Incidental Mutation 'R5889:Nop56'
| ID |
456204 |
| 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 |
044090-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.964)
|
| Stock # |
R5889 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
2 |
| Chromosomal Location |
130116350-130121233 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
G to T
at 130117902 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Arginine to Leucine
at position 126
(R126L)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000124616
(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 |
noncoding transcript
Transcript: ENSMUST00000083338
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000083353
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000083355
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000103198
AA Change: R126L
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000099487
Gene: ENSMUSG00000027405
AA Change: R126L
| 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 |
|
| SMART Domains |
Protein: ENSMUSP00000125305
Gene: ENSMUSG00000027405
AA Change: R134L
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:NOP5NT
|
14 |
79 |
3.8e-22 |
PFAM |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000136621
AA Change: R126L
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000124616
Gene: ENSMUSG00000027405
AA Change: R126L
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:NOP5NT
|
4 |
70 |
3.6e-22 |
PFAM |
|
NOSIC
|
167 |
219 |
1.18e-30 |
SMART |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000133351
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000160183
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000138163
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000153353
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000160976
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000145335
|
| 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: 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 |
noncoding transcript
Transcript: ENSMUST00000161025
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000162063
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000175746
|
| 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 |
0.9712 |
| Coding Region Coverage |
- 1x: 99.9%
- 3x: 99.5%
- 10x: 97.6%
- 20x: 92.3%
|
| Validation Efficiency |
100% (63/63) |
| 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 |
|---|
| 4930568D16Rik |
T |
C |
2: 35,244,461 (GRCm39) |
E297G |
probably damaging |
Het |
| Astn1 |
C |
T |
1: 158,427,950 (GRCm39) |
P707L |
possibly damaging |
Het |
| Cep290 |
T |
C |
10: 100,334,936 (GRCm39) |
S319P |
possibly damaging |
Het |
| Chrna4 |
A |
C |
2: 180,670,451 (GRCm39) |
L435W |
probably damaging |
Het |
| Cilp |
C |
A |
9: 65,187,625 (GRCm39) |
A1240D |
possibly damaging |
Het |
| Col17a1 |
A |
G |
19: 47,637,511 (GRCm39) |
F1249S |
possibly damaging |
Het |
| Creb3l3 |
T |
C |
10: 80,928,367 (GRCm39) |
|
probably benign |
Het |
| Cyp4f40 |
C |
A |
17: 32,894,731 (GRCm39) |
T432N |
probably benign |
Het |
| Dsg1c |
T |
G |
18: 20,416,658 (GRCm39) |
I853R |
possibly damaging |
Het |
| Ebna1bp2 |
T |
A |
4: 118,478,620 (GRCm39) |
D34E |
probably damaging |
Het |
| Edc4 |
C |
T |
8: 106,614,654 (GRCm39) |
T112I |
possibly damaging |
Het |
| Enpep |
T |
A |
3: 129,106,227 (GRCm39) |
Y333F |
probably damaging |
Het |
| Exoc6 |
A |
G |
19: 37,570,693 (GRCm39) |
H291R |
probably damaging |
Het |
| Fbln5 |
G |
T |
12: 101,731,485 (GRCm39) |
N236K |
probably damaging |
Het |
| Fndc8 |
A |
T |
11: 82,789,555 (GRCm39) |
T238S |
probably damaging |
Het |
| Frem3 |
T |
C |
8: 81,340,917 (GRCm39) |
V1070A |
probably damaging |
Het |
| Gabra4 |
A |
T |
5: 71,729,234 (GRCm39) |
N515K |
possibly damaging |
Het |
| Gemin5 |
A |
G |
11: 58,013,181 (GRCm39) |
V1422A |
possibly damaging |
Het |
| Gm10118 |
A |
G |
10: 63,762,890 (GRCm39) |
|
probably benign |
Het |
| Grm5 |
A |
G |
7: 87,252,281 (GRCm39) |
D177G |
probably damaging |
Het |
| Gtf2h4 |
G |
A |
17: 35,981,792 (GRCm39) |
P147L |
possibly damaging |
Het |
| Hgsnat |
T |
C |
8: 26,453,395 (GRCm39) |
D265G |
probably damaging |
Het |
| Hsd17b4 |
T |
A |
18: 50,310,276 (GRCm39) |
L513Q |
probably damaging |
Het |
| Hsd17b7 |
A |
T |
1: 169,783,487 (GRCm39) |
M307K |
probably benign |
Het |
| Hspa5 |
T |
C |
2: 34,664,629 (GRCm39) |
V361A |
probably damaging |
Het |
| Iqgap2 |
A |
G |
13: 95,768,550 (GRCm39) |
V1450A |
probably benign |
Het |
| Itpr3 |
A |
G |
17: 27,334,039 (GRCm39) |
E2037G |
probably damaging |
Het |
| Itprid2 |
T |
A |
2: 79,488,072 (GRCm39) |
D718E |
probably damaging |
Het |
| Lama5 |
T |
C |
2: 179,835,467 (GRCm39) |
|
probably benign |
Het |
| Manba |
G |
T |
3: 135,230,359 (GRCm39) |
G311* |
probably null |
Het |
| Mettl24 |
T |
A |
10: 40,622,486 (GRCm39) |
V236E |
probably benign |
Het |
| Myh3 |
A |
G |
11: 66,977,201 (GRCm39) |
D310G |
probably damaging |
Het |
| Ncoa4 |
A |
T |
14: 31,888,616 (GRCm39) |
|
probably benign |
Het |
| Nos3 |
C |
A |
5: 24,573,775 (GRCm39) |
|
probably benign |
Het |
| Or13c7b |
T |
C |
4: 43,820,492 (GRCm39) |
M290V |
possibly damaging |
Het |
| Pcdhga3 |
T |
A |
18: 37,809,662 (GRCm39) |
V705D |
probably damaging |
Het |
| Prom2 |
C |
T |
2: 127,371,331 (GRCm39) |
A776T |
possibly damaging |
Het |
| Prss48 |
A |
G |
3: 85,905,492 (GRCm39) |
I127T |
probably damaging |
Het |
| Rtca |
T |
C |
3: 116,293,232 (GRCm39) |
Y193C |
possibly damaging |
Het |
| Samd9l |
T |
C |
6: 3,376,460 (GRCm39) |
Y267C |
probably damaging |
Het |
| Scube3 |
A |
G |
17: 28,379,887 (GRCm39) |
R272G |
possibly damaging |
Het |
| Sprr1a |
G |
T |
3: 92,391,951 (GRCm39) |
H17N |
probably benign |
Het |
| Stard3 |
G |
C |
11: 98,266,361 (GRCm39) |
Q120H |
probably benign |
Het |
| Supt6 |
A |
G |
11: 78,103,574 (GRCm39) |
I1377T |
probably damaging |
Het |
| Svop |
A |
T |
5: 114,203,692 (GRCm39) |
S30T |
probably benign |
Het |
| Syne2 |
T |
A |
12: 76,119,026 (GRCm39) |
L5882* |
probably null |
Het |
| Tanc2 |
G |
T |
11: 105,812,633 (GRCm39) |
R1359L |
probably benign |
Het |
| Tmc7 |
A |
C |
7: 118,165,549 (GRCm39) |
L55R |
probably benign |
Het |
| Trappc11 |
G |
A |
8: 47,972,613 (GRCm39) |
A320V |
probably benign |
Het |
| Ttll8 |
G |
C |
15: 88,818,142 (GRCm39) |
P178A |
probably damaging |
Het |
| Ttn |
T |
C |
2: 76,560,993 (GRCm39) |
E20809G |
probably damaging |
Het |
| Tubb2a |
A |
T |
13: 34,259,451 (GRCm39) |
V113E |
possibly damaging |
Het |
| Ube2d1 |
A |
T |
10: 71,095,699 (GRCm39) |
|
probably benign |
Het |
| Usp48 |
T |
C |
4: 137,343,723 (GRCm39) |
V452A |
probably benign |
Het |
| Vldlr |
T |
A |
19: 27,217,064 (GRCm39) |
I39N |
probably damaging |
Het |
| Wbp1l |
C |
T |
19: 46,642,619 (GRCm39) |
R191* |
probably null |
Het |
| Zyg11b |
C |
T |
4: 108,094,577 (GRCm39) |
W669* |
probably null |
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 |
|
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'- GCTGAGATCCTTCGAGGTAAGAG -3'
(R):5'- TGAATCATCGGCCATGCTCG -3'
Sequencing Primer
(F):5'- ATCCTTCGAGGTAAGAGTCCTATTTC -3'
(R):5'- TTACCTGACGCGCATCGAGAAG -3'
|
| Posted On |
2017-02-15 |
Incidental Mutation