Mutagenetix > Incidental Mutation

Incidental Mutation 'R9443:Ybx2'

713761

Institutional Source

Beutler Lab

Gene Symbol

Ybx2

Ensembl Gene

ENSMUSG00000018554

Gene Name

Y box protein 2

Synonyms

MSY2

MMRRC Submission

Accession Numbers

Essential gene?

Probably essential (E-score: 0.857) question?

Stock #

R9443 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

69826652-69832430 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 69831188 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Proline to Leucine at position 261 (P261L)

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

SMART Domains

Protein: ENSMUSP00000018698
Gene: ENSMUSG00000018554
AA Change: P261L

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 damaging
Transcript: ENSMUST00000108601
AA Change: P184L

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000104242
Gene: ENSMUSG00000018554
AA Change: P184L

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

probably damaging
Transcript: ENSMUST00000149194
AA Change: P66L

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

SMART Domains

Protein: ENSMUSP00000136684
Gene: ENSMUSG00000018554
AA Change: P66L

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: 100.0%
3x: 99.9%
10x: 99.5%
20x: 98.4%

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: 74 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adad1	T	C	3: 37,146,140 (GRCm39)	Y503H	probably benign	Het
Adck1	T	C	12: 88,338,550 (GRCm39)		probably null	Het
Afap1l1	T	C	18: 61,879,859 (GRCm39)	D337G	probably damaging	Het
Afg1l	G	A	10: 42,189,587 (GRCm39)	T448M	probably damaging	Het
Aqp6	T	C	15: 99,499,409 (GRCm39)	S41P		Het
Atad5	T	G	11: 80,023,388 (GRCm39)	V1500G	probably benign	Het
B3galt9	C	T	2: 34,728,623 (GRCm39)	Q141*	probably null	Het
Btbd18	T	A	2: 84,497,524 (GRCm39)	D387E	probably benign	Het
Catsperd	A	G	17: 56,969,720 (GRCm39)	N605D	possibly damaging	Het
Ccdc24	C	T	4: 117,728,355 (GRCm39)	V102I	probably benign	Het
Cenpe	T	A	3: 134,976,609 (GRCm39)	D2405E	probably damaging	Het
Cfap46	T	C	7: 139,195,023 (GRCm39)	D2249G		Het
Chrm1	A	T	19: 8,655,550 (GRCm39)	Y85F	possibly damaging	Het
Clstn3	C	T	6: 124,428,358 (GRCm39)	G465S	probably damaging	Het
Col7a1	G	A	9: 108,785,059 (GRCm39)	G262D	unknown	Het
Copg2	T	C	6: 30,750,578 (GRCm39)	T736A	probably benign	Het
Coro2b	T	C	9: 62,333,080 (GRCm39)	E435G	probably benign	Het
Cp	A	T	3: 20,033,083 (GRCm39)	I637F	possibly damaging	Het
Cpne7	T	C	8: 123,853,411 (GRCm39)	F239L	probably damaging	Het
Cstdc2	C	T	2: 148,689,878 (GRCm39)	E92K	probably damaging	Het
Cul2	T	A	18: 3,434,041 (GRCm39)	Y679*	probably null	Het
Dhx8	T	C	11: 101,655,740 (GRCm39)	Y1158H	probably damaging	Het
Eda	G	T	X: 99,019,775 (GRCm39)	R130L	unknown	Het
Elp6	T	A	9: 110,150,004 (GRCm39)	V265D	probably damaging	Het
Eomes	A	G	9: 118,313,640 (GRCm39)	T562A		Het
Fam187b	A	T	7: 30,677,067 (GRCm39)	E192V	probably damaging	Het
Foxi1	T	C	11: 34,155,671 (GRCm39)	T320A	probably benign	Het
Gga1	C	T	15: 78,765,247 (GRCm39)	T18I	possibly damaging	Het
Grik4	T	A	9: 42,571,037 (GRCm39)	M223L	probably benign	Het
Hdac7	T	C	15: 97,700,352 (GRCm39)	N594S	probably benign	Het
Ifnar1	C	T	16: 91,292,367 (GRCm39)	P207L	probably benign	Het
Itpr3	T	G	17: 27,324,523 (GRCm39)	F1235C	probably damaging	Het
Klhdc4	A	G	8: 122,523,765 (GRCm39)	S484P	possibly damaging	Het
Kmt2c	A	G	5: 25,515,045 (GRCm39)	S2933P	probably damaging	Het
Lama5	T	A	2: 179,843,522 (GRCm39)	H475L	probably benign	Het
Ly6g6f	A	G	17: 35,299,826 (GRCm39)	L292P	possibly damaging	Het
Macf1	T	A	4: 123,365,668 (GRCm39)	Q3031L	probably benign	Het
Mbd5	T	G	2: 49,146,712 (GRCm39)	S307R	probably damaging	Het
Mertk	T	C	2: 128,604,029 (GRCm39)	F388L	probably benign	Het
Mmp11	A	G	10: 75,762,733 (GRCm39)	F240S	probably damaging	Het
Mroh1	T	A	15: 76,318,964 (GRCm39)	F949I	probably damaging	Het
Mroh2b	T	C	15: 4,973,821 (GRCm39)	L1113P	probably damaging	Het
Ndufv1	C	A	19: 4,057,614 (GRCm39)	A454S	probably benign	Het
Or13e8	A	G	4: 43,696,591 (GRCm39)	L194P	probably damaging	Het
Or56b2j	T	C	7: 104,352,821 (GRCm39)	S16P	probably benign	Het
Or5d46	T	A	2: 88,170,364 (GRCm39)	W152R	probably damaging	Het
Osbpl1a	C	A	18: 13,031,244 (GRCm39)	D329Y	probably benign	Het
Pcdh1	C	A	18: 38,330,633 (GRCm39)	R929L	probably damaging	Het
Phactr2	C	T	10: 13,122,841 (GRCm39)	R427K	probably benign	Het
Pip5k1c	T	C	10: 81,153,184 (GRCm39)	Y670H	probably damaging	Het
Plbd1	T	A	6: 136,611,555 (GRCm39)	N241Y	probably damaging	Het
Pmvk	C	A	3: 89,374,956 (GRCm39)	Q139K	probably benign	Het
Pramel30	T	A	4: 144,059,678 (GRCm39)	I463N	possibly damaging	Het
Rab3gap2	T	A	1: 184,967,523 (GRCm39)	C136S	probably damaging	Het
Rcor3	A	G	1: 191,786,050 (GRCm39)	V396A	probably damaging	Het
Rgs20	C	A	1: 4,982,629 (GRCm39)	E147*	probably null	Het
Rnf167	G	T	11: 70,540,777 (GRCm39)	L170F	probably damaging	Het
Scn9a	T	C	2: 66,395,553 (GRCm39)	T164A	probably damaging	Het
Skic3	A	G	13: 76,266,288 (GRCm39)	Q210R	probably benign	Het
Slc52a3	A	T	2: 151,846,299 (GRCm39)	I87F	probably benign	Het
Sntn	A	T	14: 13,682,364 (GRCm38)	M146L		Het
Svep1	C	T	4: 58,179,697 (GRCm39)	R182H	possibly damaging	Het
Taar7f	A	G	10: 23,926,311 (GRCm39)	I302V	probably benign	Het
Tm4sf20	T	C	1: 82,746,090 (GRCm39)	I17V	probably benign	Het
Traf1	T	C	2: 34,836,748 (GRCm39)	T270A	probably benign	Het
Trpm5	C	T	7: 142,638,860 (GRCm39)	E304K	probably benign	Het
Ttll8	T	C	15: 88,809,863 (GRCm39)	D311G	possibly damaging	Het
Unc79	T	A	12: 103,037,035 (GRCm39)	F608I	probably damaging	Het
Vmn2r11	A	T	5: 109,195,159 (GRCm39)	C722*	probably null	Het
Wdr7	A	G	18: 63,853,407 (GRCm39)	T36A	probably damaging	Het
Zfp101	C	T	17: 33,601,418 (GRCm39)	V113I	probably benign	Het
Zfp260	T	C	7: 29,804,249 (GRCm39)	S50P	probably benign	Het
Zfp319	A	T	8: 96,054,922 (GRCm39)	F427Y	probably benign	Het
Zfp369	T	C	13: 65,444,347 (GRCm39)	S497P	possibly 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
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
X0062:Ybx2	UTSW	11	69,829,174 (GRCm39)	missense	probably damaging	0.99

Predicted Primers

PCR Primer
(F):5'- CAACAGCCCATAGAGGTGAG -3'
(R):5'- AATTGGGCAGACTCCCTTCC -3'

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

Posted On

2022-06-15