Mutagenetix > Incidental Mutation

Incidental Mutation 'R2484:Nub1'

250798

Institutional Source

Beutler Lab

Gene Symbol

Nub1

Ensembl Gene

ENSMUSG00000028954

Gene Name

negative regulator of ubiquitin-like proteins 1

Synonyms

NY-REN-18, 6330412F12Rik, BS4, 4931404D21Rik

MMRRC Submission

040408-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.872) question?

Stock #

R2484 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

24890813-24915376 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 24913700 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glycine at position 503 (D503G)

Ref Sequence

ENSEMBL: ENSMUSP00000070265 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000068693] [ENSMUST00000068825] [ENSMUST00000197407]

AlphaFold

P54729

PDB Structure

Solution Structure of RSGI RUH-012, a UBA Domain from Mouse cDNA [SOLUTION NMR]

Predicted Effect

probably benign
Transcript: ENSMUST00000068693

SMART Domains

Protein: ENSMUSP00000064785
Gene: ENSMUSG00000055235

Domain	Start	End	E-Value	Type
WD40	4	43	1.62e-8	SMART
WD40	46	83	3.17e-2	SMART
WD40	86	123	1.9e-5	SMART
WD40	126	179	3e-3	SMART
WD40	182	221	2.78e-7	SMART
WD40	224	261	9.9e-4	SMART
WD40	264	301	1.29e-2	SMART
WD40	304	341	6.28e-6	SMART

Predicted Effect

possibly damaging
Transcript: ENSMUST00000068825
AA Change: D503G

PolyPhen 2 Score 0.906 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000070265
Gene: ENSMUSG00000028954
AA Change: D503G

Domain	Start	End	E-Value	Type
coiled coil region	37	70	N/A	INTRINSIC
PDB:1WJU\|A	71	162	2e-45	PDB
low complexity region	167	186	N/A	INTRINSIC
UBA	375	412	7.29e-8	SMART
UBA	431	468	1.61e-9	SMART
UBA	490	527	1.95e-8	SMART
low complexity region	539	565	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000127320

SMART Domains

Protein: ENSMUSP00000119649
Gene: ENSMUSG00000055235

Domain	Start	End	E-Value	Type
WD40	29	63	1.27e2	SMART
WD40	66	103	6.28e-6	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000142607

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000181925

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000196443

Predicted Effect

possibly damaging
Transcript: ENSMUST00000197407
AA Change: D527G

PolyPhen 2 Score 0.843 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000143657
Gene: ENSMUSG00000028954
AA Change: D527G

Domain	Start	End	E-Value	Type
coiled coil region	61	94	N/A	INTRINSIC
PDB:1WJU\|A	95	186	2e-45	PDB
low complexity region	191	210	N/A	INTRINSIC
UBA	399	436	3.5e-10	SMART
UBA	455	492	8.1e-12	SMART
UBA	514	551	9.5e-11	SMART
low complexity region	563	589	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000200337

Meta Mutation Damage Score

0.4042

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.5%
20x: 95.7%

Validation Efficiency

97% (72/74)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein that functions as a negative regulator of NEDD8, a ubiquitin-like protein that conjugates with cullin family members in order to regulate vital biological events. The protein encoded by this gene regulates the NEDD8 conjugation system post-transcriptionally by recruiting NEDD8 and its conjugates to the proteasome for degradation. This protein interacts with the product of the AIPL1 gene, which is associated with Leber congenital amaurosis, an inherited retinopathy, and mutations in that gene can abolish interaction with this protein, which may contribute to the pathogenesis. This protein is also known to accumulate in Lewy bodies in Parkinson's disease and dementia with Lewy bodies, and in glial cytoplasmic inclusions in multiple system atrophy, with this abnormal accumulation being specific to alpha-synucleinopathy lesions. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Aug 2011]

Allele List at MGI

Other mutations in this stock

Total: 75 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4932414N04Rik	G	A	2: 68,541,819 (GRCm39)	D46N	possibly damaging	Het
A830018L16Rik	G	T	1: 11,666,526 (GRCm39)	A278S	probably damaging	Het
Acsbg3	A	G	17: 57,189,641 (GRCm39)	N252S	probably benign	Het
Adarb2	A	T	13: 8,619,810 (GRCm39)	K99*	probably null	Het
Arsi	G	A	18: 61,049,723 (GRCm39)	G202E	probably benign	Het
Atxn1l	A	G	8: 110,458,883 (GRCm39)	S460P	probably damaging	Het
Bicra	T	A	7: 15,722,605 (GRCm39)	N304I	possibly damaging	Het
Capn10	A	T	1: 92,872,565 (GRCm39)	D470V	probably damaging	Het
Chchd3	A	G	6: 32,780,950 (GRCm39)	Y184H	possibly damaging	Het
Col6a6	T	C	9: 105,658,003 (GRCm39)	I736M	probably damaging	Het
Dhx36	T	A	3: 62,380,236 (GRCm39)	N820I	probably damaging	Het
Drd4	C	T	7: 140,874,649 (GRCm39)	P347S	probably benign	Het
Ephx1	A	T	1: 180,817,537 (GRCm39)	V378D	probably damaging	Het
Extl3	A	T	14: 65,313,184 (GRCm39)	V666E	probably damaging	Het
Fam20c	G	C	5: 138,794,872 (GRCm39)	R500S	probably benign	Het
Glod4	A	T	11: 76,130,344 (GRCm39)	D42E	probably damaging	Het
Golga2	T	C	2: 32,194,782 (GRCm39)	I643T	probably benign	Het
Hnf1b	A	T	11: 83,752,661 (GRCm39)	T73S	probably benign	Het
Hydin	A	G	8: 111,239,747 (GRCm39)	Y2009C	possibly damaging	Het
Ido2	A	G	8: 25,023,831 (GRCm39)	C336R	probably damaging	Het
Ifngr1	T	C	10: 19,477,163 (GRCm39)	V108A	probably damaging	Het
Igbp1b	A	T	6: 138,634,492 (GRCm39)	N317K	probably benign	Het
Ints14	A	G	9: 64,893,366 (GRCm39)	S511G	probably benign	Het
Itpr1	T	C	6: 108,346,071 (GRCm39)	S125P	probably damaging	Het
Jag1	T	C	2: 136,926,620 (GRCm39)	T975A	possibly damaging	Het
Klra17	A	G	6: 129,845,720 (GRCm39)	W165R	probably damaging	Het
Leo1	T	A	9: 75,352,755 (GRCm39)	N99K	possibly damaging	Het
Lonp1	C	A	17: 56,921,659 (GRCm39)	G883C	probably damaging	Het
Lpin1	C	A	12: 16,597,500 (GRCm39)	G682W	probably damaging	Het
Macf1	A	C	4: 123,367,465 (GRCm39)	L2432R	probably damaging	Het
Med12l	T	G	3: 59,205,259 (GRCm39)	I2075M	probably benign	Het
Mroh6	A	G	15: 75,756,177 (GRCm39)	S660P	probably benign	Het
Myh6	G	T	14: 55,198,699 (GRCm39)	Y309*	probably null	Het
Myof	C	T	19: 37,892,291 (GRCm39)	R1154H	probably benign	Het
Myrip	G	A	9: 120,253,685 (GRCm39)	E253K	probably benign	Het
Ndst3	T	C	3: 123,346,186 (GRCm39)	D281G	possibly damaging	Het
Nipbl	T	C	15: 8,353,182 (GRCm39)	K1788R	probably damaging	Het
Nol12	A	G	15: 78,824,717 (GRCm39)		probably benign	Het
Nptn	A	G	9: 58,550,956 (GRCm39)	T212A	possibly damaging	Het
Nptx2	C	T	5: 144,493,155 (GRCm39)	A414V	probably damaging	Het
Obscn	T	A	11: 58,898,366 (GRCm39)		probably benign	Het
Or4a80	A	G	2: 89,582,578 (GRCm39)	I198T	probably benign	Het
Or51q1	A	G	7: 103,628,545 (GRCm39)	T49A	probably benign	Het
Or5b97	C	T	19: 12,879,005 (GRCm39)	M46I	probably benign	Het
Pcnx2	T	C	8: 126,617,859 (GRCm39)	E132G	probably damaging	Het
Pkdcc	A	G	17: 83,529,667 (GRCm39)		probably benign	Het
Prdm2	T	A	4: 142,861,776 (GRCm39)	I505F	probably damaging	Het
Psmc3	C	G	2: 90,886,346 (GRCm39)	Q169E	probably damaging	Het
Ptger4	A	T	15: 5,264,654 (GRCm39)	I334N	probably benign	Het
Ptrh1	T	C	2: 32,667,183 (GRCm39)	M161T	probably benign	Het
Rapgef6	T	A	11: 54,533,582 (GRCm39)	V482D	possibly damaging	Het
Rdh16f2	T	C	10: 127,710,946 (GRCm39)	S188P	probably damaging	Het
Rrh	T	C	3: 129,616,040 (GRCm39)	Y31C	probably damaging	Het
Selp	G	T	1: 163,971,523 (GRCm39)	W659L	probably benign	Het
Selp	G	T	1: 163,971,524 (GRCm39)	W659C	probably damaging	Het
Shh	A	G	5: 28,671,740 (GRCm39)	C8R	probably benign	Het
Spdye4b	C	A	5: 143,187,848 (GRCm39)	S167R	possibly damaging	Het
Strip1	T	C	3: 107,535,537 (GRCm39)	Y62C	possibly damaging	Het
Sucla2	A	T	14: 73,819,149 (GRCm39)	I232F	probably benign	Het
Sugp1	A	G	8: 70,522,174 (GRCm39)	D437G	possibly damaging	Het
Taf1a	A	G	1: 183,177,422 (GRCm39)		probably benign	Het
Tbc1d20	T	A	2: 152,153,283 (GRCm39)	M271K	probably damaging	Het
Tecpr2	T	C	12: 110,899,752 (GRCm39)	S707P	probably benign	Het
Tert	G	A	13: 73,796,104 (GRCm39)	R1017H	probably benign	Het
Tox	C	G	4: 6,688,886 (GRCm39)	V493L	probably damaging	Het
Tpo	C	T	12: 30,153,968 (GRCm39)	A246T	probably benign	Het
Traf7	A	T	17: 24,730,613 (GRCm39)	V358D	probably damaging	Het
Trim56	C	T	5: 137,141,528 (GRCm39)	V663M	possibly damaging	Het
Unc80	C	T	1: 66,560,740 (GRCm39)	H823Y	possibly damaging	Het
Usf3	C	T	16: 44,041,045 (GRCm39)	H1842Y	probably damaging	Het
Uvrag	T	C	7: 98,537,668 (GRCm39)	E509G	probably benign	Het
Vmn2r5	T	C	3: 64,411,392 (GRCm39)	D305G	possibly damaging	Het
Vmn2r52	T	C	7: 9,903,058 (GRCm39)	R457G	probably damaging	Het
Vti1a	A	C	19: 55,369,411 (GRCm39)	N101T	possibly damaging	Het
Zfp236	A	G	18: 82,686,762 (GRCm39)	F259L	probably benign	Het

Other mutations in Nub1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL02367:Nub1	APN	5	24,894,392 (GRCm39)	start codon destroyed	probably null	0.99
IGL02626:Nub1	APN	5	24,908,462 (GRCm39)	missense	possibly damaging	0.65
IGL02629:Nub1	APN	5	24,908,462 (GRCm39)	missense	possibly damaging	0.65
IGL02633:Nub1	APN	5	24,897,931 (GRCm39)	missense	probably benign	0.00
IGL02798:Nub1	APN	5	24,897,812 (GRCm39)	missense	probably damaging	1.00
IGL03384:Nub1	APN	5	24,902,424 (GRCm39)	splice site	probably null
IGL03384:Nub1	APN	5	24,902,425 (GRCm39)	splice site	probably benign
R2679:Nub1	UTSW	5	24,897,923 (GRCm39)	missense	possibly damaging	0.93
R3825:Nub1	UTSW	5	24,912,851 (GRCm39)	missense	probably benign	0.21
R4180:Nub1	UTSW	5	24,897,875 (GRCm39)	missense	probably damaging	0.99
R4593:Nub1	UTSW	5	24,914,119 (GRCm39)	missense	probably damaging	1.00
R4921:Nub1	UTSW	5	24,906,467 (GRCm39)	missense	probably benign	0.38
R5175:Nub1	UTSW	5	24,907,446 (GRCm39)	missense	probably benign	0.28
R5282:Nub1	UTSW	5	24,900,533 (GRCm39)	missense	probably benign	0.04
R5346:Nub1	UTSW	5	24,902,414 (GRCm39)	missense	probably damaging	0.96
R5533:Nub1	UTSW	5	24,907,379 (GRCm39)	missense	possibly damaging	0.93
R5567:Nub1	UTSW	5	24,913,814 (GRCm39)	missense	possibly damaging	0.54
R5802:Nub1	UTSW	5	24,907,439 (GRCm39)	missense	possibly damaging	0.95
R6966:Nub1	UTSW	5	24,894,470 (GRCm39)	missense	probably damaging	1.00
R6967:Nub1	UTSW	5	24,913,709 (GRCm39)	missense	probably benign
R7540:Nub1	UTSW	5	24,906,527 (GRCm39)	missense	probably damaging	1.00
R7787:Nub1	UTSW	5	24,913,801 (GRCm39)	missense	probably benign	0.03
R8478:Nub1	UTSW	5	24,906,422 (GRCm39)	missense	probably benign	0.01
R9746:Nub1	UTSW	5	24,908,483 (GRCm39)	missense	probably damaging	1.00
R9760:Nub1	UTSW	5	24,897,965 (GRCm39)	missense	possibly damaging	0.76
Z1177:Nub1	UTSW	5	24,907,456 (GRCm39)	missense	probably benign	0.00

Predicted Primers

PCR Primer
(F):5'- TTAGACCAGGTCTTCAGAGGC -3'
(R):5'- CAGACCTCAGATCTACCTGCAG -3'

Sequencing Primer
(F):5'- AGAGGCCCTTTCTACATGGC -3'
(R):5'- TCAGATCTACCTGCAGAGTCAGATG -3'

Posted On

2014-12-04