Mutagenetix > Incidental Mutation

Incidental Mutation 'R2869:Ybx3'

500421

Institutional Source

Beutler Lab

Gene Symbol

Ybx3

Ensembl Gene

ENSMUSG00000030189

Gene Name

Y box protein 3

Synonyms

dbpA, MSY4, MSY3, Dpba, Yb2, oxyR, Csda

MMRRC Submission

040457-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R2869 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

131341821-131365413 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 131347376 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Alanine to Valine at position 253 (A253V)

Ref Sequence

ENSEMBL: ENSMUSP00000032309 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000032309] [ENSMUST00000087865]

AlphaFold

Q9JKB3

Predicted Effect

probably damaging
Transcript: ENSMUST00000032309
AA Change: A253V

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000032309
Gene: ENSMUSG00000030189
AA Change: A253V

Domain	Start	End	E-Value	Type
low complexity region	3	13	N/A	INTRINSIC
low complexity region	14	71	N/A	INTRINSIC
CSP	84	152	8.65e-24	SMART
low complexity region	166	182	N/A	INTRINSIC
low complexity region	186	198	N/A	INTRINSIC
low complexity region	212	232	N/A	INTRINSIC
low complexity region	278	293	N/A	INTRINSIC
low complexity region	315	329	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000087865
AA Change: A184V

PolyPhen 2 Score 0.843 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000085172
Gene: ENSMUSG00000030189
AA Change: A184V

Domain	Start	End	E-Value	Type
low complexity region	3	13	N/A	INTRINSIC
low complexity region	14	71	N/A	INTRINSIC
CSP	84	152	8.65e-24	SMART
low complexity region	166	182	N/A	INTRINSIC
low complexity region	209	224	N/A	INTRINSIC
low complexity region	246	260	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000203157

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000205035

Meta Mutation Damage Score

0.0970

Coding Region Coverage

1x: 99.6%
3x: 98.4%
10x: 93.9%
20x: 77.8%

Validation Efficiency

MGI Phenotype

PHENOTYPE: Half of mice homozygous for a knock-out allele exhibit male infertility associated with smaller testes and reduced sperm production, partly due to increased spermatocyte apoptosis during mid to late spermatogenesis and progressive seminiferous tubule degeneration. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 57 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Als2	A	G	1: 59,250,296 (GRCm39)	S483P	probably damaging	Het
Ccl27a	C	T	4: 41,769,640 (GRCm39)	R73Q	probably benign	Het
Cd6	A	G	19: 10,771,990 (GRCm39)	I307T	possibly damaging	Het
Ch25h	T	A	19: 34,452,210 (GRCm39)	H106L	probably benign	Het
Dennd2b	A	T	7: 109,156,637 (GRCm39)	Y38N	probably benign	Het
Dhx57	A	T	17: 80,558,805 (GRCm39)	D1051E	probably benign	Het
Eef2	GCCC	GCCCC	10: 81,014,601 (GRCm39)		probably null	Het
Eif4enif1	C	T	11: 3,192,586 (GRCm39)	P805S	probably damaging	Het
Fan1	A	G	7: 64,012,938 (GRCm39)	I668T	probably benign	Het
Frmpd4	A	T	X: 166,260,243 (GRCm39)	D1166E	probably benign	Het
Gbp11	C	T	5: 105,478,866 (GRCm39)	D191N	probably benign	Het
Ggt6	A	T	11: 72,328,187 (GRCm39)	N229I	probably benign	Het
Gria2	G	A	3: 80,609,799 (GRCm39)	T670I	probably damaging	Het
Gsdme	A	T	6: 50,185,157 (GRCm39)	C432*	probably null	Het
Hjurp	GT	GTT	1: 88,194,246 (GRCm39)		probably null	Het
Hmcn1	A	T	1: 150,614,467 (GRCm39)	V1313D	possibly damaging	Het
Kcnb1	A	G	2: 166,947,855 (GRCm39)	L331P	probably damaging	Het
Klf8	A	T	X: 152,165,678 (GRCm39)	E82D	probably damaging	Het
Krt13	A	G	11: 100,008,475 (GRCm39)	S421P	unknown	Het
Lactbl1	G	A	4: 136,354,097 (GRCm39)	C37Y	probably damaging	Het
Lzts2	C	A	19: 45,012,534 (GRCm39)	S321*	probably null	Het
Meikin	T	C	11: 54,264,333 (GRCm39)	V103A	possibly damaging	Het
Mki67	G	A	7: 135,309,878 (GRCm39)	P191L	probably benign	Het
Mlxip	A	G	5: 123,590,730 (GRCm39)	M878V	probably benign	Het
Mpp7	G	A	18: 7,461,678 (GRCm39)	P65L	possibly damaging	Het
Mroh2a	GCCC	GC	1: 88,159,979 (GRCm39)		probably null	Het
Myo9b	G	A	8: 71,786,981 (GRCm39)	R721Q	probably benign	Het
Nbn	T	A	4: 15,963,810 (GRCm39)	D70E	probably damaging	Het
Nomo1	C	A	7: 45,696,361 (GRCm39)	T293N	probably damaging	Het
Notum	A	G	11: 120,551,022 (GRCm39)	V48A	probably benign	Het
Nwd2	A	T	5: 63,957,671 (GRCm39)	I334L	probably benign	Het
Or10z1	T	C	1: 174,078,092 (GRCm39)	S134G	probably benign	Het
Or4k2	T	C	14: 50,423,811 (GRCm39)	T288A	probably benign	Het
Or6c211	A	T	10: 129,505,628 (GRCm39)	C253*	probably null	Het
Ostc	T	C	3: 130,497,157 (GRCm39)	N80S	probably damaging	Het
Otud4	T	A	8: 80,387,702 (GRCm39)	N300K	possibly damaging	Het
Palmd	T	C	3: 116,717,400 (GRCm39)	R366G	possibly damaging	Het
Parp1	A	G	1: 180,401,230 (GRCm39)	D45G	probably damaging	Het
Pes1	C	A	11: 3,926,834 (GRCm39)	T372K	probably benign	Het
Plcl1	A	T	1: 55,736,309 (GRCm39)	D550V	probably benign	Het
Ppp1r7	T	A	1: 93,285,585 (GRCm39)		probably null	Het
Prdx4	A	G	X: 154,123,460 (GRCm39)	V15A	probably benign	Het
Psmb8	T	C	17: 34,419,144 (GRCm39)	I146T	probably damaging	Het
Psmd13	A	T	7: 140,466,968 (GRCm39)	T116S	probably damaging	Het
Pzp	A	T	6: 128,462,519 (GRCm39)		probably null	Het
Serinc2	A	G	4: 130,159,005 (GRCm39)	S29P	probably damaging	Het
Slc39a8	T	A	3: 135,592,554 (GRCm39)		probably null	Het
Sppl2c	C	T	11: 104,078,141 (GRCm39)	P314S	probably benign	Het
St7	C	T	6: 17,819,276 (GRCm39)	P60L	probably damaging	Het
Stx3	A	T	19: 11,766,938 (GRCm39)	V91D	probably damaging	Het
Tafa2	A	T	10: 123,540,270 (GRCm39)	H42L	possibly damaging	Het
Tnni3k	C	T	3: 154,644,387 (GRCm39)		probably null	Het
Tprg1	T	C	16: 25,231,590 (GRCm39)	W189R	probably damaging	Het
Trim32	A	G	4: 65,532,694 (GRCm39)	D417G	probably damaging	Het
Vmn2r68	A	C	7: 84,882,834 (GRCm39)	M306R	probably benign	Het
Vwa7	G	A	17: 35,240,218 (GRCm39)	M395I	probably damaging	Het
Zfp53	A	T	17: 21,728,340 (GRCm39)	E124D	probably benign	Het

Other mutations in Ybx3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL02135:Ybx3	APN	6	131,357,892 (GRCm39)	missense	probably damaging	1.00
IGL02203:Ybx3	APN	6	131,345,371 (GRCm39)	missense	probably benign	0.01
PIT1430001:Ybx3	UTSW	6	131,356,422 (GRCm39)	missense	probably damaging	1.00
R2869:Ybx3	UTSW	6	131,347,376 (GRCm39)	missense	probably damaging	1.00
R2870:Ybx3	UTSW	6	131,347,376 (GRCm39)	missense	probably damaging	1.00
R2870:Ybx3	UTSW	6	131,347,376 (GRCm39)	missense	probably damaging	1.00
R2873:Ybx3	UTSW	6	131,347,376 (GRCm39)	missense	probably damaging	1.00
R4654:Ybx3	UTSW	6	131,347,290 (GRCm39)	missense	probably damaging	0.99
R5878:Ybx3	UTSW	6	131,344,726 (GRCm39)	critical splice donor site	probably null
R5881:Ybx3	UTSW	6	131,345,451 (GRCm39)	missense	possibly damaging	0.71
R7796:Ybx3	UTSW	6	131,345,479 (GRCm39)	missense	probably damaging	0.98
R7833:Ybx3	UTSW	6	131,344,826 (GRCm39)	missense	possibly damaging	0.83
R7986:Ybx3	UTSW	6	131,356,362 (GRCm39)	nonsense	probably null
R8003:Ybx3	UTSW	6	131,345,400 (GRCm39)	nonsense	probably null
R8043:Ybx3	UTSW	6	131,361,469 (GRCm39)	missense	probably benign	0.13
R9802:Ybx3	UTSW	6	131,345,426 (GRCm39)	missense	probably benign	0.01
X0024:Ybx3	UTSW	6	131,357,867 (GRCm39)	missense	possibly damaging	0.88

Predicted Primers

Posted On

2017-12-01