Mutagenetix > Incidental Mutation

Incidental Mutation 'R4782:Xbp1'

366638

Institutional Source

Beutler Lab

Gene Symbol

Xbp1

Ensembl Gene

ENSMUSG00000020484

Gene Name

X-box binding protein 1

Synonyms

XBP-1, TREB-5, TREB5, D11Ertd39e

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R4782 (G1)

Quality Score

165

Status

Not validated

Chromosome

Chromosomal Location

5470659-5475893 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 5471167 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Methionine at position 58 (T58M)

Ref Sequence

ENSEMBL: ENSMUSP00000054852 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000063084] [ENSMUST00000149623]

AlphaFold

O35426

Predicted Effect

probably damaging
Transcript: ENSMUST00000063084
AA Change: T58M

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000054852
Gene: ENSMUSG00000020484
AA Change: T58M

Domain	Start	End	E-Value	Type
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

Domain	Start	End	E-Value	Type
BRLZ	2	57	2.62e-9	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000149623

SMART Domains

Protein: ENSMUSP00000135768
Gene: ENSMUSG00000020484

Domain	Start	End	E-Value	Type
BRLZ	11	72	3.68e-13	SMART
low complexity region	132	145	N/A	INTRINSIC

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 96.9%
20x: 94.4%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a 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: 121 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca13	A	G	11: 9,278,096 (GRCm39)	E3092G	probably damaging	Het
Abhd12b	C	G	12: 70,215,838 (GRCm39)	S170C	probably damaging	Het
Abtb2	A	T	2: 103,547,644 (GRCm39)	D1006V	probably benign	Het
Abtb3	A	C	10: 85,490,414 (GRCm39)	I1027L	probably damaging	Het
Adgrl1	A	G	8: 84,662,202 (GRCm39)	H1021R	probably benign	Het
Ago3	A	T	4: 126,241,665 (GRCm39)		probably null	Het
Ahnak	A	G	19: 8,989,863 (GRCm39)		probably benign	Het
Akap6	CA	C	12: 52,934,406 (GRCm39)		probably null	Het
Amotl2	T	G	9: 102,597,322 (GRCm39)		probably null	Het
Ankrd34b	T	A	13: 92,574,813 (GRCm39)	I15N	probably damaging	Het
Ap3d1	C	T	10: 80,557,420 (GRCm39)		probably null	Het
Appl2	A	T	10: 83,436,855 (GRCm39)	D635E	probably damaging	Het
Arid1b	C	T	17: 5,389,496 (GRCm39)	P1681S	probably damaging	Het
Atp10a	T	C	7: 58,440,843 (GRCm39)	M496T	probably benign	Het
Atp2c2	A	G	8: 120,475,891 (GRCm39)	K595E	probably damaging	Het
Atpaf2	T	C	11: 60,295,238 (GRCm39)	H204R	probably damaging	Het
Atr	G	A	9: 95,744,850 (GRCm39)	V56I	probably benign	Het
Bod1l	G	A	5: 41,991,006 (GRCm39)	T183I	probably benign	Het
Ccdc168	T	C	1: 44,098,203 (GRCm39)	D965G	possibly damaging	Het
Ccdc171	A	T	4: 83,599,253 (GRCm39)	E689D	probably damaging	Het
Cdc73	T	A	1: 143,503,613 (GRCm39)	Q346L	probably benign	Het
Cert1	T	C	13: 96,748,773 (GRCm39)	V281A	probably benign	Het
Chd2	A	T	7: 73,134,184 (GRCm39)	M721K	possibly damaging	Het
Col22a1	T	A	15: 71,673,774 (GRCm39)	T981S	unknown	Het
Cpox	G	A	16: 58,492,986 (GRCm39)	A207T	probably damaging	Het
Cym	G	A	3: 107,123,413 (GRCm39)	T160I	possibly damaging	Het
D130043K22Rik	T	C	13: 25,062,023 (GRCm39)	I664T	probably damaging	Het
Ddx4	C	T	13: 112,750,230 (GRCm39)		probably null	Het
Ddx4	A	T	13: 112,787,894 (GRCm39)	V15E	probably benign	Het
Depdc1a	G	A	3: 159,232,273 (GRCm39)	E675K	probably damaging	Het
Dglucy	A	T	12: 100,816,602 (GRCm39)	M415L	probably benign	Het
Dlg4	C	T	11: 69,917,780 (GRCm39)	P21L	probably damaging	Het
Dmxl1	A	T	18: 49,996,059 (GRCm39)	N395I	probably damaging	Het
Dzank1	A	T	2: 144,346,319 (GRCm39)	C249S	probably damaging	Het
Efnb2	A	T	8: 8,673,104 (GRCm39)		probably null	Het
Ercc6l2	T	G	13: 63,982,552 (GRCm39)	I244S	probably damaging	Het
Ewsr1	A	T	11: 5,020,423 (GRCm39)	M584K	unknown	Het
Fam193b	A	G	13: 55,691,284 (GRCm39)	S197P	probably damaging	Het
Fanca	A	G	8: 124,014,941 (GRCm39)	V689A	probably damaging	Het
Fbxo31	A	T	8: 122,279,178 (GRCm39)	Y436*	probably null	Het
Fbxo31	A	G	8: 122,279,180 (GRCm39)	Y436H	probably damaging	Het
Fcna	T	A	2: 25,515,338 (GRCm39)	D215V	probably damaging	Het
Foxj3	A	T	4: 119,478,857 (GRCm39)	S438C	unknown	Het
Gcm2	T	C	13: 41,256,970 (GRCm39)	K260E	possibly damaging	Het
Gcnt4	A	T	13: 97,083,914 (GRCm39)	L403F	possibly damaging	Het
Gdf10	A	G	14: 33,653,870 (GRCm39)	T126A	probably benign	Het
Ggcx	A	G	6: 72,405,875 (GRCm39)	K569E	probably benign	Het
Gm10250	C	T	15: 5,150,578 (GRCm39)		probably benign	Het
Gpnmb	G	T	6: 49,022,417 (GRCm39)		probably null	Het
Ifi44	G	A	3: 151,451,229 (GRCm39)	P241S	probably damaging	Het
Irs1	T	C	1: 82,265,184 (GRCm39)	T1011A	probably benign	Het
Jag2	A	T	12: 112,877,869 (GRCm39)	S595T	probably benign	Het
Kif5a	T	A	10: 127,066,823 (GRCm39)	Q960L	probably benign	Het
Kifc2	A	G	15: 76,548,548 (GRCm39)	E430G	possibly damaging	Het
Lama3	T	A	18: 12,544,627 (GRCm39)	C323*	probably null	Het
Lgsn	T	C	1: 31,242,823 (GRCm39)	Y302H	probably benign	Het
Lmbrd1	G	A	1: 24,784,056 (GRCm39)		probably null	Het
Lrpap1	A	G	5: 35,256,622 (GRCm39)	V120A	probably damaging	Het
Macrod2	T	A	2: 140,261,858 (GRCm39)	D46E	possibly damaging	Het
Mbd4	C	A	6: 115,822,283 (GRCm39)	R63L	possibly damaging	Het
Mfsd10	T	C	5: 34,792,293 (GRCm39)		probably benign	Het
Mib2	G	T	4: 155,744,229 (GRCm39)	S144R	probably benign	Het
Muc5b	T	A	7: 141,401,453 (GRCm39)	C566*	probably null	Het
Ndufs1	C	A	1: 63,200,108 (GRCm39)	G268V	probably damaging	Het
Nfs1	A	G	2: 155,976,369 (GRCm39)	V175A	possibly damaging	Het
Ngb	G	A	12: 87,146,999 (GRCm39)	H73Y	probably benign	Het
Npepps	G	A	11: 97,117,652 (GRCm39)	T549I	probably damaging	Het
Nr1h2	A	G	7: 44,199,923 (GRCm39)	V329A	possibly damaging	Het
Nsun6	T	C	2: 15,041,137 (GRCm39)	I151M	possibly damaging	Het
Ofcc1	T	C	13: 40,155,368 (GRCm39)		probably null	Het
Or1e31	C	T	11: 73,689,665 (GRCm39)	C306Y	probably benign	Het
Or2y16	T	A	11: 49,334,696 (GRCm39)	F6Y	probably benign	Het
Or2z8	A	G	8: 72,811,938 (GRCm39)	N138S	probably benign	Het
Or51h1	T	A	7: 102,308,041 (GRCm39)	N4K	possibly damaging	Het
Or5an1c	C	T	19: 12,218,936 (GRCm39)	V30I	probably benign	Het
Or8b46	A	G	9: 38,450,371 (GRCm39)	Y60C	probably damaging	Het
Parp6	A	G	9: 59,542,267 (GRCm39)		probably null	Het
Pcnt	C	A	10: 76,245,411 (GRCm39)	R1075S	possibly damaging	Het
Pla2g4f	T	C	2: 120,133,757 (GRCm39)	E548G	probably damaging	Het
Polrmt	G	T	10: 79,575,357 (GRCm39)	H725N	probably benign	Het
Pou2f3	T	C	9: 43,051,153 (GRCm39)	T178A	probably damaging	Het
Prtn3	C	A	10: 79,717,899 (GRCm39)	P169H	probably damaging	Het
Ptprd	A	G	4: 76,009,769 (GRCm39)	I764T	probably benign	Het
Ptprh	A	T	7: 4,572,576 (GRCm39)	H467Q	probably benign	Het
Raph1	A	T	1: 60,528,273 (GRCm39)	I996N	probably damaging	Het
Rasa4	G	A	5: 136,120,083 (GRCm39)	W53*	probably null	Het
Rasgrp1	C	T	2: 117,115,356 (GRCm39)	R744Q	probably benign	Het
Rmnd5a	T	C	6: 71,390,333 (GRCm39)	E141G	probably damaging	Het
Rps12	T	C	10: 23,662,688 (GRCm39)	I51M	possibly damaging	Het
Scn10a	T	G	9: 119,451,976 (GRCm39)	S1316R	possibly damaging	Het
Sdhb	A	G	4: 140,704,777 (GRCm39)	H246R	possibly damaging	Het
Setx	G	A	2: 29,034,058 (GRCm39)	R332Q	probably damaging	Het
Siglec1	A	C	2: 130,917,843 (GRCm39)	S1011R	probably damaging	Het
Sin3b	A	C	8: 73,452,271 (GRCm39)	I126L	probably benign	Het
Slc11a1	T	G	1: 74,423,247 (GRCm39)	L366R	probably damaging	Het
Slc12a1	C	T	2: 125,002,999 (GRCm39)	R177*	probably null	Het
Slc30a1	A	C	1: 191,641,160 (GRCm39)	K269Q	probably benign	Het
Slco1a5	T	C	6: 142,194,533 (GRCm39)	Y370C	possibly damaging	Het
Slf2	T	A	19: 44,923,364 (GRCm39)		probably null	Het
Sltm	A	G	9: 70,496,339 (GRCm39)	H958R	probably damaging	Het
Snrnp40	A	G	4: 130,256,549 (GRCm39)	I91M	probably damaging	Het
Spta1	A	T	1: 174,058,232 (GRCm39)	Q1900L	probably benign	Het
Srgn	C	T	10: 62,333,631 (GRCm39)	E49K	possibly damaging	Het
Ssu2	A	C	6: 112,353,411 (GRCm39)	C238G	probably damaging	Het
Terf2	G	T	8: 107,803,307 (GRCm39)	H425Q	probably benign	Het
Thra	G	A	11: 98,646,990 (GRCm39)	S37N	probably benign	Het
Toporsl	A	G	4: 52,610,845 (GRCm39)	D246G	probably damaging	Het
Ubap2l	G	A	3: 89,928,210 (GRCm39)	T553M	probably damaging	Het
Usp10	A	G	8: 120,667,930 (GRCm39)	Y77C	probably benign	Het
Utrn	T	C	10: 12,625,813 (GRCm39)	T123A	probably damaging	Het
Vmn1r204	T	G	13: 22,740,867 (GRCm39)	F166C	probably benign	Het
Vmn2r14	T	C	5: 109,369,370 (GRCm39)	I68V	probably benign	Het
Wls	C	T	3: 159,603,082 (GRCm39)	T165I	probably benign	Het
Wsb1	A	G	11: 79,131,199 (GRCm39)	M399T	probably benign	Het
Zbtb46	A	T	2: 181,032,929 (GRCm39)	D577E	probably benign	Het
Zfp366	A	G	13: 99,382,991 (GRCm39)	D718G	probably damaging	Het
Zfp408	A	T	2: 91,475,369 (GRCm39)	V595E	possibly damaging	Het
Zfp493	T	A	13: 67,934,322 (GRCm39)	W60R	probably null	Het
Zfp606	A	T	7: 12,227,932 (GRCm39)	K626N	probably damaging	Het
Zfp820	A	T	17: 22,037,966 (GRCm39)	L454Q	probably benign	Het
Zswim5	A	G	4: 116,830,169 (GRCm39)	I515V	probably benign	Het

Other mutations in Xbp1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH 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
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
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'- GATGAATATACCCGCGCGTCAC -3'
(R):5'- AGCGAGCATTTACAGAGGAC -3'

Sequencing Primer
(F):5'- CACGACCCTAGAAAGGCTGG -3'
(R):5'- GGAGCTCCTGCACACAC -3'

Posted On

2015-12-29