Mutagenetix > Incidental Mutation

Incidental Mutation 'IGL02000:Ybx1'

183003

Institutional Source

Australian Phenomics Network (link to record)

Gene Symbol

Ybx1

Ensembl Gene

ENSMUSG00000028639

Gene Name

Y box protein 1

Synonyms

Nsep1, DNA binding protein B, dbpB, EF1A, YB-1, MSY1

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

IGL02000

Quality Score

Status

Chromosome

Chromosomal Location

119135178-119151801 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 119139509 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Isoleucine at position 50 (N50I)

Ref Sequence

ENSEMBL: ENSMUSP00000117225 (fasta)

Gene Model

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

AlphaFold

P62960

Predicted Effect

possibly damaging
Transcript: ENSMUST00000079644
AA Change: N162I

PolyPhen 2 Score 0.772 (Sensitivity: 0.85; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000078589
Gene: ENSMUSG00000028639
AA Change: N162I

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 damaging
Transcript: ENSMUST00000127737
AA Change: N50I

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000117225
Gene: ENSMUSG00000028639
AA Change: N50I

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

Coding Region Coverage

Validation Efficiency

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: 42 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Arid5a	T	C	1: 36,358,578 (GRCm39)	F450S	probably damaging	Het
Astn1	C	T	1: 158,502,184 (GRCm39)	R1133C	probably damaging	Het
Cd101	G	A	3: 100,919,398 (GRCm39)	P568L	probably benign	Het
Cdkl4	T	C	17: 80,851,192 (GRCm39)	E170G	probably damaging	Het
Chit1	A	G	1: 134,074,413 (GRCm39)	E240G	probably benign	Het
Duox2	T	C	2: 122,121,190 (GRCm39)	T741A	probably benign	Het
Eef2	T	C	10: 81,015,845 (GRCm39)	V427A	probably benign	Het
Ewsr1	T	C	11: 5,038,077 (GRCm39)	D105G	probably damaging	Het
Ftsj3	C	T	11: 106,141,233 (GRCm39)	R629Q	probably benign	Het
Gm10406	C	T	14: 18,341,703 (GRCm39)	G181E	probably benign	Het
Ilk	A	G	7: 105,390,376 (GRCm39)	H185R	probably benign	Het
Lamc1	A	T	1: 153,116,179 (GRCm39)	C1001S	probably damaging	Het
Mcidas	T	C	13: 113,133,974 (GRCm39)	S153P	probably benign	Het
Mtcl1	T	C	17: 66,661,185 (GRCm39)	E931G	probably benign	Het
Myo10	C	T	15: 25,808,152 (GRCm39)	R1925C	probably damaging	Het
Notch3	A	G	17: 32,341,716 (GRCm39)	V2012A	probably damaging	Het
Or6c76	C	A	10: 129,611,938 (GRCm39)	H67N	probably benign	Het
Parp6	A	G	9: 59,556,175 (GRCm39)	M542V	probably benign	Het
Rab27a	G	A	9: 72,992,254 (GRCm39)	G94D	probably damaging	Het
Ralgapb	A	G	2: 158,296,034 (GRCm39)		probably benign	Het
Rassf4	T	C	6: 116,622,933 (GRCm39)	E26G	probably benign	Het
Rnf166	C	T	8: 123,193,961 (GRCm39)	D221N	probably damaging	Het
Rptn	G	T	3: 93,303,735 (GRCm39)	G356V	probably benign	Het
Rwdd2b	T	A	16: 87,233,828 (GRCm39)		probably benign	Het
Scfd1	T	A	12: 51,460,900 (GRCm39)	S337T	probably benign	Het
Sel1l3	T	A	5: 53,302,835 (GRCm39)	D678V	probably damaging	Het
Sidt1	A	T	16: 44,106,732 (GRCm39)	F233I	probably damaging	Het
Slc12a4	T	C	8: 106,671,864 (GRCm39)	D917G	probably damaging	Het
Slc22a2	A	T	17: 12,803,270 (GRCm39)	I35F	possibly damaging	Het
Smco1	A	T	16: 32,092,751 (GRCm39)	T141S	possibly damaging	Het
Svs6	T	C	2: 164,159,352 (GRCm39)		probably benign	Het
Syne2	C	T	12: 76,062,419 (GRCm39)	A4247V	probably damaging	Het
Tacc2	T	A	7: 130,330,898 (GRCm39)		probably null	Het
Tgm4	A	T	9: 122,885,531 (GRCm39)	I358F	probably damaging	Het
Thnsl2	A	G	6: 71,111,203 (GRCm39)	S222P	probably damaging	Het
Tmem25	G	A	9: 44,709,568 (GRCm39)	R78*	probably null	Het
Ube2l6	T	C	2: 84,639,506 (GRCm39)		probably benign	Het
Usp10	T	A	8: 120,675,480 (GRCm39)	Y63N	possibly damaging	Het
Vit	A	G	17: 78,912,915 (GRCm39)	I283V	possibly damaging	Het
Vmn1r214	G	A	13: 23,219,270 (GRCm39)	V255I	possibly damaging	Het
Xpo1	A	G	11: 23,246,003 (GRCm39)	R1038G	probably damaging	Het
Zhx1	T	C	15: 57,917,683 (GRCm39)	K188E	probably damaging	Het

Other mutations in Ybx1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
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
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

Posted On

2014-05-07