTCCTGCCCACCC -3'
Posted On 2020-01-23