Incidental Mutation 'R3969:Ybx2'
| ID |
310889 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Ybx2
|
| Ensembl Gene |
ENSMUSG00000018554 |
| Gene Name |
Y box protein 2 |
| Synonyms |
MSY2 |
| MMRRC Submission |
040937-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.860)
|
| Stock # |
R3969 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
11 |
| Chromosomal Location |
69826652-69832430 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
G to A
at 69831242 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Arginine to Glutamine
at position 84
(R84Q)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000136684
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000018698]
[ENSMUST00000018710]
[ENSMUST00000108601]
[ENSMUST00000141837]
[ENSMUST00000149194]
[ENSMUST00000178363]
|
| AlphaFold |
no structure available at present |
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000018698
AA Change: R279Q
PolyPhen 2
Score 0.930 (Sensitivity: 0.81; Specificity: 0.94)
|
| SMART Domains |
Protein: ENSMUSP00000018698
Gene: ENSMUSG00000018554
AA Change: R279Q
| 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 |
possibly damaging
Transcript: ENSMUST00000108601
AA Change: R202Q
PolyPhen 2
Score 0.930 (Sensitivity: 0.81; Specificity: 0.94)
|
| SMART Domains |
Protein: ENSMUSP00000104242
Gene: ENSMUSG00000018554
AA Change: R202Q
| 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: 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 |
noncoding transcript
Transcript: ENSMUST00000148395
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000149194
AA Change: R84Q
PolyPhen 2
Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)
|
| SMART Domains |
Protein: ENSMUSP00000136684
Gene: ENSMUSG00000018554
AA Change: R84Q
| 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: 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 |
0.0829 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.0%
- 20x: 94.1%
|
| Validation Efficiency |
100% (48/48) |
| 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: 40 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Ahi1 |
A |
G |
10: 20,835,846 (GRCm39) |
K60E |
probably damaging |
Het |
| Arhgef12 |
C |
A |
9: 42,916,847 (GRCm39) |
R432L |
probably damaging |
Het |
| Armcx6 |
G |
T |
X: 133,650,505 (GRCm39) |
H109N |
possibly damaging |
Het |
| Camk2d |
G |
T |
3: 126,590,608 (GRCm39) |
C273F |
possibly damaging |
Het |
| Camk4 |
T |
A |
18: 33,312,634 (GRCm39) |
I258N |
possibly damaging |
Het |
| Chia1 |
T |
G |
3: 106,028,951 (GRCm39) |
|
probably null |
Het |
| Commd9 |
C |
A |
2: 101,727,486 (GRCm39) |
N93K |
probably benign |
Het |
| Cpeb4 |
T |
C |
11: 31,822,811 (GRCm39) |
I175T |
possibly damaging |
Het |
| Dnah17 |
G |
A |
11: 117,931,984 (GRCm39) |
|
probably benign |
Het |
| E2f1 |
C |
G |
2: 154,405,942 (GRCm39) |
G144R |
probably damaging |
Het |
| Faap100 |
A |
T |
11: 120,269,531 (GRCm39) |
M1K |
probably null |
Het |
| Flna |
A |
T |
X: 73,279,273 (GRCm39) |
V1253E |
probably damaging |
Het |
| Fryl |
A |
T |
5: 73,269,766 (GRCm39) |
S396R |
probably damaging |
Het |
| Gm12185 |
A |
T |
11: 48,798,172 (GRCm39) |
C774S |
probably benign |
Het |
| Habp2 |
A |
G |
19: 56,300,133 (GRCm39) |
Y194C |
probably damaging |
Het |
| Insyn2b |
A |
T |
11: 34,369,739 (GRCm39) |
Q481L |
probably damaging |
Het |
| Irf5 |
A |
T |
6: 29,536,781 (GRCm39) |
Q497H |
probably benign |
Het |
| Lama3 |
A |
T |
18: 12,713,398 (GRCm39) |
K3230M |
probably damaging |
Het |
| Lins1 |
C |
T |
7: 66,357,946 (GRCm39) |
T27I |
probably benign |
Het |
| Ncstn |
A |
C |
1: 171,897,576 (GRCm39) |
V439G |
probably damaging |
Het |
| Nlrx1 |
A |
T |
9: 44,166,722 (GRCm39) |
|
probably benign |
Het |
| Nol8 |
A |
T |
13: 49,813,492 (GRCm39) |
K162* |
probably null |
Het |
| Or7g21 |
A |
G |
9: 19,032,956 (GRCm39) |
E232G |
probably benign |
Het |
| Or8b54 |
A |
G |
9: 38,686,664 (GRCm39) |
T38A |
probably benign |
Het |
| Pabpc5 |
A |
G |
X: 118,838,321 (GRCm39) |
E212G |
probably benign |
Het |
| Pecr |
G |
A |
1: 72,315,468 (GRCm39) |
T94I |
probably damaging |
Het |
| Piezo2 |
A |
T |
18: 63,144,767 (GRCm39) |
V2776E |
probably damaging |
Het |
| Pik3r2 |
G |
A |
8: 71,223,065 (GRCm39) |
R452C |
probably benign |
Het |
| Pole3 |
G |
T |
4: 62,443,198 (GRCm39) |
N12K |
possibly damaging |
Het |
| Prl2a1 |
A |
G |
13: 27,990,263 (GRCm39) |
S71G |
probably benign |
Het |
| Rab39 |
G |
A |
9: 53,597,932 (GRCm39) |
A111V |
possibly damaging |
Het |
| Rb1cc1 |
T |
A |
1: 6,318,494 (GRCm39) |
|
probably benign |
Het |
| Shroom3 |
T |
C |
5: 93,088,738 (GRCm39) |
V496A |
probably benign |
Het |
| Slc26a1 |
A |
G |
5: 108,821,818 (GRCm39) |
S24P |
probably benign |
Het |
| Tspoap1 |
A |
T |
11: 87,653,272 (GRCm39) |
N113Y |
probably damaging |
Het |
| Usp17lc |
A |
T |
7: 103,067,626 (GRCm39) |
H307L |
probably damaging |
Het |
| Vmn2r79 |
T |
C |
7: 86,652,801 (GRCm39) |
W498R |
probably damaging |
Het |
| Vmn2r94 |
C |
A |
17: 18,478,647 (GRCm39) |
Q33H |
possibly damaging |
Het |
| Wwc2 |
T |
C |
8: 48,309,358 (GRCm39) |
D808G |
unknown |
Het |
| Zfp462 |
C |
T |
4: 55,012,402 (GRCm39) |
S308F |
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 |
|
|
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 |
|
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'- AGCAACAGCCCATAGAGGTG -3'
(R):5'- CTGGAAGTAGGGACGGTTTC -3'
Sequencing Primer
(F):5'- CCGGGGAGGCTAGTTCTCTTAC -3'
(R):5'- AGCCATCAGTGGGGCCTTG -3'
|
| Posted On |
2015-04-29 |
Incidental Mutation