Incidental Mutation 'R0270:Ybx1'
ID 35200
Institutional Source Beutler Lab
Gene Symbol Ybx1
Ensembl Gene ENSMUSG00000028639
Gene Name Y box protein 1
Synonyms Nsep1, DNA binding protein B, dbpB, EF1A, YB-1, MSY1
MMRRC Submission 038496-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R0270 (G1)
Quality Score 190
Status Validated
Chromosome 4
Chromosomal Location 119135178-119151801 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to T at 119138788 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Glycine to Aspartic acid at position 126 (G126D)
Ref Sequence ENSEMBL: ENSMUSP00000117225 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000079644] [ENSMUST00000127737]
AlphaFold P62960
Predicted Effect probably benign
Transcript: ENSMUST00000079644
AA Change: G238D

PolyPhen 2 Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)
SMART Domains Protein: ENSMUSP00000078589
Gene: ENSMUSG00000028639
AA Change: G238D

DomainStartEndE-ValueType
low complexity region 10 21 N/A INTRINSIC
low complexity region 25 48 N/A INTRINSIC
CSP 58 126 8.65e-24 SMART
low complexity region 140 159 N/A INTRINSIC
low complexity region 162 174 N/A INTRINSIC
low complexity region 179 206 N/A INTRINSIC
low complexity region 236 254 N/A INTRINSIC
low complexity region 277 289 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000127737
AA Change: G126D

PolyPhen 2 Score 0.110 (Sensitivity: 0.93; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000117225
Gene: ENSMUSG00000028639
AA Change: G126D

DomainStartEndE-ValueType
low complexity region 28 47 N/A INTRINSIC
low complexity region 50 62 N/A INTRINSIC
low complexity region 67 94 N/A INTRINSIC
low complexity region 169 181 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000139897
Predicted Effect noncoding transcript
Transcript: ENSMUST00000142884
Predicted Effect noncoding transcript
Transcript: ENSMUST00000144992
Predicted Effect noncoding transcript
Transcript: ENSMUST00000145976
Meta Mutation Damage Score 0.0898 question?
Coding Region Coverage
  • 1x: 98.7%
  • 3x: 97.7%
  • 10x: 96.0%
  • 20x: 93.2%
Validation Efficiency 99% (113/114)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a highly conserved cold shock domain protein that has broad nucleic acid binding properties. The encoded protein functions as both a DNA and RNA binding protein and has been implicated in numerous cellular processes including regulation of transcription and translation, pre-mRNA splicing, DNA reparation and mRNA packaging. This protein is also a component of messenger ribonucleoprotein (mRNP) complexes and may have a role in microRNA processing. This protein can be secreted through non-classical pathways and functions as an extracellular mitogen. Aberrant expression of the gene is associated with cancer proliferation in numerous tissues. This gene may be a prognostic marker for poor outcome and drug resistance in certain cancers. Alternate splicing results in multiple transcript variants. Pseudogenes of this gene are found on multiple chromosomes. [provided by RefSeq, Sep 2015]
PHENOTYPE: Homozygous null mice exhibit embryonic and perinatal lethality and are severely growth retarded. Some mice exhibit craniofacial defects and respiratory failure. MEFs are more sensitive to oxidative stress resulting in premature senescence. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 109 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
3110009E18Rik T A 1: 120,093,906 (GRCm39) probably benign Het
Aadacl2fm3 T A 3: 59,784,440 (GRCm39) N304K probably benign Het
Abcf3 T A 16: 20,378,918 (GRCm39) probably null Het
Acadm C T 3: 153,641,961 (GRCm39) M190I possibly damaging Het
Adamtsl3 G A 7: 82,206,032 (GRCm39) R739Q probably damaging Het
Ank1 T A 8: 23,578,941 (GRCm39) probably benign Het
Ap3b1 T A 13: 94,540,626 (GRCm39) probably benign Het
Arhgdib A G 6: 136,903,732 (GRCm39) V31A probably damaging Het
Arid4a A G 12: 71,119,406 (GRCm39) R342G probably damaging Het
Asic3 C T 5: 24,622,700 (GRCm39) L517F probably benign Het
Atxn7l1 C T 12: 33,392,150 (GRCm39) P242L possibly damaging Het
AY761185 T A 8: 21,434,616 (GRCm39) E37D possibly damaging Het
Babam1 T A 8: 71,851,050 (GRCm39) D104E probably damaging Het
Batf A T 12: 85,755,446 (GRCm39) T100S probably benign Het
Blcap A T 2: 157,399,897 (GRCm39) Y59* probably null Het
Cacnb3 G A 15: 98,540,440 (GRCm39) A350T probably damaging Het
Cdk15 T A 1: 59,349,965 (GRCm39) V319D probably damaging Het
Cenpf T C 1: 189,382,911 (GRCm39) H2661R probably benign Het
Cenpq T C 17: 41,240,941 (GRCm39) E106G probably damaging Het
Cfap43 A G 19: 47,785,642 (GRCm39) probably benign Het
Cfb G A 17: 35,079,362 (GRCm39) S778L possibly damaging Het
Clec2m A T 6: 129,302,571 (GRCm39) L152* probably null Het
Clspn T A 4: 126,467,029 (GRCm39) N631K probably damaging Het
Cntn2 T A 1: 132,449,462 (GRCm39) T660S probably damaging Het
Cntrob T A 11: 69,202,167 (GRCm39) H475L possibly damaging Het
Ddx46 T C 13: 55,821,917 (GRCm39) I863T probably benign Het
Dnah11 G A 12: 118,004,748 (GRCm39) T2191I probably damaging Het
Dock9 T C 14: 121,813,411 (GRCm39) T1703A probably benign Het
Fam13c C T 10: 70,380,343 (GRCm39) P424S probably benign Het
Fan1 T C 7: 63,998,619 (GRCm39) N968D probably benign Het
Fbxl20 A T 11: 97,989,329 (GRCm39) probably benign Het
Fkbp1b A T 12: 4,888,229 (GRCm39) probably benign Het
G930045G22Rik T A 6: 50,824,039 (GRCm39) noncoding transcript Het
Gm28042 C A 2: 119,872,073 (GRCm39) R1008S probably benign Het
Gon4l G A 3: 88,765,707 (GRCm39) S376N probably damaging Het
Gstt3 C A 10: 75,616,749 (GRCm39) R15L probably damaging Het
Gtdc1 A T 2: 44,642,186 (GRCm39) S73T possibly damaging Het
Hhatl A G 9: 121,613,786 (GRCm39) S419P probably benign Het
Hirip3 T G 7: 126,462,363 (GRCm39) S46R probably damaging Het
Hsf2 A G 10: 57,378,735 (GRCm39) T204A probably benign Het
Impg2 G A 16: 56,089,378 (GRCm39) E1108K possibly damaging Het
Itgb2l G T 16: 96,224,130 (GRCm39) probably benign Het
Itih5 A T 2: 10,256,075 (GRCm39) N847I probably benign Het
Kif1a T C 1: 92,982,164 (GRCm39) probably benign Het
Klhl1 T A 14: 96,755,780 (GRCm39) probably benign Het
Ktn1 T A 14: 47,952,119 (GRCm39) D963E probably benign Het
Lclat1 T A 17: 73,547,022 (GRCm39) V313E probably benign Het
Lrrn4 T C 2: 132,712,639 (GRCm39) S395G probably benign Het
Macroh2a1 G A 13: 56,243,927 (GRCm39) probably benign Het
Mbtps1 G A 8: 120,264,856 (GRCm39) probably benign Het
Me1 A G 9: 86,478,257 (GRCm39) probably benign Het
Mov10 C A 3: 104,702,721 (GRCm39) C948F probably benign Het
Mterf1a G A 5: 3,940,990 (GRCm39) Q293* probably null Het
Nfkb2 A T 19: 46,300,065 (GRCm39) M838L possibly damaging Het
Nhlrc2 T A 19: 56,540,302 (GRCm39) L97Q probably damaging Het
Nr6a1 A T 2: 38,629,032 (GRCm39) Y331N possibly damaging Het
Nup214 C T 2: 31,924,826 (GRCm39) A1785V probably damaging Het
Ogg1 C T 6: 113,306,217 (GRCm39) T138I probably benign Het
Or5ac20 A G 16: 59,104,116 (GRCm39) V248A probably damaging Het
Or5b107 A G 19: 13,143,251 (GRCm39) Y291C probably damaging Het
Or5b124 A G 19: 13,611,048 (GRCm39) Y191C probably damaging Het
Or7g17 T A 9: 18,768,127 (GRCm39) Y60N probably damaging Het
Plod2 G T 9: 92,466,574 (GRCm39) R178L probably benign Het
Polr3b T A 10: 84,554,339 (GRCm39) L1017Q probably benign Het
Postn C A 3: 54,291,971 (GRCm39) T724N probably damaging Het
Ppm1l T G 3: 69,225,309 (GRCm39) probably benign Het
Prpf8 T G 11: 75,396,075 (GRCm39) L1983R probably damaging Het
Psma7 A G 2: 179,681,193 (GRCm39) V59A probably benign Het
Qser1 T A 2: 104,619,306 (GRCm39) Y502F probably benign Het
Rad50 T C 11: 53,558,852 (GRCm39) D1129G probably damaging Het
Rasal1 C A 5: 120,812,794 (GRCm39) P606Q probably damaging Het
Rgs6 A G 12: 83,180,463 (GRCm39) Y438C probably damaging Het
Rnf180 A G 13: 105,388,774 (GRCm39) C73R probably benign Het
Rnf216 T A 5: 143,065,996 (GRCm39) I474F possibly damaging Het
Sdha A T 13: 74,480,366 (GRCm39) L371Q probably damaging Het
Sdk1 T G 5: 142,070,321 (GRCm39) L1162R possibly damaging Het
Sh3rf2 T C 18: 42,237,146 (GRCm39) I223T probably damaging Het
Sirpb1a A G 3: 15,475,587 (GRCm39) V316A probably damaging Het
Slc12a4 A T 8: 106,672,021 (GRCm39) I897N probably benign Het
Slc35d1 A T 4: 103,048,035 (GRCm39) V243E probably damaging Het
Slc4a11 T A 2: 130,532,852 (GRCm39) K200N possibly damaging Het
Slc9a8 T A 2: 167,293,216 (GRCm39) M188K probably damaging Het
Slco1a8 T A 6: 141,918,137 (GRCm39) I580F possibly damaging Het
Snrnp200 T C 2: 127,074,902 (GRCm39) S1492P probably damaging Het
Sphk2 T C 7: 45,360,149 (GRCm39) *618W probably null Het
Sytl2 T C 7: 90,052,228 (GRCm39) probably benign Het
Tdpoz3 A G 3: 93,734,231 (GRCm39) N302S probably benign Het
Tdrd6 T C 17: 43,935,199 (GRCm39) M1950V probably benign Het
Tmem39a A G 16: 38,384,675 (GRCm39) probably benign Het
Trip4 A T 9: 65,765,640 (GRCm39) I353K probably damaging Het
Trip6 A T 5: 137,311,103 (GRCm39) F204L probably benign Het
Trpm4 T A 7: 44,968,677 (GRCm39) I419F possibly damaging Het
Ttn C A 2: 76,775,140 (GRCm39) E1967D probably damaging Het
Uba2 C T 7: 33,850,281 (GRCm39) V391M possibly damaging Het
Ubr4 T G 4: 139,206,746 (GRCm39) probably benign Het
Upf1 G A 8: 70,788,295 (GRCm39) probably benign Het
Vmn1r228 A C 17: 20,996,858 (GRCm39) V220G possibly damaging Het
Vmn2r79 A G 7: 86,652,594 (GRCm39) M429V probably benign Het
Vps36 C T 8: 22,700,472 (GRCm39) T210I possibly damaging Het
Wdr17 C T 8: 55,146,131 (GRCm39) A90T possibly damaging Het
Yipf5 C A 18: 40,339,460 (GRCm39) probably benign Het
Zbtb47 A G 9: 121,596,641 (GRCm39) T666A probably benign Het
Zdhhc5 A C 2: 84,520,459 (GRCm39) S573A probably benign Het
Zfp457 A T 13: 67,441,991 (GRCm39) C99S probably damaging Het
Zfp52 T A 17: 21,781,564 (GRCm39) C471S probably damaging Het
Zfp558 C T 9: 18,379,252 (GRCm39) V71I probably damaging Het
Zfp655 A G 5: 145,181,267 (GRCm39) Y375C probably damaging Het
Zfp882 A T 8: 72,668,459 (GRCm39) T429S probably benign Het
Zmym2 T C 14: 57,187,141 (GRCm39) probably null Het
Other mutations in Ybx1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL02000:Ybx1 APN 4 119,139,509 (GRCm39) missense probably damaging 1.00
IGL02635:Ybx1 APN 4 119,136,286 (GRCm39) missense possibly damaging 0.88
BB001:Ybx1 UTSW 4 119,139,476 (GRCm39) missense probably damaging 0.97
BB011:Ybx1 UTSW 4 119,139,476 (GRCm39) missense probably damaging 0.97
R0136:Ybx1 UTSW 4 119,139,551 (GRCm39) missense possibly damaging 0.57
R4911:Ybx1 UTSW 4 119,140,010 (GRCm39) missense probably benign 0.13
R4957:Ybx1 UTSW 4 119,136,135 (GRCm39) utr 3 prime probably benign
R4986:Ybx1 UTSW 4 119,139,627 (GRCm39) missense probably damaging 0.99
R5205:Ybx1 UTSW 4 119,136,348 (GRCm39) missense probably damaging 1.00
R7098:Ybx1 UTSW 4 119,140,050 (GRCm39) missense possibly damaging 0.65
R7706:Ybx1 UTSW 4 119,136,164 (GRCm39) makesense probably null
R7924:Ybx1 UTSW 4 119,139,476 (GRCm39) missense probably damaging 0.97
R8901:Ybx1 UTSW 4 119,138,785 (GRCm39) missense probably damaging 0.97
R9213:Ybx1 UTSW 4 119,138,794 (GRCm39) missense possibly damaging 0.86
Predicted Primers PCR Primer
(F):5'- TGGTAGCAGACACCTCCCAGTAAG -3'
(R):5'- ATTGCCCTGTTAGCCACAGAGTG -3'

Sequencing Primer
(F):5'- gccagagcacttgcctac -3'
(R):5'- ataggcagggcaggtgg -3'
Posted On 2013-05-09