Mutagenetix > Incidental Mutation

Incidental Mutation 'R4679:Nop56'

349892

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

041932-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.964) question?

Stock #

R4679 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

130116350-130121233 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 130120193 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Alanine at position 183 (T183A)

Ref Sequence

ENSEMBL: ENSMUSP00000028890 (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: T183A

PolyPhen 2 Score 0.363 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000028890
Gene: ENSMUSG00000027405
AA Change: T183A

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 benign
Transcript: ENSMUST00000103198
AA Change: T467A

PolyPhen 2 Score 0.029 (Sensitivity: 0.95; Specificity: 0.82)

SMART Domains

Protein: ENSMUSP00000099487
Gene: ENSMUSG00000027405
AA Change: T467A

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: ENSMUST00000133351

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000153353

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000150745

Predicted Effect

unknown
Transcript: ENSMUST00000146454
AA Change: T211A

SMART Domains

Protein: ENSMUSP00000125304
Gene: ENSMUSG00000027405
AA Change: T211A

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: T162A

SMART Domains

Protein: ENSMUSP00000123890
Gene: ENSMUSG00000027405
AA Change: T162A

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: ENSMUST00000138163

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000145335

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000160183

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000149843

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: 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: 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: 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

noncoding transcript
Transcript: ENSMUST00000175746

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000162063

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000160976

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000161543

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000161025

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

0.0601

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 96.7%
20x: 93.9%

Validation Efficiency

98% (112/114)

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: 93 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
AA986860	T	A	1: 130,670,140 (GRCm39)	S121T	possibly damaging	Het
Abcb9	A	G	5: 124,216,867 (GRCm39)	V450A	probably benign	Het
Abcg1	A	T	17: 31,333,235 (GRCm39)	R659S	probably benign	Het
Acad9	A	T	3: 36,142,989 (GRCm39)	N508I	possibly damaging	Het
Acrbp	T	A	6: 125,037,881 (GRCm39)	C393S	probably damaging	Het
Adcy7	T	C	8: 89,044,565 (GRCm39)	V486A	probably benign	Het
Adgrf1	G	T	17: 43,621,384 (GRCm39)	L540F	probably damaging	Het
Ap5m1	T	C	14: 49,316,285 (GRCm39)	I285T	probably benign	Het
Arhgap27	G	T	11: 103,251,775 (GRCm39)		probably benign	Het
Armc5	A	T	7: 127,839,276 (GRCm39)	E198V	possibly damaging	Het
Atp8b5	A	T	4: 43,365,955 (GRCm39)	K742M	probably benign	Het
Atp9a	T	G	2: 168,503,884 (GRCm39)	T603P	possibly damaging	Het
Bsn	A	G	9: 107,987,329 (GRCm39)	S2808P	unknown	Het
C9orf72	C	T	4: 35,226,033 (GRCm39)		probably benign	Het
Catsper4	T	C	4: 133,953,916 (GRCm39)	N81S	probably damaging	Het
Ccl17	C	G	8: 95,537,128 (GRCm39)	T10S	probably benign	Het
Cdc123	A	T	2: 5,849,703 (GRCm39)	V6D	probably damaging	Het
Cdca2	T	C	14: 67,952,415 (GRCm39)	K14E	possibly damaging	Het
Cdh3	C	A	8: 107,266,488 (GRCm39)	T302K	probably damaging	Het
Cdh9	A	G	15: 16,851,045 (GRCm39)	M605V	probably benign	Het
Cdk4	A	G	10: 126,900,780 (GRCm39)	E144G	possibly damaging	Het
Clasp1	C	T	1: 118,471,001 (GRCm39)	A879V	probably damaging	Het
Cldn8	G	A	16: 88,359,296 (GRCm39)	H210Y	probably benign	Het
Cntn5	T	C	9: 9,970,536 (GRCm39)	D518G	probably benign	Het
Cog1	C	T	11: 113,543,116 (GRCm39)	A208V	probably damaging	Het
Col4a2	T	A	8: 11,481,337 (GRCm39)	H836Q	possibly damaging	Het
Copb1	T	C	7: 113,848,211 (GRCm39)	D108G	probably damaging	Het
Csmd3	A	T	15: 48,024,479 (GRCm39)	Y600*	probably null	Het
Cyb5r1	T	A	1: 134,335,571 (GRCm39)	H164Q	probably benign	Het
Dkc1	A	G	X: 74,144,598 (GRCm39)	I215V	probably benign	Het
Enpep	A	G	3: 129,097,362 (GRCm39)		probably null	Het
Fam110d	A	G	4: 133,978,747 (GRCm39)	S244P	probably damaging	Het
Fbln7	A	G	2: 128,736,806 (GRCm39)	Y311C	probably damaging	Het
Fign	A	C	2: 63,809,605 (GRCm39)	L555R	probably damaging	Het
Fkbp7	A	T	2: 76,502,032 (GRCm39)		probably benign	Het
Fmn2	T	C	1: 174,330,728 (GRCm39)	S373P	unknown	Het
Frmd4b	C	T	6: 97,272,627 (GRCm39)	D868N	possibly damaging	Het
Garin3	T	A	11: 46,295,640 (GRCm39)	M4K	possibly damaging	Het
Gfpt2	A	G	11: 49,714,564 (GRCm39)	N321S	probably benign	Het
Glmn	G	T	5: 107,708,941 (GRCm39)	T372K	probably damaging	Het
Gm26602	C	T	10: 79,746,808 (GRCm39)		probably benign	Het
Gm6797	A	G	X: 8,505,933 (GRCm39)		noncoding transcript	Het
Gpat3	T	A	5: 101,041,322 (GRCm39)	F383L	probably damaging	Het
H2-M11	C	T	17: 36,859,042 (GRCm39)	T194I	possibly damaging	Het
Hcn1	C	T	13: 117,793,551 (GRCm39)	H268Y	probably benign	Het
Hectd4	G	T	5: 121,463,314 (GRCm39)	C2345F	possibly damaging	Het
Htt	A	G	5: 34,977,424 (GRCm39)	D770G	probably benign	Het
Ints3	T	C	3: 90,315,817 (GRCm39)	T316A	possibly damaging	Het
Ipo9	A	G	1: 135,321,907 (GRCm39)	F608L	probably benign	Het
Irak1	A	C	X: 73,065,995 (GRCm39)		probably benign	Het
Jam2	G	A	16: 84,609,840 (GRCm39)	V151M	probably damaging	Het
Lag3	T	A	6: 124,881,508 (GRCm39)	Q488L	possibly damaging	Het
Large2	A	T	2: 92,197,903 (GRCm39)	L266Q	probably benign	Het
Lrp3	T	G	7: 34,903,365 (GRCm39)	D327A	probably damaging	Het
Mamstr	C	A	7: 45,294,116 (GRCm39)		probably benign	Het
Mettl14	G	A	3: 123,163,063 (GRCm39)		probably benign	Het
Miga1	A	G	3: 152,028,112 (GRCm39)	V139A	probably damaging	Het
Mthfd2l	A	C	5: 91,096,770 (GRCm39)	R130S	probably benign	Het
Myo1b	A	G	1: 51,797,132 (GRCm39)	I970T	possibly damaging	Het
Nat10	C	A	2: 103,562,515 (GRCm39)	W607L	probably damaging	Het
Or10h1	A	G	17: 33,418,367 (GRCm39)	H115R	probably benign	Het
Or2d4	A	T	7: 106,544,152 (GRCm39)	S19T	probably benign	Het
Or4c10	A	G	2: 89,761,008 (GRCm39)	Y285C	possibly damaging	Het
Or4d1	T	A	11: 87,805,136 (GRCm39)	M199L	probably benign	Het
Or52j3	A	G	7: 102,836,309 (GRCm39)	Y167C	probably benign	Het
Or5ae2	T	A	7: 84,506,112 (GRCm39)	Y178*	probably null	Het
Pcdhb12	T	C	18: 37,570,002 (GRCm39)	F383L	probably damaging	Het
Pde4dip	C	A	3: 97,602,321 (GRCm39)	D2252Y	probably damaging	Het
Peg10	GC	GCTCC	6: 4,756,452 (GRCm39)		probably benign	Het
Plscr2	T	G	9: 92,169,823 (GRCm39)	L91R	probably benign	Het
Plxnc1	T	A	10: 94,630,306 (GRCm39)	Y1531F	probably damaging	Het
Ptprq	A	T	10: 107,521,043 (GRCm39)	F710I	probably benign	Het
Rad51ap2	A	G	12: 11,506,552 (GRCm39)	E158G	probably damaging	Het
Rasip1	T	A	7: 45,277,247 (GRCm39)	H18Q	possibly damaging	Het
Rcsd1	T	A	1: 165,483,493 (GRCm39)	N166I	probably damaging	Het
Ripor1	T	A	8: 106,344,417 (GRCm39)	I517K	possibly damaging	Het
Ryr2	T	A	13: 11,839,255 (GRCm39)	H506L	probably benign	Het
Secisbp2l	C	T	2: 125,582,657 (GRCm39)	G933D	possibly damaging	Het
Septin14	T	C	5: 129,770,090 (GRCm39)	D202G	possibly damaging	Het
Siglec1	A	T	2: 130,915,331 (GRCm39)	L1420Q	possibly damaging	Het
Slc22a29	T	A	19: 8,138,948 (GRCm39)	I505F	possibly damaging	Het
Sorcs1	T	A	19: 50,171,107 (GRCm39)	Y927F	probably benign	Het
Spats2	T	G	15: 99,078,603 (GRCm39)	M191R	possibly damaging	Het
Sycp1	C	T	3: 102,829,778 (GRCm39)		probably null	Het
T2	A	G	17: 8,609,848 (GRCm39)	E99G	possibly damaging	Het
Taf3	G	A	2: 10,053,375 (GRCm39)		probably benign	Het
Tnfsf10	A	T	3: 27,389,728 (GRCm39)	N263I	probably damaging	Het
Treml2	A	T	17: 48,615,203 (GRCm39)	R229S	probably benign	Het
Trmt13	T	C	3: 116,383,404 (GRCm39)	K125E	probably damaging	Het
Ttc9	G	T	12: 81,678,375 (GRCm39)	C66F	probably damaging	Het
Vmn2r63	C	T	7: 42,577,544 (GRCm39)	M331I	probably benign	Het
Zfp353-ps	T	C	8: 42,535,251 (GRCm39)		noncoding transcript	Het
Zfp932	A	T	5: 110,157,760 (GRCm39)	H486L	probably damaging	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
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'- ACTAGGAGTGTTGTGGCAAGTC -3'
(R):5'- GCACACTTGCCCATGGAATG -3'

Sequencing Primer
(F):5'- GGCAAGTCAGGGGTCTTC -3'
(R):5'- ATGGGCCATGTGCTACAAC -3'

Posted On

2015-10-08