Mutagenetix > Incidental Mutation

Incidental Mutation 'R5963:Ybx2'

471892

Institutional Source

Beutler Lab

Gene Symbol

Ybx2

Ensembl Gene

ENSMUSG00000018554

Gene Name

Y box protein 2

Synonyms

MSY2

MMRRC Submission

044148-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.857) question?

Stock #

R5963 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

69826652-69832430 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 69831918 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glutamic Acid to Glycine at position 164 (E164G)

Ref Sequence

ENSEMBL: ENSMUSP00000136684 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000018698] [ENSMUST00000018710] [ENSMUST00000108601] [ENSMUST00000135437] [ENSMUST00000141837] [ENSMUST00000142500] [ENSMUST00000149194] [ENSMUST00000179298] [ENSMUST00000178363]

AlphaFold

no structure available at present

Predicted Effect

probably damaging
Transcript: ENSMUST00000018698
AA Change: E359G

PolyPhen 2 Score 0.959 (Sensitivity: 0.78; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000018698
Gene: ENSMUSG00000018554
AA Change: E359G

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: E282G

PolyPhen 2 Score 0.959 (Sensitivity: 0.78; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000104242
Gene: ENSMUSG00000018554
AA Change: E282G

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: ENSMUST00000135437

SMART Domains

Protein: ENSMUSP00000137092
Gene: ENSMUSG00000018566

Domain	Start	End	E-Value	Type
Pfam:Sugar_tr	1	57	5.3e-13	PFAM

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 benign
Transcript: ENSMUST00000142500

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000148395

Predicted Effect

probably damaging
Transcript: ENSMUST00000149194
AA Change: E164G

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000136684
Gene: ENSMUSG00000018554
AA Change: E164G

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

Predicted Effect

probably benign
Transcript: ENSMUST00000179298

SMART Domains

Protein: ENSMUSP00000136726
Gene: ENSMUSG00000018566

Domain	Start	End	E-Value	Type
Pfam:Sugar_tr	26	242	6.9e-65	PFAM
Pfam:MFS_1	27	239	2e-10	PFAM

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

Predicted Effect

probably benign
Transcript: ENSMUST00000152487

Meta Mutation Damage Score

0.0920

Coding Region Coverage

1x: 99.9%
3x: 99.5%
10x: 97.7%
20x: 92.5%

Validation Efficiency

99% (68/69)

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: 55 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Alg8	A	G	7: 97,029,037 (GRCm39)	K131E	probably benign	Het
Ank3	T	A	10: 69,823,056 (GRCm39)	L575*	probably null	Het
Aqr	T	C	2: 113,957,442 (GRCm39)	T819A	probably damaging	Het
Bbs2	A	T	8: 94,807,659 (GRCm39)	S407T	probably benign	Het
Bmper	T	A	9: 23,286,889 (GRCm39)	C272S	probably benign	Het
Btbd9	C	T	17: 30,553,192 (GRCm39)		probably null	Het
C5ar1	A	G	7: 15,982,747 (GRCm39)	V91A	possibly damaging	Het
Ccdc138	A	G	10: 58,411,579 (GRCm39)	H649R	possibly damaging	Het
Cfap43	A	T	19: 47,734,013 (GRCm39)	V1451E	probably benign	Het
Cfap46	T	A	7: 139,231,511 (GRCm39)	M901L	probably damaging	Het
Cherp	G	T	8: 73,215,379 (GRCm39)		probably benign	Het
D430041D05Rik	C	T	2: 104,078,630 (GRCm39)	V1229I	possibly damaging	Het
Fat4	A	C	3: 39,064,696 (GRCm39)	D4884A	probably damaging	Het
Fcrl5	T	C	3: 87,351,480 (GRCm39)	F243L	probably damaging	Het
Garem1	T	A	18: 21,262,487 (GRCm39)	I776F	probably benign	Het
Gpr87	T	A	3: 59,086,690 (GRCm39)	R272*	probably null	Het
Gsdmc	A	T	15: 63,651,965 (GRCm39)		probably null	Het
Hydin	T	A	8: 111,220,926 (GRCm39)	F1441I	possibly damaging	Het
Ints11	T	A	4: 155,957,369 (GRCm39)	C63*	probably null	Het
Kdm4b	A	T	17: 56,706,732 (GRCm39)	T908S	probably damaging	Het
Lipn	A	G	19: 34,058,700 (GRCm39)	D304G	probably damaging	Het
Man2a1	T	G	17: 64,982,117 (GRCm39)	N544K	probably benign	Het
Mapkapk5	G	T	5: 121,676,544 (GRCm39)	H66N	probably damaging	Het
Mog	G	A	17: 37,323,240 (GRCm39)	R233*	probably null	Het
Mrps24	A	T	11: 5,657,481 (GRCm39)		probably benign	Het
Nom1	T	C	5: 29,642,768 (GRCm39)	L423P	probably damaging	Het
Or51b6	T	A	7: 103,556,168 (GRCm39)	V174E	probably benign	Het
Pcdha1	T	A	18: 37,064,224 (GRCm39)	V296E	probably damaging	Het
Pdcd2	T	C	17: 15,746,656 (GRCm39)	K168E	possibly damaging	Het
Pdcd2	G	T	17: 15,746,657 (GRCm39)	H167Q	probably damaging	Het
Pla2g12b	T	A	10: 59,239,780 (GRCm39)	V63D	probably damaging	Het
Pnn	C	T	12: 59,114,617 (GRCm39)	R56*	probably null	Het
Primpol	T	A	8: 47,046,615 (GRCm39)	E227V	possibly damaging	Het
Rad54l	A	T	4: 115,967,584 (GRCm39)	W233R	probably damaging	Het
Rims2	A	T	15: 39,300,578 (GRCm39)	D103V	probably damaging	Het
Rttn	T	C	18: 89,091,819 (GRCm39)	S1511P	probably benign	Het
Septin5	T	C	16: 18,442,962 (GRCm39)		probably null	Het
Simc1	T	A	13: 54,673,632 (GRCm39)	I660K	possibly damaging	Het
Slc15a5	A	G	6: 138,056,691 (GRCm39)	L75P	probably damaging	Het
Slc9a2	A	G	1: 40,721,196 (GRCm39)	S55G	possibly damaging	Het
Slit3	C	T	11: 35,591,063 (GRCm39)	R1292C	probably damaging	Het
Slitrk3	A	G	3: 72,958,046 (GRCm39)	V242A	probably benign	Het
St14	A	T	9: 31,017,853 (GRCm39)		probably benign	Het
Tnnt2	T	C	1: 135,771,600 (GRCm39)		probably benign	Het
Traf5	G	A	1: 191,731,977 (GRCm39)	T288I	probably benign	Het
Trerf1	C	T	17: 47,625,263 (GRCm39)		noncoding transcript	Het
Vegfc	A	G	8: 54,634,319 (GRCm39)	N333D	probably benign	Het
Vmn1r65	T	A	7: 6,011,608 (GRCm39)	I209F	probably damaging	Het
Vps51	A	G	19: 6,118,320 (GRCm39)	L725P	probably damaging	Het
Vps8	T	C	16: 21,288,871 (GRCm39)	I408T	possibly damaging	Het
Wdr72	T	C	9: 74,052,310 (GRCm39)	Y114H	probably damaging	Het
Zcchc14	A	T	8: 122,355,362 (GRCm39)		probably benign	Het
Zfp383	A	G	7: 29,615,103 (GRCm39)	T453A	possibly damaging	Het
Zfp84	G	T	7: 29,476,378 (GRCm39)	G357C	probably damaging	Het
Zmynd11	G	T	13: 9,745,931 (GRCm39)		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
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
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'- CCTATGCAGGCAAGTCAAGC -3'
(R):5'- AAGCCGATGTTTTGATGTCATG -3'

Sequencing Primer
(F):5'- AAGTCAAGCCCAGGGTGC -3'
(R):5'- TGATGTCATGAATTATGGGAAAGTG -3'

Posted On

2017-03-31