Incidental Mutation 'R7867:Nop56'
ID 607817
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 045919-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.964) question?
Stock # R7867 (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 130120205 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Cysteine to Serine at position 471 (C471S)
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
AA Change: C187S

PolyPhen 2 Score 0.336 (Sensitivity: 0.90; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000028890
Gene: ENSMUSG00000027405
AA Change: C187S

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 possibly damaging
Transcript: ENSMUST00000103198
AA Change: C471S

PolyPhen 2 Score 0.533 (Sensitivity: 0.88; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000099487
Gene: ENSMUSG00000027405
AA Change: C471S

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
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 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: ENSMUST00000143547
Predicted Effect
SMART Domains Protein: ENSMUSP00000125304
Gene: ENSMUSG00000027405
AA Change: C215S

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
SMART Domains Protein: ENSMUSP00000123890
Gene: ENSMUSG00000027405
AA Change: C166S

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: 99.9%
  • 10x: 99.7%
  • 20x: 98.9%
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
Abca13 T A 11: 9,212,139 (GRCm39) probably null Het
Abcf1 C A 17: 36,272,890 (GRCm39) K252N probably damaging Het
Abi3 C T 11: 95,724,851 (GRCm39) A211T possibly damaging Het
Acaca A T 11: 84,140,350 (GRCm39) D608V possibly damaging Het
Akap10 A G 11: 61,791,272 (GRCm39) Y396H probably damaging Het
Ap3b1 C G 13: 94,619,771 (GRCm39) S778W unknown Het
Arb2a T C 13: 78,050,837 (GRCm39) M165T probably benign Het
Baat G A 4: 49,502,925 (GRCm39) L66F probably benign Het
Cachd1 A G 4: 100,845,759 (GRCm39) N981S probably damaging Het
Cacna1c C T 6: 118,753,407 (GRCm39) R243H Het
Cdh23 T A 10: 60,150,390 (GRCm39) I2527F probably damaging Het
Cinp A G 12: 110,840,557 (GRCm39) V198A probably benign Het
Clec4d T C 6: 123,244,123 (GRCm39) probably null Het
Cnn3 A G 3: 121,248,704 (GRCm39) I204V probably benign Het
Cpxm2 C A 7: 131,650,800 (GRCm39) G620V probably damaging Het
Ctrl A C 8: 106,659,497 (GRCm39) S93A probably benign Het
Cyp2d34 A G 15: 82,501,425 (GRCm39) V301A possibly damaging Het
Dnaaf5 G T 5: 139,147,565 (GRCm39) K376N probably damaging Het
Eno2 C T 6: 124,740,137 (GRCm39) D300N probably damaging Het
Entrep3 T A 3: 89,093,083 (GRCm39) Y280* probably null Het
Fam117b T A 1: 60,014,046 (GRCm39) N440K probably damaging Het
Fam131a A G 16: 20,514,584 (GRCm39) S62G probably benign Het
Fancm T A 12: 65,163,240 (GRCm39) probably null Het
Fancm A G 12: 65,165,173 (GRCm39) D1506G probably benign Het
Fhad1 C A 4: 141,632,902 (GRCm39) V1201L probably benign Het
Gdpd4 T A 7: 97,623,185 (GRCm39) C265* probably null Het
Gm3127 A T 14: 15,425,888 (GRCm39) T98S probably null Het
Gpsm1 A T 2: 26,230,448 (GRCm39) D466V probably benign Het
Gramd1a T G 7: 30,842,992 (GRCm39) K76Q probably damaging Het
Gstp3 T C 19: 4,108,808 (GRCm39) D24G probably damaging Het
Kalrn G A 16: 33,810,161 (GRCm39) T2531I possibly damaging Het
Klk7 C A 7: 43,462,333 (GRCm39) D108E probably damaging Het
Klkb1 A G 8: 45,740,002 (GRCm39) S97P probably damaging Het
Krt13 T C 11: 100,012,008 (GRCm39) D105G probably damaging Het
Lingo2 T A 4: 35,709,302 (GRCm39) H226L probably benign Het
Lrba T C 3: 86,275,896 (GRCm39) S1755P probably damaging Het
Marf1 A G 16: 13,946,470 (GRCm39) V1217A probably damaging Het
Mtss1 A T 15: 58,842,858 (GRCm39) V118E possibly damaging Het
Mug1 T A 6: 121,850,593 (GRCm39) D696E probably benign Het
Ndufa3 C T 7: 3,623,003 (GRCm39) P56L probably damaging Het
Obscn T A 11: 58,891,652 (GRCm39) H6960L unknown Het
Or13a22 C T 7: 140,073,049 (GRCm39) T166I probably benign Het
Pcdhb10 A C 18: 37,546,619 (GRCm39) Q565P probably benign Het
Pde6g T A 11: 120,338,953 (GRCm39) H79L possibly damaging Het
Phrf1 G T 7: 140,836,524 (GRCm39) M265I unknown Het
Pkd2 T C 5: 104,630,986 (GRCm39) F470S probably damaging Het
Plekhm1 T A 11: 103,271,153 (GRCm39) D446V probably damaging Het
Prkaca A T 8: 84,721,963 (GRCm39) T325S probably benign Het
Proz A T 8: 13,111,027 (GRCm39) probably benign Het
Pten T C 19: 32,792,894 (GRCm39) F238L probably benign Het
Ptpn21 G A 12: 98,671,435 (GRCm39) L198F probably damaging Het
Rbm5 A T 9: 107,628,930 (GRCm39) S394T probably benign Het
Scaf8 T G 17: 3,227,994 (GRCm39) S408A unknown Het
Slc41a3 T A 6: 90,617,909 (GRCm39) F312I probably damaging Het
Soat2 T A 15: 102,059,598 (GRCm39) probably null Het
Sorcs1 C A 19: 50,218,698 (GRCm39) G595* probably null Het
Spopfm1 G C 3: 94,173,154 (GRCm39) S50T probably benign Het
Stox1 G T 10: 62,500,723 (GRCm39) D612E probably benign Het
Suco T C 1: 161,665,365 (GRCm39) I530M possibly damaging Het
Syne2 A G 12: 76,030,501 (GRCm39) probably null Het
Thbd G A 2: 148,249,664 (GRCm39) A68V probably damaging Het
Tmem109 A T 19: 10,855,466 (GRCm39) M4K unknown Het
Tmub1 G C 5: 24,651,664 (GRCm39) P85R possibly damaging Het
Tnk2 A C 16: 32,500,053 (GRCm39) Q1039H probably damaging Het
Tpm3 T C 3: 89,993,775 (GRCm39) L89S probably damaging Het
Unc13b C T 4: 43,232,573 (GRCm39) R432* probably null Het
Vmn2r59 T A 7: 41,661,707 (GRCm39) I703F probably damaging Het
Xylt1 T A 7: 117,074,749 (GRCm39) I122N probably benign Het
Zc3h12c T C 9: 52,055,248 (GRCm39) E187G probably 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
R7393:Nop56 UTSW 2 130,116,558 (GRCm39) missense probably benign 0.06
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'- GCCTGATCCAGCAAGACTAG -3'
(R):5'- GAATGGGCCATGTGCTACAAC -3'

Sequencing Primer
(F):5'- CCTGATCCAGCAAGACTAGGAGTG -3'
(R):5'- TTGGTCCAAAGAGCCCAA -3'
Posted On 2019-12-20