Incidental Mutation 'R6389:Nop56'
| ID |
515673 |
| 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 |
044538-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.964)
|
| Stock # |
R6389 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
2 |
| Chromosomal Location |
130116350-130121233 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
C to A
at 130119807 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Glutamine to Lysine
at position 83
(Q83K)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000124080
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000028890]
[ENSMUST00000028892]
[ENSMUST00000103198]
[ENSMUST00000159373]
[ENSMUST00000136621]
[ENSMUST00000184538]
|
| AlphaFold |
Q9D6Z1 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000028890
AA Change: Q116K
PolyPhen 2
Score 0.292 (Sensitivity: 0.91; Specificity: 0.89)
|
| SMART Domains |
Protein: ENSMUSP00000028890
Gene: ENSMUSG00000027405
AA Change: Q116K
| 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 |
probably benign
Transcript: ENSMUST00000103198
AA Change: Q400K
PolyPhen 2
Score 0.168 (Sensitivity: 0.92; Specificity: 0.87)
|
| SMART Domains |
Protein: ENSMUSP00000099487
Gene: ENSMUSG00000027405
AA Change: Q400K
| 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 |
probably damaging
Transcript: ENSMUST00000159373
AA Change: Q83K
PolyPhen 2
Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)
|
| SMART Domains |
Protein: ENSMUSP00000124080
Gene: ENSMUSG00000027405
AA Change: Q83K
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Nop
|
10 |
94 |
6e-28 |
PFAM |
|
coiled coil region
|
98 |
135 |
N/A |
INTRINSIC |
|
| Predicted Effect |
unknown
Transcript: ENSMUST00000150401
AA Change: Q95K
|
| SMART Domains |
Protein: ENSMUSP00000123890
Gene: ENSMUSG00000027405
AA Change: Q95K
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Nop
|
26 |
103 |
3.9e-26 |
PFAM |
|
coiled coil region
|
110 |
155 |
N/A |
INTRINSIC |
|
| Predicted Effect |
unknown
Transcript: ENSMUST00000146454
AA Change: Q144K
|
| SMART Domains |
Protein: ENSMUSP00000125304
Gene: ENSMUSG00000027405
AA Change: Q144K
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Nop
|
1 |
152 |
7.8e-66 |
PFAM |
|
coiled coil region
|
159 |
204 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000145335
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000150745
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000133351
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000153353
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000149843
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000143547
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000138163
|
| 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 |
noncoding transcript
Transcript: ENSMUST00000160183
|
| 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: ENSMUST00000149955
|
| SMART Domains |
Protein: ENSMUSP00000123879
Gene: ENSMUSG00000027405
| Domain | Start | End | E-Value | Type |
|---|
|
NOSIC
|
2 |
35 |
1.24e-6 |
SMART |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000161543
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000161025
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000175746
|
| 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 |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000162063
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000160976
|
| Meta Mutation Damage Score |
0.4773 |
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 99.9%
- 10x: 99.2%
- 20x: 96.9%
|
| Validation Efficiency |
100% (57/57) |
| 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: 57 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 4931406B18Rik |
A |
C |
7: 43,147,254 (GRCm39) |
L326R |
possibly damaging |
Het |
| Abcb11 |
A |
T |
2: 69,154,238 (GRCm39) |
N109K |
probably damaging |
Het |
| Actn1 |
T |
A |
12: 80,221,296 (GRCm39) |
M586L |
probably benign |
Het |
| Ago4 |
T |
A |
4: 126,401,037 (GRCm39) |
I603F |
probably damaging |
Het |
| Bicc1 |
A |
T |
10: 70,794,752 (GRCm39) |
V135D |
probably damaging |
Het |
| Bms1 |
T |
C |
6: 118,380,196 (GRCm39) |
N704D |
possibly damaging |
Het |
| Cadm4 |
A |
C |
7: 24,198,959 (GRCm39) |
Q78P |
probably benign |
Het |
| Cfap74 |
T |
C |
4: 155,507,793 (GRCm39) |
I248T |
possibly damaging |
Het |
| Clu |
G |
C |
14: 66,208,771 (GRCm39) |
|
probably benign |
Het |
| Cnnm3 |
T |
C |
1: 36,559,603 (GRCm39) |
V514A |
probably damaging |
Het |
| Cntd1 |
A |
T |
11: 101,176,577 (GRCm39) |
I225F |
probably damaging |
Het |
| Col20a1 |
T |
C |
2: 180,634,376 (GRCm39) |
|
probably null |
Het |
| Ctnnal1 |
A |
G |
4: 56,813,849 (GRCm39) |
V640A |
probably benign |
Het |
| Cul4a |
A |
G |
8: 13,190,278 (GRCm39) |
T572A |
probably benign |
Het |
| D16Ertd472e |
A |
G |
16: 78,342,071 (GRCm39) |
S270P |
probably damaging |
Het |
| Dmp1 |
A |
T |
5: 104,360,788 (GRCm39) |
N488I |
probably damaging |
Het |
| Dnah14 |
G |
A |
1: 181,478,767 (GRCm39) |
|
probably null |
Het |
| Dst |
T |
C |
1: 34,232,265 (GRCm39) |
L3464P |
probably damaging |
Het |
| Fnbp4 |
C |
T |
2: 90,575,879 (GRCm39) |
P27S |
unknown |
Het |
| Fpr-rs3 |
A |
T |
17: 20,844,230 (GRCm39) |
F304I |
probably damaging |
Het |
| Gm13941 |
T |
C |
2: 110,928,734 (GRCm39) |
Q108R |
unknown |
Het |
| Hcn3 |
C |
T |
3: 89,058,240 (GRCm39) |
A339T |
possibly damaging |
Het |
| Inpp5f |
A |
G |
7: 128,279,780 (GRCm39) |
D460G |
probably damaging |
Het |
| Ism2 |
T |
C |
12: 87,329,145 (GRCm39) |
E253G |
possibly damaging |
Het |
| Klrg1 |
T |
C |
6: 122,248,431 (GRCm39) |
N156S |
probably damaging |
Het |
| Ksr2 |
A |
G |
5: 117,552,907 (GRCm39) |
N5S |
probably benign |
Het |
| Lrrc7 |
T |
G |
3: 157,891,063 (GRCm39) |
E368A |
probably damaging |
Het |
| Ly9 |
G |
C |
1: 171,424,105 (GRCm39) |
S482C |
probably damaging |
Het |
| Map3k1 |
T |
C |
13: 111,905,975 (GRCm39) |
D289G |
probably damaging |
Het |
| Mcub |
T |
C |
3: 129,712,357 (GRCm39) |
T173A |
probably benign |
Het |
| Mup16 |
T |
C |
4: 61,437,177 (GRCm39) |
E48G |
probably damaging |
Het |
| Naf1 |
C |
T |
8: 67,313,680 (GRCm39) |
S24L |
possibly damaging |
Het |
| Ncoa6 |
A |
G |
2: 155,237,736 (GRCm39) |
S2024P |
probably damaging |
Het |
| Nt5e |
T |
C |
9: 88,245,524 (GRCm39) |
Y265H |
probably damaging |
Het |
| Odad1 |
G |
T |
7: 45,597,940 (GRCm39) |
V617F |
probably benign |
Het |
| Or4a27 |
A |
G |
2: 88,559,016 (GRCm39) |
V309A |
probably benign |
Het |
| Or52p2 |
A |
T |
7: 102,237,679 (GRCm39) |
N90K |
probably benign |
Het |
| Or5w8 |
C |
T |
2: 87,688,367 (GRCm39) |
P283S |
probably damaging |
Het |
| Oxct2a |
T |
A |
4: 123,217,220 (GRCm39) |
K54* |
probably null |
Het |
| Oxct2b |
G |
T |
4: 123,010,367 (GRCm39) |
D96Y |
probably benign |
Het |
| Pisd |
A |
G |
5: 32,922,191 (GRCm39) |
Y250H |
probably damaging |
Het |
| Plekhm1 |
G |
T |
11: 103,257,720 (GRCm39) |
N1071K |
probably benign |
Het |
| Prr11 |
G |
A |
11: 86,989,564 (GRCm39) |
T269I |
possibly damaging |
Het |
| Ptpn4 |
T |
A |
1: 119,649,684 (GRCm39) |
H304L |
probably damaging |
Het |
| Rrp1b |
A |
G |
17: 32,275,601 (GRCm39) |
K383E |
possibly damaging |
Het |
| Sel1l2 |
C |
A |
2: 140,087,274 (GRCm39) |
A466S |
probably damaging |
Het |
| Slc9a4 |
A |
G |
1: 40,619,844 (GRCm39) |
I57V |
probably benign |
Het |
| Spag9 |
A |
G |
11: 93,977,137 (GRCm39) |
E81G |
probably damaging |
Het |
| Tbr1 |
A |
G |
2: 61,636,631 (GRCm39) |
|
probably benign |
Het |
| Tnrc6c |
A |
G |
11: 117,613,567 (GRCm39) |
D735G |
probably damaging |
Het |
| Tspan17 |
A |
T |
13: 54,943,429 (GRCm39) |
|
probably null |
Het |
| Tyw5 |
T |
C |
1: 57,430,658 (GRCm39) |
K175R |
probably damaging |
Het |
| Ube2o |
A |
C |
11: 116,439,684 (GRCm39) |
I162R |
probably null |
Het |
| Ubr1 |
G |
T |
2: 120,711,520 (GRCm39) |
T1458K |
probably benign |
Het |
| Vmn2r16 |
A |
T |
5: 109,478,344 (GRCm39) |
Q33L |
probably benign |
Het |
| Zfp1007 |
G |
A |
5: 109,823,885 (GRCm39) |
P522S |
possibly damaging |
Het |
| Zfp799 |
A |
G |
17: 33,039,552 (GRCm39) |
L238P |
probably damaging |
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 |
|
|
R0421:Nop56
|
UTSW |
2 |
130,118,692 (GRCm39) |
missense |
possibly damaging |
0.96 |
|
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 |
|
|
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'- CTTGGCAGCTTCTACAATGATG -3'
(R):5'- AGTCTTGCTGGATCAGGCTC -3'
Sequencing Primer
(F):5'- GGTAATATTTTTCGTCAACAGAGTTC -3'
(R):5'- GCTGGATCAGGCTCATTAAATCAG -3'
|
| Posted On |
2018-05-04 |
Incidental Mutation