Incidental Mutation 'R0421:Nop56'
| ID |
37037 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Nop56
|
| Ensembl Gene |
ENSMUSG00000027405 |
| Gene Name |
NOP56 ribonucleoprotein |
| Synonyms |
NOP56, 56kDa with KKE/D repeat, Nol5a, 2310044F10Rik |
| MMRRC Submission |
038623-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.964)
|
| Stock # |
R0421 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
2 |
| Chromosomal Location |
130116350-130121233 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 130118692 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Serine to Proline
at position 275
(S275P)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000099487
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000028890]
[ENSMUST00000028892]
[ENSMUST00000103198]
[ENSMUST00000159373]
[ENSMUST00000136621]
[ENSMUST00000184538]
|
| AlphaFold |
Q9D6Z1 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000028890
|
| SMART Domains |
Protein: ENSMUSP00000028890
Gene: ENSMUSG00000027405
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
18 |
N/A |
INTRINSIC |
|
Pfam:Nop
|
44 |
127 |
1.1e-26 |
PFAM |
|
coiled coil region
|
131 |
176 |
N/A |
INTRINSIC |
|
low complexity region
|
185 |
204 |
N/A |
INTRINSIC |
|
low complexity region
|
213 |
228 |
N/A |
INTRINSIC |
|
low complexity region
|
242 |
264 |
N/A |
INTRINSIC |
|
low complexity region
|
280 |
292 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000028892
|
| SMART Domains |
Protein: ENSMUSP00000028892
Gene: ENSMUSG00000027406
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
28 |
40 |
N/A |
INTRINSIC |
|
Iso_dh
|
49 |
375 |
1.43e-140 |
SMART |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000083338
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000083353
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000083355
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000103198
AA Change: S275P
PolyPhen 2
Score 0.956 (Sensitivity: 0.79; Specificity: 0.95)
|
| SMART Domains |
Protein: ENSMUSP00000099487
Gene: ENSMUSG00000027405
AA Change: S275P
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:NOP5NT
|
5 |
70 |
4.3e-20 |
PFAM |
|
NOSIC
|
167 |
219 |
1.18e-30 |
SMART |
|
internal_repeat_1
|
257 |
305 |
4.06e-5 |
PROSPERO |
|
coiled coil region
|
415 |
460 |
N/A |
INTRINSIC |
|
low complexity region
|
469 |
488 |
N/A |
INTRINSIC |
|
low complexity region
|
497 |
512 |
N/A |
INTRINSIC |
|
low complexity region
|
526 |
548 |
N/A |
INTRINSIC |
|
low complexity region
|
564 |
576 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000116960
|
| Predicted Effect |
unknown
Transcript: ENSMUST00000146454
AA Change: S19P
|
| SMART Domains |
Protein: ENSMUSP00000125304
Gene: ENSMUSG00000027405
AA Change: S19P
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Nop
|
1 |
152 |
7.8e-66 |
PFAM |
|
coiled coil region
|
159 |
204 |
N/A |
INTRINSIC |
|
| Predicted Effect |
unknown
Transcript: ENSMUST00000149955
AA Change: S90P
|
| SMART Domains |
Protein: ENSMUSP00000123879
Gene: ENSMUSG00000027405
AA Change: S90P
| Domain | Start | End | E-Value | Type |
|---|
|
NOSIC
|
2 |
35 |
1.24e-6 |
SMART |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000138163
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000160183
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000133351
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000160976
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000145335
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000153353
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000150745
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000159373
|
| SMART Domains |
Protein: ENSMUSP00000124080
Gene: ENSMUSG00000027405
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Nop
|
10 |
94 |
6e-28 |
PFAM |
|
coiled coil region
|
98 |
135 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000141872
|
| SMART Domains |
Protein: ENSMUSP00000125305
Gene: ENSMUSG00000027405
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:NOP5NT
|
14 |
79 |
3.8e-22 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000150401
|
| SMART Domains |
Protein: ENSMUSP00000123890
Gene: ENSMUSG00000027405
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Nop
|
26 |
103 |
3.9e-26 |
PFAM |
|
coiled coil region
|
110 |
155 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000136621
|
| SMART Domains |
Protein: ENSMUSP00000124616
Gene: ENSMUSG00000027405
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:NOP5NT
|
4 |
70 |
3.6e-22 |
PFAM |
|
NOSIC
|
167 |
219 |
1.18e-30 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000143547
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000162063
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000175746
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000161025
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000161543
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000184538
|
| SMART Domains |
Protein: ENSMUSP00000139331
Gene: ENSMUSG00000027406
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Iso_dh
|
6 |
71 |
1.8e-15 |
PFAM |
|
| Meta Mutation Damage Score |
0.3660 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.3%
- 10x: 96.4%
- 20x: 92.7%
|
| Validation Efficiency |
97% (67/69) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] Nop56p is a yeast nucleolar protein that is part of a complex with the nucleolar proteins Nop58p and fibrillarin. Nop56p is required for assembly of the 60S ribosomal subunit and is involved in pre-rRNA processing. The protein encoded by this gene is similar in sequence to Nop56p and is also found in the nucleolus. Expansion of a GGCCTG repeat from 3-8 copies to 1500-2500 copies in an intron of this gene results in spinocerebellar ataxia 36. Multiple transcript variants encoding several different isoforms have been found for this gene, but the full-length nature of most of them has not been determined. [provided by RefSeq, Jul 2016]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 69 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abi1 |
G |
A |
2: 22,850,839 (GRCm39) |
T195I |
probably damaging |
Het |
| Afap1l1 |
T |
C |
18: 61,884,945 (GRCm39) |
N180S |
probably damaging |
Het |
| Arsg |
A |
G |
11: 109,418,592 (GRCm39) |
Y196C |
probably damaging |
Het |
| Ascc3 |
G |
T |
10: 50,625,022 (GRCm39) |
V1637L |
probably benign |
Het |
| Atp2b2 |
C |
A |
6: 113,790,849 (GRCm39) |
R185L |
probably damaging |
Het |
| Ccr9 |
A |
T |
9: 123,608,671 (GRCm39) |
M118L |
probably benign |
Het |
| Cdh12 |
A |
T |
15: 21,480,310 (GRCm39) |
|
probably null |
Het |
| Cdk13 |
T |
C |
13: 17,937,755 (GRCm39) |
S763G |
probably damaging |
Het |
| Cenpk |
C |
A |
13: 104,378,911 (GRCm39) |
N177K |
probably benign |
Het |
| Cfap43 |
T |
G |
19: 47,824,014 (GRCm39) |
N119T |
probably benign |
Het |
| Chrna6 |
T |
C |
8: 27,898,415 (GRCm39) |
E101G |
probably null |
Het |
| Clasp2 |
G |
A |
9: 113,683,370 (GRCm39) |
R400H |
probably benign |
Het |
| Col6a6 |
T |
C |
9: 105,661,405 (GRCm39) |
M235V |
probably benign |
Het |
| Ddx49 |
A |
T |
8: 70,748,282 (GRCm39) |
L291Q |
probably damaging |
Het |
| Dhrs7 |
A |
T |
12: 72,699,860 (GRCm39) |
|
probably benign |
Het |
| Dnah5 |
A |
T |
15: 28,229,687 (GRCm39) |
K107M |
possibly damaging |
Het |
| Dsg2 |
C |
T |
18: 20,712,448 (GRCm39) |
R151C |
probably damaging |
Het |
| Dsn1 |
T |
C |
2: 156,847,789 (GRCm39) |
T2A |
possibly damaging |
Het |
| Edem3 |
A |
G |
1: 151,668,189 (GRCm39) |
|
probably benign |
Het |
| Eif3c |
T |
C |
7: 126,162,884 (GRCm39) |
N133S |
possibly damaging |
Het |
| F10 |
A |
G |
8: 13,095,097 (GRCm39) |
K85E |
probably benign |
Het |
| Fbn2 |
T |
A |
18: 58,160,876 (GRCm39) |
|
probably benign |
Het |
| Gtpbp10 |
A |
T |
5: 5,607,290 (GRCm39) |
H50Q |
probably benign |
Het |
| Hephl1 |
A |
G |
9: 14,970,456 (GRCm39) |
F1013L |
probably benign |
Het |
| Hps3 |
C |
A |
3: 20,083,480 (GRCm39) |
V238F |
probably benign |
Het |
| Kcna10 |
A |
C |
3: 107,101,820 (GRCm39) |
K150N |
probably damaging |
Het |
| Kirrel1 |
C |
T |
3: 86,990,914 (GRCm39) |
G636D |
probably damaging |
Het |
| Kndc1 |
G |
A |
7: 139,488,912 (GRCm39) |
R189H |
probably damaging |
Het |
| Knop1 |
C |
T |
7: 118,454,852 (GRCm39) |
E50K |
possibly damaging |
Het |
| Kplce |
T |
C |
3: 92,776,291 (GRCm39) |
T131A |
probably damaging |
Het |
| Kpna7 |
T |
A |
5: 144,926,551 (GRCm39) |
H467L |
possibly damaging |
Het |
| Lcn4 |
T |
C |
2: 26,558,661 (GRCm39) |
N142D |
possibly damaging |
Het |
| Map3k3 |
T |
C |
11: 106,039,741 (GRCm39) |
|
probably benign |
Het |
| Mdn1 |
A |
G |
4: 32,684,707 (GRCm39) |
T806A |
probably benign |
Het |
| Nbeal1 |
T |
A |
1: 60,307,598 (GRCm39) |
N1703K |
probably benign |
Het |
| Neurl4 |
T |
C |
11: 69,799,360 (GRCm39) |
V914A |
probably damaging |
Het |
| Niban1 |
T |
A |
1: 151,584,833 (GRCm39) |
|
probably benign |
Het |
| Or1j20 |
A |
G |
2: 36,759,653 (GRCm39) |
E25G |
possibly damaging |
Het |
| Or52ac1 |
A |
G |
7: 104,245,929 (GRCm39) |
V153A |
probably benign |
Het |
| Or7e174 |
A |
G |
9: 20,012,771 (GRCm39) |
K239E |
probably damaging |
Het |
| Otof |
A |
C |
5: 30,528,912 (GRCm39) |
I1827S |
possibly damaging |
Het |
| Pappa2 |
A |
T |
1: 158,675,650 (GRCm39) |
I1032N |
probably damaging |
Het |
| Pcdh7 |
A |
G |
5: 57,877,402 (GRCm39) |
E319G |
probably damaging |
Het |
| Pcdhb11 |
T |
A |
18: 37,555,533 (GRCm39) |
S288T |
probably benign |
Het |
| Phip |
A |
T |
9: 82,808,510 (GRCm39) |
D488E |
probably damaging |
Het |
| Pla2g7 |
A |
T |
17: 43,922,303 (GRCm39) |
H394L |
probably damaging |
Het |
| Plk3 |
A |
G |
4: 116,990,641 (GRCm39) |
V69A |
probably damaging |
Het |
| Prob1 |
C |
A |
18: 35,786,083 (GRCm39) |
A724S |
possibly damaging |
Het |
| Prune2 |
T |
C |
19: 17,100,675 (GRCm39) |
F2060L |
probably benign |
Het |
| Rgl3 |
G |
A |
9: 21,887,328 (GRCm39) |
R498C |
probably benign |
Het |
| Rnf213 |
A |
C |
11: 119,338,083 (GRCm39) |
N3362H |
probably damaging |
Het |
| Sbds |
A |
G |
5: 130,282,774 (GRCm39) |
|
probably benign |
Het |
| Scn9a |
T |
C |
2: 66,373,621 (GRCm39) |
S453G |
probably benign |
Het |
| Sh3rf3 |
T |
C |
10: 58,819,897 (GRCm39) |
L236P |
probably damaging |
Het |
| Skint1 |
A |
G |
4: 111,876,211 (GRCm39) |
N44S |
possibly damaging |
Het |
| Slc5a1 |
T |
A |
5: 33,291,996 (GRCm39) |
I141N |
probably damaging |
Het |
| Tlcd3b |
G |
A |
7: 126,424,187 (GRCm39) |
V44M |
probably damaging |
Het |
| Trank1 |
T |
A |
9: 111,220,907 (GRCm39) |
I2548N |
probably damaging |
Het |
| Tsc22d2 |
G |
A |
3: 58,324,749 (GRCm39) |
|
probably benign |
Het |
| Unc13c |
T |
A |
9: 73,840,492 (GRCm39) |
I120F |
possibly damaging |
Het |
| Vmn2r11 |
T |
G |
5: 109,207,294 (GRCm39) |
I9L |
probably benign |
Het |
| Vmn2r58 |
T |
G |
7: 41,514,628 (GRCm39) |
N114H |
probably benign |
Het |
| Vps53 |
A |
G |
11: 75,973,496 (GRCm39) |
L166P |
probably damaging |
Het |
| Zfp119a |
T |
A |
17: 56,172,248 (GRCm39) |
K532* |
probably null |
Het |
| Zfp472 |
A |
G |
17: 33,194,897 (GRCm39) |
T11A |
possibly damaging |
Het |
| Zfp512b |
T |
A |
2: 181,230,051 (GRCm39) |
K87* |
probably null |
Het |
| Zfp518b |
G |
A |
5: 38,831,918 (GRCm39) |
P29L |
probably damaging |
Het |
| Zfp599 |
A |
G |
9: 22,161,843 (GRCm39) |
|
probably benign |
Het |
| Zic2 |
CCCACCACCACCATCACCACCACCACC |
CCCACCATCACCACCACCACC |
14: 122,713,776 (GRCm39) |
|
probably benign |
Het |
|
| Other mutations in Nop56 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00834:Nop56
|
APN |
2 |
130,117,915 (GRCm39) |
missense |
possibly damaging |
0.77 |
|
IGL02330:Nop56
|
APN |
2 |
130,118,686 (GRCm39) |
missense |
probably damaging |
0.99 |
|
IGL02939:Nop56
|
APN |
2 |
130,120,117 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL03149:Nop56
|
APN |
2 |
130,119,445 (GRCm39) |
missense |
probably damaging |
1.00 |
|
bookish
|
UTSW |
2 |
130,118,692 (GRCm39) |
missense |
possibly damaging |
0.96 |
|
escholar
|
UTSW |
2 |
130,119,807 (GRCm39) |
missense |
probably damaging |
1.00 |
|
messy
|
UTSW |
2 |
130,117,902 (GRCm39) |
missense |
probably damaging |
1.00 |
|
scholar
|
UTSW |
2 |
130,117,902 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL03046:Nop56
|
UTSW |
2 |
130,117,489 (GRCm39) |
unclassified |
probably benign |
|
|
R1405:Nop56
|
UTSW |
2 |
130,119,868 (GRCm39) |
missense |
probably benign |
0.22 |
|
R1405:Nop56
|
UTSW |
2 |
130,119,868 (GRCm39) |
missense |
probably benign |
0.22 |
|
R1713:Nop56
|
UTSW |
2 |
130,119,886 (GRCm39) |
missense |
possibly damaging |
0.85 |
|
R2202:Nop56
|
UTSW |
2 |
130,119,488 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2203:Nop56
|
UTSW |
2 |
130,119,488 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2204:Nop56
|
UTSW |
2 |
130,119,488 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R3697:Nop56
|
UTSW |
2 |
130,119,507 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4114:Nop56
|
UTSW |
2 |
130,118,593 (GRCm39) |
splice site |
probably null |
|
|
R4679:Nop56
|
UTSW |
2 |
130,120,193 (GRCm39) |
missense |
probably benign |
0.36 |
|
R4788:Nop56
|
UTSW |
2 |
130,120,820 (GRCm39) |
missense |
probably benign |
0.05 |
|
R4792:Nop56
|
UTSW |
2 |
130,119,784 (GRCm39) |
missense |
possibly damaging |
0.96 |
|
R4999:Nop56
|
UTSW |
2 |
130,117,645 (GRCm39) |
missense |
probably benign |
0.00 |
|
R5889:Nop56
|
UTSW |
2 |
130,117,902 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6016:Nop56
|
UTSW |
2 |
130,118,545 (GRCm39) |
critical splice donor site |
probably null |
|
|
R6389:Nop56
|
UTSW |
2 |
130,119,807 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7025:Nop56
|
UTSW |
2 |
130,119,801 (GRCm39) |
nonsense |
probably null |
|
|
R7393:Nop56
|
UTSW |
2 |
130,116,558 (GRCm39) |
missense |
probably benign |
0.06 |
|
R7867:Nop56
|
UTSW |
2 |
130,120,205 (GRCm39) |
missense |
possibly damaging |
0.53 |
|
R8026:Nop56
|
UTSW |
2 |
130,119,188 (GRCm39) |
missense |
probably benign |
|
|
R8886:Nop56
|
UTSW |
2 |
130,117,902 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9450:Nop56
|
UTSW |
2 |
130,117,601 (GRCm39) |
missense |
probably damaging |
1.00 |
|
| Predicted Primers |
PCR Primer
(F):5'- AAGGCCATCTTGGATGCTTCTCG -3'
(R):5'- CTGTACTGTGGACGCTGGATACTTG -3'
Sequencing Primer
(F):5'- GGATGCTTCTCGGTCCTC -3'
(R):5'- GTAAGTGGGAACCTGACCTC -3'
|
| Posted On |
2013-05-09 |
Incidental Mutation