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

Unp, F730026I20Rik

MMRRC Submission

045370-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.139) question?

Stock #

R7320 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

108225052-108269744 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 108265505 bp (GRCm39)

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
Abcc3	A	G	11: 94,258,471 (GRCm39)	I458T	probably benign	Het
Adam29	A	G	8: 56,325,749 (GRCm39)	I235T	possibly damaging	Het
Afap1	G	A	5: 36,105,567 (GRCm39)	V174I	probably damaging	Het
Ak8	A	T	2: 28,703,004 (GRCm39)	D456V	probably damaging	Het
Alb	T	C	5: 90,612,846 (GRCm39)		probably null	Het
Alox12	C	T	11: 70,145,298 (GRCm39)	A92T	probably benign	Het
Arhgap23	T	C	11: 97,342,371 (GRCm39)	S218P	probably benign	Het
Blm	G	A	7: 80,105,102 (GRCm39)	Q1389*	probably null	Het
C1ql4	A	T	15: 98,985,605 (GRCm39)	V2E	unknown	Het
Casp12	A	G	9: 5,348,897 (GRCm39)		probably null	Het
Ccdc73	A	T	2: 104,829,521 (GRCm39)	I1065F	possibly damaging	Het
Ccdc83	C	T	7: 89,873,242 (GRCm39)	G371D	probably damaging	Het
Cfap65	A	G	1: 74,965,763 (GRCm39)	S416P	probably damaging	Het
Cftr	T	A	6: 18,319,012 (GRCm39)	C1351S	probably damaging	Het
Clcn4	A	T	7: 7,294,827 (GRCm39)	H311Q	probably benign	Het
Cldn13	T	G	5: 134,943,874 (GRCm39)	I104L	probably benign	Het
Cul9	A	G	17: 46,821,835 (GRCm39)	V1880A	possibly damaging	Het
Ddx17	A	T	15: 79,416,105 (GRCm39)	D407E	probably damaging	Het
Ddx28	G	A	8: 106,737,957 (GRCm39)	P34S	probably damaging	Het
Dnah5	A	T	15: 28,270,616 (GRCm39)	N973Y	probably null	Het
Dnai4	A	T	4: 102,907,384 (GRCm39)	I634N	possibly damaging	Het
Dock10	A	G	1: 80,527,421 (GRCm39)		probably null	Het
Dock3	T	C	9: 106,772,723 (GRCm39)	D510G	probably benign	Het
Dst	T	A	1: 34,230,175 (GRCm39)	D2589E	probably benign	Het
E2f7	T	C	10: 110,599,991 (GRCm39)	Y249H	not run	Het
Eef2kmt	T	C	16: 5,068,373 (GRCm39)	Y69C	possibly damaging	Het
Elapor1	T	A	3: 108,371,619 (GRCm39)	K650*	probably null	Het
Erlin1	T	C	19: 44,047,504 (GRCm39)	Y139C	probably damaging	Het
Exog	G	T	9: 119,291,544 (GRCm39)	V274L	possibly damaging	Het
Fam83e	G	A	7: 45,371,896 (GRCm39)	V98M	probably benign	Het
Fras1	C	T	5: 96,857,745 (GRCm39)	T2013I	probably benign	Het
Gart	G	T	16: 91,418,569 (GRCm39)	A970E	probably benign	Het
Gga2	T	A	7: 121,601,326 (GRCm39)	H259L	probably benign	Het
Glis3	C	A	19: 28,508,998 (GRCm39)	V329F	probably damaging	Het
Gm6356	T	A	14: 6,972,923 (GRCm38)	N53I	probably damaging	Het
Golgb1	C	A	16: 36,736,313 (GRCm39)	C1894*	probably null	Het
Ifi203	T	C	1: 173,756,733 (GRCm39)	N350S	unknown	Het
Isy1	T	A	6: 87,810,688 (GRCm39)	R55S	unknown	Het
Itsn1	A	T	16: 91,636,587 (GRCm39)	D678V	unknown	Het
Lhcgr	T	A	17: 89,049,506 (GRCm39)	R673S	probably benign	Het
Lnx2	C	A	5: 146,956,943 (GRCm39)	R601L	possibly damaging	Het
Map4	A	G	9: 109,910,585 (GRCm39)	T1093A	probably benign	Het
Minar1	A	G	9: 89,483,679 (GRCm39)	S573P	probably benign	Het
Mink1	A	G	11: 70,489,899 (GRCm39)	K92E	probably benign	Het
Moxd1	A	G	10: 24,177,363 (GRCm39)	I560V	probably benign	Het
Mrc2	C	A	11: 105,220,061 (GRCm39)	D327E	possibly damaging	Het
Notch2	A	G	3: 98,038,643 (GRCm39)	E1262G	possibly damaging	Het
Or2g1	T	A	17: 38,107,248 (GRCm39)	N304K	probably benign	Het
Or4k48	A	G	2: 111,476,297 (GRCm39)	L15S	probably benign	Het
Or52d3	C	A	7: 104,229,645 (GRCm39)	S264*	probably null	Het
Or5an1	G	A	19: 12,261,180 (GRCm39)	G256D	possibly damaging	Het
Or5b120	T	A	19: 13,480,544 (GRCm39)	M279K	possibly damaging	Het
Or5j3	GTACTTTTT	GT	2: 86,128,338 (GRCm39)		probably null	Het
Or5m13	A	T	2: 85,748,718 (GRCm39)	I150F	probably benign	Het
Or6c5b	A	T	10: 129,245,654 (GRCm39)	T140S	possibly damaging	Het
Pcbp2	T	A	15: 102,381,782 (GRCm39)	V5E	probably damaging	Het
Pcp4l1	G	A	1: 171,002,034 (GRCm39)	A42V	possibly damaging	Het
Pgghg	A	T	7: 140,522,953 (GRCm39)	Y104F	probably benign	Het
Plscr2	T	C	9: 92,173,193 (GRCm39)		probably null	Het
Ppfibp1	C	T	6: 146,879,551 (GRCm39)	A25V	probably damaging	Het
Ptgfr	C	T	3: 151,541,034 (GRCm39)	G158D	probably benign	Het
Ptgs2	T	C	1: 149,978,446 (GRCm39)	F186S	probably damaging	Het
Ptpn14	A	G	1: 189,564,956 (GRCm39)	E181G	probably benign	Het
Rpgrip1	A	G	14: 52,368,673 (GRCm39)	K291E	possibly damaging	Het
Rtn4rl1	T	C	11: 75,085,122 (GRCm39)		probably null	Het
Sema3b	T	A	9: 107,478,141 (GRCm39)	M415L	probably benign	Het
Sh3bp4	A	G	1: 89,073,216 (GRCm39)	E688G	probably damaging	Het
Slco6c1	G	A	1: 97,055,887 (GRCm39)	R5C	possibly damaging	Het
Slmap	A	G	14: 26,181,227 (GRCm39)	F369L	possibly damaging	Het
Sphk2	T	C	7: 45,361,894 (GRCm39)	N181S	possibly damaging	Het
Sqor	A	G	2: 122,641,730 (GRCm39)	T235A	probably benign	Het
St13	A	G	15: 81,273,854 (GRCm39)	L80P	probably damaging	Het
St3gal6	A	G	16: 58,314,074 (GRCm39)	Y20H	probably benign	Het
Sun1	T	G	5: 139,234,239 (GRCm39)	Y899D	probably damaging	Het
Synm	C	T	7: 67,385,128 (GRCm39)	E845K	possibly damaging	Het
Tg	A	T	15: 66,566,633 (GRCm39)	D1227V	possibly damaging	Het
Thbs1	A	G	2: 117,945,438 (GRCm39)	N306D	possibly damaging	Het
Tmcc3	A	T	10: 94,414,357 (GRCm39)	N51Y	possibly damaging	Het
Vil1	G	A	1: 74,457,603 (GRCm39)	A79T	probably damaging	Het
Vmn1r119	T	A	7: 20,746,271 (GRCm39)	H37L	probably damaging	Het
Vmn2r110	A	T	17: 20,816,316 (GRCm39)	M69K	probably benign	Het
Ywhaq	A	G	12: 21,444,982 (GRCm39)	L221P	probably damaging	Het
Zfp142	G	A	1: 74,609,167 (GRCm39)	Q1543*	probably null	Het
Zfp384	T	A	6: 125,001,793 (GRCm39)	M146K	possibly damaging	Het

Other mutations in Usp4

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01530:Usp4	APN	9	108,240,099 (GRCm39)	critical splice donor site	probably null
IGL01663:Usp4	APN	9	108,243,079 (GRCm39)	missense	possibly damaging	0.80
IGL02105:Usp4	APN	9	108,262,131 (GRCm39)	missense	probably damaging	1.00
IGL02486:Usp4	APN	9	108,228,228 (GRCm39)	missense	probably damaging	1.00
kleinesrot	UTSW	9	108,233,661 (GRCm39)	missense	possibly damaging	0.95
R0148:Usp4	UTSW	9	108,268,870 (GRCm39)	splice site	probably null
R0285:Usp4	UTSW	9	108,255,763 (GRCm39)	missense	probably benign	0.33
R0591:Usp4	UTSW	9	108,225,228 (GRCm39)	splice site	probably benign
R0594:Usp4	UTSW	9	108,248,080 (GRCm39)	splice site	probably null
R0616:Usp4	UTSW	9	108,244,003 (GRCm39)	missense	probably benign
R1329:Usp4	UTSW	9	108,249,765 (GRCm39)	missense	probably damaging	1.00
R1508:Usp4	UTSW	9	108,249,873 (GRCm39)	missense	probably benign	0.14
R1752:Usp4	UTSW	9	108,251,441 (GRCm39)	missense	probably damaging	1.00
R1824:Usp4	UTSW	9	108,225,207 (GRCm39)	missense	probably damaging	1.00
R1846:Usp4	UTSW	9	108,249,935 (GRCm39)	missense	probably benign
R2196:Usp4	UTSW	9	108,250,885 (GRCm39)	missense	probably benign	0.07
R2925:Usp4	UTSW	9	108,245,055 (GRCm39)	missense	probably damaging	1.00
R4126:Usp4	UTSW	9	108,237,316 (GRCm39)	missense	probably benign	0.10
R4345:Usp4	UTSW	9	108,245,222 (GRCm39)	intron	probably benign
R4965:Usp4	UTSW	9	108,239,819 (GRCm39)	missense	probably damaging	1.00
R4981:Usp4	UTSW	9	108,258,617 (GRCm39)	missense	probably benign	0.00
R5110:Usp4	UTSW	9	108,239,877 (GRCm39)	missense	probably damaging	1.00
R5580:Usp4	UTSW	9	108,243,058 (GRCm39)	missense	probably benign	0.09
R5586:Usp4	UTSW	9	108,233,661 (GRCm39)	missense	possibly damaging	0.95
R5927:Usp4	UTSW	9	108,268,959 (GRCm39)	missense	probably benign	0.09
R6025:Usp4	UTSW	9	108,237,322 (GRCm39)	missense	possibly damaging	0.70
R6112:Usp4	UTSW	9	108,233,703 (GRCm39)	missense	probably damaging	1.00
R6197:Usp4	UTSW	9	108,248,154 (GRCm39)	missense	probably damaging	1.00
R6742:Usp4	UTSW	9	108,251,438 (GRCm39)	missense	possibly damaging	0.74
R7458:Usp4	UTSW	9	108,245,055 (GRCm39)	missense	probably damaging	1.00
R7531:Usp4	UTSW	9	108,249,879 (GRCm39)	missense	probably damaging	1.00
R7563:Usp4	UTSW	9	108,256,543 (GRCm39)	missense	probably benign
R8022:Usp4	UTSW	9	108,255,670 (GRCm39)	missense	probably damaging	0.99
R8510:Usp4	UTSW	9	108,265,581 (GRCm39)	critical splice donor site	probably null
R8996:Usp4	UTSW	9	108,268,909 (GRCm39)	missense	probably damaging	1.00
R9151:Usp4	UTSW	9	108,244,011 (GRCm39)	missense	probably benign	0.00
R9775:Usp4	UTSW	9	108,239,780 (GRCm39)	missense	probably damaging	1.00
X0026:Usp4	UTSW	9	108,225,069 (GRCm39)	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