Mutagenetix > Incidental Mutation

Incidental Mutation 'R8022:Usp4'

617465

Institutional Source

Beutler Lab

Gene Symbol

Usp4

Ensembl Gene

ENSMUSG00000032612

Gene Name

ubiquitin specific peptidase 4 (proto-oncogene)

Synonyms

F730026I20Rik, Unp

MMRRC Submission

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.121) question?

Stock #

R8022 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

108347853-108392545 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 108378471 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Glutamic Acid to Glycine at position 576 (E576G)

Ref Sequence

ENSEMBL: ENSMUSP00000035237 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000035237] [ENSMUST00000194224] [ENSMUST00000194959]

AlphaFold

P35123

PDB Structure

Crystal structure of the N-terminal domains of the ubiquitin specific peptidase 4 (USP4) [X-RAY DIFFRACTION]

Predicted Effect

probably damaging
Transcript: ENSMUST00000035237
AA Change: E576G

PolyPhen 2 Score 0.991 (Sensitivity: 0.71; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000035237
Gene: ENSMUSG00000032612
AA Change: E576G

Domain	Start	End	E-Value	Type
DUSP	27	125	1.39e-46	SMART
Pfam:Ubiquitin_3	139	226	6.7e-34	PFAM
low complexity region	263	286	N/A	INTRINSIC
Pfam:UCH	301	919	2.2e-84	PFAM
Pfam:UCH_1	302	507	2.8e-8	PFAM
Pfam:UCH_1	605	901	1.4e-15	PFAM
low complexity region	927	938	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000194224
AA Change: E576G

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000141321
Gene: ENSMUSG00000032612
AA Change: E576G

Domain	Start	End	E-Value	Type
DUSP	27	125	5.5e-49	SMART
Pfam:Ubiquitin_3	139	226	1.3e-30	PFAM
low complexity region	263	286	N/A	INTRINSIC
Pfam:UCH	301	633	1.4e-50	PFAM
Pfam:UCH_1	302	520	2.3e-8	PFAM
low complexity region	657	673	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000194959
AA Change: E529G

PolyPhen 2 Score 0.982 (Sensitivity: 0.75; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000141368
Gene: ENSMUSG00000032612
AA Change: E529G

Domain	Start	End	E-Value	Type
DUSP	27	125	5.5e-49	SMART
Pfam:Ubiquitin_3	139	226	1.7e-30	PFAM
Pfam:UCH	254	872	7e-89	PFAM
Pfam:UCH_1	255	469	3.5e-8	PFAM
Pfam:UCH_1	566	854	2.5e-14	PFAM
low complexity region	880	891	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000195608

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.6%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is a protease that deubiquitinates target proteins such as ADORA2A and TRIM21. The encoded protein shuttles between the nucleus and cytoplasm and is involved in maintaining operational fidelity in the endoplasmic reticulum. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2011]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit increased irradiation-induced apoptosis, slow cellular growth, resistance to oncogenic transformation, and early cellular replicative senescence. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 87 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acacb	A	T	5: 114,223,854	T1386S	probably benign	Het
AI661453	T	G	17: 47,466,236	S296A	unknown	Het
Ambp	G	T	4: 63,144,197	N268K	probably damaging	Het
Ankrd11	T	C	8: 122,887,593	K2503E	probably damaging	Het
Ap1g1	C	A	8: 109,832,735	R221S	possibly damaging	Het
Ap5z1	T	C	5: 142,470,149		probably null	Het
Aspa	A	C	11: 73,322,206	N103K	probably benign	Het
BC049730	T	A	7: 24,714,174	I205N	possibly damaging	Het
Bend7	G	A	2: 4,752,779	V211I	probably benign	Het
Bsn	A	G	9: 108,114,404	M1383T	probably benign	Het
Cad	G	T	5: 31,068,806	V1117F	probably damaging	Het
Cdh2	A	G	18: 16,590,301	L856S	probably damaging	Het
Cdh7	T	A	1: 110,061,108	S247T	probably benign	Het
Ces1b	A	G	8: 93,069,315		probably null	Het
Chd7	T	A	4: 8,751,605	V34E	unknown	Het
Clca3a2	A	T	3: 144,805,766	F623I	probably damaging	Het
Cope	T	G	8: 70,312,803	M217R	probably benign	Het
Crim1	T	A	17: 78,315,555	I394N	possibly damaging	Het
Crnkl1	A	T	2: 145,918,566	I644N	probably damaging	Het
Cry1	G	A	10: 85,146,402	A360V	probably damaging	Het
Ctcfl	A	T	2: 173,118,766	V8D	probably benign	Het
Cyp2d34	G	A	15: 82,616,114	Q475*	probably null	Het
Cyp39a1	T	C	17: 43,746,577	Y436H	probably damaging	Het
Cyp3a25	T	A	5: 145,977,668	Q484L	probably benign	Het
Dnah1	A	G	14: 31,265,014	F3607S	probably damaging	Het
Dnali1	T	A	4: 125,065,530	K23N	possibly damaging	Het
Ecel1	T	C	1: 87,153,330	I313V	probably benign	Het
Ehhadh	C	A	16: 21,777,820	A53S	probably benign	Het
Epcam	T	C	17: 87,646,308	S277P	probably benign	Het
Fbxo10	T	C	4: 45,062,062	I155V	possibly damaging	Het
Fgd6	A	T	10: 94,044,344	K353N	possibly damaging	Het
Glce	A	T	9: 62,060,591	M426K	probably benign	Het
Glmp	A	T	3: 88,326,520	N228I	probably damaging	Het
Gm4787	C	A	12: 81,377,720	V555F	possibly damaging	Het
Gm5114	T	A	7: 39,409,376	H273L	probably benign	Het
Gzmg	T	A	14: 56,157,446	T122S	probably benign	Het
Hace1	T	C	10: 45,700,970	V820A	probably damaging	Het
Igf2r	T	A	17: 12,718,795	D535V	probably damaging	Het
Kcnd3	A	G	3: 105,458,873	M20V	probably benign	Het
Kcnn3	T	G	3: 89,609,703	I473S	possibly damaging	Het
Klhl35	T	A	7: 99,473,239	F94Y	unknown	Het
Kmt2c	C	T	5: 25,281,680	V4712I	possibly damaging	Het
Lepr	A	G	4: 101,782,557	E740G	probably benign	Het
Lmod3	T	C	6: 97,248,299	D187G	probably benign	Het
Lsm3	C	T	6: 91,519,561	H49Y	probably benign	Het
Magi1	T	C	6: 93,697,365	S962G	probably damaging	Het
Man2b1	G	A	8: 85,095,613	R782Q	probably damaging	Het
Mical2	A	T	7: 112,303,767	K148N	probably damaging	Het
Nbeal1	C	T	1: 60,260,272	Q1256*	probably null	Het
Ncam1	G	T	9: 49,564,892	A299D	possibly damaging	Het
Ncapg	A	G	5: 45,681,794	D512G	probably damaging	Het
Nkiras2	A	G	11: 100,624,287	N28D	probably benign	Het
Nprl2	A	C	9: 107,543,061	K53T	probably damaging	Het
Nr4a3	T	A	4: 48,051,510	I88N	probably damaging	Het
Oas3	A	G	5: 120,756,966	I986T	possibly damaging	Het
Olfr809	A	T	10: 129,776,785	L305F	possibly damaging	Het
Pcsk1	A	T	13: 75,099,293	Y187F	possibly damaging	Het
Pgc	A	G	17: 47,728,776	T32A	probably benign	Het
Ranbp2	A	C	10: 58,485,861	D2660A	possibly damaging	Het
Retreg1	A	G	15: 25,843,479	R46G		Het
Rrbp1	C	A	2: 143,956,792	K1100N	probably benign	Het
Rsph10b	A	T	5: 143,967,232	T676S	probably benign	Het
Setdb1	A	T	3: 95,338,599	F672I	probably damaging	Het
Setdb1	T	A	3: 95,347,085	D195V	probably damaging	Het
Slc12a8	A	G	16: 33,625,086	E450G	probably benign	Het
Slc1a7	G	A	4: 108,012,276	V513M	probably benign	Het
Slc25a12	A	T	2: 71,275,189	V667E	unknown	Het
Slc39a3	T	C	10: 81,031,277	T212A	probably benign	Het
Slc45a1	C	T	4: 150,638,309	G373S	possibly damaging	Het
Snx11	G	A	11: 96,772,854	T53M	probably damaging	Het
Snx33	A	G	9: 56,925,340	F482L	possibly damaging	Het
Srebf2	C	T	15: 82,178,765	R468C	probably damaging	Het
Stk32a	C	T	18: 43,315,101	Q382*	probably null	Het
Sun3	C	A	11: 9,023,376	S167I	probably damaging	Het
Sycp2	A	G	2: 178,355,062	L1116P	probably damaging	Het
Thbs4	T	G	13: 92,752,447	T913P	probably damaging	Het
Trav8d-1	C	T	14: 52,778,827	Q57*	probably null	Het
Trio	C	G	15: 27,749,866	V2250L	probably benign	Het
Unc119b	A	T	5: 115,127,043	I204N	probably damaging	Het
Uvssa	T	A	5: 33,409,504	L515Q	probably damaging	Het
Xkr8	T	C	4: 132,732,338	Y43C	probably damaging	Het
Xpo6	G	A	7: 126,169,254	L94F	probably benign	Het
Zbtb11	A	G	16: 56,006,020	K804R	probably damaging	Het
Zfp616	A	G	11: 74,084,068	R479G	probably benign	Het
Zfp661	T	C	2: 127,577,924	T99A	probably benign	Het
Zfp839	A	T	12: 110,855,098	Q115H	probably damaging	Het
Zyg11a	C	T	4: 108,189,568		probably null	Het

Other mutations in Usp4

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01530:Usp4	APN	9	108362900	critical splice donor site	probably null
IGL01663:Usp4	APN	9	108365880	missense	possibly damaging	0.80
IGL02105:Usp4	APN	9	108384932	missense	probably damaging	1.00
IGL02486:Usp4	APN	9	108351029	missense	probably damaging	1.00
kleinesrot	UTSW	9	108356462	missense	possibly damaging	0.95
R0148:Usp4	UTSW	9	108391671	splice site	probably null
R0285:Usp4	UTSW	9	108378564	missense	probably benign	0.33
R0591:Usp4	UTSW	9	108348029	splice site	probably benign
R0594:Usp4	UTSW	9	108370881	splice site	probably null
R0616:Usp4	UTSW	9	108366804	missense	probably benign
R1329:Usp4	UTSW	9	108372566	missense	probably damaging	1.00
R1508:Usp4	UTSW	9	108372674	missense	probably benign	0.14
R1752:Usp4	UTSW	9	108374242	missense	probably damaging	1.00
R1824:Usp4	UTSW	9	108348008	missense	probably damaging	1.00
R1846:Usp4	UTSW	9	108372736	missense	probably benign
R2196:Usp4	UTSW	9	108373686	missense	probably benign	0.07
R2925:Usp4	UTSW	9	108367856	missense	probably damaging	1.00
R4126:Usp4	UTSW	9	108360117	missense	probably benign	0.10
R4345:Usp4	UTSW	9	108368023	intron	probably benign
R4965:Usp4	UTSW	9	108362620	missense	probably damaging	1.00
R4981:Usp4	UTSW	9	108381418	missense	probably benign	0.00
R5110:Usp4	UTSW	9	108362678	missense	probably damaging	1.00
R5580:Usp4	UTSW	9	108365859	missense	probably benign	0.09
R5586:Usp4	UTSW	9	108356462	missense	possibly damaging	0.95
R5927:Usp4	UTSW	9	108391760	missense	probably benign	0.09
R6025:Usp4	UTSW	9	108360123	missense	possibly damaging	0.70
R6112:Usp4	UTSW	9	108356504	missense	probably damaging	1.00
R6197:Usp4	UTSW	9	108370955	missense	probably damaging	1.00
R6742:Usp4	UTSW	9	108374239	missense	possibly damaging	0.74
R7320:Usp4	UTSW	9	108388306	missense	probably benign	0.00
R7458:Usp4	UTSW	9	108367856	missense	probably damaging	1.00
R7531:Usp4	UTSW	9	108372680	missense	probably damaging	1.00
R7563:Usp4	UTSW	9	108379344	missense	probably benign
R8510:Usp4	UTSW	9	108388382	critical splice donor site	probably null
R8996:Usp4	UTSW	9	108391710	missense	probably damaging	1.00
R9151:Usp4	UTSW	9	108366812	missense	probably benign	0.00
R9775:Usp4	UTSW	9	108362581	missense	probably damaging	1.00
X0026:Usp4	UTSW	9	108347870	unclassified	probably benign

Predicted Primers

PCR Primer
(F):5'- TCAACCTGTAATCACCTTGGAAATGG -3'
(R):5'- GTGCAAAACCCATTCATCTCAG -3'

Sequencing Primer
(F):5'- AATCACCTTGGAAATGGCTTATCTCC -3'
(R):5'- ACCATGCGATTACATTTCCAGTAC -3'

Posted On

2020-01-23