Mutagenetix > Incidental Mutation

Incidental Mutation 'R2870:Ybx3'

266508

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

040458-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R2870 (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: 99.1%
3x: 98.6%
10x: 97.3%
20x: 95.0%

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: 87 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Actrt3	A	G	3: 30,653,847 (GRCm39)	V51A	probably damaging	Het
Adgb	C	T	10: 10,307,025 (GRCm39)		probably null	Het
Als2	A	G	1: 59,250,296 (GRCm39)	S483P	probably damaging	Het
Ankrd10	C	T	8: 11,665,682 (GRCm39)	R306H	probably damaging	Het
Arhgef10	T	C	8: 15,025,093 (GRCm39)		probably null	Het
Arhgef10	A	G	8: 15,025,666 (GRCm39)	I459V	probably benign	Het
Armc2	C	T	10: 41,842,696 (GRCm39)		probably null	Het
Atp12a	A	G	14: 56,624,407 (GRCm39)	R952G	possibly damaging	Het
Atp6v1g1	A	G	4: 63,468,258 (GRCm39)	Y87C	probably benign	Het
C030034I22Rik	T	A	17: 69,725,106 (GRCm39)		noncoding transcript	Het
Cacna2d1	G	A	5: 16,517,566 (GRCm39)	C404Y	probably damaging	Het
Ccdc163	T	C	4: 116,599,058 (GRCm39)		silent	Het
Ccdc59	A	T	10: 105,677,388 (GRCm39)	K9M	possibly damaging	Het
Cd6	A	G	19: 10,771,990 (GRCm39)	I307T	possibly damaging	Het
Cimap1d	G	A	10: 79,481,487 (GRCm39)	T14I	probably benign	Het
Clasrp	C	A	7: 19,319,165 (GRCm39)		probably benign	Het
Csmd2	T	C	4: 128,451,511 (GRCm39)	F113S	unknown	Het
Csmd3	C	T	15: 47,721,320 (GRCm39)	G1437D	probably damaging	Het
Cyp4a14	C	A	4: 115,344,498 (GRCm39)	G456W	probably damaging	Het
Cyp4a30b	A	G	4: 115,315,559 (GRCm39)	H260R	possibly damaging	Het
Dcp1b	C	T	6: 119,191,735 (GRCm39)	S217L	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
Dmp1	A	G	5: 104,359,974 (GRCm39)	S217G	probably benign	Het
Eif4enif1	C	T	11: 3,192,586 (GRCm39)	P805S	probably damaging	Het
Eral1	A	G	11: 77,967,104 (GRCm39)	I164T	possibly damaging	Het
Esr1	G	A	10: 4,947,890 (GRCm39)	R481H	probably damaging	Het
Fan1	A	G	7: 64,012,938 (GRCm39)	I668T	probably benign	Het
Gbp11	C	T	5: 105,478,866 (GRCm39)	D191N	probably benign	Het
Gm21759	T	A	5: 8,230,863 (GRCm39)		probably benign	Het
Gm5454	C	A	13: 103,494,031 (GRCm39)		noncoding transcript	Het
Gm9874	A	T	17: 30,704,763 (GRCm39)		probably benign	Het
Gria2	G	A	3: 80,609,799 (GRCm39)	T670I	probably damaging	Het
Gria4	T	A	9: 4,503,614 (GRCm39)	N334I	probably damaging	Het
Grm5	T	C	7: 87,251,930 (GRCm39)	V60A	possibly damaging	Het
Ift172	C	T	5: 31,415,205 (GRCm39)	V1335I	probably benign	Het
Ino80d	C	T	1: 63,100,198 (GRCm39)		probably null	Het
Kif1c	A	G	11: 70,614,907 (GRCm39)	E567G	probably damaging	Het
Krt31	T	G	11: 99,938,699 (GRCm39)	N298T	possibly damaging	Het
Mapk7	C	A	11: 61,381,038 (GRCm39)		probably benign	Het
Marchf8	C	T	6: 116,378,106 (GRCm39)		probably benign	Het
Matr3	T	A	18: 35,705,349 (GRCm39)	S91R	probably benign	Het
Mdm1	A	G	10: 117,986,847 (GRCm39)	T267A	probably benign	Het
Mlxip	A	G	5: 123,590,730 (GRCm39)	M878V	probably benign	Het
Mtm1	T	C	X: 70,339,968 (GRCm39)		probably benign	Homo
Mtor	T	A	4: 148,624,487 (GRCm39)	M2089K	probably benign	Het
Mylk2	A	G	2: 152,761,268 (GRCm39)	K457R	probably damaging	Het
Nell1	A	T	7: 49,899,405 (GRCm39)		probably benign	Het
Nomo1	C	A	7: 45,696,361 (GRCm39)	T293N	probably damaging	Het
Or10g1	T	G	14: 52,648,318 (GRCm39)	T4P	probably benign	Het
Or6c211	A	T	10: 129,505,628 (GRCm39)	C253*	probably null	Het
Or8k33	T	C	2: 86,383,928 (GRCm39)	D180G	possibly damaging	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
Otx1	A	G	11: 21,948,681 (GRCm39)		probably benign	Het
Palmd	T	C	3: 116,717,400 (GRCm39)	R366G	possibly damaging	Het
Pcdhb20	A	T	18: 37,638,833 (GRCm39)	Q453L	possibly damaging	Het
Pcdhga9	T	A	18: 37,870,524 (GRCm39)	Y118N	possibly 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
Plekhg5	T	A	4: 152,191,960 (GRCm39)	C433S	probably benign	Het
Plin2	A	G	4: 86,586,915 (GRCm39)	M1T	probably null	Het
Pold1	C	T	7: 44,192,771 (GRCm39)		silent	Het
Ppp1r7	T	A	1: 93,285,585 (GRCm39)		probably null	Het
Psmb8	T	C	17: 34,419,144 (GRCm39)	I146T	probably damaging	Het
Pzp	A	T	6: 128,462,519 (GRCm39)		probably null	Het
Rel	T	C	11: 23,711,129 (GRCm39)	I13V	probably benign	Het
Reln	C	T	5: 22,254,789 (GRCm39)	V527I	possibly damaging	Het
Retnla	A	G	16: 48,663,975 (GRCm39)	R90G	probably benign	Het
Semp2l2b	A	T	10: 21,943,278 (GRCm39)	I234N	probably benign	Het
Shoc1	A	C	4: 59,093,850 (GRCm39)	L226R	probably damaging	Het
Slc39a8	T	A	3: 135,592,554 (GRCm39)		probably null	Het
Slc5a8	A	G	10: 88,740,825 (GRCm39)	I247V	probably benign	Het
Son	A	G	16: 91,461,205 (GRCm39)		probably null	Het
Spcs2	T	C	7: 99,488,968 (GRCm39)	D240G	probably damaging	Het
Stx3	A	T	19: 11,766,938 (GRCm39)	V91D	probably damaging	Het
Taf6l	A	G	19: 8,755,992 (GRCm39)		probably benign	Het
Tafa2	A	T	10: 123,540,270 (GRCm39)	H42L	possibly damaging	Het
Tbc1d8	A	G	1: 39,444,398 (GRCm39)	F187S	probably damaging	Het
Thbs1	C	G	2: 117,949,859 (GRCm39)	N611K	probably damaging	Het
Tipin	A	C	9: 64,211,609 (GRCm39)	S232R	probably benign	Het
Tmem132b	A	G	5: 125,715,332 (GRCm39)	D347G	probably benign	Het
Tmem161a	C	T	8: 70,631,565 (GRCm39)		probably benign	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
Zzz3	T	A	3: 152,152,481 (GRCm39)		silent	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
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
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

PCR Primer
(F):5'- ATCAGGCTCATGACCAAAGC -3'
(R):5'- GTGAAAAGCTAGGTGCCCTG -3'

Sequencing Primer
(F):5'- TCATGACCAAAGCAACCATATCTTC -3'
(R):5'- AAGCTAGGTGCCCTGTGCTAAG -3'

Posted On

2015-02-18