Mutagenetix > Incidental Mutation

Incidental Mutation 'PIT4515001:Ybx2'

556333

Institutional Source

Beutler Lab

Gene Symbol

Ybx2

Ensembl Gene

ENSMUSG00000018554

Gene Name

Y box protein 2

Synonyms

MSY2

Accession Numbers

Essential gene?

Probably essential (E-score: 0.860) question?

Stock #

PIT4515001 (G1)

Quality Score

155.008

Status

Not validated

Chromosome

Chromosomal Location

69826652-69832430 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 69831224 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Glutamic Acid at position 273 (V273E)

Ref Sequence

ENSEMBL: ENSMUSP00000018698 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000018698] [ENSMUST00000018710] [ENSMUST00000108601] [ENSMUST00000141837] [ENSMUST00000149194] [ENSMUST00000178363]

AlphaFold

no structure available at present

Predicted Effect

probably benign
Transcript: ENSMUST00000018698
AA Change: V273E

PolyPhen 2 Score 0.411 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000018698
Gene: ENSMUSG00000018554
AA Change: V273E

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: V196E

PolyPhen 2 Score 0.174 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000104242
Gene: ENSMUSG00000018554
AA Change: V196E

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

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

possibly damaging
Transcript: ENSMUST00000149194
AA Change: V78E

PolyPhen 2 Score 0.673 (Sensitivity: 0.86; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000136684
Gene: ENSMUSG00000018554
AA Change: V78E

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

probably benign
Transcript: ENSMUST00000152487

Predicted Effect

probably benign
Transcript: ENSMUST00000178363

SMART Domains

Protein: ENSMUSP00000136455
Gene: ENSMUSG00000018566

Domain	Start	End	E-Value	Type
PDB:4PYP\|A	14	50	3e-10	PDB

Coding Region Coverage

1x: 93.4%
3x: 91.0%
10x: 86.0%
20x: 75.1%

Validation Efficiency

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: 66 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
3425401B19Rik	T	A	14: 32,383,068 (GRCm39)	R966*	probably null	Het
Adam32	A	T	8: 25,404,342 (GRCm39)	I221K	possibly damaging	Het
Adcy6	T	C	15: 98,493,027 (GRCm39)	T880A	probably benign	Het
Agpat5	T	A	8: 18,896,657 (GRCm39)	Y28N	probably damaging	Het
Atg2a	A	G	19: 6,303,615 (GRCm39)	I1125V	probably damaging	Het
B4galt6	A	G	18: 20,821,524 (GRCm39)	Y335H	probably benign	Het
Bend3	A	T	10: 43,386,630 (GRCm39)	E341V	probably damaging	Het
Bltp1	T	A	3: 37,028,385 (GRCm39)	Y2351N	probably damaging	Het
Ccdc136	T	A	6: 29,417,225 (GRCm39)	V682E	probably benign	Het
Ccdc142	T	C	6: 83,080,238 (GRCm39)	C394R	probably benign	Het
Cfap58	A	G	19: 48,023,122 (GRCm39)	N845D	probably benign	Het
Col4a3	G	A	1: 82,660,024 (GRCm39)	G890R	unknown	Het
Cyp1a2	C	A	9: 57,589,242 (GRCm39)	V191L	probably benign	Het
Cyp51	A	T	5: 4,149,122 (GRCm39)		probably null	Het
Diras2	T	C	13: 52,661,783 (GRCm39)	S175G	possibly damaging	Het
Dnah6	A	G	6: 73,091,565 (GRCm39)	F2242S	probably damaging	Het
Erg	T	A	16: 95,210,619 (GRCm39)	N78Y	probably benign	Het
Fdft1	T	A	14: 63,402,032 (GRCm39)	Q49L	probably benign	Het
Frem1	G	T	4: 82,818,663 (GRCm39)	H2183Q	probably damaging	Het
Fut2	G	A	7: 45,299,890 (GRCm39)	T294I	probably damaging	Het
Gabrb1	A	C	5: 71,858,160 (GRCm39)	D62A	probably damaging	Het
Gbe1	T	A	16: 70,238,004 (GRCm39)	Y263*	probably null	Het
Gimap6	T	C	6: 48,679,502 (GRCm39)	D178G	probably benign	Het
Gss	T	A	2: 155,420,261 (GRCm39)	T147S	probably damaging	Het
Hlcs	A	T	16: 94,068,275 (GRCm39)	V315E	probably benign	Het
Hoxa3	C	T	6: 52,147,164 (GRCm39)	G363E	unknown	Het
Ift140	A	G	17: 25,305,834 (GRCm39)	N807S	probably damaging	Het
Iglc1	T	G	16: 18,880,701 (GRCm39)	D40A		Het
Itga10	T	A	3: 96,569,948 (GRCm39)	I1120N	probably damaging	Het
Jak3	T	C	8: 72,132,286 (GRCm39)	V217A	probably benign	Het
Kank2	T	G	9: 21,706,179 (GRCm39)	I280L	probably benign	Het
Kcnk1	G	T	8: 126,752,081 (GRCm39)	G229V	probably damaging	Het
Kpna7	T	C	5: 144,941,862 (GRCm39)	T143A	probably benign	Het
Letmd1	C	T	15: 100,374,683 (GRCm39)	R310C	probably damaging	Het
Mga	G	A	2: 119,746,985 (GRCm39)	V379I	probably damaging	Het
Mto1	T	A	9: 78,364,699 (GRCm39)	Y313N	probably damaging	Het
Muc5ac	G	A	7: 141,361,153 (GRCm39)	C1488Y	probably damaging	Het
Nde1	T	A	16: 13,988,357 (GRCm39)		probably null	Het
Nfatc3	T	C	8: 106,805,835 (GRCm39)	S235P	possibly damaging	Het
Nup88	T	C	11: 70,835,547 (GRCm39)	D602G	probably benign	Het
Or11g25	T	A	14: 50,723,536 (GRCm39)	M207K	probably benign	Het
Or2h1b	A	C	17: 37,462,270 (GRCm39)	S198A	probably benign	Het
Pcnx1	G	A	12: 82,038,561 (GRCm39)	C1309Y		Het
Phldb1	A	G	9: 44,627,257 (GRCm39)	I396T	probably benign	Het
Pramel38	T	C	5: 94,368,831 (GRCm39)	M442T	probably benign	Het
Pramel41	A	C	5: 94,594,694 (GRCm39)	K185Q	probably benign	Het
Prss53	G	A	7: 127,487,963 (GRCm39)	T173I	probably benign	Het
Ptpn11	C	A	5: 121,302,617 (GRCm39)	D156Y	probably damaging	Het
Rfx8	A	G	1: 39,729,265 (GRCm39)	Y167H	probably benign	Het
Rpsa	T	A	9: 119,960,214 (GRCm39)	I259N	probably benign	Het
Rrm2b	G	T	15: 37,947,048 (GRCm39)	D84E	probably benign	Het
Scgb2b19	A	T	7: 32,979,036 (GRCm39)		probably null	Het
Sik3	T	C	9: 46,120,029 (GRCm39)	L706P	probably damaging	Het
Slc4a4	A	T	5: 89,281,112 (GRCm39)	E426D	probably damaging	Het
Slc8a2	C	A	7: 15,874,504 (GRCm39)	L251I	possibly damaging	Het
Taf6	T	C	5: 138,180,504 (GRCm39)	K287E	probably benign	Het
Tiam1	G	A	16: 89,657,130 (GRCm39)	T702I	probably damaging	Het
Tle1	A	T	4: 72,117,556 (GRCm39)	F35I	possibly damaging	Het
Tle2	A	G	10: 81,422,964 (GRCm39)	Q454R	possibly damaging	Het
Tsc2	T	C	17: 24,840,121 (GRCm39)	N425S	probably benign	Het
Utp3	A	G	5: 88,702,564 (GRCm39)	D31G	probably benign	Het
Vmn1r173	A	T	7: 23,401,911 (GRCm39)	R49*	probably null	Het
Zbtb22	G	A	17: 34,137,672 (GRCm39)	A606T	probably benign	Het
Zcchc8	A	T	5: 123,838,995 (GRCm39)	D514E	probably benign	Het
Zfy2	T	A	Y: 2,117,096 (GRCm39)	I244F	probably benign	Het
Zglp1	T	C	9: 20,977,485 (GRCm39)	N110S	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
R0158:Ybx2	UTSW	11	69,831,145 (GRCm39)	unclassified	probably benign
R1697:Ybx2	UTSW	11	69,830,887 (GRCm39)	missense	probably benign	0.40
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'- AGCAACAGCCCATAGAGGTG -3'
(R):5'- CTGGAAGTAGGGACGGTTTC -3'

Sequencing Primer
(F):5'- CCGGGGAGGCTAGTTCTCTTAC -3'
(R):5'- AGCCATCAGTGGGGCCTTG -3'

Posted On

2019-06-07