Incidental Mutation 'R7393:Nop56'
ID 573575
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 045475-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.964) question?
Stock # R7393 (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 A at 130116558 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Leucine to Glutamine at position 3 (L3Q)
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

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 probably benign
Transcript: ENSMUST00000103198
AA Change: L3Q

PolyPhen 2 Score 0.058 (Sensitivity: 0.94; Specificity: 0.84)
SMART Domains Protein: ENSMUSP00000099487
Gene: ENSMUSG00000027405
AA Change: L3Q

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 probably benign
Transcript: ENSMUST00000136621
AA Change: L3Q

PolyPhen 2 Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)
SMART Domains Protein: ENSMUSP00000124616
Gene: ENSMUSG00000027405
AA Change: L3Q

DomainStartEndE-ValueType
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: L11Q

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
NOSIC 2 35 1.24e-6 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000150401
SMART Domains Protein: ENSMUSP00000123890
Gene: ENSMUSG00000027405

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
Pfam:Iso_dh 6 71 1.8e-15 PFAM
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 100.0%
  • 10x: 99.7%
  • 20x: 99.1%
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: 69 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcb11 C T 2: 69,130,211 (GRCm39) D282N probably damaging Het
Abi2 T C 1: 60,473,541 (GRCm39) M86T possibly damaging Het
Adam26a T C 8: 44,022,725 (GRCm39) N255S probably benign Het
Adam4 G A 12: 81,466,434 (GRCm39) S729L probably benign Het
Adcy1 G T 11: 7,087,381 (GRCm39) W418C probably damaging Het
Add2 T A 6: 86,075,629 (GRCm39) Y259* probably null Het
Agl A T 3: 116,584,805 (GRCm39) C172S probably benign Het
Ankfy1 A G 11: 72,629,134 (GRCm39) T319A possibly damaging Het
Armc8 A T 9: 99,366,052 (GRCm39) C621S possibly damaging Het
Atp5mj A G 12: 111,929,711 (GRCm39) V26A probably benign Het
Bbc3 A G 7: 16,047,714 (GRCm39) D146G probably benign Het
Btnl10 T C 11: 58,814,532 (GRCm39) L404P probably damaging Het
Cbl A G 9: 44,065,485 (GRCm39) probably null Het
Ccdc170 T A 10: 4,464,314 (GRCm39) probably null Het
Ccdc91 T A 6: 147,435,527 (GRCm39) V37E possibly damaging Het
Ces1e G T 8: 93,937,045 (GRCm39) T343K probably benign Het
Chfr T A 5: 110,300,224 (GRCm39) F323I probably damaging Het
Clcnkb T A 4: 141,136,756 (GRCm39) M370L probably benign Het
Col11a1 A G 3: 113,890,755 (GRCm39) D364G unknown Het
Ctbp2 A G 7: 132,590,021 (GRCm39) I381T probably benign Het
Cyp4a29 A C 4: 115,099,393 (GRCm39) Y38S probably damaging Het
Ddx1 T C 12: 13,280,354 (GRCm39) D382G probably benign Het
Dhx57 T A 17: 80,563,000 (GRCm39) N876Y probably damaging Het
Dsel C T 1: 111,789,303 (GRCm39) G411S probably damaging Het
Enpp5 G A 17: 44,396,155 (GRCm39) G356S probably damaging Het
Fam234a T C 17: 26,435,598 (GRCm39) D262G probably benign Het
Fnbp4 C A 2: 90,609,660 (GRCm39) Q1035K probably damaging Het
Gbp11 T A 5: 105,475,443 (GRCm39) N302Y possibly damaging Het
Gm11554 T A 11: 99,694,698 (GRCm39) T172S unknown Het
Hamp2 A T 7: 30,622,030 (GRCm39) M53K possibly damaging Het
Kcnj1 A G 9: 32,308,314 (GRCm39) D246G probably damaging Het
Kctd20 T C 17: 29,182,312 (GRCm39) F209L probably damaging Het
Klra2 T C 6: 131,207,165 (GRCm39) Y148C probably damaging Het
Krtap15-1 T C 16: 88,625,985 (GRCm39) probably null Het
Mrps23 T C 11: 88,095,284 (GRCm39) L6P probably damaging Het
Ms4a6d G A 19: 11,567,437 (GRCm39) Q155* probably null Het
Myo7a G A 7: 97,712,906 (GRCm39) R1690C possibly damaging Het
Nbas T C 12: 13,443,493 (GRCm39) S1183P probably damaging Het
Ndufaf4 T A 4: 24,903,177 (GRCm39) M122K probably benign Het
Nop2 C A 6: 125,110,509 (GRCm39) S45* probably null Het
Nrp2 T C 1: 62,784,583 (GRCm39) I244T probably damaging Het
Or4d10c T A 19: 12,065,992 (GRCm39) T55S probably benign Het
Or51v14 A G 7: 103,261,198 (GRCm39) S121P possibly damaging Het
Otof T C 5: 30,527,614 (GRCm39) D1941G probably benign Het
Pcyox1l T C 18: 61,830,712 (GRCm39) K387E probably benign Het
Plcg2 A G 8: 118,306,564 (GRCm39) Y306C possibly damaging Het
Ppp1r13b G A 12: 111,805,188 (GRCm39) P333S probably damaging Het
Rcc2 A G 4: 140,444,341 (GRCm39) D344G probably damaging Het
Reln A T 5: 22,181,349 (GRCm39) N1810K probably damaging Het
Rfesd G T 13: 76,151,149 (GRCm39) A90E probably benign Het
Rsf1 CGGCGGCGG CGGCGGCGGGGGCGGCGG 7: 97,229,124 (GRCm39) probably benign Het
Scg2 T C 1: 79,412,948 (GRCm39) K552E probably damaging Het
Sdccag8 A G 1: 176,667,872 (GRCm39) I190V probably benign Het
Sele C A 1: 163,881,492 (GRCm39) T533K probably benign Het
Sh3bp4 T A 1: 89,072,170 (GRCm39) H339Q possibly damaging Het
Slc6a19 A G 13: 73,841,093 (GRCm39) S106P probably benign Het
Spidr C T 16: 15,964,695 (GRCm39) probably benign Het
Stk36 A T 1: 74,650,352 (GRCm39) K295* probably null Het
Synj1 A T 16: 90,748,887 (GRCm39) D1056E probably damaging Het
Tnks1bp1 T C 2: 84,893,210 (GRCm39) S1046P probably benign Het
Ttc27 T G 17: 75,077,259 (GRCm39) F385V possibly damaging Het
Ttn C A 2: 76,774,689 (GRCm39) G2164W unknown Het
Ubap1 T A 4: 41,379,764 (GRCm39) L326* probably null Het
Ubr4 A G 4: 139,154,096 (GRCm39) N812S probably damaging Het
Vmn1r160 A G 7: 22,570,778 (GRCm39) T44A possibly damaging Het
Vmn1r28 G A 6: 58,242,574 (GRCm39) S139N possibly damaging Het
Vmn2r116 A G 17: 23,605,099 (GRCm39) I137M probably benign Het
Vmn2r67 A T 7: 84,805,086 (GRCm39) W9R probably null Het
Zfp101 T C 17: 33,605,674 (GRCm39) N45D 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
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
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'- CTCTGATTGGTCAAACCGGAG -3'
(R):5'- AAGAGTCCCCTCATTCTAGAGC -3'

Sequencing Primer
(F):5'- AAGGTGTGGTCTCCGCAGTC -3'
(R):5'- CCCTCATTCTAGAGCTCCCC -3'
Posted On 2019-09-13