Mutagenetix > Incidental Mutation

Incidental Mutation 'R5586:Usp4'

438728

Institutional Source

Beutler Lab

Gene Symbol

Usp4

Ensembl Gene

ENSMUSG00000032612

Gene Name

ubiquitin specific peptidase 4 (proto-oncogene)

Synonyms

F730026I20Rik, Unp

MMRRC Submission

043140-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.150) question?

Stock #

R5586 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

108347853-108392545 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 108356462 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 94 (V94A)

Ref Sequence

ENSEMBL: ENSMUSP00000141321 (fasta)

Gene Model

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

AlphaFold

P35123

Predicted Effect

possibly damaging
Transcript: ENSMUST00000035237
AA Change: V94A

PolyPhen 2 Score 0.803 (Sensitivity: 0.84; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000035237
Gene: ENSMUSG00000032612
AA Change: V94A

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

noncoding transcript
Transcript: ENSMUST00000192750

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000193093

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000194034

Predicted Effect

possibly damaging
Transcript: ENSMUST00000194224
AA Change: V94A

PolyPhen 2 Score 0.952 (Sensitivity: 0.79; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000141321
Gene: ENSMUSG00000032612
AA Change: V94A

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

possibly damaging
Transcript: ENSMUST00000194959
AA Change: V94A

PolyPhen 2 Score 0.917 (Sensitivity: 0.81; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000141368
Gene: ENSMUSG00000032612
AA Change: V94A

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

noncoding transcript
Transcript: ENSMUST00000195283

Meta Mutation Damage Score

0.6609

Coding Region Coverage

1x: 99.9%
3x: 99.7%
10x: 98.6%
20x: 96.0%

Validation Efficiency

98% (101/103)

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: 92 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930432E11Rik	A	G	7: 29,577,728		noncoding transcript	Het
Aaas	A	T	15: 102,346,676		probably null	Het
Abcc3	G	A	11: 94,364,421	R600W	probably damaging	Het
Abhd13	A	T	8: 9,988,318	Q305L	probably benign	Het
Adcy5	A	T	16: 35,157,116	I340F	probably damaging	Het
Adgrl3	T	A	5: 81,724,147	I964N	probably damaging	Het
Anks1b	T	A	10: 90,077,064	H316Q	probably damaging	Het
Ap3d1	A	T	10: 80,719,130	F454I	possibly damaging	Het
Apol7c	T	C	15: 77,526,399	R116G	possibly damaging	Het
Arhgap5	A	G	12: 52,519,912	E1222G	possibly damaging	Het
AW551984	A	G	9: 39,591,263	V673A	probably benign	Het
Baiap2l1	A	G	5: 144,282,139	S220P	probably damaging	Het
Bcl6	A	G	16: 23,973,176	F143L	probably benign	Het
Calb1	A	T	4: 15,900,811	T165S	probably benign	Het
Ccdc66	C	A	14: 27,506,711	G6C	probably damaging	Het
Ccdc88a	A	G	11: 29,503,484	I344V	probably benign	Het
Cdh19	T	A	1: 110,929,857	D249V	probably damaging	Het
Ces1c	T	A	8: 93,127,599	T103S	probably benign	Het
Cfap54	T	A	10: 92,972,611	K1401*	probably null	Het
Copa	T	A	1: 172,105,222	N371K	probably damaging	Het
Cyp2b10	A	T	7: 25,917,012	Y348F	probably damaging	Het
Dennd5a	T	C	7: 109,905,721	R861G	possibly damaging	Het
Dhx8	T	C	11: 101,733,036		probably benign	Het
Dido1	C	T	2: 180,659,652	W2153*	probably null	Het
Dlgap1	T	A	17: 70,818,161	V969D	probably damaging	Het
Dvl3	A	G	16: 20,517,289	D32G	probably damaging	Het
Epdr1	T	C	13: 19,594,548	D24G	probably benign	Het
Etnk2	T	A	1: 133,379,305		probably null	Het
Fam129a	C	T	1: 151,717,556	T664I	probably benign	Het
Fhad1	C	T	4: 141,905,131	M1232I	probably benign	Het
Gcnt2	A	C	13: 40,860,953	E200A	probably damaging	Het
Gm12800	T	A	4: 101,910,120	F189I	probably benign	Het
Gm5174	A	G	10: 86,656,545		noncoding transcript	Het
Gm6408	T	A	5: 146,484,457	F299I	possibly damaging	Het
Gpr85	G	T	6: 13,836,001	Y301*	probably null	Het
Gucy2e	G	T	11: 69,226,256	P780T	probably damaging	Het
Icam5	A	T	9: 21,034,820	N316I	probably damaging	Het
Ifit1bl1	C	T	19: 34,594,277	R260Q	probably damaging	Het
Il1r1	A	C	1: 40,225,251		probably benign	Het
Kif3c	A	T	12: 3,389,656	I86F	probably benign	Het
Klhdc2	A	G	12: 69,307,693		probably null	Het
Mast2	A	G	4: 116,435,563	L9P	probably damaging	Het
Mcoln1	G	T	8: 3,510,389	C316F	probably damaging	Het
Mon1a	A	T	9: 107,898,695	D4V	probably damaging	Het
Ms4a18	T	A	19: 11,013,674	M19L	probably benign	Het
Nbea	T	C	3: 55,631,971	K2790E	probably benign	Het
Noc3l	C	T	19: 38,814,695	E167K	possibly damaging	Het
Nol10	G	A	12: 17,416,828	E570K	possibly damaging	Het
Nr2e3	T	C	9: 59,949,201	R69G	probably damaging	Het
Obscn	G	A	11: 59,001,468	R1358*	probably null	Het
Olfr115	A	T	17: 37,610,254	F166I	probably damaging	Het
Olfr1472	A	T	19: 13,454,382	M45K	probably benign	Het
Olfr1535	C	A	13: 21,555,096	V309F	probably damaging	Het
Olfr675	A	G	7: 105,024,221	I253T	probably damaging	Het
Pak2	A	T	16: 32,041,519	D175E	probably benign	Het
Pccb	C	T	9: 100,985,803	V357I	possibly damaging	Het
Pcdhb4	C	T	18: 37,308,981	P448L	probably damaging	Het
Pcdhb9	A	G	18: 37,401,114	M54V	probably benign	Het
Ppp3cb	A	G	14: 20,520,690		probably benign	Het
Ppp4r1	A	G	17: 65,824,568	D452G	probably benign	Het
Prmt3	T	A	7: 49,826,751	D369E	probably damaging	Het
Psmd12	T	A	11: 107,486,475	V120D	probably benign	Het
Ptprb	T	C	10: 116,353,827	L1797P	probably damaging	Het
Ptprm	A	G	17: 66,920,196	S653P	probably damaging	Het
Pxdn	T	A	12: 30,003,142	V926D	probably damaging	Het
Retreg3	T	G	11: 101,106,339	Q105P	probably damaging	Het
Sacs	A	T	14: 61,206,441	R1979*	probably null	Het
Scn2a	T	A	2: 65,707,295	L696*	probably null	Het
Sema3c	A	T	5: 17,711,424	N465Y	probably damaging	Het
Slc25a32	A	T	15: 39,099,913	V171E	possibly damaging	Het
Slc30a7	C	T	3: 115,990,051	V158I	probably benign	Het
Slc44a5	G	A	3: 154,270,165		probably benign	Het
Slc4a8	A	G	15: 100,787,164	D140G	probably damaging	Het
Slc7a11	G	A	3: 50,443,083	S60L	possibly damaging	Het
Spryd3	A	T	15: 102,131,937	H59Q	probably benign	Het
Sqstm1	T	C	11: 50,203,022	D256G	probably damaging	Het
Sst	A	T	16: 23,889,737	S115T	probably damaging	Het
Surf1	T	C	2: 26,915,951		probably benign	Het
Synj1	A	T	16: 91,009,977		probably benign	Het
Tet1	C	A	10: 62,878,294	C574F	probably damaging	Het
Thnsl1	T	A	2: 21,212,390	Y318*	probably null	Het
Tmem110	A	G	14: 30,870,819	K166E	probably damaging	Het
Tomm70a	A	G	16: 57,122,130	E90G	probably damaging	Het
Treml4	A	G	17: 48,264,899	D110G	probably damaging	Het
Ttn	A	T	2: 76,811,243	L5176Q	possibly damaging	Het
Txnl1	C	T	18: 63,664,325	G283D	probably damaging	Het
Uba6	T	C	5: 86,135,047	D559G	probably damaging	Het
Vmn2r25	A	C	6: 123,825,296	C549W	probably damaging	Het
Vmn2r59	G	T	7: 42,045,681	Q436K	probably benign	Het
Wdr70	A	T	15: 7,884,288	Y627N	possibly damaging	Het
Xpr1	T	C	1: 155,312,863	I344V	probably benign	Het
Zfp423	T	A	8: 87,859,340	Q61L	possibly damaging	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
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
R8022:Usp4	UTSW	9	108378471	missense	probably damaging	0.99
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'- AGCCAGTGACAGTGTTTTGG -3'
(R):5'- GCTTCATTTTCAACCATGTAACCG -3'

Sequencing Primer
(F):5'- CCAGTGACAGTGTTTTGGAATATTG -3'
(R):5'- AACCATGTAACCGTTTTCATCC -3'

Posted On

2016-10-26