Mutagenetix > Incidental Mutation

Incidental Mutation 'R4957:Ybx1'

381637

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

042554-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R4957 (G1)

Quality Score

138

Status

Validated

Chromosome

Chromosomal Location

119135178-119151801 bp(-) (GRCm39)

Type of Mutation

utr 3 prime

DNA Base Change (assembly)

A to T at 119136135 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000117225 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000079644] [ENSMUST00000127737]

AlphaFold

P62960

Predicted Effect

probably benign
Transcript: ENSMUST00000079644

SMART Domains

Protein: ENSMUSP00000078589
Gene: ENSMUSG00000028639

Domain	Start	End	E-Value	Type
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

probably benign
Transcript: ENSMUST00000127737

SMART Domains

Protein: ENSMUSP00000117225
Gene: ENSMUSG00000028639

Domain	Start	End	E-Value	Type
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

1x: 99.1%
3x: 98.3%
10x: 96.3%
20x: 92.5%

Validation Efficiency

99% (80/81)

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: 69 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
3110009E18Rik	G	C	1: 120,096,840 (GRCm39)		probably benign	Het
3110009E18Rik	C	T	1: 120,096,850 (GRCm39)		probably benign	Het
3110009E18Rik	G	T	1: 120,096,849 (GRCm39)		probably benign	Het
6820408C15Rik	T	A	2: 152,286,013 (GRCm39)	V342D	probably damaging	Het
Arhgap33	C	T	7: 30,231,786 (GRCm39)	G101R	probably damaging	Het
Atf7ip	C	T	6: 136,583,808 (GRCm39)	R1280C	probably damaging	Het
Cacnb4	T	C	2: 52,448,303 (GRCm39)	H8R	probably damaging	Het
Ccdc150	T	A	1: 54,404,027 (GRCm39)		probably benign	Het
Cd74	A	G	18: 60,942,109 (GRCm39)	N113D	probably benign	Het
Cdc25b	T	C	2: 131,035,525 (GRCm39)	V341A	possibly damaging	Het
Clptm1l	T	A	13: 73,759,315 (GRCm39)	I245N	possibly damaging	Het
Clptm1l	T	C	13: 73,760,547 (GRCm39)	I310T	probably damaging	Het
Creb5	A	T	6: 53,670,907 (GRCm39)		probably null	Het
Crebbp	T	C	16: 3,935,231 (GRCm39)	Q460R	probably benign	Het
Dnah17	A	T	11: 117,965,124 (GRCm39)	I2306N	probably benign	Het
Dync1h1	C	A	12: 110,624,560 (GRCm39)	T3700N	probably damaging	Het
Elovl1	A	T	4: 118,289,120 (GRCm39)	H215L	probably damaging	Het
Enkd1	A	G	8: 106,431,121 (GRCm39)	I202T	probably benign	Het
Epha7	C	T	4: 28,871,892 (GRCm39)	A407V	probably damaging	Het
Ercc3	G	T	18: 32,376,170 (GRCm39)	G130W	probably damaging	Het
Fbxl8	A	G	8: 105,994,827 (GRCm39)	E113G	probably damaging	Het
Frmpd1	T	G	4: 45,273,099 (GRCm39)	N339K	probably damaging	Het
Frrs1	G	A	3: 116,678,897 (GRCm39)	D240N	probably benign	Het
Gemin2	A	G	12: 59,063,954 (GRCm39)	S105G	probably benign	Het
Glra1	T	A	11: 55,418,224 (GRCm39)	I257F	probably damaging	Het
Gmcl1	G	A	6: 86,687,503 (GRCm39)	P354S	probably damaging	Het
Gpr15	G	T	16: 58,538,537 (GRCm39)	A184E	probably damaging	Het
Grm7	G	A	6: 111,335,824 (GRCm39)	G745E	probably damaging	Het
H2-T10	T	A	17: 36,428,308 (GRCm39)		probably benign	Het
Hdac5	C	A	11: 102,096,082 (GRCm39)		probably benign	Het
Ift22	G	A	5: 136,937,070 (GRCm39)		probably benign	Het
Ighg3	T	C	12: 113,324,750 (GRCm39)	E34G	unknown	Het
Itga11	A	T	9: 62,674,930 (GRCm39)	T821S	probably benign	Het
Lmod2	T	C	6: 24,603,871 (GRCm39)	V282A	possibly damaging	Het
Maml2	A	G	9: 13,531,572 (GRCm39)	K262R	probably damaging	Het
Mme	T	A	3: 63,250,910 (GRCm39)		probably benign	Het
Mnat1	A	G	12: 73,170,652 (GRCm39)	Y14C	probably damaging	Het
Mtdh	A	T	15: 34,083,281 (GRCm39)	T34S	possibly damaging	Het
Ncaph	T	C	2: 126,963,177 (GRCm39)	D352G	possibly damaging	Het
Or2t43	A	G	11: 58,457,344 (GRCm39)	Y276H	probably damaging	Het
Or4f17-ps1	C	A	2: 111,358,569 (GRCm39)	N321K	probably benign	Het
Or5m9b	T	A	2: 85,905,854 (GRCm39)	Y257N	probably damaging	Het
Or9g8	T	C	2: 85,607,459 (GRCm39)	F177S	probably damaging	Het
Pcdhb13	T	A	18: 37,577,837 (GRCm39)	D738E	possibly damaging	Het
Pla2g4f	C	T	2: 120,130,980 (GRCm39)	R825Q	probably benign	Het
Pnliprp2	C	T	19: 58,763,577 (GRCm39)	L409F	possibly damaging	Het
Prlr	G	T	15: 10,319,281 (GRCm39)	C70F	probably damaging	Het
Ptpn14	C	T	1: 189,583,469 (GRCm39)	T772I	probably benign	Het
Ryr2	T	C	13: 11,799,966 (GRCm39)	Q927R	probably damaging	Het
Scarf1	A	G	11: 75,416,460 (GRCm39)	E634G	probably benign	Het
Scart1	T	C	7: 139,808,435 (GRCm39)	V782A	probably damaging	Het
Skic3	T	G	13: 76,333,232 (GRCm39)		probably null	Het
Slc39a14	A	T	14: 70,553,260 (GRCm39)	S158R	probably damaging	Het
Slc9c1	A	T	16: 45,365,194 (GRCm39)	T176S	probably benign	Het
Srsf10	T	C	4: 135,583,541 (GRCm39)	S2P	probably damaging	Het
Tcam1	T	A	11: 106,173,705 (GRCm39)	C50S	probably damaging	Het
Tcf7l2	A	G	19: 55,919,864 (GRCm39)		probably null	Het
Tdrd3	T	A	14: 87,743,223 (GRCm39)	H390Q	probably benign	Het
Tlk2	T	C	11: 105,144,185 (GRCm39)		probably null	Het
Tnc	G	C	4: 63,894,793 (GRCm39)	P1531R	probably damaging	Het
Tnfrsf1b	C	A	4: 144,973,327 (GRCm39)	Q15H	probably damaging	Het
Tnfrsf1b	T	G	4: 144,973,328 (GRCm39)	Q15P	possibly damaging	Het
Tssk4	A	T	14: 55,889,266 (GRCm39)	E264V	probably damaging	Het
Ugt3a1	G	A	15: 9,365,274 (GRCm39)	V296I	probably benign	Het
Usp5	C	G	6: 124,799,593 (GRCm39)	K318N	possibly damaging	Het
Vmn2r8	T	G	5: 108,947,129 (GRCm39)	E541A	probably benign	Het
Zfp39	T	A	11: 58,782,057 (GRCm39)	Y235F	possibly damaging	Het
Zfp422	T	A	6: 116,603,904 (GRCm39)	K32*	probably null	Het
Zpbp2	T	A	11: 98,442,150 (GRCm39)		probably null	Het

Other mutations in Ybx1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH 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
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

Predicted Primers

PCR Primer
(F):5'- CTGTCTTCAGAGCACAGGAAG -3'
(R):5'- TCGCCAAAGACAGCCTAGAG -3'

Sequencing Primer
(F):5'- CACAGGAAGTAAGACTTTGCTTAGC -3'
(R):5'- AGGTCAGCAGCCACCTC -3'

Posted On

2016-04-27