Mutagenetix > Incidental Mutation

Incidental Mutation 'R7320:Usp4'

568149

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: 0.143) question?

Stock #

R7320 (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 108388306 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glycine at position 856 (D856G)

Ref Sequence

ENSEMBL: ENSMUSP00000035237 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000035234] [ENSMUST00000035237] [ENSMUST00000192995] [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 benign
Transcript: ENSMUST00000035234

Predicted Effect

probably benign
Transcript: ENSMUST00000035237
AA Change: D856G

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)

SMART Domains

Protein: ENSMUSP00000035237
Gene: ENSMUSG00000032612
AA Change: D856G

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 benign
Transcript: ENSMUST00000192995

Predicted Effect

probably benign
Transcript: ENSMUST00000193288

Predicted Effect

probably benign
Transcript: ENSMUST00000194224

SMART Domains

Protein: ENSMUSP00000141321
Gene: ENSMUSG00000032612

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 benign
Transcript: ENSMUST00000194959
AA Change: D809G

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000141368
Gene: ENSMUSG00000032612
AA Change: D809G

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: 98.8%

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: 84 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
5330417C22Rik	T	A	3: 108,464,303	K650*	probably null	Het
Abcc3	A	G	11: 94,367,645	I458T	probably benign	Het
Adam29	A	G	8: 55,872,714	I235T	possibly damaging	Het
AF529169	A	G	9: 89,601,626	S573P	probably benign	Het
Afap1	G	A	5: 35,948,223	V174I	probably damaging	Het
Ak8	A	T	2: 28,812,992	D456V	probably damaging	Het
Alb	T	C	5: 90,464,987		probably null	Het
Alox12	C	T	11: 70,254,472	A92T	probably benign	Het
Arhgap23	T	C	11: 97,451,545	S218P	probably benign	Het
Blm	G	A	7: 80,455,354	Q1389*	probably null	Het
C1ql4	A	T	15: 99,087,724	V2E	unknown	Het
Casp12	A	G	9: 5,348,897		probably null	Het
Ccdc73	A	T	2: 104,999,176	I1065F	possibly damaging	Het
Ccdc83	C	T	7: 90,224,034	G371D	probably damaging	Het
Cfap65	A	G	1: 74,926,604	S416P	probably damaging	Het
Cftr	T	A	6: 18,319,013	C1351S	probably damaging	Het
Clcn4	A	T	7: 7,291,828	H311Q	probably benign	Het
Cldn13	T	G	5: 134,915,020	I104L	probably benign	Het
Cul9	A	G	17: 46,510,909	V1880A	possibly damaging	Het
Ddx17	A	T	15: 79,531,904	D407E	probably damaging	Het
Ddx28	G	A	8: 106,011,325	P34S	probably damaging	Het
Dnah5	A	T	15: 28,270,470	N973Y	probably null	Het
Dock10	A	G	1: 80,549,704		probably null	Het
Dock3	T	C	9: 106,895,524	D510G	probably benign	Het
Dst	T	A	1: 34,191,094	D2589E	probably benign	Het
E2f7	T	C	10: 110,764,130	Y249H	not run	Het
Eef2kmt	T	C	16: 5,250,509	Y69C	possibly damaging	Het
Erlin1	T	C	19: 44,059,065	Y139C	probably damaging	Het
Exog	G	T	9: 119,462,478	V274L	possibly damaging	Het
Fam83e	G	A	7: 45,722,472	V98M	probably benign	Het
Fras1	C	T	5: 96,709,886	T2013I	probably benign	Het
Gart	G	T	16: 91,621,681	A970E	probably benign	Het
Gga2	T	A	7: 122,002,103	H259L	probably benign	Het
Glis3	C	A	19: 28,531,598	V329F	probably damaging	Het
Gm6356	T	A	14: 6,972,923	N53I	probably damaging	Het
Golgb1	C	A	16: 36,915,951	C1894*	probably null	Het
Ifi203	T	C	1: 173,929,167	N350S	unknown	Het
Isy1	T	A	6: 87,833,706	R55S	unknown	Het
Itsn1	A	T	16: 91,839,699	D678V	unknown	Het
Lhcgr	T	A	17: 88,742,078	R673S	probably benign	Het
Lnx2	C	A	5: 147,020,133	R601L	possibly damaging	Het
Map4	A	G	9: 110,081,517	T1093A	probably benign	Het
Mink1	A	G	11: 70,599,073	K92E	probably benign	Het
Moxd1	A	G	10: 24,301,465	I560V	probably benign	Het
Mrc2	C	A	11: 105,329,235	D327E	possibly damaging	Het
Notch2	A	G	3: 98,131,327	E1262G	possibly damaging	Het
Olfr1025-ps1	A	T	2: 85,918,374	I150F	probably benign	Het
Olfr1052	GTACTTTTT	GT	2: 86,297,994		probably null	Het
Olfr123	T	A	17: 37,796,357	N304K	probably benign	Het
Olfr1298	A	G	2: 111,645,952	L15S	probably benign	Het
Olfr1434	G	A	19: 12,283,816	G256D	possibly damaging	Het
Olfr1477	T	A	19: 13,503,180	M279K	possibly damaging	Het
Olfr653	C	A	7: 104,580,438	S264*	probably null	Het
Olfr785	A	T	10: 129,409,785	T140S	possibly damaging	Het
Pcbp2	T	A	15: 102,473,347	V5E	probably damaging	Het
Pcp4l1	G	A	1: 171,174,465	A42V	possibly damaging	Het
Pgghg	A	T	7: 140,943,040	Y104F	probably benign	Het
Plscr2	T	C	9: 92,291,140		probably null	Het
Ppfibp1	C	T	6: 146,978,053	A25V	probably damaging	Het
Ptgfr	C	T	3: 151,835,397	G158D	probably benign	Het
Ptgs2	T	C	1: 150,102,695	F186S	probably damaging	Het
Ptpn14	A	G	1: 189,832,759	E181G	probably benign	Het
Rpgrip1	A	G	14: 52,131,216	K291E	possibly damaging	Het
Rtn4rl1	T	C	11: 75,194,296		probably null	Het
Sema3b	T	A	9: 107,600,942	M415L	probably benign	Het
Sh3bp4	A	G	1: 89,145,494	E688G	probably damaging	Het
Slco6c1	G	A	1: 97,128,162	R5C	possibly damaging	Het
Slmap	A	G	14: 26,460,072	F369L	possibly damaging	Het
Sphk2	T	C	7: 45,712,470	N181S	possibly damaging	Het
Sqor	A	G	2: 122,799,810	T235A	probably benign	Het
St13	A	G	15: 81,389,653	L80P	probably damaging	Het
St3gal6	A	G	16: 58,493,711	Y20H	probably benign	Het
Sun1	T	G	5: 139,248,484	Y899D	probably damaging	Het
Synm	C	T	7: 67,735,380	E845K	possibly damaging	Het
Tg	A	T	15: 66,694,784	D1227V	possibly damaging	Het
Thbs1	A	G	2: 118,114,957	N306D	possibly damaging	Het
Tmcc3	A	T	10: 94,578,495	N51Y	possibly damaging	Het
Vil1	G	A	1: 74,418,444	A79T	probably damaging	Het
Vmn1r119	T	A	7: 21,012,346	H37L	probably damaging	Het
Vmn2r110	A	T	17: 20,596,054	M69K	probably benign	Het
Wdr78	A	T	4: 103,050,187	I634N	possibly damaging	Het
Ywhaq	A	G	12: 21,394,981	L221P	probably damaging	Het
Zfp142	G	A	1: 74,570,008	Q1543*	probably null	Het
Zfp384	T	A	6: 125,024,830	M146K	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
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
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'- AGTTTCTGCTCCCACAAACC -3'
(R):5'- GATCGTTACCACCACTGAGG -3'

Sequencing Primer
(F):5'- AAACCATCACTGTGCCTTGG -3'
(R):5'- CGTTACCACCACTGAGGAAGGTAG -3'

Posted On

2019-06-26