Mutagenetix > Incidental Mutation

Incidental Mutation 'R4911:Ybx1'

379497

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

042513-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R4911 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

119135178-119151801 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 119140010 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Alanine at position 106 (T106A)

Ref Sequence

ENSEMBL: ENSMUSP00000078589 (fasta)

Gene Model

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

AlphaFold

P62960

Predicted Effect

probably benign
Transcript: ENSMUST00000079644
AA Change: T106A

PolyPhen 2 Score 0.127 (Sensitivity: 0.93; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000078589
Gene: ENSMUSG00000028639
AA Change: T106A

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: ENSMUST00000142884

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000144992

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000145976

Meta Mutation Damage Score

0.1789

Coding Region Coverage

1x: 99.0%
3x: 98.1%
10x: 95.5%
20x: 89.7%

Validation Efficiency

97% (149/153)

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: 132 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aacs	A	G	5: 125,583,224 (GRCm39)	D260G	possibly damaging	Het
Aadacl4	T	A	4: 144,340,362 (GRCm39)	L29H	probably damaging	Het
Abca7	T	C	10: 79,848,022 (GRCm39)		probably null	Het
Adgre1	G	A	17: 57,754,832 (GRCm39)	M643I	possibly damaging	Het
Adgrl2	A	T	3: 148,596,099 (GRCm39)	M79K	probably damaging	Het
Ankrd55	T	A	13: 112,459,573 (GRCm39)		probably null	Het
Aopep	A	T	13: 63,318,753 (GRCm39)		probably null	Het
Arhgap21	A	G	2: 20,863,800 (GRCm39)	I1257T	probably damaging	Het
Arhgap26	T	A	18: 39,126,690 (GRCm39)		probably benign	Het
Arhgap39	A	G	15: 76,622,005 (GRCm39)	S199P	probably damaging	Het
Arhgef5	A	G	6: 43,249,762 (GRCm39)	D171G	probably benign	Het
Atp7a	T	C	X: 105,163,980 (GRCm39)	V1305A	probably damaging	Het
B3gnt3	T	A	8: 72,145,578 (GRCm39)	R263S	probably benign	Het
B9d1	A	C	11: 61,398,497 (GRCm39)	D59A	probably benign	Het
Bag2	A	T	1: 33,787,357 (GRCm39)	I55N	probably benign	Het
Bank1	T	C	3: 135,990,004 (GRCm39)	I29V	probably benign	Het
Bbs2	A	T	8: 94,815,743 (GRCm39)	D174E	probably damaging	Het
Bmp8b	T	C	4: 123,009,030 (GRCm39)	W203R	probably damaging	Het
Cacnb2	A	T	2: 14,986,151 (GRCm39)	E359D	possibly damaging	Het
Camp	T	A	9: 109,676,651 (GRCm39)		probably null	Het
Casp4	C	T	9: 5,328,580 (GRCm39)		probably benign	Het
Ccdc110	A	T	8: 46,395,944 (GRCm39)	T612S	probably benign	Het
Cd209b	T	A	8: 3,976,640 (GRCm39)		probably null	Het
Cemip	T	C	7: 83,632,461 (GRCm39)	D367G	probably damaging	Het
Cers5	T	A	15: 99,644,960 (GRCm39)	N131I	probably damaging	Het
Cfhr4	T	G	1: 139,702,301 (GRCm39)	D61A	probably damaging	Het
Chd5	T	G	4: 152,445,129 (GRCm39)	V370G	probably damaging	Het
Cipc	C	A	12: 86,999,531 (GRCm39)	Q20K	probably benign	Het
Cnr2	T	A	4: 135,644,512 (GRCm39)	F197I	possibly damaging	Het
Col7a1	G	A	9: 108,804,287 (GRCm39)	G2233S	unknown	Het
Dcdc2b	T	A	4: 129,505,060 (GRCm39)	I125F	possibly damaging	Het
Ddi2	A	G	4: 141,411,713 (GRCm39)	S400P	probably benign	Het
Ddx31	C	A	2: 28,794,696 (GRCm39)	T664K	probably benign	Het
Dhx30	C	A	9: 109,929,992 (GRCm39)	G35C	probably damaging	Het
Dmxl2	G	A	9: 54,318,937 (GRCm39)	T1576I	probably damaging	Het
Dnah1	T	C	14: 31,017,280 (GRCm39)	Y1510C	probably damaging	Het
Dnah2	C	T	11: 69,389,930 (GRCm39)		probably null	Het
Dock10	C	A	1: 80,583,953 (GRCm39)	G163C	probably damaging	Het
Edar	T	C	10: 58,457,146 (GRCm39)	N144S	probably benign	Het
Elavl2	T	A	4: 91,196,915 (GRCm39)	E54D	possibly damaging	Het
Enam	T	G	5: 88,650,173 (GRCm39)	S561A	probably benign	Het
Ercc5	C	A	1: 44,206,031 (GRCm39)	H315N	possibly damaging	Het
Esp31	A	G	17: 38,955,552 (GRCm39)	E65G	possibly damaging	Het
Faap100	T	C	11: 120,262,939 (GRCm39)	I806M	probably benign	Het
Fbxw21	T	C	9: 108,974,731 (GRCm39)	Y263C	probably damaging	Het
Fsip2	T	A	2: 82,811,837 (GRCm39)	S2719T	possibly damaging	Het
Fv1	T	C	4: 147,953,875 (GRCm39)	V147A	probably benign	Het
Gal	T	C	19: 3,461,590 (GRCm39)	E65G	probably benign	Het
Galnt2l	A	G	8: 123,807,343 (GRCm39)		probably benign	Het
Galnt6	T	C	15: 100,614,059 (GRCm39)	T81A	probably benign	Het
Gcc2	A	G	10: 58,106,261 (GRCm39)	E399G	probably damaging	Het
Gfi1b	A	T	2: 28,500,114 (GRCm39)	C306S	probably damaging	Het
Gm10654	T	A	8: 71,384,496 (GRCm39)		noncoding transcript	Het
Gm4953	T	A	1: 158,995,929 (GRCm39)		noncoding transcript	Het
Gorasp2	T	C	2: 70,518,683 (GRCm39)		probably benign	Het
Gse1	T	C	8: 121,295,205 (GRCm39)		probably benign	Het
H2-D1	A	G	17: 35,484,973 (GRCm39)	E278G	probably damaging	Het
Herc2	T	C	7: 55,877,640 (GRCm39)	L4569P	probably damaging	Het
Hgs	T	A	11: 120,368,028 (GRCm39)	S246T	probably damaging	Het
Hs2st1	T	C	3: 144,170,843 (GRCm39)	T110A	probably benign	Het
Hydin	A	G	8: 111,322,070 (GRCm39)	Y4574C	probably benign	Het
Ighv1-23	C	A	12: 114,728,372 (GRCm39)	V17F	possibly damaging	Het
Ighv8-14	A	T	12: 115,772,185 (GRCm39)		noncoding transcript	Het
Igsf21	C	T	4: 139,761,934 (GRCm39)	R248H	probably benign	Het
Il22b	T	C	10: 118,130,894 (GRCm39)	M1V	probably null	Het
Il23r	T	C	6: 67,400,545 (GRCm39)	N595S	probably benign	Het
Il5ra	G	T	6: 106,692,629 (GRCm39)	P372Q	probably damaging	Het
Inppl1	A	G	7: 101,481,516 (GRCm39)	V222A	possibly damaging	Het
Ints10	T	C	8: 69,279,964 (GRCm39)	V697A	probably damaging	Het
Isg15	T	A	4: 156,284,217 (GRCm39)	T104S	probably benign	Het
Kif11	A	G	19: 37,406,385 (GRCm39)	T983A	probably benign	Het
Kif3b	A	T	2: 153,159,212 (GRCm39)	K338*	probably null	Het
Kpna2	T	A	11: 106,881,545 (GRCm39)	I362F	probably damaging	Het
Lama2	G	A	10: 27,014,923 (GRCm39)	T1595M	probably damaging	Het
Lrrc36	A	G	8: 106,153,567 (GRCm39)	T126A	probably benign	Het
Lrrk1	T	A	7: 65,945,202 (GRCm39)	D604V	probably damaging	Het
Map7d1	T	C	4: 126,130,484 (GRCm39)	K409E	probably damaging	Het
Mast2	T	C	4: 116,210,254 (GRCm39)	T110A	probably benign	Het
Micall2	G	A	5: 139,702,580 (GRCm39)	T221M	probably damaging	Het
Morc2b	T	A	17: 33,356,351 (GRCm39)	N474Y	probably damaging	Het
Myo1e	T	A	9: 70,250,378 (GRCm39)	M528K	probably benign	Het
Nlrp1c-ps	G	T	11: 71,151,195 (GRCm39)		noncoding transcript	Het
Nostrin	T	C	2: 68,991,486 (GRCm39)	S160P	possibly damaging	Het
Nup133	T	C	8: 124,653,870 (GRCm39)	R530G	possibly damaging	Het
Or2f2	T	A	6: 42,767,138 (GRCm39)	L55H	probably damaging	Het
Or5p64	T	C	7: 107,855,244 (GRCm39)	I34V	possibly damaging	Het
Or8c16	A	G	9: 38,130,392 (GRCm39)	E91G	probably damaging	Het
Pabpc4l	A	T	3: 46,400,597 (GRCm39)	M349K	possibly damaging	Het
Pah	G	A	10: 87,406,129 (GRCm39)	G256S	probably benign	Het
Pigk	T	C	3: 152,445,841 (GRCm39)	S151P	probably damaging	Het
Plcd4	A	C	1: 74,603,572 (GRCm39)	T658P	possibly damaging	Het
Pld4	A	T	12: 112,730,951 (GRCm39)	S178C	probably benign	Het
Polr1a	G	A	6: 71,886,213 (GRCm39)	E23K	possibly damaging	Het
Pomt1	T	C	2: 32,131,691 (GRCm39)	S127P	probably damaging	Het
Pon2	A	G	6: 5,269,029 (GRCm39)	V215A	possibly damaging	Het
Ppp3cb	A	T	14: 20,559,508 (GRCm39)	M416K	probably damaging	Het
Prdm1	A	T	10: 44,318,048 (GRCm39)	N273K	possibly damaging	Het
Prg4	T	A	1: 150,331,574 (GRCm39)		probably benign	Het
Prkn	G	T	17: 11,059,359 (GRCm39)		probably benign	Het
Ptch1	G	A	13: 63,670,866 (GRCm39)	T888M	probably damaging	Het
Pusl1	T	G	4: 155,975,899 (GRCm39)		probably benign	Het
Rapgef6	A	T	11: 54,513,143 (GRCm39)	E122D	probably damaging	Het
Rif1	C	T	2: 52,000,530 (GRCm39)	T1328I	probably damaging	Het
Rngtt	T	G	4: 33,500,292 (GRCm39)		probably null	Het
Runx2	G	A	17: 45,125,079 (GRCm39)	P80L	probably damaging	Het
Samd1	A	G	8: 84,725,618 (GRCm39)		probably benign	Het
Scamp5	A	T	9: 57,358,735 (GRCm39)	F14I	probably damaging	Het
Shank3	C	T	15: 89,388,547 (GRCm39)	R380C	probably damaging	Het
Shisal2a	T	C	4: 108,234,658 (GRCm39)	T70A	probably benign	Het
Slc1a4	C	A	11: 20,282,166 (GRCm39)	A103S	probably damaging	Het
Slc39a14	A	G	14: 70,547,371 (GRCm39)	V325A	probably benign	Het
Slc5a9	C	A	4: 111,748,941 (GRCm39)		probably null	Het
Spata6l	G	A	19: 28,874,903 (GRCm39)		probably benign	Het
Spta1	T	A	1: 174,013,213 (GRCm39)	S375T	probably damaging	Het
Sval1	A	G	6: 41,932,378 (GRCm39)	N76S	probably benign	Het
Synpo	C	T	18: 60,762,936 (GRCm39)		probably benign	Het
Sytl5	C	T	X: 9,781,841 (GRCm39)	P181L	possibly damaging	Het
Tacc1	A	G	8: 25,672,622 (GRCm39)	M111T	possibly damaging	Het
Tec	T	C	5: 72,913,694 (GRCm39)	D613G	probably benign	Het
Tecpr2	C	T	12: 110,897,921 (GRCm39)	T391I	possibly damaging	Het
Thop1	G	A	10: 80,909,125 (GRCm39)	G52D	probably damaging	Het
Tmco5	T	A	2: 116,722,689 (GRCm39)	V270D	possibly damaging	Het
Ttn	C	T	2: 76,556,973 (GRCm39)	E28265K	possibly damaging	Het
Tuft1	T	C	3: 94,542,750 (GRCm39)	D72G	probably damaging	Het
Tyrp1	C	T	4: 80,769,144 (GRCm39)		probably benign	Het
Usp9y	T	C	Y: 1,308,041 (GRCm39)	D2265G	probably damaging	Het
Vmn2r104	G	A	17: 20,250,288 (GRCm39)	A661V	probably benign	Het
Vwa5a	A	T	9: 38,649,268 (GRCm39)	N672I	probably benign	Het
Wdr95	A	T	5: 149,535,157 (GRCm39)	K772*	probably null	Het
Ypel3	T	C	7: 126,376,961 (GRCm39)	S14P	probably benign	Het
Zfp518a	T	A	19: 40,903,972 (GRCm39)	S1300R	probably benign	Het
Zscan5b	A	T	7: 6,242,189 (GRCm39)	*469Y	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
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

Predicted Primers

PCR Primer
(F):5'- TTAGGCTCGATGCACCTGTG -3'
(R):5'- TAAAACGCTGGGGCCTTGTAAG -3'

Sequencing Primer
(F):5'- TGTTCATGTGGTCACCAGAAC -3'
(R):5'- GCTTTCCTAAACTATTGACAGTTTGG -3'

Posted On

2016-04-15