Incidental Mutation 'IGL02635:Ybx1'
ID 301463
Institutional Source Australian Phenomics Network (link to record)
Gene Symbol Ybx1
Ensembl Gene ENSMUSG00000028639
Gene Name Y box protein 1
Synonyms Nsep1, DNA binding protein B, dbpB, EF1A, YB-1, MSY1
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # IGL02635
Quality Score
Status
Chromosome 4
Chromosomal Location 119135178-119151801 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 119136286 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Asparagine to Serine at position 282 (N282S)
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: N282S

PolyPhen 2 Score 0.883 (Sensitivity: 0.82; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000078589
Gene: ENSMUSG00000028639
AA Change: N282S

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: N174S

PolyPhen 2 Score 0.684 (Sensitivity: 0.86; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000117225
Gene: ENSMUSG00000028639
AA Change: N174S

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: ENSMUST00000144992
Predicted Effect noncoding transcript
Transcript: ENSMUST00000145976
Coding Region Coverage
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: 44 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
A730018C14Rik A C 12: 112,381,586 (GRCm39) noncoding transcript Het
Abcc12 C T 8: 87,236,311 (GRCm39) probably benign Het
Akap9 T C 5: 4,120,500 (GRCm39) S3639P possibly damaging Het
Ankar C T 1: 72,691,590 (GRCm39) V1124I possibly damaging Het
AW209491 C T 13: 14,811,852 (GRCm39) A235V possibly damaging Het
Cask A T X: 13,581,009 (GRCm39) D58E probably damaging Het
Cdhr4 T A 9: 107,870,070 (GRCm39) M25K probably benign Het
Clasp2 A G 9: 113,737,910 (GRCm39) I1096V probably damaging Het
Fam234a T A 17: 26,433,427 (GRCm39) I410F possibly damaging Het
Gbe1 T C 16: 70,365,902 (GRCm39) L693P probably damaging Het
Golgb1 G T 16: 36,735,375 (GRCm39) V1541L probably benign Het
Gpr143 G A X: 151,591,257 (GRCm39) E382K probably damaging Het
Gpr171 C T 3: 59,005,017 (GRCm39) V253I probably benign Het
Gsap T A 5: 21,494,814 (GRCm39) W10R probably damaging Het
Hsd17b12 T A 2: 93,913,556 (GRCm39) D116V possibly damaging Het
Ifih1 A T 2: 62,442,173 (GRCm39) L348Q probably damaging Het
Ighv1-50 G A 12: 115,083,615 (GRCm39) A35V probably benign Het
Lrcol1 A C 5: 110,502,459 (GRCm39) M112L probably benign Het
Lrrc59 T A 11: 94,534,282 (GRCm39) V280E probably damaging Het
Med17 A T 9: 15,185,845 (GRCm39) I223K probably damaging Het
Oog3 T C 4: 143,884,715 (GRCm39) N407S probably damaging Het
Or4e1 T C 14: 52,701,251 (GRCm39) I72V probably damaging Het
Pear1 T C 3: 87,657,453 (GRCm39) *1035W probably null Het
Pkd1 T A 17: 24,791,785 (GRCm39) F1157L probably damaging Het
Pkp4 T C 2: 59,135,842 (GRCm39) probably benign Het
Ppl T C 16: 4,907,631 (GRCm39) E888G probably benign Het
Prh1 G A 6: 132,549,246 (GRCm39) G251E unknown Het
Prkar2a A G 9: 108,605,476 (GRCm39) E178G probably damaging Het
Rfx6 A T 10: 51,592,122 (GRCm39) T352S possibly damaging Het
S1pr1 T C 3: 115,505,739 (GRCm39) K285R probably benign Het
Slc12a1 A G 2: 125,067,898 (GRCm39) H995R probably benign Het
Slc25a54 T A 3: 109,020,133 (GRCm39) N382K possibly damaging Het
Snrnp48 T G 13: 38,393,845 (GRCm39) probably benign Het
Spg11 T C 2: 121,943,549 (GRCm39) D201G possibly damaging Het
Stox1 T C 10: 62,500,685 (GRCm39) D625G probably benign Het
Supt6 T C 11: 78,103,565 (GRCm39) H1380R probably damaging Het
Tcp1 T A 17: 13,142,296 (GRCm39) M430K probably benign Het
Tlr12 A T 4: 128,510,609 (GRCm39) V547E probably damaging Het
Tmem255b G T 8: 13,505,195 (GRCm39) D167Y probably damaging Het
Trpc7 T C 13: 56,923,981 (GRCm39) R735G probably damaging Het
Trpm1 A G 7: 63,848,972 (GRCm39) T73A probably benign Het
Ubr3 A T 2: 69,850,827 (GRCm39) L1748F probably damaging Het
Xirp2 T C 2: 67,338,254 (GRCm39) I165T possibly damaging Het
Zdhhc12 T A 2: 29,983,531 (GRCm39) I24F probably damaging Het
Other mutations in Ybx1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL02000:Ybx1 APN 4 119,139,509 (GRCm39) missense probably damaging 1.00
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
R9213:Ybx1 UTSW 4 119,138,794 (GRCm39) missense possibly damaging 0.86
Posted On 2015-04-16