Incidental Mutation 'R2873:Ybx3'
ID 260407
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 040461-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R2873 (G1)
Quality Score 215
Status Validated
Chromosome 6
Chromosomal Location 131341821-131365413 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to A at 131347376 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Alanine to Valine at position 253 (A253V)
Ref Sequence ENSEMBL: ENSMUSP00000032309 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000032309] [ENSMUST00000087865]
AlphaFold Q9JKB3
Predicted Effect probably damaging
Transcript: ENSMUST00000032309
AA Change: A253V

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000032309
Gene: ENSMUSG00000030189
AA Change: A253V

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 possibly damaging
Transcript: ENSMUST00000087865
AA Change: A184V

PolyPhen 2 Score 0.843 (Sensitivity: 0.83; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000085172
Gene: ENSMUSG00000030189
AA Change: A184V

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
Predicted Effect noncoding transcript
Transcript: ENSMUST00000203157
Predicted Effect noncoding transcript
Transcript: ENSMUST00000205035
Meta Mutation Damage Score 0.0970 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.3%
  • 20x: 95.2%
Validation Efficiency 100% (81/81)
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: 73 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca8b A G 11: 109,846,002 (GRCm39) C811R possibly damaging Het
Acvr1 G A 2: 58,367,808 (GRCm39) Q118* probably null Het
Als2 A G 1: 59,250,296 (GRCm39) S483P probably damaging Het
Ankrd40 T C 11: 94,224,771 (GRCm39) V60A possibly damaging Het
Armc2 C T 10: 41,842,696 (GRCm39) probably null Het
Atp12a A G 14: 56,624,407 (GRCm39) R952G possibly damaging Het
Atp13a2 T C 4: 140,730,294 (GRCm39) I773T probably benign Het
Atp6v1g1 A G 4: 63,468,258 (GRCm39) Y87C probably benign Het
Ccdc162 G T 10: 41,531,095 (GRCm39) T537N possibly damaging Het
Ccdc59 A T 10: 105,677,388 (GRCm39) K9M possibly damaging Het
Cd101 A T 3: 100,911,164 (GRCm39) D831E probably benign Het
Ch25h T A 19: 34,452,210 (GRCm39) H106L probably benign Het
Chek2 C A 5: 111,011,202 (GRCm39) Y333* probably null Het
Cimap1d G A 10: 79,481,487 (GRCm39) T14I probably benign Het
Csmd2 T C 4: 128,451,511 (GRCm39) F113S unknown Het
Cyp4a14 C A 4: 115,344,498 (GRCm39) G456W probably damaging Het
Cyp4a30b A G 4: 115,315,559 (GRCm39) H260R possibly damaging Het
Dennd2b A T 7: 109,156,637 (GRCm39) Y38N probably benign Het
Eif4enif1 C T 11: 3,192,586 (GRCm39) P805S probably damaging Het
Fan1 A G 7: 64,012,938 (GRCm39) I668T probably benign Het
Flnc A G 6: 29,447,542 (GRCm39) D1115G probably damaging Het
Ftdc1 A T 16: 58,434,342 (GRCm39) I125K probably benign Het
Gbp11 C T 5: 105,478,866 (GRCm39) D191N probably benign Het
Gm5519 A C 19: 33,802,410 (GRCm39) D151A possibly damaging Het
Grid2ip C A 5: 143,343,684 (GRCm39) Q127K probably benign Het
Hdhd2 T C 18: 77,042,702 (GRCm39) F44L probably damaging Het
Hmcn1 A T 1: 150,614,467 (GRCm39) V1313D possibly damaging Het
Kpna7 T C 5: 144,930,745 (GRCm39) T367A probably benign Het
Matr3 T A 18: 35,705,349 (GRCm39) S91R probably benign Het
Mdm1 A G 10: 117,986,847 (GRCm39) T267A probably benign Het
Mlxip A G 5: 123,590,730 (GRCm39) M878V probably benign Het
Mtor T A 4: 148,624,487 (GRCm39) M2089K probably benign Het
Myo9b G A 8: 71,786,981 (GRCm39) R721Q probably benign Het
Ndufs1 A G 1: 63,203,882 (GRCm39) probably benign Het
Nlrp4b C T 7: 10,444,170 (GRCm39) Q40* probably null Het
Nomo1 C A 7: 45,696,361 (GRCm39) T293N probably damaging Het
Notch1 A G 2: 26,350,247 (GRCm39) C2298R possibly damaging Het
Notum A G 11: 120,551,022 (GRCm39) V48A probably benign Het
Or10g1 T G 14: 52,648,318 (GRCm39) T4P probably benign Het
Or10z1 T C 1: 174,078,092 (GRCm39) S134G probably benign Het
Or6c211 A T 10: 129,505,628 (GRCm39) C253* probably null Het
Ostc T C 3: 130,497,157 (GRCm39) N80S probably damaging Het
Palmd T C 3: 116,717,400 (GRCm39) R366G possibly damaging Het
Parp1 A G 1: 180,401,230 (GRCm39) D45G probably damaging Het
Pcdhga9 T A 18: 37,870,524 (GRCm39) Y118N possibly damaging Het
Pes1 C A 11: 3,926,834 (GRCm39) T372K probably benign Het
Plcl1 A T 1: 55,736,309 (GRCm39) D550V probably benign Het
Plekhg5 T A 4: 152,191,960 (GRCm39) C433S probably benign Het
Plin2 A G 4: 86,586,915 (GRCm39) M1T probably null Het
Pms2 G A 5: 143,848,732 (GRCm39) probably benign Het
Ppp1r7 T A 1: 93,285,585 (GRCm39) probably null Het
Psmb8 T C 17: 34,419,144 (GRCm39) I146T probably damaging Het
Ptger4 T C 15: 5,264,286 (GRCm39) R457G probably benign Het
Pzp A T 6: 128,462,519 (GRCm39) probably null Het
Ralgds A G 2: 28,438,781 (GRCm39) probably null Het
Rnf6 T C 5: 146,147,215 (GRCm39) Y601C probably benign Het
Sgk2 A G 2: 162,836,449 (GRCm39) probably benign Het
Shoc1 A C 4: 59,093,850 (GRCm39) L226R probably damaging Het
Slc39a8 T A 3: 135,592,554 (GRCm39) probably null Het
Slc4a4 G T 5: 89,283,623 (GRCm39) V481L probably damaging Het
Slc5a8 A G 10: 88,740,825 (GRCm39) I247V probably benign Het
Slit3 G T 11: 35,435,620 (GRCm39) E184* probably null Het
Sppl2c C T 11: 104,078,141 (GRCm39) P314S probably benign Het
St7 C T 6: 17,819,276 (GRCm39) P60L probably damaging Het
Tafa2 A T 10: 123,540,270 (GRCm39) H42L possibly damaging Het
Tbc1d8 A G 1: 39,444,398 (GRCm39) F187S probably damaging Het
Tet2 C T 3: 133,192,715 (GRCm39) G573E probably damaging Het
Tnni3k C T 3: 154,644,387 (GRCm39) probably null Het
Trpa1 A G 1: 14,957,844 (GRCm39) C705R probably damaging Het
Usp9y T A Y: 1,310,502 (GRCm39) probably benign Het
Vmn2r68 A C 7: 84,882,834 (GRCm39) M306R probably benign Het
Vwa7 G A 17: 35,240,218 (GRCm39) M395I probably damaging Het
Zfp53 A T 17: 21,728,340 (GRCm39) E124D 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
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
R8003:Ybx3 UTSW 6 131,345,400 (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'- ATCAGGCTCATGACCAAAGC -3'
(R):5'- AAAAGCTAGGTGCCCTGTGC -3'

Sequencing Primer
(F):5'- TCATGACCAAAGCAACCATATCTTC -3'
(R):5'- CTAGGTGCCCTGTGCTAAGGAAG -3'
Posted On 2015-01-23