Mutagenetix > Incidental Mutation

Incidental Mutation 'R6016:Nop56'

478591

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

043255-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.964) question?

Stock #

R6016 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

130116350-130121233 bp(+) (GRCm39)

Type of Mutation

critical splice donor site (2 bp from exon)

DNA Base Change (assembly)

T to C at 130118545 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

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

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 null
Transcript: ENSMUST00000103198

SMART Domains

Protein: ENSMUSP00000099487
Gene: ENSMUSG00000027405

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

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

silent
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

silent
Transcript: ENSMUST00000143547

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000160976

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000145335

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000160183

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000150745

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000138163

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000153353

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000133351

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: 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: 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: 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: ENSMUST00000175746

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000162063

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

Coding Region Coverage

1x: 99.9%
3x: 99.4%
10x: 97.0%
20x: 90.5%

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: 32 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Apol9b	T	C	15: 77,620,058 (GRCm39)	S285P	probably damaging	Het
Casz1	C	A	4: 149,019,041 (GRCm39)	N447K	probably damaging	Het
Cltb	T	C	13: 54,754,480 (GRCm39)	T71A	possibly damaging	Het
Dcaf12	A	G	4: 41,313,267 (GRCm39)	F93L	probably damaging	Het
Dnah5	T	C	15: 28,328,030 (GRCm39)	Y2135H	probably damaging	Het
Entpd2	C	T	2: 25,288,568 (GRCm39)	R191W	probably damaging	Het
Gm17067	G	T	7: 42,357,654 (GRCm39)	P283T	probably benign	Het
Gm3250	A	G	10: 77,618,367 (GRCm39)		probably benign	Het
Gne	T	C	4: 44,039,063 (GRCm39)	E532G	probably damaging	Het
Gsdmc3	T	G	15: 63,740,261 (GRCm39)	D86A	probably benign	Het
Hs3st2	A	G	7: 121,099,922 (GRCm39)	H256R	probably damaging	Het
Il19	T	A	1: 130,863,718 (GRCm39)	D16V	probably damaging	Het
Lats2	A	T	14: 57,971,632 (GRCm39)	N14K	probably damaging	Het
Mill2	G	T	7: 18,590,373 (GRCm39)	S151I	probably benign	Het
Ncapg2	G	A	12: 116,390,227 (GRCm39)	R392H	probably damaging	Het
Or14j8	A	T	17: 38,262,967 (GRCm39)	V316D	probably benign	Het
Or2bd2	A	T	7: 6,443,613 (GRCm39)	H238L	probably benign	Het
Or5p5	A	T	7: 107,414,219 (GRCm39)	I143F	probably benign	Het
Pde1a	T	C	2: 79,695,406 (GRCm39)	R446G	probably benign	Het
Pes1	T	A	11: 3,928,004 (GRCm39)	M552K	possibly damaging	Het
Plxnb2	T	A	15: 89,045,225 (GRCm39)	T1074S	possibly damaging	Het
Psg23	G	T	7: 18,346,112 (GRCm39)	H194Q	probably benign	Het
Rprd2	A	G	3: 95,694,685 (GRCm39)	V116A	probably damaging	Het
Shkbp1	A	G	7: 27,053,826 (GRCm39)	V124A	possibly damaging	Het
Slc38a8	A	T	8: 120,221,044 (GRCm39)		probably null	Het
Slitrk6	A	G	14: 110,987,958 (GRCm39)	V583A	probably benign	Het
Sptbn5	G	T	2: 119,880,573 (GRCm39)		noncoding transcript	Het
Stab1	A	T	14: 30,880,950 (GRCm39)	I614N	probably damaging	Het
Tgm6	A	G	2: 129,983,148 (GRCm39)	T246A	probably damaging	Het
Tnks1bp1	T	C	2: 84,882,734 (GRCm39)	L187P	probably damaging	Het
Vmn1r157	A	G	7: 22,461,272 (GRCm39)	R51G	possibly damaging	Het
Vmn2r68	A	T	7: 84,871,453 (GRCm39)	I610K	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
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
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'- CTACAGGGAGTGGTATGGGTAC -3'
(R):5'- GGGCTACTTGGCTCATCTTG -3'

Sequencing Primer
(F):5'- GGTACCACTTTCCAGAGCTG -3'
(R):5'- CTCATCTTGGAGCGAAGGTAAGTG -3'

Posted On

2017-06-26