Incidental Mutation 'IGL02939:Nop56'
| ID |
365955 |
| Institutional Source |
Australian Phenomics Network
(link to record)
|
| Gene Symbol |
Nop56
|
| Ensembl Gene |
ENSMUSG00000027405 |
| Gene Name |
NOP56 ribonucleoprotein |
| Synonyms |
NOP56, 56kDa with KKE/D repeat, Nol5a, 2310044F10Rik |
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.964)
|
| Stock # |
IGL02939
|
| Quality Score |
|
|
Status
|
|
| Chromosome |
2 |
| Chromosomal Location |
130116350-130121233 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to T
at 130120117 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Lysine to Asparagine
at position 157
(K157N)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000028890
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000028890]
[ENSMUST00000028892]
[ENSMUST00000103198]
[ENSMUST00000159373]
[ENSMUST00000136621]
[ENSMUST00000184538]
|
| AlphaFold |
Q9D6Z1 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000028890
AA Change: K157N
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000028890
Gene: ENSMUSG00000027405
AA Change: K157N
| 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: K441N
PolyPhen 2
Score 0.719 (Sensitivity: 0.86; Specificity: 0.92)
|
| SMART Domains |
Protein: ENSMUSP00000099487
Gene: ENSMUSG00000027405
AA Change: K441N
| 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: ENSMUST00000159373
AA Change: K124N
|
| SMART Domains |
Protein: ENSMUSP00000124080
Gene: ENSMUSG00000027405
AA Change: K124N
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Nop
|
10 |
94 |
6e-28 |
PFAM |
|
coiled coil region
|
98 |
135 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000153353
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000133351
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000150745
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000145335
|
| Predicted Effect |
unknown
Transcript: ENSMUST00000146454
AA Change: K185N
|
| SMART Domains |
Protein: ENSMUSP00000125304
Gene: ENSMUSG00000027405
AA Change: K185N
| 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: ENSMUST00000150401
AA Change: K136N
|
| SMART Domains |
Protein: ENSMUSP00000123890
Gene: ENSMUSG00000027405
AA Change: K136N
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Nop
|
26 |
103 |
3.9e-26 |
PFAM |
|
coiled coil region
|
110 |
155 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000138163
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000160183
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000149843
|
| 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 |
probably benign
Transcript: ENSMUST00000143547
|
| 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: ENSMUST00000161543
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000160976
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000161025
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000162063
|
| 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 |
|
| Coding Region Coverage |
|
| 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: 52 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Atp6ap1 |
A |
G |
X: 73,340,924 (GRCm39) |
D47G |
probably benign |
Het |
| Atr |
T |
C |
9: 95,747,314 (GRCm39) |
F199L |
probably benign |
Het |
| Bivm |
C |
A |
1: 44,182,120 (GRCm39) |
H443N |
probably benign |
Het |
| Btnl2 |
A |
T |
17: 34,580,043 (GRCm39) |
H192L |
probably benign |
Het |
| Ccdc178 |
A |
T |
18: 22,253,775 (GRCm39) |
C155S |
probably benign |
Het |
| Celsr1 |
C |
A |
15: 85,785,673 (GRCm39) |
V2934L |
probably benign |
Het |
| Celsr3 |
T |
C |
9: 108,726,652 (GRCm39) |
S3294P |
probably damaging |
Het |
| Ddx10 |
T |
A |
9: 53,115,579 (GRCm39) |
E585V |
possibly damaging |
Het |
| Elapor2 |
T |
C |
5: 9,511,478 (GRCm39) |
Y947H |
probably damaging |
Het |
| Eps15l1 |
A |
T |
8: 73,138,606 (GRCm39) |
|
probably benign |
Het |
| Erlin1 |
G |
T |
19: 44,051,491 (GRCm39) |
T70K |
probably damaging |
Het |
| Ext2 |
A |
T |
2: 93,534,964 (GRCm39) |
|
probably null |
Het |
| Fam124a |
G |
A |
14: 62,793,368 (GRCm39) |
|
probably null |
Het |
| Fam53a |
T |
C |
5: 33,765,103 (GRCm39) |
D201G |
probably damaging |
Het |
| Fgf14 |
C |
T |
14: 124,369,891 (GRCm39) |
G136D |
possibly damaging |
Het |
| Gdi2 |
A |
T |
13: 3,614,623 (GRCm39) |
T323S |
probably benign |
Het |
| Gemin5 |
A |
T |
11: 58,047,556 (GRCm39) |
N339K |
probably damaging |
Het |
| Golga4 |
A |
G |
9: 118,364,522 (GRCm39) |
E286G |
probably benign |
Het |
| Golga4 |
A |
C |
9: 118,363,700 (GRCm39) |
K233T |
probably damaging |
Het |
| Gosr1 |
A |
G |
11: 76,641,732 (GRCm39) |
|
probably benign |
Het |
| Haus8 |
A |
G |
8: 71,708,361 (GRCm39) |
|
probably benign |
Het |
| Itgb3bp |
T |
C |
4: 99,690,373 (GRCm39) |
T49A |
probably null |
Het |
| Ldlrad4 |
A |
G |
18: 68,387,585 (GRCm39) |
D299G |
probably damaging |
Het |
| Lpo |
A |
G |
11: 87,706,004 (GRCm39) |
M273T |
possibly damaging |
Het |
| Map3k4 |
T |
A |
17: 12,491,036 (GRCm39) |
S132C |
probably damaging |
Het |
| Mycbp2 |
T |
G |
14: 103,414,715 (GRCm39) |
T2566P |
probably benign |
Het |
| Nalcn |
T |
C |
14: 123,536,284 (GRCm39) |
E1255G |
probably null |
Het |
| Or10g9 |
C |
T |
9: 39,912,194 (GRCm39) |
E110K |
probably benign |
Het |
| Or6c1 |
A |
T |
10: 129,517,857 (GRCm39) |
Y250* |
probably null |
Het |
| Pcdh15 |
A |
G |
10: 74,340,648 (GRCm39) |
|
probably benign |
Het |
| Pi4ka |
T |
C |
16: 17,172,074 (GRCm39) |
H557R |
probably damaging |
Het |
| Plekha4 |
C |
T |
7: 45,181,787 (GRCm39) |
Q64* |
probably null |
Het |
| Ppp2r3c |
G |
A |
12: 55,345,192 (GRCm39) |
|
probably benign |
Het |
| Rgmb |
C |
T |
17: 16,027,755 (GRCm39) |
M321I |
probably benign |
Het |
| Rnf31 |
T |
C |
14: 55,833,131 (GRCm39) |
S363P |
probably benign |
Het |
| Sap18b |
T |
A |
8: 96,552,329 (GRCm39) |
M113K |
probably benign |
Het |
| Scara3 |
T |
A |
14: 66,169,105 (GRCm39) |
M171L |
probably benign |
Het |
| Slc9a2 |
T |
G |
1: 40,781,863 (GRCm39) |
M364R |
probably damaging |
Het |
| Sorcs1 |
C |
T |
19: 50,666,368 (GRCm39) |
W180* |
probably null |
Het |
| Stat6 |
T |
A |
10: 127,482,809 (GRCm39) |
M10K |
probably benign |
Het |
| Sun1 |
T |
C |
5: 139,221,243 (GRCm39) |
|
probably benign |
Het |
| Tead2 |
T |
C |
7: 44,869,858 (GRCm39) |
|
probably benign |
Het |
| Tjp1 |
T |
G |
7: 64,964,638 (GRCm39) |
E844D |
probably damaging |
Het |
| Tmtc2 |
A |
G |
10: 105,206,411 (GRCm39) |
S295P |
probably damaging |
Het |
| Ttn |
G |
A |
2: 76,612,756 (GRCm39) |
R17108C |
probably damaging |
Het |
| Ubr1 |
T |
C |
2: 120,711,664 (GRCm39) |
|
probably null |
Het |
| Vmn2r108 |
T |
A |
17: 20,691,545 (GRCm39) |
H326L |
probably benign |
Het |
| Xdh |
A |
G |
17: 74,250,840 (GRCm39) |
|
probably null |
Het |
| Zfp385b |
A |
G |
2: 77,242,403 (GRCm39) |
S439P |
probably benign |
Het |
| Zfp597 |
G |
A |
16: 3,683,805 (GRCm39) |
S317L |
probably benign |
Het |
| Zfp638 |
A |
G |
6: 83,946,214 (GRCm39) |
D1081G |
probably damaging |
Het |
| Zfp93 |
C |
T |
7: 23,974,509 (GRCm39) |
H165Y |
possibly 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 |
|
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 |
|
R9450:Nop56
|
UTSW |
2 |
130,117,601 (GRCm39) |
missense |
probably damaging |
1.00 |
|
| Posted On |
2015-12-18 |
Incidental Mutation