Incidental Mutation 'R2202:Nop56'
ID 238709
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 040204-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.964) question?
Stock # R2202 (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] [ENSMUST00000136621] [ENSMUST00000159373] [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

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
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: ENSMUST00000133351
Predicted Effect probably benign
Transcript: ENSMUST00000136621
SMART Domains Protein: ENSMUSP00000124616
Gene: ENSMUSG00000027405

DomainStartEndE-ValueType
Pfam:NOP5NT 4 70 3.6e-22 PFAM
NOSIC 167 219 1.18e-30 SMART
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

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
Pfam:Nop 26 103 3.9e-26 PFAM
coiled coil region 110 155 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000160976
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: ENSMUST00000161543
Predicted Effect noncoding transcript
Transcript: ENSMUST00000162063
Predicted Effect noncoding transcript
Transcript: ENSMUST00000161025
Predicted Effect noncoding transcript
Transcript: ENSMUST00000175746
Predicted Effect noncoding transcript
Transcript: ENSMUST00000149843
Predicted Effect probably benign
Transcript: ENSMUST00000141872
SMART Domains Protein: ENSMUSP00000125305
Gene: ENSMUSG00000027405

DomainStartEndE-ValueType
Pfam:NOP5NT 14 79 3.8e-22 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000184538
SMART Domains Protein: ENSMUSP00000139331
Gene: ENSMUSG00000027406

DomainStartEndE-ValueType
Pfam:Iso_dh 6 71 1.8e-15 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000143547
Predicted Effect probably benign
Transcript: ENSMUST00000149955
SMART Domains Protein: ENSMUSP00000123879
Gene: ENSMUSG00000027405

DomainStartEndE-ValueType
NOSIC 2 35 1.24e-6 SMART
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.5%
  • 20x: 95.6%
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: 91 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
0610040J01Rik T C 5: 64,056,011 (GRCm39) V249A possibly damaging Het
9930111J21Rik2 C G 11: 48,910,149 (GRCm39) L761F probably damaging Het
Abca1 G A 4: 53,090,291 (GRCm39) T386I probably damaging Het
Abca14 T C 7: 119,888,764 (GRCm39) Y1237H probably benign Het
Abi3bp C T 16: 56,471,088 (GRCm39) R578* probably null Het
Abi3bp T G 16: 56,433,566 (GRCm39) L550R probably benign Het
Adamts7 A T 9: 90,062,729 (GRCm39) K394N probably damaging Het
Ahdc1 A G 4: 132,793,220 (GRCm39) E1487G possibly damaging Het
AI987944 T C 7: 41,023,950 (GRCm39) E343G probably damaging Het
Ankrd26 T A 6: 118,500,843 (GRCm39) H876L possibly damaging Het
Atg16l1 A C 1: 87,694,737 (GRCm39) Q138P probably benign Het
Atp1b1 G T 1: 164,281,084 (GRCm39) T11K probably benign Het
Calr3 A G 8: 73,188,683 (GRCm39) L40S probably damaging Het
Ccar1 A C 10: 62,581,066 (GRCm39) D1119E unknown Het
Cdan1 C A 2: 120,551,241 (GRCm39) C1093F probably damaging Het
Cdk12 T G 11: 98,101,464 (GRCm39) S441A unknown Het
Ces4a T A 8: 105,872,746 (GRCm39) V333E probably damaging Het
Cfap61 T C 2: 146,056,600 (GRCm39) L1193P probably damaging Het
Chd2 A T 7: 73,128,416 (GRCm39) D856E probably benign Het
Chil3 T C 3: 106,071,562 (GRCm39) D34G probably benign Het
Cln3 T A 7: 126,178,390 (GRCm39) H211L probably benign Het
Cpa1 A G 6: 30,641,818 (GRCm39) D214G probably damaging Het
Cttnbp2 T G 6: 18,408,693 (GRCm39) D976A probably benign Het
Dcstamp T A 15: 39,617,708 (GRCm39) V39E probably damaging Het
Dicer1 C T 12: 104,697,297 (GRCm39) V87M possibly damaging Het
Duox1 A G 2: 122,175,194 (GRCm39) T1331A probably benign 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
Fcer2a T C 8: 3,738,557 (GRCm39) E60G possibly damaging Het
Flnc C T 6: 29,459,507 (GRCm39) P2536S probably damaging Het
Fnbp1l A T 3: 122,340,611 (GRCm39) M463K probably benign Het
Garem2 A G 5: 30,319,762 (GRCm39) D408G probably benign Het
Gm6370 T A 5: 146,430,539 (GRCm39) D241E probably benign Het
Gpc3 T A X: 51,486,083 (GRCm39) I344F probably damaging Het
Gtf2e1 T A 16: 37,331,904 (GRCm39) E390D possibly damaging Het
Hmgcs2 T A 3: 98,198,499 (GRCm39) I134N probably damaging Het
Il15ra T A 2: 11,723,155 (GRCm39) probably null Het
Ints8 A T 4: 11,225,712 (GRCm39) M615K possibly damaging Het
Irak1 G A X: 73,060,744 (GRCm39) T193I probably damaging Het
Jmjd1c A G 10: 67,075,242 (GRCm39) probably null Het
Knstrn T A 2: 118,661,456 (GRCm39) probably null Het
Letm1 C A 5: 33,926,830 (GRCm39) V156L possibly damaging Het
Lrrc24 G A 15: 76,607,111 (GRCm39) P95L probably damaging Het
Map2k2 T C 10: 80,955,213 (GRCm39) S14P probably damaging Het
Me3 T C 7: 89,499,589 (GRCm39) Y535H probably damaging Het
Nfatc2ip T C 7: 125,990,467 (GRCm39) E178G probably benign 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
Or10a2 T A 7: 106,673,523 (GRCm39) W163R probably damaging Het
Or2m12 C T 16: 19,105,047 (GRCm39) A149T probably benign 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
Pdlim2 C T 14: 70,402,228 (GRCm39) R296H probably damaging Het
Pid1 T A 1: 84,016,159 (GRCm39) I69F probably damaging Het
Pkhd1 A G 1: 20,607,584 (GRCm39) S1091P probably benign Het
Plcb4 T C 2: 135,844,514 (GRCm39) I144T probably benign Het
Plxnd1 T C 6: 115,939,725 (GRCm39) N1418S probably benign Het
Pmm1 T C 15: 81,840,601 (GRCm39) T82A probably benign Het
Prrc2b C A 2: 32,113,476 (GRCm39) Q1970K probably damaging Het
Ptprz1 C T 6: 23,000,649 (GRCm39) T913M possibly damaging Het
Ralgapa1 T C 12: 55,659,585 (GRCm39) probably null Het
Rbm8a2 T C 1: 175,806,420 (GRCm39) E19G possibly damaging Het
Rgs3 T C 4: 62,608,741 (GRCm39) S336P probably damaging Het
Saxo5 A T 8: 3,529,028 (GRCm39) D201V probably benign Het
Serpina11 G T 12: 103,952,233 (GRCm39) T179K probably damaging Het
Serpina1f T C 12: 103,659,655 (GRCm39) N209S possibly damaging Het
Serpinf2 G A 11: 75,327,588 (GRCm39) T159I probably benign Het
Slc19a1 T C 10: 76,877,758 (GRCm39) C98R possibly damaging Het
Slc22a20 A T 19: 6,021,553 (GRCm39) I483N possibly damaging 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
Timd5 A G 11: 46,419,394 (GRCm39) N70S probably benign Het
Tln1 C T 4: 43,553,083 (GRCm39) probably null Het
Tmem39b A C 4: 129,587,716 (GRCm39) S32A probably benign Het
Tmx3 T C 18: 90,546,037 (GRCm39) F206S probably damaging Het
Tnfsf14 T C 17: 57,497,638 (GRCm39) D198G possibly damaging Het
Trappc10 A G 10: 78,034,876 (GRCm39) probably null Het
Tssk2 A G 16: 17,716,603 (GRCm39) D2G possibly damaging Het
Ttn T C 2: 76,601,985 (GRCm39) N18559S possibly damaging Het
Ube3b G A 5: 114,527,135 (GRCm39) V118M probably damaging Het
Vmn1r23 T C 6: 57,903,604 (GRCm39) D58G probably benign Het
Vmn2r53 T A 7: 12,335,366 (GRCm39) Y98F probably damaging Het
Vmn2r58 T A 7: 41,513,594 (GRCm39) N350Y probably benign Het
Vmn2r82 A T 10: 79,192,519 (GRCm39) H32L probably benign Het
Wsb1 T C 11: 79,131,212 (GRCm39) I395V probably benign Het
Zbtb47 A G 9: 121,591,703 (GRCm39) T8A possibly damaging Het
Zfat T C 15: 68,051,709 (GRCm39) D695G probably benign Het
Zfp358 G T 8: 3,546,995 (GRCm39) V526F possibly damaging Het
Zmat1 A G X: 133,873,861 (GRCm39) L476P possibly damaging Het
Other mutations in Nop56
AlleleSourceChrCoordTypePredicted EffectPPH 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
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
Predicted Primers PCR Primer
(F):5'- TTGGTGAGGTAGAAAGTTCAGCC -3'
(R):5'- TTCACTCAGACCCAAGGTGTC -3'

Sequencing Primer
(F):5'- AAGTTCAGCCAAGCCTGGTG -3'
(R):5'- GGTGTCAACACTCACTAGGTG -3'
Posted On 2014-10-02