Incidental Mutation 'R7502:Xbp1'
ID 581568
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 045575-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R7502 (G1)
Quality Score 225.009
Status Not validated
Chromosome 11
Chromosomal Location 5470659-5475893 bp(+) (GRCm39)
Type of Mutation critical splice acceptor site
DNA Base Change (assembly) A to G at 5474683 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change
Ref Sequence ENSEMBL: ENSMUSP00000054852 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000020776] [ENSMUST00000063084] [ENSMUST00000063084] [ENSMUST00000149623] [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 null
Transcript: ENSMUST00000063084
SMART Domains Protein: ENSMUSP00000054852
Gene: ENSMUSG00000020484

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 probably null
Transcript: ENSMUST00000063084
SMART Domains Protein: ENSMUSP00000054852
Gene: ENSMUSG00000020484

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 probably benign
Transcript: ENSMUST00000149159
SMART Domains Protein: ENSMUSP00000134088
Gene: ENSMUSG00000020484

DomainStartEndE-ValueType
BRLZ 2 57 2.62e-9 SMART
Predicted Effect probably null
Transcript: ENSMUST00000149623
SMART Domains Protein: ENSMUSP00000135768
Gene: ENSMUSG00000020484

DomainStartEndE-ValueType
BRLZ 11 72 3.68e-13 SMART
low complexity region 132 145 N/A INTRINSIC
Predicted Effect probably null
Transcript: ENSMUST00000149623
SMART Domains Protein: ENSMUSP00000135768
Gene: ENSMUSG00000020484

DomainStartEndE-ValueType
BRLZ 11 72 3.68e-13 SMART
low complexity region 132 145 N/A INTRINSIC
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 100.0%
  • 10x: 99.7%
  • 20x: 99.1%
Validation Efficiency
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: 87 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Acan A G 7: 78,743,951 (GRCm39) T661A probably damaging Het
Actrt2 T C 4: 154,751,383 (GRCm39) Y251C probably benign Het
Adat3 T A 10: 80,442,255 (GRCm39) V31D probably damaging Het
Adgrf4 T C 17: 42,980,548 (GRCm39) H179R possibly damaging Het
Ahcyl1 A T 3: 107,578,513 (GRCm39) Y241* probably null Het
Anks1 C A 17: 28,227,114 (GRCm39) T589K possibly damaging Het
Arhgap15 A G 2: 43,670,630 (GRCm39) T5A probably benign Het
Cacna1e A T 1: 154,344,734 (GRCm39) M1130K probably null Het
Ccdc121rt1 G A 1: 181,338,443 (GRCm39) Q170* probably null Het
Ceacam18 A T 7: 43,286,298 (GRCm39) D57V probably damaging Het
Celf1 C T 2: 90,835,100 (GRCm39) Q194* probably null Het
Celsr2 T A 3: 108,306,218 (GRCm39) T2029S probably benign Het
Cep170 T C 1: 176,583,595 (GRCm39) D163G probably damaging Het
Cfap210 A T 2: 69,606,488 (GRCm39) D309E probably benign Het
Cftr T C 6: 18,214,295 (GRCm39) F157S probably damaging Het
Chchd3 T C 6: 32,945,164 (GRCm39) E114G probably damaging Het
Cntnap2 T A 6: 46,460,963 (GRCm39) S666R possibly damaging Het
Col6a5 C T 9: 105,753,075 (GRCm39) V2266I probably benign Het
Ctr9 A G 7: 110,633,133 (GRCm39) D127G probably benign Het
Ctsl A T 13: 64,514,882 (GRCm39) F141I probably damaging Het
Dcpp1 T A 17: 24,101,615 (GRCm39) Y121* probably null Het
Ddx42 T C 11: 106,138,565 (GRCm39) V788A probably benign Het
Ehd4 T C 2: 119,921,874 (GRCm39) I461V probably benign Het
Elp6 C A 9: 110,134,376 (GRCm39) L5I possibly damaging Het
Faap20 T C 4: 155,334,793 (GRCm39) S2P Het
Fam98b A C 2: 117,094,344 (GRCm39) Y218S probably damaging Het
Fbxl4 T A 4: 22,376,655 (GRCm39) D30E probably benign Het
Fcrlb T C 1: 170,736,210 (GRCm39) T189A probably damaging Het
Gfpt1 A G 6: 87,043,671 (GRCm39) D302G probably benign Het
Gzmg T G 14: 56,394,284 (GRCm39) E203D not run Het
Hsph1 A C 5: 149,553,838 (GRCm39) V210G probably damaging Het
Il20rb A T 9: 100,350,479 (GRCm39) M138K probably damaging Het
Itpr1 A T 6: 108,360,639 (GRCm39) E688D probably benign Het
Jmjd1c T G 10: 67,067,794 (GRCm39) S1585A probably damaging Het
Kcnk3 A T 5: 30,780,062 (GRCm39) T371S possibly damaging Het
Kif11 T A 19: 37,398,255 (GRCm39) S694T possibly damaging Het
Kpna7 T A 5: 144,942,731 (GRCm39) H85L probably benign Het
Lipf A T 19: 33,954,006 (GRCm39) I366F probably damaging Het
Lrrc27 A G 7: 138,794,748 (GRCm39) H37R probably benign Het
Mki67 T C 7: 135,302,512 (GRCm39) T841A possibly damaging Het
Mtss1 A G 15: 58,820,210 (GRCm39) S120P probably damaging Het
Nav1 A G 1: 135,397,404 (GRCm39) W922R probably damaging Het
Nwd1 A G 8: 73,434,021 (GRCm39) E1206G probably damaging Het
Obscn T C 11: 58,885,635 (GRCm39) S7933G unknown Het
Or13j1 T C 4: 43,706,316 (GRCm39) H84R probably damaging Het
Or1p4-ps1 T C 11: 74,208,010 (GRCm39) V53A probably benign Het
Or2g25 T A 17: 37,971,122 (GRCm39) Y34F probably damaging Het
Or2k2 T C 4: 58,785,648 (GRCm39) I25V probably benign Het
Or4c52 T C 2: 89,845,355 (GRCm39) L27S probably benign Het
Otog A T 7: 45,948,039 (GRCm39) I162F probably damaging Het
Paf1 G A 7: 28,095,293 (GRCm39) V153I possibly damaging Het
Pcdhga11 T A 18: 37,889,554 (GRCm39) D187E probably benign Het
Peg10 CCACATCAGGATCCACATCAGGATGCACATCAGCATCAGGATCCCCATCAGGATGCACATCAGGATCCACATCAGGATGCACATCAG CCACATCAGGATCCACATCAGGATGCACATCAG 6: 4,756,398 (GRCm39) probably benign Het
Pitrm1 G T 13: 6,610,658 (GRCm39) R424L probably damaging Het
Pla2g4e T A 2: 120,004,819 (GRCm39) probably null Het
Plaat1 T C 16: 29,046,919 (GRCm39) V146A probably benign Het
Prorp T C 12: 55,351,206 (GRCm39) Y172H probably damaging Het
Prrc2a T C 17: 35,381,286 (GRCm39) N61S unknown Het
Ror1 T A 4: 100,190,827 (GRCm39) D61E probably benign Het
Ryr3 G A 2: 112,542,706 (GRCm39) P3168S probably benign Het
Serinc4 T A 2: 121,284,250 (GRCm39) I289F probably damaging Het
Sez6l A T 5: 112,623,347 (GRCm39) L68H possibly damaging Het
Sez6l2 A G 7: 126,560,915 (GRCm39) E460G probably benign Het
Sh3tc1 C T 5: 35,863,406 (GRCm39) G927D probably damaging Het
Slc22a27 G C 19: 7,903,747 (GRCm39) T130S probably damaging Het
Slc38a8 C A 8: 120,227,820 (GRCm39) A37S possibly damaging Het
Slc40a1 T C 1: 45,958,134 (GRCm39) N100D probably damaging Het
Slc49a3 G A 5: 108,591,646 (GRCm39) probably null Het
Snx30 T C 4: 59,894,567 (GRCm39) F382L possibly damaging Het
Sox1 A G 8: 12,446,913 (GRCm39) N185D possibly damaging Het
Spsb1 C T 4: 149,991,385 (GRCm39) R61H possibly damaging Het
Sptbn2 T C 19: 4,798,110 (GRCm39) V1945A probably benign Het
St18 T A 1: 6,898,194 (GRCm39) N665K probably benign Het
Syne1 A G 10: 5,283,446 (GRCm39) S1540P probably damaging Het
Syne2 G A 12: 76,141,100 (GRCm39) V1331M probably damaging Het
Tfap2c T C 2: 172,393,639 (GRCm39) S185P probably benign Het
Tnfsf8 T A 4: 63,769,398 (GRCm39) D71V probably damaging Het
Tnn T C 1: 159,937,929 (GRCm39) D1196G probably benign Het
Ttll8 A G 15: 88,817,639 (GRCm39) probably null Het
Tubgcp3 A G 8: 12,691,207 (GRCm39) F444L probably damaging Het
Txndc11 G A 16: 10,905,742 (GRCm39) P596L probably benign Het
Ubr4 C T 4: 139,139,983 (GRCm39) P1189S possibly damaging Het
Usp32 T C 11: 84,913,724 (GRCm39) D869G possibly damaging Het
Vmn1r202 G T 13: 22,686,188 (GRCm39) N76K probably damaging Het
Wfdc6a C T 2: 164,421,761 (GRCm39) M132I probably benign Het
Wnk2 A T 13: 49,300,720 (GRCm39) probably null Het
Zfp551 A T 7: 12,149,725 (GRCm39) Y561* probably null 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
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
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'- CACTTTCCTAGTCTGCTTAAGTGG -3'
(R):5'- TGAGTTCATTAATGGCTTCCAGC -3'

Sequencing Primer
(F):5'- CCTAGTCTGCTTAAGTGGATGGAG -3'
(R):5'- AATGGCTTCCAGCTTGGC -3'
Posted On 2019-10-17