Incidental Mutation 'R9450:Nop56'
ID |
714173 |
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 |
|
Accession Numbers |
|
Essential gene? |
Probably essential
(E-score: 0.964)
|
Stock # |
R9450 (G1)
|
Quality Score |
225.009 |
Status
|
Not validated
|
Chromosome |
2 |
Chromosomal Location |
130116350-130121233 bp(+) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
T to C
at 130117601 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Leucine to Proline
at position 76
(L76P)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000099487
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000028890]
[ENSMUST00000028892]
[ENSMUST00000103198]
[ENSMUST00000136621]
[ENSMUST00000159373]
[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 |
probably damaging
Transcript: ENSMUST00000103198
AA Change: L76P
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000099487 Gene: ENSMUSG00000027405 AA Change: L76P
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 |
probably damaging
Transcript: ENSMUST00000136621
AA Change: L76P
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000124616 Gene: ENSMUSG00000027405 AA Change: L76P
Domain | Start | End | E-Value | Type |
Pfam:NOP5NT
|
4 |
70 |
3.6e-22 |
PFAM |
NOSIC
|
167 |
219 |
1.18e-30 |
SMART |
|
Predicted Effect |
|
SMART Domains |
Protein: ENSMUSP00000125305 Gene: ENSMUSG00000027405 AA Change: L84P
Domain | Start | End | E-Value | Type |
Pfam:NOP5NT
|
14 |
79 |
3.8e-22 |
PFAM |
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000143547
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000146454
|
SMART Domains |
Protein: ENSMUSP00000125304 Gene: ENSMUSG00000027405
Domain | Start | End | E-Value | Type |
Pfam:Nop
|
1 |
152 |
7.8e-66 |
PFAM |
coiled coil region
|
159 |
204 |
N/A |
INTRINSIC |
|
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 |
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: 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: ENSMUST00000184538
|
SMART Domains |
Protein: ENSMUSP00000139331 Gene: ENSMUSG00000027406
Domain | Start | End | E-Value | Type |
Pfam:Iso_dh
|
6 |
71 |
1.8e-15 |
PFAM |
|
Coding Region Coverage |
- 1x: 100.0%
- 3x: 99.9%
- 10x: 99.7%
- 20x: 98.9%
|
Validation Efficiency |
|
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: 61 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
2200002D01Rik |
CCTTCTCCTTCTTCTCCTTCTTCTCCTTCTTCTCCATCTTCTCCTTCTTC |
CCTTCTCCTTCTTCTCCTTCTTCTCCATCTTCTCCTTCTTC |
7: 28,947,048 (GRCm39) |
|
probably benign |
Het |
2810004N23Rik |
T |
C |
8: 125,567,215 (GRCm39) |
K229E |
probably damaging |
Het |
Abca8b |
T |
C |
11: 109,859,930 (GRCm39) |
T523A |
probably damaging |
Het |
Adamts18 |
G |
T |
8: 114,490,942 (GRCm39) |
D508E |
probably benign |
Het |
Arap2 |
T |
C |
5: 62,855,762 (GRCm39) |
E558G |
probably benign |
Het |
Arid4a |
A |
T |
12: 71,119,374 (GRCm39) |
D331V |
|
Het |
Ash1l |
A |
T |
3: 88,915,139 (GRCm39) |
K1923M |
possibly damaging |
Het |
Atad2b |
T |
A |
12: 5,063,859 (GRCm39) |
S947T |
probably benign |
Het |
B4galt1 |
A |
T |
4: 40,853,804 (GRCm39) |
M1K |
probably null |
Het |
Ccpg1 |
G |
A |
9: 72,904,703 (GRCm39) |
S4N |
unknown |
Het |
Cfap43 |
A |
T |
19: 47,886,310 (GRCm39) |
L102M |
probably benign |
Het |
Clic6 |
T |
C |
16: 92,327,644 (GRCm39) |
I483T |
possibly damaging |
Het |
Col6a6 |
A |
T |
9: 105,661,373 (GRCm39) |
D245E |
probably benign |
Het |
Cpsf7 |
G |
A |
19: 10,518,213 (GRCm39) |
|
probably null |
Het |
Depdc5 |
A |
G |
5: 33,091,354 (GRCm39) |
D721G |
probably benign |
Het |
Dhx29 |
C |
T |
13: 113,083,862 (GRCm39) |
T639I |
possibly damaging |
Het |
Dock7 |
T |
C |
4: 98,861,426 (GRCm39) |
E1397G |
unknown |
Het |
Dsp |
C |
T |
13: 38,376,379 (GRCm39) |
T1388M |
probably damaging |
Het |
Fam186b |
C |
T |
15: 99,183,425 (GRCm39) |
G73D |
probably damaging |
Het |
Ganab |
A |
G |
19: 8,893,076 (GRCm39) |
D960G |
probably damaging |
Het |
Gria1 |
T |
C |
11: 57,200,615 (GRCm39) |
V764A |
probably damaging |
Het |
Grk3 |
T |
C |
5: 113,062,913 (GRCm39) |
K645E |
probably benign |
Het |
Hecw2 |
A |
T |
1: 53,878,188 (GRCm39) |
Y1339* |
probably null |
Het |
Hmcn2 |
C |
A |
2: 31,316,845 (GRCm39) |
T3808N |
probably damaging |
Het |
Il20rb |
A |
T |
9: 100,355,055 (GRCm39) |
N129K |
possibly damaging |
Het |
Iqca1l |
T |
A |
5: 24,754,447 (GRCm39) |
I395F |
probably benign |
Het |
Itgb4 |
T |
C |
11: 115,874,097 (GRCm39) |
Y340H |
probably damaging |
Het |
Itgb6 |
T |
C |
2: 60,458,372 (GRCm39) |
I460M |
probably benign |
Het |
Kat14 |
T |
C |
2: 144,242,739 (GRCm39) |
I599T |
possibly damaging |
Het |
Kif1b |
A |
C |
4: 149,322,467 (GRCm39) |
D817E |
probably benign |
Het |
Lamb2 |
T |
A |
9: 108,357,760 (GRCm39) |
C94* |
probably null |
Het |
Larp1 |
T |
C |
11: 57,941,890 (GRCm39) |
S743P |
probably damaging |
Het |
Ldlrap1 |
T |
C |
4: 134,474,490 (GRCm39) |
N267S |
probably damaging |
Het |
Ltbp2 |
G |
A |
12: 84,837,864 (GRCm39) |
P1192L |
probably benign |
Het |
Ltf |
T |
C |
9: 110,851,064 (GRCm39) |
L92P |
probably damaging |
Het |
Ly6g2 |
T |
A |
15: 75,092,574 (GRCm39) |
C98S |
probably damaging |
Het |
Mns1 |
C |
A |
9: 72,359,890 (GRCm39) |
Q347K |
probably benign |
Het |
Myof |
A |
T |
19: 37,949,374 (GRCm39) |
F611I |
probably damaging |
Het |
Nphp1 |
T |
C |
2: 127,616,008 (GRCm39) |
H114R |
|
Het |
Or10g3 |
G |
C |
14: 52,610,110 (GRCm39) |
Y133* |
probably null |
Het |
Or1e30 |
C |
A |
11: 73,678,101 (GRCm39) |
N112K |
possibly damaging |
Het |
Or4k36 |
T |
A |
2: 111,146,398 (GRCm39) |
N191K |
probably benign |
Het |
Pcdha12 |
A |
G |
18: 37,153,992 (GRCm39) |
D237G |
probably damaging |
Het |
Pierce1 |
TCTCTGGGGCAGGCTTAGCCTTGGGCTCCCCCGGCTCCGGCTCCTCTGGGGCAGGCTTAGCCTTGGGCTCCCCCGGCTCCGGCTCCTCTGGGGCGGGCTTAGCCTTGGGCTCCCCCGGCTCCGGCTCCTC |
TCTCTGGGGCAGGCTTAGCCTTGGGCTCCCCCGGCTCCGGCTCCTCTGGGGCGGGCTTAGCCTTGGGCTCCCCCGGCTCCGGCTCCTC |
2: 28,356,122 (GRCm39) |
|
probably benign |
Het |
Pitpnm3 |
A |
T |
11: 71,952,412 (GRCm39) |
M593K |
possibly damaging |
Het |
Plxdc1 |
C |
T |
11: 97,845,681 (GRCm39) |
V211I |
probably damaging |
Het |
Prkn |
C |
A |
17: 12,057,521 (GRCm39) |
H301N |
possibly damaging |
Het |
Prpf38a |
A |
T |
4: 108,430,072 (GRCm39) |
H143Q |
probably damaging |
Het |
Sdk2 |
T |
C |
11: 113,697,105 (GRCm39) |
T1769A |
probably benign |
Het |
Spata31f1e |
G |
T |
4: 42,793,833 (GRCm39) |
Q100K |
probably benign |
Het |
Stab1 |
T |
C |
14: 30,884,896 (GRCm39) |
D153G |
possibly damaging |
Het |
Tm7sf3 |
C |
T |
6: 146,525,179 (GRCm39) |
D89N |
possibly damaging |
Het |
Tnrc6b |
T |
A |
15: 80,764,637 (GRCm39) |
M713K |
probably benign |
Het |
Top2a |
T |
C |
11: 98,894,434 (GRCm39) |
K966E |
possibly damaging |
Het |
Vars2 |
T |
C |
17: 35,973,027 (GRCm39) |
T421A |
probably damaging |
Het |
Vmn1r1 |
A |
T |
1: 181,984,770 (GRCm39) |
C298* |
probably null |
Het |
Vps35l |
T |
C |
7: 118,352,118 (GRCm39) |
|
probably null |
Het |
Vwa3a |
T |
C |
7: 120,403,253 (GRCm39) |
|
probably null |
Het |
Vwa5b1 |
G |
T |
4: 138,315,940 (GRCm39) |
Q601K |
possibly damaging |
Het |
Zbtb46 |
T |
C |
2: 181,037,281 (GRCm39) |
K454E |
probably damaging |
Het |
Zfp426 |
T |
C |
9: 20,381,577 (GRCm39) |
H470R |
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 |
|
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 |
|
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 |
|
Predicted Primers |
PCR Primer
(F):5'- GCCAGGCTTTGCAATGATGAC -3'
(R):5'- TGGAAATGCAGACGAACTCC -3'
Sequencing Primer
(F):5'- ACTTATATATCTGTCAATCCCCTGAG -3'
(R):5'- GGGACTTTAAGAATAGATCCTCCAG -3'
|
Posted On |
2022-06-15 |