Mutagenetix > Incidental Mutation

Incidental Mutation 'R1713:Nop56'

190742

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

039746-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.964) question?

Stock #

R1713 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

130116350-130121233 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 130119886 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 109 (V109A)

Ref Sequence

ENSEMBL: ENSMUSP00000124080 (fasta)

Gene Model

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

AlphaFold

Q9D6Z1

Predicted Effect

possibly damaging
Transcript: ENSMUST00000028890
AA Change: V142A

PolyPhen 2 Score 0.697 (Sensitivity: 0.86; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000028890
Gene: ENSMUSG00000027405
AA Change: V142A

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

possibly damaging
Transcript: ENSMUST00000103198
AA Change: V426A

PolyPhen 2 Score 0.483 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000099487
Gene: ENSMUSG00000027405
AA Change: V426A

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

possibly damaging
Transcript: ENSMUST00000159373
AA Change: V109A

PolyPhen 2 Score 0.845 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000124080
Gene: ENSMUSG00000027405
AA Change: V109A

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: ENSMUST00000146454
AA Change: V170A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000125304
Gene: ENSMUSG00000027405
AA Change: V170A

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
AA Change: V121A

PolyPhen 2 Score 0.056 (Sensitivity: 0.94; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000123890
Gene: ENSMUSG00000027405
AA Change: V121A

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: ENSMUST00000150745

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000133351

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000149843

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000153353

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000145335

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000160183

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000138163

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: 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: ENSMUST00000162063

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000161543

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000175746

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000161025

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000160976

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

0.0592

Coding Region Coverage

1x: 99.1%
3x: 98.5%
10x: 96.7%
20x: 93.6%

Validation Efficiency

98% (96/98)

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: 90 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4921539E11Rik	T	A	4: 103,127,964 (GRCm39)	I54F	possibly damaging	Het
Ackr1	A	T	1: 173,159,916 (GRCm39)	H134Q	probably benign	Het
Agtr1b	A	T	3: 20,370,473 (GRCm39)	F44L	probably benign	Het
Ahnak	G	A	19: 8,989,173 (GRCm39)	D3486N	possibly damaging	Het
Akap9	T	C	5: 4,089,345 (GRCm39)		probably null	Het
Anks6	T	A	4: 47,039,726 (GRCm39)	Q495L	probably benign	Het
Arpp21	A	G	9: 111,896,237 (GRCm39)	S684P	probably damaging	Het
Ash1l	A	G	3: 88,983,531 (GRCm39)	E2911G	probably damaging	Het
Avpi1	C	T	19: 42,113,248 (GRCm39)	E70K	probably damaging	Het
Btbd17	G	T	11: 114,686,650 (GRCm39)	P9T	probably benign	Het
C4b	A	G	17: 34,948,245 (GRCm39)		probably benign	Het
Carm1	T	C	9: 21,497,785 (GRCm39)	V385A	probably damaging	Het
Casd1	A	G	6: 4,624,104 (GRCm39)	D299G	probably damaging	Het
Clca3a1	T	A	3: 144,730,307 (GRCm39)	K179N	probably benign	Het
Col1a2	T	C	6: 4,538,691 (GRCm39)	S1204P	unknown	Het
Col24a1	C	T	3: 145,072,624 (GRCm39)	Q780*	probably null	Het
Cxadr	C	A	16: 78,131,133 (GRCm39)	N216K	probably damaging	Het
Daam1	C	T	12: 71,942,656 (GRCm39)	T40I	unknown	Het
Dab2	C	T	15: 6,459,182 (GRCm39)	P365S	possibly damaging	Het
Dnah1	A	T	14: 31,001,139 (GRCm39)	I2402N	probably damaging	Het
Dscaml1	T	A	9: 45,663,988 (GRCm39)	S1954R	possibly damaging	Het
Dync2h1	T	C	9: 7,131,891 (GRCm39)	T1639A	probably benign	Het
Ebf1	A	T	11: 44,815,393 (GRCm39)	I336F	probably damaging	Het
Ebna1bp2	A	G	4: 118,482,881 (GRCm39)	N290S	possibly damaging	Het
Gabra2	A	G	5: 71,171,906 (GRCm39)	I110T	probably benign	Het
Galk2	A	G	2: 125,773,210 (GRCm39)	N203S	probably benign	Het
Gria4	T	C	9: 4,424,448 (GRCm39)	T806A	probably benign	Het
Impg2	A	G	16: 56,080,889 (GRCm39)	T789A	probably benign	Het
Itga6	A	G	2: 71,617,546 (GRCm39)	T22A	probably benign	Het
Itgb4	T	A	11: 115,894,315 (GRCm39)	I1312N	probably damaging	Het
Kdm4c	A	G	4: 74,216,721 (GRCm39)	D160G	probably benign	Het
Kdr	A	G	5: 76,129,127 (GRCm39)	V173A	probably benign	Het
Kif14	T	C	1: 136,455,202 (GRCm39)	S1575P	probably benign	Het
Lcp1	G	A	14: 75,436,884 (GRCm39)		probably null	Het
Lipe	C	A	7: 25,084,750 (GRCm39)	S516I	probably damaging	Het
Lrrc61	G	A	6: 48,545,708 (GRCm39)	R177Q	possibly damaging	Het
Macf1	A	G	4: 123,272,487 (GRCm39)	I6429T	probably damaging	Het
Map3k4	C	T	17: 12,468,458 (GRCm39)	E1012K	probably benign	Het
Map3k5	T	C	10: 19,986,593 (GRCm39)	F936L	possibly damaging	Het
Mllt3	A	T	4: 87,701,901 (GRCm39)	N497K	probably damaging	Het
Moxd1	G	A	10: 24,157,394 (GRCm39)	G342D	probably damaging	Het
Mtdh	A	C	15: 34,114,985 (GRCm39)	Q202H	possibly damaging	Het
Nav1	A	G	1: 135,522,972 (GRCm39)		probably benign	Het
Obscn	T	C	11: 58,970,712 (GRCm39)	D2540G	probably damaging	Het
Omg	T	C	11: 79,393,679 (GRCm39)	I60V	probably benign	Het
Or10q12	A	T	19: 13,746,659 (GRCm39)	T318S	probably benign	Het
Or12e9	A	T	2: 87,202,290 (GRCm39)	Y138F	probably damaging	Het
Osbpl5	G	A	7: 143,248,110 (GRCm39)	H652Y	probably damaging	Het
Parvb	T	C	15: 84,182,192 (GRCm39)		probably benign	Het
Pcdhb3	A	C	18: 37,436,375 (GRCm39)	E780D	probably benign	Het
Pik3c3	A	G	18: 30,456,639 (GRCm39)	D723G	possibly damaging	Het
Prkdc	T	C	16: 15,612,958 (GRCm39)	V3172A	probably benign	Het
Psme4	G	T	11: 30,756,310 (GRCm39)	W272L	probably damaging	Het
Rem1	G	A	2: 152,476,455 (GRCm39)	V238M	probably damaging	Het
Rhobtb1	A	C	10: 69,108,601 (GRCm39)	S434R	probably benign	Het
Rhobtb1	G	C	10: 69,108,602 (GRCm39)	S434T	possibly damaging	Het
Rnf8	T	C	17: 29,853,735 (GRCm39)	F413S	probably damaging	Het
Rpn2	A	G	2: 157,156,888 (GRCm39)	N497S	probably damaging	Het
Rsbn1l	G	T	5: 21,156,488 (GRCm39)	P99Q	probably benign	Het
Serpinb3b	A	T	1: 107,083,164 (GRCm39)	M246K	probably benign	Het
Sgsm2	T	C	11: 74,787,652 (GRCm39)	E19G	probably null	Het
Shank1	A	G	7: 43,969,161 (GRCm39)	H352R	unknown	Het
Slc17a7	A	G	7: 44,819,728 (GRCm39)	I177V	probably benign	Het
Slc28a2	T	A	2: 122,281,494 (GRCm39)	F228I	probably damaging	Het
Slc35b4	C	T	6: 34,147,484 (GRCm39)	V35I	probably benign	Het
Slc38a1	T	C	15: 96,476,641 (GRCm39)	I407V	probably damaging	Het
Slc39a13	A	G	2: 90,893,442 (GRCm39)	V326A	probably damaging	Het
Slc44a5	T	C	3: 153,944,743 (GRCm39)	L120P	probably damaging	Het
Slfn3	T	C	11: 83,104,140 (GRCm39)	I214T	probably damaging	Het
Slitrk3	A	C	3: 72,957,024 (GRCm39)	S583A	probably benign	Het
Snx14	T	C	9: 88,297,728 (GRCm39)	Y180C	probably damaging	Het
Sorl1	T	A	9: 41,907,538 (GRCm39)	K1483I	probably benign	Het
Ssrp1	C	A	2: 84,871,104 (GRCm39)	H247N	probably damaging	Het
Stk39	A	T	2: 68,137,460 (GRCm39)		probably benign	Het
Syde1	C	T	10: 78,421,530 (GRCm39)	G674R	probably damaging	Het
Tent4a	A	T	13: 69,651,170 (GRCm39)	I565N	probably benign	Het
Themis3	G	A	17: 66,862,848 (GRCm39)	S370L	probably benign	Het
Tll1	T	A	8: 64,554,907 (GRCm39)	N259Y	probably damaging	Het
Tnip2	T	G	5: 34,661,175 (GRCm39)		probably benign	Het
Top2b	T	C	14: 16,409,823 (GRCm38)	V830A	probably benign	Het
Trpm8	T	A	1: 88,292,802 (GRCm39)	N934K	probably damaging	Het
Ttc14	A	G	3: 33,857,069 (GRCm39)	Y179C	probably damaging	Het
Ttn	T	G	2: 76,573,965 (GRCm39)	I17316L	possibly damaging	Het
Tufm	T	C	7: 126,086,871 (GRCm39)	V52A	probably benign	Het
Vamp8	T	A	6: 72,365,270 (GRCm39)	N20I	probably benign	Het
Vmn1r170	A	T	7: 23,306,288 (GRCm39)	H230L	probably benign	Het
Vmn2r50	T	G	7: 9,771,731 (GRCm39)	T657P	probably damaging	Het
Xirp2	G	A	2: 67,342,762 (GRCm39)	G1668R	probably benign	Het
Zik1	C	A	7: 10,224,311 (GRCm39)	R262L	possibly damaging	Het
Zscan25	T	G	5: 145,220,501 (GRCm39)	Y99D	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
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
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'- ACCTTGGCAGCTTCTACAATGATGG -3'
(R):5'- TGGTGATTTCAGCAGCCGCTTC -3'

Sequencing Primer
(F):5'- TCGTCAACAGAGTTCACCTAGTG -3'
(R):5'- TTCCTCTGCCTGGCAAAAAAG -3'

Posted On

2014-05-14