Incidental Mutation 'R6038:Xbp1'
ID 486683
Institutional Source Beutler Lab
Gene Symbol Xbp1
Ensembl Gene ENSMUSG00000020484
Gene Name X-box binding protein 1
Synonyms XBP-1, TREB-5, TREB5, D11Ertd39e
MMRRC Submission 044208-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R6038 (G1)
Quality Score 225.009
Status Validated
Chromosome 11
Chromosomal Location 5470659-5475893 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 5474798 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Leucine to Proline at position 233 (L233P)
Ref Sequence ENSEMBL: ENSMUSP00000054852 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000020776] [ENSMUST00000063084] [ENSMUST00000149623]
AlphaFold O35426
Predicted Effect probably benign
Transcript: ENSMUST00000020776
SMART Domains Protein: ENSMUSP00000020776
Gene: ENSMUSG00000020482

DomainStartEndE-ValueType
low complexity region 22 37 N/A INTRINSIC
Pfam:CCDC117 139 277 1.9e-56 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000063084
AA Change: L233P

PolyPhen 2 Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)
SMART Domains Protein: ENSMUSP00000054852
Gene: ENSMUSG00000020484
AA Change: L233P

DomainStartEndE-ValueType
low complexity region 2 17 N/A INTRINSIC
BRLZ 61 125 9.12e-18 SMART
low complexity region 185 198 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000145588
Predicted Effect probably benign
Transcript: ENSMUST00000149159
SMART Domains Protein: ENSMUSP00000134088
Gene: ENSMUSG00000020484

DomainStartEndE-ValueType
BRLZ 2 57 2.62e-9 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000149623
AA Change: L180P

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000135768
Gene: ENSMUSG00000020484
AA Change: L180P

DomainStartEndE-ValueType
BRLZ 11 72 3.68e-13 SMART
low complexity region 132 145 N/A INTRINSIC
Meta Mutation Damage Score 0.0898 question?
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.7%
  • 10x: 98.4%
  • 20x: 95.7%
Validation Efficiency 100% (65/65)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a transcription factor that regulates MHC class II genes by binding to a promoter element referred to as an X box. This gene product is a bZIP protein, which was also identified as a cellular transcription factor that binds to an enhancer in the promoter of the T cell leukemia virus type 1 promoter. It may increase expression of viral proteins by acting as the DNA binding partner of a viral transactivator. It has been found that upon accumulation of unfolded proteins in the endoplasmic reticulum (ER), the mRNA of this gene is processed to an active form by an unconventional splicing mechanism that is mediated by the endonuclease inositol-requiring enzyme 1 (IRE1). The resulting loss of 26 nt from the spliced mRNA causes a frame-shift and an isoform XBP1(S), which is the functionally active transcription factor. The isoform encoded by the unspliced mRNA, XBP1(U), is constitutively expressed, and thought to function as a negative feedback regulator of XBP1(S), which shuts off transcription of target genes during the recovery phase of ER stress. A pseudogene of XBP1 has been identified and localized to chromosome 5. [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygous mutants exhibit markedly impaired liver development resulting in severe anemia, necrosis of cardiac myocytes, morphological abnormalities of the neural tube, and fetal death around embryonic day 14. [provided by MGI curators]
Allele List at MGI

All alleles(16) : Targeted, knock-out(3) Targeted, other(6) Gene trapped(7)
Other mutations in this stock
Total: 62 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcc10 A G 17: 46,615,286 (GRCm39) C1327R probably damaging Het
Adcy7 A G 8: 89,049,608 (GRCm39) T704A probably benign Het
Adgra3 A T 5: 50,156,487 (GRCm39) Y414* probably null Het
Adgrf1 T C 17: 43,606,100 (GRCm39) S75P probably benign Het
Akirin1 A G 4: 123,643,956 (GRCm39) M1T probably null Het
Antxr1 C A 6: 87,263,982 (GRCm39) probably null Het
Arid1b A T 17: 5,386,957 (GRCm39) Y1470F probably benign Het
Baiap3 T C 17: 25,465,308 (GRCm39) D649G probably damaging Het
Cabin1 A G 10: 75,575,200 (GRCm39) V615A probably benign Het
Cntnap1 G A 11: 101,075,462 (GRCm39) R880Q probably benign Het
Col28a1 T C 6: 8,013,140 (GRCm39) T971A probably benign Het
Coro7 A T 16: 4,497,414 (GRCm39) probably null Het
Cspg4b G A 13: 113,455,153 (GRCm39) V400M possibly damaging Het
Defb19 T G 2: 152,418,187 (GRCm39) probably null Het
Dnah17 T C 11: 117,946,715 (GRCm39) D3045G probably benign Het
Dock4 A T 12: 40,783,350 (GRCm39) probably null Het
Egln3 A G 12: 54,228,476 (GRCm39) V210A probably damaging Het
Epb41l4a T C 18: 33,987,388 (GRCm39) S330G probably benign Het
Epha7 G A 4: 28,821,521 (GRCm39) E229K probably damaging Het
Fetub C T 16: 22,751,081 (GRCm39) R143C probably damaging Het
Garin4 C T 1: 190,894,919 (GRCm39) E575K probably damaging Het
Garin5a C T 7: 44,149,719 (GRCm39) R147W probably damaging Het
Garin5b T C 7: 4,756,594 (GRCm39) probably null Het
Gm29587 G A 12: 74,269,309 (GRCm39) probably null Het
Gxylt2 T A 6: 100,781,555 (GRCm39) L410Q probably damaging Het
H2-M10.3 C A 17: 36,679,287 (GRCm39) C6F probably benign Het
Hecw1 G T 13: 14,520,647 (GRCm39) Q197K probably benign Het
Hk3 T C 13: 55,154,373 (GRCm39) M778V probably benign Het
Hydin A G 8: 111,325,663 (GRCm39) T4691A probably benign Het
Larp1 A G 11: 57,932,431 (GRCm39) E204G possibly damaging Het
Lrp12 A C 15: 39,735,776 (GRCm39) W738G probably damaging Het
Mdga2 A T 12: 66,676,827 (GRCm39) D488E probably damaging Het
Mrc1 G C 2: 14,261,882 (GRCm39) W290C probably damaging Het
Mtrex A T 13: 113,027,824 (GRCm39) S679T probably benign Het
Nhp2 T C 11: 51,510,912 (GRCm39) V55A probably benign Het
Nrm T C 17: 36,172,397 (GRCm39) S41P possibly damaging Het
Or10ag54 T A 2: 87,099,611 (GRCm39) I141N possibly damaging Het
Or11g25 T C 14: 50,723,677 (GRCm39) L254P probably damaging Het
Or7e165 A G 9: 19,694,858 (GRCm39) Y143C probably benign Het
Osbpl7 C T 11: 96,941,542 (GRCm39) P22S probably benign Het
Pebp1 A T 5: 117,422,170 (GRCm39) L124Q probably benign Het
Pfkp G T 13: 6,648,005 (GRCm39) H524N probably benign Het
Pnmt G A 11: 98,278,594 (GRCm39) D187N probably damaging Het
Ppl A T 16: 4,920,445 (GRCm39) I355K possibly damaging Het
Prom1 A T 5: 44,159,135 (GRCm39) Y836N probably damaging Het
Rubcnl T C 14: 75,269,410 (GRCm39) S23P probably benign Het
Sap130 T A 18: 31,813,539 (GRCm39) I532N probably damaging Het
Serpina1e A T 12: 103,913,095 (GRCm39) probably null Het
Slc12a3 T G 8: 95,057,100 (GRCm39) S124R probably benign Het
Slc24a5 A G 2: 124,927,651 (GRCm39) T317A probably benign Het
Smarcad1 T C 6: 65,050,232 (GRCm39) S284P possibly damaging Het
Spag9 C G 11: 94,002,918 (GRCm39) R724G probably damaging Het
Speg T C 1: 75,395,103 (GRCm39) probably null Het
Steap3 A G 1: 120,169,371 (GRCm39) Y271H probably damaging Het
Syne2 C T 12: 75,925,158 (GRCm39) Q44* probably null Het
Tas2r114 A T 6: 131,666,444 (GRCm39) C195S possibly damaging Het
Tcl1b4 T C 12: 105,168,766 (GRCm39) M10T possibly damaging Het
Tln1 G C 4: 43,555,052 (GRCm39) F259L probably damaging Het
Vmn2r60 C A 7: 41,844,386 (GRCm39) A583D probably benign Het
Wdhd1 T C 14: 47,501,037 (GRCm39) Q455R possibly damaging Het
Wdr17 A G 8: 55,085,346 (GRCm39) probably null Het
Zbtb17 A G 4: 141,191,752 (GRCm39) E288G probably benign Het
Other mutations in Xbp1
AlleleSourceChrCoordTypePredicted EffectPPH Score
R1601:Xbp1 UTSW 11 5,471,975 (GRCm39) missense probably damaging 1.00
R2256:Xbp1 UTSW 11 5,474,841 (GRCm39) missense probably damaging 1.00
R4647:Xbp1 UTSW 11 5,472,006 (GRCm39) missense probably damaging 1.00
R4782:Xbp1 UTSW 11 5,471,167 (GRCm39) missense probably damaging 1.00
R4964:Xbp1 UTSW 11 5,471,125 (GRCm39) missense probably damaging 0.98
R5367:Xbp1 UTSW 11 5,471,910 (GRCm39) missense probably benign
R5718:Xbp1 UTSW 11 5,471,903 (GRCm39) missense probably benign 0.00
R5928:Xbp1 UTSW 11 5,473,514 (GRCm39) intron probably benign
R6038:Xbp1 UTSW 11 5,474,798 (GRCm39) missense probably benign 0.00
R6492:Xbp1 UTSW 11 5,471,005 (GRCm39) missense probably benign
R6835:Xbp1 UTSW 11 5,471,809 (GRCm39) start gained probably benign
R6955:Xbp1 UTSW 11 5,472,018 (GRCm39) missense probably null 0.97
R7067:Xbp1 UTSW 11 5,474,275 (GRCm39) missense probably damaging 1.00
R7483:Xbp1 UTSW 11 5,471,098 (GRCm39) missense probably benign 0.02
R7502:Xbp1 UTSW 11 5,474,683 (GRCm39) critical splice acceptor site probably null
R7819:Xbp1 UTSW 11 5,474,886 (GRCm39) missense probably benign 0.01
R8024:Xbp1 UTSW 11 5,471,910 (GRCm39) missense probably benign
R8512:Xbp1 UTSW 11 5,474,266 (GRCm39) missense probably damaging 1.00
R8933:Xbp1 UTSW 11 5,474,741 (GRCm39) missense probably benign 0.00
Predicted Primers PCR Primer
(F):5'- AGTGTAAGCCCTAAGTAACATTGTG -3'
(R):5'- TGAAGAGCTTAGAGGTGCTTCC -3'

Sequencing Primer
(F):5'- AGTAACATTGTGGAACCCAGTAC -3'
(R):5'- CCTCAATTTTCACTACCACGTTAG -3'
Posted On 2017-08-16