Mutagenetix > Incidental Mutation

Incidental Mutation 'R7325:Ybx2'

568833

Institutional Source

Beutler Lab

Gene Symbol

Ybx2

Ensembl Gene

ENSMUSG00000018554

Gene Name

Y box protein 2

Synonyms

MSY2

MMRRC Submission

045419-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.860) question?

Stock #

R7325 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

69826652-69832430 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 69831181 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Serine at position 259 (T259S)

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: T259S

PolyPhen 2 Score 0.223 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000018698
Gene: ENSMUSG00000018554
AA Change: T259S

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: T182S

PolyPhen 2 Score 0.080 (Sensitivity: 0.93; Specificity: 0.85)

SMART Domains

Protein: ENSMUSP00000104242
Gene: ENSMUSG00000018554
AA Change: T182S

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: T64S

PolyPhen 2 Score 0.459 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000136684
Gene: ENSMUSG00000018554
AA Change: T64S

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

Meta Mutation Damage Score

0.0613

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.7%
20x: 99.1%

Validation Efficiency

100% (62/62)

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: 61 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adgrb3	T	A	1: 25,571,711 (GRCm39)	Q402L	probably benign	Het
Afap1l1	T	C	18: 61,869,917 (GRCm39)	T638A	probably benign	Het
Agtr1a	A	C	13: 30,565,890 (GRCm39)	K318N	possibly damaging	Het
Anks1b	A	G	10: 90,777,294 (GRCm39)	T1095A	probably damaging	Het
Ap3d1	A	T	10: 80,559,637 (GRCm39)	I207N	probably damaging	Het
Arhgef11	T	C	3: 87,620,599 (GRCm39)	L484P	possibly damaging	Het
Astn2	C	T	4: 65,460,906 (GRCm39)	S1076N	probably benign	Het
Baat	C	A	4: 49,490,213 (GRCm39)	L290F	probably benign	Het
Boll	T	C	1: 55,343,757 (GRCm39)	Y222C	probably damaging	Het
Bphl	A	T	13: 34,234,324 (GRCm39)	I147F	possibly damaging	Het
Cadps2	T	G	6: 23,409,934 (GRCm39)	D766A	unknown	Het
Cd300lb	T	A	11: 114,815,858 (GRCm39)	K210M	probably damaging	Het
Cdan1	T	C	2: 120,555,185 (GRCm39)	Q797R	probably benign	Het
Celsr1	T	A	15: 85,917,209 (GRCm39)	S255C	probably damaging	Het
Cfap91	T	A	16: 38,141,963 (GRCm39)		probably null	Het
Cip2a	T	A	16: 48,826,184 (GRCm39)	M417K	probably benign	Het
Csmd1	G	A	8: 16,108,721 (GRCm39)	S1894L	probably damaging	Het
Dennd5b	T	A	6: 148,922,068 (GRCm39)	K815N	probably benign	Het
Exd1	A	G	2: 119,350,620 (GRCm39)	V547A	probably benign	Het
Fbxo15	C	T	18: 84,977,243 (GRCm39)	R52C	probably damaging	Het
Fip1l1	A	G	5: 74,697,460 (GRCm39)		probably null	Het
Flg2	T	A	3: 93,110,679 (GRCm39)	N902K	unknown	Het
Fyttd1	T	A	16: 32,704,618 (GRCm39)	N76K	probably benign	Het
Gins1	T	A	2: 150,758,086 (GRCm39)	D57E	probably benign	Het
Gm5565	G	C	5: 146,095,171 (GRCm39)		probably null	Het
Gpsm2	T	C	3: 108,610,244 (GRCm39)	Y72C	probably damaging	Het
Hace1	C	A	10: 45,465,603 (GRCm39)	S53*	probably null	Het
Insig2	A	G	1: 121,234,666 (GRCm39)	V188A	possibly damaging	Het
Ism1	T	C	2: 139,598,963 (GRCm39)	V312A	probably damaging	Het
Jmy	A	T	13: 93,609,251 (GRCm39)	Y353N	probably damaging	Het
Maz	A	C	7: 126,624,725 (GRCm39)	V265G	probably benign	Het
Mtmr14	T	A	6: 113,246,509 (GRCm39)	I426N	probably damaging	Het
Or1e34	C	T	11: 73,779,101 (GRCm39)	M32I	probably benign	Het
Or5b113	A	G	19: 13,342,001 (GRCm39)	E3G	probably benign	Het
Or8k22	A	G	2: 86,163,344 (GRCm39)	S119P	possibly damaging	Het
Pcdhac2	T	A	18: 37,278,413 (GRCm39)	N464K	probably damaging	Het
Pcdhb7	T	A	18: 37,476,440 (GRCm39)	H525Q	probably benign	Het
Pcp4l1	G	A	1: 171,002,034 (GRCm39)	A42V	possibly damaging	Het
Podn	C	T	4: 107,874,899 (GRCm39)		probably null	Het
Prim1	A	G	10: 127,858,788 (GRCm39)	D232G	probably null	Het
Prrt1	T	A	17: 34,851,161 (GRCm39)	M283K	possibly damaging	Het
Rgs9	A	T	11: 109,167,407 (GRCm39)	I65N	probably damaging	Het
Scgb2b26	C	A	7: 33,643,782 (GRCm39)	V53L	probably benign	Het
Shank2	C	A	7: 143,965,422 (GRCm39)	P1010Q	probably benign	Het
Slc12a4	C	T	8: 106,682,347 (GRCm39)	G121S	probably damaging	Het
Slc17a6	G	T	7: 51,294,766 (GRCm39)	A158S	probably damaging	Het
Slc9a9	C	T	9: 94,594,951 (GRCm39)	H154Y	probably benign	Het
Slco1a8	T	C	6: 141,934,951 (GRCm39)	K379E	probably damaging	Het
Slco2a1	T	A	9: 102,962,948 (GRCm39)		probably null	Het
Snapc3	T	C	4: 83,353,507 (GRCm39)	I182T	probably benign	Het
Taok2	A	G	7: 126,470,260 (GRCm39)	V856A	probably benign	Het
Tep1	T	A	14: 51,103,495 (GRCm39)	N265I	probably damaging	Het
Tespa1	A	T	10: 130,197,910 (GRCm39)	N311Y	probably damaging	Het
Tpmt	G	A	13: 47,194,960 (GRCm39)	Q14*	probably null	Het
Trim33	T	C	3: 103,228,952 (GRCm39)	F353L	possibly damaging	Het
Upp1	T	C	11: 9,084,743 (GRCm39)	V154A	probably damaging	Het
Usp34	T	C	11: 23,369,052 (GRCm39)	I1747T		Het
Vmn1r47	T	C	6: 89,999,254 (GRCm39)	S129P	probably benign	Het
Vmn2r93	A	G	17: 18,524,249 (GRCm39)	Y81C	probably benign	Het
Zfp536	T	C	7: 37,179,285 (GRCm39)	T1107A	probably benign	Het
Zfp583	C	T	7: 6,319,585 (GRCm39)	A476T	probably damaging	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
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
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'- CAACAGCCCATAGAGGTGAG -3'
(R):5'- AGACTCCCTTCCCAGGATTC -3'

Sequencing Primer
(F):5'- TGAGAGGAGAGTTGCAGCC -3'
(R):5'- TCCCAGGATTCCTTGGTTTG -3'

Posted On

2019-09-13