Incidental Mutation 'R9213:Ybx1'
ID 698986
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
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R9213 (G1)
Quality Score 225.009
Status Not validated
Chromosome 4
Chromosomal Location 119135178-119151801 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 119138794 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Tyrosine to Phenylalanine at position 236 (Y236F)
Ref Sequence ENSEMBL: ENSMUSP00000078589 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000079644] [ENSMUST00000127737]
AlphaFold P62960
Predicted Effect possibly damaging
Transcript: ENSMUST00000079644
AA Change: Y236F

PolyPhen 2 Score 0.856 (Sensitivity: 0.83; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000078589
Gene: ENSMUSG00000028639
AA Change: Y236F

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 possibly damaging
Transcript: ENSMUST00000127737
AA Change: Y124F

PolyPhen 2 Score 0.583 (Sensitivity: 0.88; Specificity: 0.91)
SMART Domains Protein: ENSMUSP00000117225
Gene: ENSMUSG00000028639
AA Change: Y124F

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
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 100.0%
  • 10x: 99.8%
  • 20x: 99.4%
Validation Efficiency
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: 61 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adamts6 T A 13: 104,581,440 (GRCm39) C852S probably damaging Het
Arf1 A G 11: 59,104,186 (GRCm39) V43A probably damaging Het
Arhgef26 T A 3: 62,340,000 (GRCm39) M674K probably benign Het
Asb1 A C 1: 91,482,531 (GRCm39) K314N probably damaging Het
Aste1 T C 9: 105,274,294 (GRCm39) F178S probably damaging Het
Avl9 T C 6: 56,720,441 (GRCm39) F493S probably damaging Het
BC024139 T C 15: 76,009,422 (GRCm39) Y220C probably benign Het
Ccdc60 T C 5: 116,328,185 (GRCm39) E93G probably damaging Het
Cep112 A G 11: 108,377,779 (GRCm39) H295R probably benign Het
Chd3 T C 11: 69,255,628 (GRCm39) K87E possibly damaging Het
Chordc1 G T 9: 18,223,789 (GRCm39) probably null Het
Ciita A T 16: 10,319,742 (GRCm39) D55V probably damaging Het
Cklf T C 8: 104,988,125 (GRCm39) V86A probably damaging Het
Clock T A 5: 76,393,376 (GRCm39) N189I possibly damaging Het
Dnah14 T C 1: 181,444,205 (GRCm39) probably null Het
Dpep3 C G 8: 106,700,245 (GRCm39) C487S probably benign Het
Dtwd2 A G 18: 49,856,799 (GRCm39) F163L probably benign Het
Eln C T 5: 134,735,456 (GRCm39) V776M unknown Het
Fanci T A 7: 79,055,971 (GRCm39) M201K possibly damaging Het
Frmd4a A G 2: 4,608,372 (GRCm39) T747A probably damaging Het
Galnt9 T A 5: 110,767,108 (GRCm39) C526* probably null Het
Garnl3 T C 2: 32,895,080 (GRCm39) E663G probably damaging Het
Gdpd5 T C 7: 99,100,945 (GRCm39) S247P probably damaging Het
Gm4846 C T 1: 166,322,142 (GRCm39) D142N probably damaging Het
Kbtbd2 T A 6: 56,756,917 (GRCm39) E273V probably damaging Het
Klk1b11 A G 7: 43,648,428 (GRCm39) E145G possibly damaging Het
Mmp1a G T 9: 7,475,364 (GRCm39) V378F possibly damaging Het
Mon2 G T 10: 122,872,016 (GRCm39) S336* probably null Het
Mrgprh T A 17: 13,095,917 (GRCm39) N52K probably damaging Het
Myo9a T C 9: 59,772,922 (GRCm39) F985L probably benign Het
Nek3 T C 8: 22,638,677 (GRCm39) N207S probably benign Het
Nkpd1 A G 7: 19,258,009 (GRCm39) D596G probably damaging Het
Oc90 C A 15: 65,761,557 (GRCm39) E154* probably null Het
Or8b101 T A 9: 38,020,426 (GRCm39) M143K possibly damaging Het
Or8b3 C A 9: 38,315,047 (GRCm39) Y292* probably null Het
Peg10 T TCCC 6: 4,756,451 (GRCm39) probably benign Het
Pkhd1l1 A G 15: 44,358,874 (GRCm39) Y361C probably damaging Het
Polr2h T C 16: 20,539,285 (GRCm39) Y90H possibly damaging Het
Potefam1 T A 2: 111,020,699 (GRCm39) R136S unknown Het
Ppp1r26 A G 2: 28,343,649 (GRCm39) N1093S probably benign Het
Prex1 G T 2: 166,417,669 (GRCm39) R1313S probably damaging Het
Ptprh A T 7: 4,583,911 (GRCm39) V227E probably damaging Het
Pycr2 A G 1: 180,733,473 (GRCm39) D58G probably benign Het
Rad54b G T 4: 11,609,321 (GRCm39) E591* probably null Het
Rptor T C 11: 119,494,765 (GRCm39) S44P probably benign Het
Safb2 T A 17: 56,882,602 (GRCm39) T344S probably benign Het
Samd9l T C 6: 3,376,856 (GRCm39) E135G probably benign Het
Sec23a A T 12: 59,048,708 (GRCm39) I167N probably damaging Het
Shoc2 C T 19: 54,016,231 (GRCm39) T415I probably benign Het
Sobp T C 10: 42,898,374 (GRCm39) I404V probably benign Het
Ssbp4 G T 8: 71,052,395 (GRCm39) L147I probably benign Het
Sspo G A 6: 48,440,869 (GRCm39) R1777H possibly damaging Het
Syt14 A G 1: 192,612,814 (GRCm39) V379A probably damaging Het
Tat T G 8: 110,722,820 (GRCm39) I294S probably damaging Het
Tcf19 A G 17: 35,825,899 (GRCm39) V86A probably damaging Het
Tfap2a T A 13: 40,870,875 (GRCm39) I338F possibly damaging Het
Tmco6 C A 18: 36,872,384 (GRCm39) N365K probably damaging Het
Tmub2 G A 11: 102,178,475 (GRCm39) R164K Het
Togaram1 A G 12: 65,065,906 (GRCm39) I1637V possibly damaging Het
Wdr49 A C 3: 75,205,419 (GRCm39) S666A probably benign Het
Zfhx3 T A 8: 109,676,756 (GRCm39) I2602N probably benign 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
R0270:Ybx1 UTSW 4 119,138,788 (GRCm39) missense probably benign 0.11
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
Predicted Primers PCR Primer
(F):5'- TGAGGACTGGTAGCAGACAC -3'
(R):5'- GTGTGCTTTTGAACCTCCAGG -3'

Sequencing Primer
(F):5'- TGCCAGAGCACTTGCCTACTAG -3'
(R):5'- TTAACCCCAGTACTCTATAGGCAGGG -3'
Posted On 2022-02-07