Incidental Mutation 'R2203:Nop56'
| ID |
238814 |
| 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 |
040205-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.964)
|
| Stock # |
R2203 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
2 |
| Chromosomal Location |
130116350-130121233 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to A
at 130119488 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Isoleucine to Asparagine
at position 51
(I51N)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000124080
(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: I84N
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000028890
Gene: ENSMUSG00000027405
AA Change: I84N
| 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 damaging
Transcript: ENSMUST00000103198
AA Change: I368N
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000099487
Gene: ENSMUSG00000027405
AA Change: I368N
| 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 |
noncoding transcript
Transcript: ENSMUST00000153353
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000159373
AA Change: I51N
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000124080
Gene: ENSMUSG00000027405
AA Change: I51N
| 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: ENSMUST00000146454
AA Change: I112N
|
| SMART Domains |
Protein: ENSMUSP00000125304
Gene: ENSMUSG00000027405
AA Change: I112N
| 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: I63N
|
| SMART Domains |
Protein: ENSMUSP00000123890
Gene: ENSMUSG00000027405
AA Change: I63N
| 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: ENSMUST00000133351
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000138163
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000160183
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000145335
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000150745
|
| 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: 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: ENSMUST00000143547
|
| 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: ENSMUST00000160976
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000161543
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000162063
|
| 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 |
|
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.3%
- 20x: 95.3%
|
| 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: 60 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abca1 |
G |
A |
4: 53,090,291 (GRCm39) |
T386I |
probably damaging |
Het |
| Abcc5 |
C |
G |
16: 20,224,632 (GRCm39) |
L44F |
possibly damaging |
Het |
| Abi3bp |
T |
G |
16: 56,433,566 (GRCm39) |
L550R |
probably benign |
Het |
| Brca2 |
T |
A |
5: 150,462,967 (GRCm39) |
D910E |
possibly damaging |
Het |
| Cacna1h |
C |
T |
17: 25,599,234 (GRCm39) |
A1742T |
probably damaging |
Het |
| Cartpt |
A |
T |
13: 100,037,133 (GRCm39) |
S4T |
probably benign |
Het |
| Ccdc66 |
T |
A |
14: 27,208,790 (GRCm39) |
D488V |
probably benign |
Het |
| Cdan1 |
C |
A |
2: 120,551,241 (GRCm39) |
C1093F |
probably damaging |
Het |
| Cfap45 |
T |
C |
1: 172,359,728 (GRCm39) |
V76A |
probably benign |
Het |
| Clptm1 |
G |
T |
7: 19,367,817 (GRCm39) |
F598L |
possibly damaging |
Het |
| Cntrl |
G |
A |
2: 35,033,749 (GRCm39) |
V257I |
possibly damaging |
Het |
| Cpa1 |
A |
G |
6: 30,641,818 (GRCm39) |
D214G |
probably damaging |
Het |
| Crebbp |
A |
C |
16: 3,956,641 (GRCm39) |
M394R |
possibly damaging |
Het |
| Ctnnd1 |
A |
G |
2: 84,447,024 (GRCm39) |
L407P |
probably damaging |
Het |
| Cttnbp2 |
T |
G |
6: 18,408,693 (GRCm39) |
D976A |
probably benign |
Het |
| Dicer1 |
C |
T |
12: 104,697,297 (GRCm39) |
V87M |
possibly damaging |
Het |
| Elapor1 |
C |
T |
3: 108,382,359 (GRCm39) |
G270E |
probably damaging |
Het |
| Fam184a |
T |
A |
10: 53,528,530 (GRCm39) |
Q29L |
probably damaging |
Het |
| Flnc |
C |
T |
6: 29,459,507 (GRCm39) |
P2536S |
probably damaging |
Het |
| Gapdh |
A |
T |
6: 125,139,569 (GRCm39) |
S165T |
probably benign |
Het |
| Gm6370 |
T |
A |
5: 146,430,539 (GRCm39) |
D241E |
probably benign |
Het |
| Grik4 |
T |
A |
9: 42,458,951 (GRCm39) |
S596C |
probably damaging |
Het |
| Gtf2e1 |
T |
A |
16: 37,331,904 (GRCm39) |
E390D |
possibly damaging |
Het |
| Hmgcr |
A |
G |
13: 96,793,141 (GRCm39) |
L497P |
probably damaging |
Het |
| Hmgcs2 |
T |
A |
3: 98,198,499 (GRCm39) |
I134N |
probably damaging |
Het |
| Htr5b |
T |
C |
1: 121,455,693 (GRCm39) |
T76A |
probably damaging |
Het |
| Iars1 |
A |
G |
13: 49,876,151 (GRCm39) |
E812G |
probably benign |
Het |
| Ints8 |
A |
T |
4: 11,225,712 (GRCm39) |
M615K |
possibly damaging |
Het |
| Jmjd1c |
A |
G |
10: 67,075,242 (GRCm39) |
|
probably null |
Het |
| Kcnj5 |
T |
C |
9: 32,234,196 (GRCm39) |
T40A |
probably benign |
Het |
| Knstrn |
T |
A |
2: 118,661,456 (GRCm39) |
|
probably null |
Het |
| Map2k2 |
T |
C |
10: 80,955,213 (GRCm39) |
S14P |
probably damaging |
Het |
| Med26 |
T |
C |
8: 73,249,746 (GRCm39) |
E451G |
probably damaging |
Het |
| Nbeal1 |
T |
A |
1: 60,323,165 (GRCm39) |
M2081K |
probably benign |
Het |
| Nectin4 |
G |
A |
1: 171,213,797 (GRCm39) |
V433M |
possibly damaging |
Het |
| Ntn4 |
C |
T |
10: 93,543,215 (GRCm39) |
R314W |
probably damaging |
Het |
| Nudt5 |
A |
T |
2: 5,860,794 (GRCm39) |
I22F |
possibly damaging |
Het |
| Or4p23 |
C |
G |
2: 88,576,953 (GRCm39) |
G93A |
probably benign |
Het |
| Pbrm1 |
A |
G |
14: 30,754,406 (GRCm39) |
D142G |
possibly damaging |
Het |
| Pdcl |
A |
T |
2: 37,242,056 (GRCm39) |
N231K |
probably benign |
Het |
| Pkd1 |
G |
T |
17: 24,799,863 (GRCm39) |
A591S |
probably benign |
Het |
| Plcb4 |
T |
C |
2: 135,844,514 (GRCm39) |
I144T |
probably benign |
Het |
| Prrc2b |
C |
A |
2: 32,113,476 (GRCm39) |
Q1970K |
probably damaging |
Het |
| Rabep1 |
A |
C |
11: 70,825,400 (GRCm39) |
E689A |
probably damaging |
Het |
| Ralgapa1 |
T |
C |
12: 55,659,585 (GRCm39) |
|
probably null |
Het |
| Robo4 |
CGG |
CG |
9: 37,322,786 (GRCm39) |
|
probably null |
Het |
| Saxo1 |
A |
C |
4: 86,363,998 (GRCm39) |
Y162D |
probably damaging |
Het |
| Shroom3 |
G |
T |
5: 93,090,945 (GRCm39) |
V1151F |
probably damaging |
Het |
| Sipa1l2 |
A |
T |
8: 126,218,366 (GRCm39) |
W324R |
probably damaging |
Het |
| Slc19a1 |
T |
C |
10: 76,877,758 (GRCm39) |
C98R |
possibly damaging |
Het |
| Slc26a8 |
G |
T |
17: 28,866,981 (GRCm39) |
L583I |
probably benign |
Het |
| Spata31d1d |
A |
G |
13: 59,879,435 (GRCm39) |
C34R |
possibly damaging |
Het |
| Stoml2 |
G |
T |
4: 43,030,243 (GRCm39) |
Y119* |
probably null |
Het |
| Susd1 |
A |
G |
4: 59,349,843 (GRCm39) |
L531P |
possibly damaging |
Het |
| Tnfsf14 |
T |
C |
17: 57,497,638 (GRCm39) |
D198G |
possibly damaging |
Het |
| Ttc39a |
A |
G |
4: 109,288,785 (GRCm39) |
N293S |
probably benign |
Het |
| Ttn |
T |
C |
2: 76,601,985 (GRCm39) |
N18559S |
possibly damaging |
Het |
| Vmn2r104 |
A |
T |
17: 20,250,083 (GRCm39) |
N729K |
probably benign |
Het |
| Zbtb47 |
A |
G |
9: 121,591,703 (GRCm39) |
T8A |
possibly damaging |
Het |
| Zfp712 |
T |
A |
13: 67,190,048 (GRCm39) |
T160S |
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 |
|
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'- TTGGTGAGGTAGAAAGTTCAGC -3'
(R):5'- TTCACTCAGACCCAAGGTGTC -3'
Sequencing Primer
(F):5'- AAGTTCAGCCAAGCCTGGTG -3'
(R):5'- GGTGTCAACACTCACTAGGTG -3'
|
| Posted On |
2014-10-02 |
Incidental Mutation