Mutagenetix > Incidental Mutation

Incidental Mutation 'R0136:Ybx1'

21935

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

038421-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R0136 (G1)

Quality Score

205

Status

Validated (trace)

Chromosome

Chromosomal Location

119135178-119151801 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to A at 119139551 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Arginine to Leucine at position 36 (R36L)

Ref Sequence

ENSEMBL: ENSMUSP00000117225 (fasta)

Gene Model

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

AlphaFold

P62960

Predicted Effect

probably benign
Transcript: ENSMUST00000079644
AA Change: R148L

PolyPhen 2 Score 0.185 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000078589
Gene: ENSMUSG00000028639
AA Change: R148L

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

possibly damaging
Transcript: ENSMUST00000127737
AA Change: R36L

PolyPhen 2 Score 0.575 (Sensitivity: 0.88; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000117225
Gene: ENSMUSG00000028639
AA Change: R36L

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

0.1438

Coding Region Coverage

1x: 99.0%
3x: 98.3%
10x: 96.5%
20x: 93.3%

Validation Efficiency

89% (56/63)

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: 64 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Ap4b1	T	C	3: 103,717,262 (GRCm39)	M1T	probably null	Het
Arg2	T	C	12: 79,196,780 (GRCm39)	L167P	probably damaging	Het
Atxn1	A	G	13: 45,720,645 (GRCm39)	S417P	probably damaging	Het
Baz2b	A	G	2: 59,732,298 (GRCm39)	V1949A	probably benign	Het
Bcl3	A	G	7: 19,543,494 (GRCm39)	V324A	probably damaging	Het
Btbd10	A	T	7: 112,929,085 (GRCm39)	S230T	possibly damaging	Het
Camta1	A	G	4: 151,163,426 (GRCm39)	S1479P	probably damaging	Het
Cd69	C	T	6: 129,247,025 (GRCm39)	S64N	probably benign	Het
Col5a1	T	C	2: 27,914,843 (GRCm39)	L153P	probably damaging	Het
Crat	C	A	2: 30,297,042 (GRCm39)	V304L	probably benign	Het
Csmd3	T	C	15: 47,710,527 (GRCm39)	T1687A	probably benign	Het
Dnah1	C	T	14: 30,998,115 (GRCm39)	G2574D	probably damaging	Het
Fau	T	C	19: 6,109,210 (GRCm39)	V86A	possibly damaging	Het
Garem1	T	G	18: 21,263,048 (GRCm39)	S589R	probably damaging	Het
Gbp3	T	G	3: 142,269,862 (GRCm39)		probably null	Het
Gin1	T	A	1: 97,710,741 (GRCm39)	S141R	possibly damaging	Het
Gtf2h1	A	T	7: 46,464,840 (GRCm39)	Q419L	possibly damaging	Het
Hipk3	A	G	2: 104,269,638 (GRCm39)	I517T	probably benign	Het
Hivep2	T	C	10: 14,007,622 (GRCm39)	S1407P	probably benign	Het
Hnrnpk	G	T	13: 58,542,991 (GRCm39)	D211E	probably benign	Het
Hnrnpul2	T	C	19: 8,804,165 (GRCm39)	L588P	probably damaging	Het
Il18rap	A	T	1: 40,564,218 (GRCm39)	H112L	probably benign	Het
Itgb1	T	G	8: 129,449,335 (GRCm39)	Y585D	possibly damaging	Het
Kmt2d	C	T	15: 98,752,159 (GRCm39)		probably benign	Het
Map7d1	A	T	4: 126,130,424 (GRCm39)		probably null	Het
Me2	A	G	18: 73,903,744 (GRCm39)	S575P	probably benign	Het
Med13l	A	G	5: 118,862,115 (GRCm39)	T353A	probably benign	Het
Mgat4b	T	C	11: 50,121,908 (GRCm39)	V143A	possibly damaging	Het
Mlxip	T	A	5: 123,580,369 (GRCm39)	W211R	probably damaging	Het
Morc2a	T	G	11: 3,635,907 (GRCm39)		probably null	Het
Muc4	A	T	16: 32,569,013 (GRCm39)		probably benign	Het
Ndufa10	A	T	1: 92,390,850 (GRCm39)	Y233*	probably null	Het
Nek8	C	T	11: 78,062,033 (GRCm39)	S237N	probably benign	Het
Neto1	G	A	18: 86,479,445 (GRCm39)	R211Q	probably benign	Het
Nfatc2ip	A	G	7: 125,990,507 (GRCm39)	S165P	probably benign	Het
Nsd2	A	G	5: 34,012,880 (GRCm39)	K404E	possibly damaging	Het
Nsd3	G	T	8: 26,149,870 (GRCm39)	E352*	probably null	Het
Nudt9	A	G	5: 104,194,972 (GRCm39)	T23A	probably benign	Het
Or1e34	T	C	11: 73,778,611 (GRCm39)	M196V	probably benign	Het
Or1e34	C	T	11: 73,778,656 (GRCm39)	V181I	probably benign	Het
Or8b57	A	G	9: 40,003,315 (GRCm39)	*312Q	probably null	Het
Patj	C	A	4: 98,555,885 (GRCm39)	Q297K	probably damaging	Het
Pelo	A	T	13: 115,225,439 (GRCm39)	C40*	probably null	Het
Pnpla3	G	A	15: 84,058,679 (GRCm39)		probably null	Het
Pramel1	C	A	4: 143,124,016 (GRCm39)	N230K	probably damaging	Het
Psg20	A	C	7: 18,416,432 (GRCm39)	L228R	probably damaging	Het
Rsph10b	T	C	5: 143,896,639 (GRCm39)	F44L	probably benign	Het
Septin2	G	A	1: 93,434,772 (GRCm39)	G358R	possibly damaging	Het
Slamf7	G	A	1: 171,476,499 (GRCm39)		probably benign	Het
Slc12a8	A	G	16: 33,428,583 (GRCm39)	D297G	probably damaging	Het
Slc17a5	G	A	9: 78,485,956 (GRCm39)	A43V	probably damaging	Het
Slc22a1	A	T	17: 12,881,483 (GRCm39)	F335L	probably benign	Het
Slc26a5	T	C	5: 22,039,345 (GRCm39)	N216S	probably damaging	Het
Snrnp27	T	C	6: 86,653,187 (GRCm39)	S144G	probably benign	Het
Spata20	T	A	11: 94,371,435 (GRCm39)	D643V	probably damaging	Het
Spata24	T	C	18: 35,793,515 (GRCm39)	K99R	probably damaging	Het
Taar5	A	G	10: 23,847,607 (GRCm39)	Y335C	probably damaging	Het
Tpr	A	G	1: 150,306,346 (GRCm39)	H1540R	probably benign	Het
Vmn1r27	A	G	6: 58,192,704 (GRCm39)	F100S	possibly damaging	Het
Vmn2r37	A	T	7: 9,220,782 (GRCm39)	Y360*	probably null	Het
Zfp369	A	G	13: 65,445,016 (GRCm39)	K720E	probably benign	Het
Zfp599	A	G	9: 22,161,038 (GRCm39)	S376P	probably benign	Het
Zic2	A	G	14: 122,713,953 (GRCm39)	E289G	probably damaging	Het
Zzef1	T	C	11: 72,712,677 (GRCm39)	V199A	probably benign	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
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

Predicted Primers

PCR Primer
(F):5'- AGGTTCAATTCCCAGGACAAGCAC -3'
(R):5'- TGATGTAGCATTCCCATGCACCC -3'

Sequencing Primer
(F):5'- AAACCCTTGTTACACTCAATGTC -3'
(R):5'- CTTTGCCCATGCACACAG -3'

Posted On

2013-04-12