Mutagenetix > Incidental Mutation

Incidental Mutation 'R3697:Nop56'

269845

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

040691-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.964) question?

Stock #

R3697 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

130116350-130121233 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to A at 130119507 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Lysine at position 57 (N57K)

Ref Sequence

ENSEMBL: ENSMUSP00000124080 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000028890] [ENSMUST00000028892] [ENSMUST00000103198] [ENSMUST00000159373] [ENSMUST00000136621] [ENSMUST00000184538]

AlphaFold

Q9D6Z1

Predicted Effect

probably damaging
Transcript: ENSMUST00000028890
AA Change: N90K

PolyPhen 2 Score 0.993 (Sensitivity: 0.70; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000028890
Gene: ENSMUSG00000027405
AA Change: N90K

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 damaging
Transcript: ENSMUST00000103198
AA Change: N374K

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000099487
Gene: ENSMUSG00000027405
AA Change: N374K

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 damaging
Transcript: ENSMUST00000159373
AA Change: N57K

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000124080
Gene: ENSMUSG00000027405
AA Change: N57K

Domain	Start	End	E-Value	Type
Pfam:Nop	10	94	6e-28	PFAM
coiled coil region	98	135	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000133351

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000150745

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000153353

Predicted Effect

unknown
Transcript: ENSMUST00000150401
AA Change: N69K

SMART Domains

Protein: ENSMUSP00000123890
Gene: ENSMUSG00000027405
AA Change: N69K

Domain	Start	End	E-Value	Type
Pfam:Nop	26	103	3.9e-26	PFAM
coiled coil region	110	155	N/A	INTRINSIC

Predicted Effect

unknown
Transcript: ENSMUST00000146454
AA Change: N118K

SMART Domains

Protein: ENSMUSP00000125304
Gene: ENSMUSG00000027405
AA Change: N118K

Domain	Start	End	E-Value	Type
Pfam:Nop	1	152	7.8e-66	PFAM
coiled coil region	159	204	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000149843

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000145335

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000138163

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000160183

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: 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: 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: ENSMUST00000143547

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000161543

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000162063

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000161025

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000160976

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000175746

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: 99.1%
3x: 98.5%
10x: 97.1%
20x: 94.4%

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: 28 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aldh4a1	A	G	4: 139,369,562 (GRCm39)	H371R	possibly damaging	Het
Arhgef4	A	G	1: 34,761,521 (GRCm39)	D259G	unknown	Het
Bckdk	C	A	7: 127,504,590 (GRCm39)	R105S	probably damaging	Het
Clcn3	T	C	8: 61,366,157 (GRCm39)	D805G	probably benign	Het
Cnmd	C	A	14: 79,875,421 (GRCm39)	R333L	probably damaging	Het
Col4a4	A	T	1: 82,518,958 (GRCm39)	I79N	unknown	Het
Emc1	T	G	4: 139,092,697 (GRCm39)	S546A	possibly damaging	Het
Ermard	T	C	17: 15,273,638 (GRCm39)	S408P	probably benign	Het
Gls	C	T	1: 52,238,923 (GRCm39)	M364I	possibly damaging	Het
Gm16380	A	G	9: 53,791,736 (GRCm39)		noncoding transcript	Het
Il12a	TCAC	TC	3: 68,605,320 (GRCm39)		probably null	Het
Il6st	T	G	13: 112,640,916 (GRCm39)	D897E	probably benign	Het
Itga3	T	C	11: 94,953,551 (GRCm39)	T233A	probably benign	Het
Kcnd3	C	T	3: 105,566,082 (GRCm39)	A421V	probably damaging	Het
Lemd3	CCCTCCTCCTCCTCCTCCTCC	CCCTCCTCCTCCTCCTCC	10: 120,814,432 (GRCm39)		probably benign	Het
Miga1	T	C	3: 152,028,073 (GRCm39)	N152S	probably damaging	Het
Nckipsd	G	A	9: 108,688,320 (GRCm39)	G83S	probably damaging	Het
Nedd4	T	C	9: 72,647,469 (GRCm39)	F728L	probably damaging	Het
Nid1	G	A	13: 13,661,344 (GRCm39)	C748Y	probably damaging	Het
Nup205	A	G	6: 35,165,646 (GRCm39)	N197S	probably benign	Het
Pglyrp3	T	A	3: 91,935,481 (GRCm39)	C244S	probably damaging	Het
Rgs22	C	T	15: 36,100,038 (GRCm39)	V226I	probably benign	Het
Rtp3	T	A	9: 110,816,262 (GRCm39)	R96S	possibly damaging	Het
Serpinb8	A	T	1: 107,534,876 (GRCm39)	K316*	probably null	Het
Sp6	C	A	11: 96,912,580 (GRCm39)	P98T	possibly damaging	Het
Vmn1r15	A	T	6: 57,235,321 (GRCm39)	D63V	possibly damaging	Het
Vmn1r216	G	A	13: 23,283,849 (GRCm39)	W177*	probably null	Het
Zfp414	CAAACTCTTCCGA	CAAACTCTTCCGAAACTCTTCCGA	17: 33,849,551 (GRCm39)		probably null	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
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

2015-03-18