Mutagenetix > Incidental Mutation

Incidental Mutation 'R1697:Ybx2'

192344

Institutional Source

Beutler Lab

Gene Symbol

Ybx2

Ensembl Gene

ENSMUSG00000018554

Gene Name

Y box protein 2

Synonyms

MSY2

MMRRC Submission

039730-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.860) question?

Stock #

R1697 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

69826652-69832430 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 69830887 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Leucine at position 217 (S217L)

Ref Sequence

ENSEMBL: ENSMUSP00000018698 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000018698] [ENSMUST00000018710] [ENSMUST00000108601] [ENSMUST00000141837] [ENSMUST00000149194]

AlphaFold

no structure available at present

Predicted Effect

probably benign
Transcript: ENSMUST00000018698
AA Change: S217L

PolyPhen 2 Score 0.399 (Sensitivity: 0.89; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000018698
Gene: ENSMUSG00000018554
AA Change: S217L

Domain	Start	End	E-Value	Type
low complexity region	2	68	N/A	INTRINSIC
low complexity region	71	82	N/A	INTRINSIC
CSP	96	164	2.54e-21	SMART
low complexity region	173	212	N/A	INTRINSIC
low complexity region	220	242	N/A	INTRINSIC
low complexity region	274	294	N/A	INTRINSIC
low complexity region	317	339	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000018710

SMART Domains

Protein: ENSMUSP00000018710
Gene: ENSMUSG00000018566

Domain	Start	End	E-Value	Type
Pfam:MFS_1	24	436	3.9e-16	PFAM
Pfam:Sugar_tr	27	483	1.7e-155	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000108601
AA Change: S140L

PolyPhen 2 Score 0.018 (Sensitivity: 0.95; Specificity: 0.80)

SMART Domains

Protein: ENSMUSP00000104242
Gene: ENSMUSG00000018554
AA Change: S140L

Domain	Start	End	E-Value	Type
CSP	19	87	2.54e-21	SMART
low complexity region	96	135	N/A	INTRINSIC
low complexity region	143	165	N/A	INTRINSIC
low complexity region	197	217	N/A	INTRINSIC
low complexity region	240	262	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000130377

Predicted Effect

probably benign
Transcript: ENSMUST00000141837

SMART Domains

Protein: ENSMUSP00000136806
Gene: ENSMUSG00000018566

Domain	Start	End	E-Value	Type
Pfam:MFS_1	24	438	4.7e-17	PFAM
Pfam:Sugar_tr	26	453	6e-140	PFAM
low complexity region	462	478	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000148395

Predicted Effect

probably benign
Transcript: ENSMUST00000149194
AA Change: S22L

PolyPhen 2 Score 0.123 (Sensitivity: 0.93; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000136684
Gene: ENSMUSG00000018554
AA Change: S22L

Domain	Start	End	E-Value	Type
low complexity region	4	17	N/A	INTRINSIC
low complexity region	25	47	N/A	INTRINSIC
low complexity region	79	99	N/A	INTRINSIC
low complexity region	122	144	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000178809

Meta Mutation Damage Score

0.0898

Coding Region Coverage

1x: 99.1%
3x: 98.4%
10x: 96.6%
20x: 93.3%

Validation Efficiency

99% (67/68)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a nucleic acid binding protein which is highly expressed in germ cells. The encoded protein binds to a Y-box element in the promoters of certain genes but also binds to mRNA transcribed from these genes. Pseudogenes for this gene are located on chromosome 10 and 15. [provided by RefSeq, Feb 2012]
PHENOTYPE: Homozygous disruption of this gene leads to both male and female infertility. Spermatogenesis terminates in postmeiotic germ cells with no sperm seen in the epididymis and a marked increase of apoptosis during meiosis. Adult females exhibit a few growingfollicles and no corpora lutea. [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
4930486L24Rik	A	T	13: 60,992,928 (GRCm39)	D250E	probably damaging	Het
4930571K23Rik	A	G	7: 124,968,201 (GRCm39)		noncoding transcript	Het
Acsl3	T	C	1: 78,683,114 (GRCm39)		probably benign	Het
Acsl6	C	A	11: 54,220,792 (GRCm39)	T244K	probably damaging	Het
Adam26b	T	A	8: 43,974,000 (GRCm39)	N334I	probably damaging	Het
Adgrl4	C	T	3: 151,223,248 (GRCm39)	T608M	probably damaging	Het
Aldh2	A	G	5: 121,716,404 (GRCm39)		probably null	Het
Alms1	A	G	6: 85,599,436 (GRCm39)	T1890A	possibly damaging	Het
Capn7	C	T	14: 31,082,117 (GRCm39)	T441M	probably damaging	Het
Cd9	A	T	6: 125,441,367 (GRCm39)	C85S	probably damaging	Het
Chrm3	T	C	13: 9,928,794 (GRCm39)	T81A	probably damaging	Het
Ctif	A	G	18: 75,757,376 (GRCm39)		probably benign	Het
Dcc	T	A	18: 71,503,808 (GRCm39)	D950V	probably damaging	Het
Eif4g1	T	C	16: 20,498,530 (GRCm39)	V422A	probably damaging	Het
Enthd1	A	G	15: 80,337,124 (GRCm39)	S437P	probably damaging	Het
Fads1	A	G	19: 10,171,464 (GRCm39)		probably benign	Het
Fat3	T	A	9: 15,856,176 (GRCm39)	I3869L	probably benign	Het
Fbxw5	T	A	2: 25,392,473 (GRCm39)	V85E	possibly damaging	Het
Fcgbpl1	T	A	7: 27,853,772 (GRCm39)	C1579S	probably damaging	Het
Fem1b	T	C	9: 62,704,456 (GRCm39)	D268G	possibly damaging	Het
Focad	T	C	4: 88,327,225 (GRCm39)	L1772P	probably damaging	Het
Gtf3a	C	A	5: 146,888,723 (GRCm39)	Q145K	possibly damaging	Het
Hacl1	T	C	14: 31,342,957 (GRCm39)		probably null	Het
Herc2	T	A	7: 55,803,653 (GRCm39)	F2229L	probably benign	Het
Hs3st4	A	T	7: 123,996,080 (GRCm39)	I249L	probably benign	Het
Iqsec1	A	T	6: 90,786,752 (GRCm39)	Y7*	probably null	Het
Irag2	A	G	6: 145,083,341 (GRCm39)		probably benign	Het
Klk1b1	T	A	7: 43,619,750 (GRCm39)	M103K	probably benign	Het
Krt5	A	G	15: 101,619,020 (GRCm39)	V287A	probably benign	Het
Lgals12	T	A	19: 7,581,530 (GRCm39)	Q59L	possibly damaging	Het
Loxl4	A	G	19: 42,593,379 (GRCm39)	V264A	possibly damaging	Het
Lrp1b	T	C	2: 40,712,695 (GRCm39)	D3099G	probably damaging	Het
Mical3	G	A	6: 120,984,369 (GRCm39)	T169I	possibly damaging	Het
Muc21	A	C	17: 35,931,540 (GRCm39)		probably benign	Het
Myef2l	G	A	3: 10,154,613 (GRCm39)	V461I	possibly damaging	Het
Myh7b	A	C	2: 155,462,054 (GRCm39)	S317R	probably damaging	Het
Nrbp1	T	A	5: 31,403,157 (GRCm39)	I210N	probably damaging	Het
Nsd1	A	T	13: 55,361,872 (GRCm39)		probably null	Het
Nup58	A	T	14: 60,482,119 (GRCm39)		probably benign	Het
Or1j17	C	T	2: 36,578,259 (GRCm39)	L82F	probably damaging	Het
Or2t49	A	T	11: 58,392,502 (GRCm39)	S293R	probably damaging	Het
Or5h22	A	G	16: 58,895,270 (GRCm39)	Y58H	probably damaging	Het
Or5i1	T	A	2: 87,612,929 (GRCm39)	I15N	possibly damaging	Het
Or6c2b	T	C	10: 128,947,737 (GRCm39)	T186A	probably benign	Het
Pcnx2	A	G	8: 126,577,087 (GRCm39)	Y982H	probably damaging	Het
Pias3	T	C	3: 96,609,541 (GRCm39)	L312P	probably damaging	Het
Plekhm1	G	A	11: 103,267,710 (GRCm39)	P754S	probably damaging	Het
Ppp2r5c	T	A	12: 110,512,057 (GRCm39)	L145*	probably null	Het
Ppp2r5c	T	A	12: 110,527,906 (GRCm39)		probably benign	Het
Pramel29	A	C	4: 143,935,162 (GRCm39)	I193S	probably damaging	Het
Proser3	T	C	7: 30,239,446 (GRCm39)	M553V	probably benign	Het
Shf	G	A	2: 122,199,163 (GRCm39)	P51S	probably damaging	Het
Smurf2	A	T	11: 106,715,514 (GRCm39)	D664E	possibly damaging	Het
Spag9	G	A	11: 93,887,391 (GRCm39)	A99T	probably benign	Het
Stim1	T	G	7: 102,003,713 (GRCm39)	C49G	probably damaging	Het
Stk32c	T	C	7: 138,701,740 (GRCm39)	I238V	probably benign	Het
Tenm2	C	T	11: 35,954,004 (GRCm39)	G1236R	possibly damaging	Het
Tfb2m	T	A	1: 179,372,464 (GRCm39)	E133V	probably null	Het
Tmem209	A	T	6: 30,497,867 (GRCm39)	C143S	probably benign	Het
Tnr	T	G	1: 159,679,600 (GRCm39)	N191K	probably benign	Het
Vars1	C	T	17: 35,217,198 (GRCm39)	A419T	probably benign	Het
Vmn2r111	T	C	17: 22,767,041 (GRCm39)	S819G	probably benign	Het
Wls	T	C	3: 159,602,995 (GRCm39)	V136A	probably benign	Het
Zfp82	T	C	7: 29,756,779 (GRCm39)	D37G	probably benign	Het

Other mutations in Ybx2

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01099:Ybx2	APN	11	69,831,556 (GRCm39)	missense	probably damaging	0.97
IGL02720:Ybx2	APN	11	69,831,158 (GRCm39)	missense	probably benign	0.09
IGL02720:Ybx2	APN	11	69,831,157 (GRCm39)	missense	probably benign
PIT4515001:Ybx2	UTSW	11	69,831,224 (GRCm39)	missense	probably benign	0.41
R0158:Ybx2	UTSW	11	69,831,145 (GRCm39)	unclassified	probably benign
R1985:Ybx2	UTSW	11	69,827,294 (GRCm39)	splice site	probably null
R3969:Ybx2	UTSW	11	69,831,242 (GRCm39)	missense	probably damaging	0.99
R4209:Ybx2	UTSW	11	69,826,767 (GRCm39)	start gained	probably benign
R5963:Ybx2	UTSW	11	69,831,918 (GRCm39)	missense	probably damaging	1.00
R6378:Ybx2	UTSW	11	69,831,179 (GRCm39)	missense	possibly damaging	0.73
R7325:Ybx2	UTSW	11	69,831,181 (GRCm39)	missense	probably benign	0.22
R7982:Ybx2	UTSW	11	69,831,448 (GRCm39)	missense	possibly damaging	0.94
R8310:Ybx2	UTSW	11	69,831,194 (GRCm39)	missense	probably damaging	0.96
R8830:Ybx2	UTSW	11	69,827,063 (GRCm39)	missense	probably benign	0.03
R9443:Ybx2	UTSW	11	69,831,188 (GRCm39)	missense
X0062:Ybx2	UTSW	11	69,829,174 (GRCm39)	missense	probably damaging	0.99

Predicted Primers

PCR Primer
(F):5'- GCAGAAGCTGCTAATGTCACTGGG -3'
(R):5'- TGGAACGCCTGATGTCTTTGGAGC -3'

Sequencing Primer
(F):5'- TAGGTTCCGGAGGTTCATTCCT -3'
(R):5'- TGTGAGGACCACAGTCTCTG -3'

Posted On

2014-05-14