Mutagenetix > Incidental Mutations

Incidental Mutation 'R5841:Usp54'

450461

Institutional Source

Beutler Lab

Gene Symbol

Usp54

Ensembl Gene

ENSMUSG00000034235

Gene Name

ubiquitin specific peptidase 54

Synonyms

C030002J06Rik, 4930429G18Rik

MMRRC Submission

044061-MU

Accession Numbers

Is this an essential gene?

Non essential (E-score: 0.000) question?

Stock #

R5841 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

20548912-20641063 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 20550283 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Isoleucine at position 1462 (T1462I)

Ref Sequence

ENSEMBL: ENSMUSP00000036214 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000022355] [ENSMUST00000022356] [ENSMUST00000035340] [ENSMUST00000159027] [ENSMUST00000161445] [ENSMUST00000161989]

AlphaFold

Q8BL06

Predicted Effect

probably benign
Transcript: ENSMUST00000022355

SMART Domains

Protein: ENSMUSP00000022355
Gene: ENSMUSG00000021816

Domain	Start	End	E-Value	Type
low complexity region	2	20	N/A	INTRINSIC
PP2Ac	65	356	5.03e-166	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000022356
AA Change: T1462I

PolyPhen 2 Score 0.039 (Sensitivity: 0.94; Specificity: 0.83)

SMART Domains

Protein: ENSMUSP00000022356
Gene: ENSMUSG00000034235
AA Change: T1462I

Domain	Start	End	E-Value	Type
Pfam:UCH	30	349	2.4e-23	PFAM
Pfam:UCH_1	31	324	2.1e-7	PFAM
low complexity region	403	412	N/A	INTRINSIC
low complexity region	439	445	N/A	INTRINSIC
low complexity region	498	513	N/A	INTRINSIC
low complexity region	601	616	N/A	INTRINSIC
coiled coil region	682	712	N/A	INTRINSIC
low complexity region	808	826	N/A	INTRINSIC
low complexity region	881	894	N/A	INTRINSIC
low complexity region	1002	1020	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000035340
AA Change: T1462I

PolyPhen 2 Score 0.039 (Sensitivity: 0.94; Specificity: 0.83)

SMART Domains

Protein: ENSMUSP00000036214
Gene: ENSMUSG00000034235
AA Change: T1462I

Domain	Start	End	E-Value	Type
Pfam:UCH	31	349	2.3e-21	PFAM
low complexity region	403	412	N/A	INTRINSIC
low complexity region	439	445	N/A	INTRINSIC
low complexity region	498	513	N/A	INTRINSIC
low complexity region	601	616	N/A	INTRINSIC
coiled coil region	682	712	N/A	INTRINSIC
low complexity region	808	826	N/A	INTRINSIC
low complexity region	881	894	N/A	INTRINSIC
low complexity region	1002	1020	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000128848

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000129237

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000141265

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000142099

Predicted Effect

probably benign
Transcript: ENSMUST00000159027

SMART Domains

Protein: ENSMUSP00000125722
Gene: ENSMUSG00000021816

Domain	Start	End	E-Value	Type
low complexity region	2	20	N/A	INTRINSIC
PP2Ac	65	356	5.03e-166	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000161445

SMART Domains

Protein: ENSMUSP00000125630
Gene: ENSMUSG00000021816

Domain	Start	End	E-Value	Type
low complexity region	2	20	N/A	INTRINSIC
PP2Ac	65	356	5.03e-166	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000161989

SMART Domains

Protein: ENSMUSP00000125582
Gene: ENSMUSG00000021816

Domain	Start	End	E-Value	Type
low complexity region	2	20	N/A	INTRINSIC
PP2Ac	65	356	5.03e-166	SMART
low complexity region	487	497	N/A	INTRINSIC

Meta Mutation Damage Score

0.0695

Coding Region Coverage

1x: 99.9%
3x: 99.7%
10x: 98.6%
20x: 96.2%

Validation Efficiency

100% (67/67)

Allele List at MGI

Other mutations in this stock

Total: 64 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcb6	A	T	1: 75,174,350	F565L	possibly damaging	Het
Abhd6	T	A	14: 8,049,596	V188D	probably benign	Het
Bbs12	T	G	3: 37,319,521	N39K	probably benign	Het
Bend5	A	G	4: 111,433,470	Y221C	probably damaging	Het
Brd8	A	G	18: 34,605,523	S683P	probably damaging	Het
Caskin1	A	G	17: 24,496,209	D79G	probably damaging	Het
Cdyl	T	C	13: 35,872,561	L509P	probably damaging	Het
Cenpf	G	T	1: 189,657,444	T1397N	possibly damaging	Het
Ckap5	T	A	2: 91,600,682	M1479K	probably benign	Het
Cpsf2	T	C	12: 101,985,238	S145P	probably damaging	Het
Cyp4a12a	A	T	4: 115,326,702	H235L	probably benign	Het
Cyp7b1	A	T	3: 18,097,506	F181Y	probably damaging	Het
Dennd5b	T	C	6: 149,044,755	T453A	probably benign	Het
Dlgap3	A	G	4: 127,195,400	D263G	probably damaging	Het
Dnah3	TTCCTC	TTC	7: 119,951,021		probably benign	Het
Dync2li1	G	A	17: 84,633,562	G69R	probably damaging	Het
Edc3	T	C	9: 57,744,602	V331A	probably benign	Het
Eml2	G	A	7: 19,201,163	V432I	probably damaging	Het
Ganc	C	T	2: 120,411,539	T66I	possibly damaging	Het
Gm11595	C	A	11: 99,772,317	C179F	unknown	Het
Gm13088	A	G	4: 143,655,539	S196P	possibly damaging	Het
Gm15448	T	A	7: 3,822,899	R324*	probably null	Het
Gnptg	A	G	17: 25,235,417	S159P	probably damaging	Het
Gsdmc2	C	T	15: 63,826,210	V349I	probably benign	Het
Hydin	T	C	8: 110,533,214	I2606T	possibly damaging	Het
Ino80d	A	G	1: 63,058,840	S632P	probably damaging	Het
Kcnn2	G	A	18: 45,559,396	R13H	probably benign	Het
Klb	A	T	5: 65,379,324	K666*	probably null	Het
Kmt2d	G	A	15: 98,852,109		probably benign	Het
Kpna7	T	C	5: 144,993,956	I360V	possibly damaging	Het
Lmbrd2	A	G	15: 9,182,570	K576E	possibly damaging	Het
Lrp2	T	A	2: 69,480,153	Y2692F	probably benign	Het
Meis2	T	A	2: 116,058,664	E202D	probably benign	Het
Mgat4c	A	T	10: 102,388,965	T347S	probably damaging	Het
Mmp12	G	A	9: 7,347,501	C26Y	possibly damaging	Het
Mrpl24	G	A	3: 87,922,985	R145Q	probably damaging	Het
Mtpn	C	T	6: 35,512,290	D100N	probably benign	Het
Mycbpap	T	A	11: 94,505,610	R135W	probably damaging	Het
Myo1g	T	A	11: 6,507,000	Y942F	probably benign	Het
Myrf	T	C	19: 10,223,547	K52R	probably null	Het
Ncf2	A	T	1: 152,821,518		silent	Het
Olfr585	T	C	7: 103,097,954	F71S	probably damaging	Het
Otx1	T	C	11: 21,998,594		probably benign	Het
Pcnx	T	A	12: 81,918,655	V532D	possibly damaging	Het
Pik3r5	T	C	11: 68,492,270	L305P	probably damaging	Het
Polr3a	A	T	14: 24,450,698	C1341S	probably benign	Het
Ppp1r3a	T	C	6: 14,718,984	T644A	probably benign	Het
Ptbp1	A	G	10: 79,859,932	D289G	probably benign	Het
Pwp2	A	G	10: 78,172,118	F868L	probably benign	Het
Rgs8	A	G	1: 153,692,828	E153G	probably damaging	Het
Rhbdf2	G	A	11: 116,602,354		probably benign	Het
Sbf1	T	C	15: 89,308,068	H78R	probably damaging	Het
Sdr16c6	C	T	4: 4,062,728	A197T	possibly damaging	Het
Slc36a3	A	T	11: 55,125,721	Y349*	probably null	Het
Slc38a9	T	C	13: 112,695,322	L202P	possibly damaging	Het
Slc40a1	A	T	1: 45,912,349	M216K	probably damaging	Het
Slc9a3r2	A	T	17: 24,644,877	M8K	probably benign	Het
Srebf1	T	A	11: 60,203,584	Q568H	possibly damaging	Het
Srp54b	A	G	12: 55,252,829	N315S	probably benign	Het
Strc	A	G	2: 121,365,877	F1557L	probably benign	Het
Susd3	C	A	13: 49,238,726		probably benign	Het
Vmn1r11	T	A	6: 57,137,802	N150K	probably damaging	Het
Vwa8	C	T	14: 78,994,518	H606Y	probably benign	Het
Zmym6	A	G	4: 127,100,670	I206V	possibly damaging	Het

Other mutations in Usp54

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00585:Usp54	APN	14	20573837	missense	probably damaging	1.00
IGL01090:Usp54	APN	14	20586157	unclassified	probably benign
IGL02030:Usp54	APN	14	20565946	missense	probably benign	0.44
IGL02333:Usp54	APN	14	20589395	missense	probably damaging	1.00
IGL02642:Usp54	APN	14	20565072	splice site	probably benign
IGL02970:Usp54	APN	14	20577472	missense	probably damaging	1.00
IGL03371:Usp54	APN	14	20589368	unclassified	probably benign
BB003:Usp54	UTSW	14	20576968	missense	probably damaging	1.00
BB013:Usp54	UTSW	14	20576968	missense	probably damaging	1.00
R0050:Usp54	UTSW	14	20573755	unclassified	probably benign
R0383:Usp54	UTSW	14	20561252	missense	probably benign	0.00
R0427:Usp54	UTSW	14	20570364	missense	probably benign
R0442:Usp54	UTSW	14	20607209	missense	probably damaging	1.00
R0574:Usp54	UTSW	14	20556254	missense	probably benign	0.00
R0638:Usp54	UTSW	14	20589369	unclassified	probably benign
R0789:Usp54	UTSW	14	20562157	missense	probably benign	0.01
R1272:Usp54	UTSW	14	20561110	missense	probably damaging	0.99
R1463:Usp54	UTSW	14	20550190	missense	probably benign	0.15
R1565:Usp54	UTSW	14	20607159	missense	probably damaging	1.00
R1721:Usp54	UTSW	14	20583440	nonsense	probably null
R1922:Usp54	UTSW	14	20560904	missense	probably benign	0.00
R2068:Usp54	UTSW	14	20577205	missense	probably damaging	1.00
R2216:Usp54	UTSW	14	20561840	missense	probably benign
R2285:Usp54	UTSW	14	20561178	missense	possibly damaging	0.52
R2426:Usp54	UTSW	14	20564940	missense	probably benign	0.00
R3855:Usp54	UTSW	14	20588420	missense	probably damaging	1.00
R3856:Usp54	UTSW	14	20588420	missense	probably damaging	1.00
R3907:Usp54	UTSW	14	20586113	missense	probably damaging	1.00
R4367:Usp54	UTSW	14	20561134	missense	probably benign	0.02
R4384:Usp54	UTSW	14	20550085	splice site	probably null
R4555:Usp54	UTSW	14	20561022	missense	probably benign	0.06
R4617:Usp54	UTSW	14	20550338	missense	probably benign	0.04
R4659:Usp54	UTSW	14	20564992	missense	probably damaging	1.00
R4672:Usp54	UTSW	14	20581529	intron	probably benign
R4928:Usp54	UTSW	14	20562192	missense	probably damaging	1.00
R5381:Usp54	UTSW	14	20586076	missense	probably damaging	1.00
R5408:Usp54	UTSW	14	20550433	missense	probably damaging	1.00
R5630:Usp54	UTSW	14	20565057	missense	probably damaging	1.00
R5886:Usp54	UTSW	14	20561842	missense	probably benign	0.28
R5922:Usp54	UTSW	14	20552071	splice site	probably null
R5975:Usp54	UTSW	14	20583351	missense	possibly damaging	0.77
R6074:Usp54	UTSW	14	20552099	missense	probably benign	0.02
R6183:Usp54	UTSW	14	20552245	missense	probably damaging	0.99
R6234:Usp54	UTSW	14	20583450	missense	probably damaging	1.00
R6303:Usp54	UTSW	14	20560968	missense	possibly damaging	0.95
R6304:Usp54	UTSW	14	20560968	missense	possibly damaging	0.95
R6695:Usp54	UTSW	14	20560869	missense	possibly damaging	0.94
R6774:Usp54	UTSW	14	20577228	missense	probably damaging	1.00
R6941:Usp54	UTSW	14	20562109	missense	probably benign
R7133:Usp54	UTSW	14	20561242	missense	probably benign	0.00
R7196:Usp54	UTSW	14	20588370	missense	probably damaging	1.00
R7409:Usp54	UTSW	14	20552245	missense	probably damaging	0.99
R7424:Usp54	UTSW	14	20577040	missense	probably benign	0.15
R7859:Usp54	UTSW	14	20588136	missense	probably benign	0.24
R7926:Usp54	UTSW	14	20576968	missense	probably damaging	1.00
R7954:Usp54	UTSW	14	20561913	missense	probably benign	0.01
R8489:Usp54	UTSW	14	20561536	missense	probably benign	0.31
R8745:Usp54	UTSW	14	20562108	missense	probably benign	0.00
R8775:Usp54	UTSW	14	20588398	missense	probably benign	0.03
R8775-TAIL:Usp54	UTSW	14	20588398	missense	probably benign	0.03
R9080:Usp54	UTSW	14	20562240	missense	probably damaging	1.00
R9121:Usp54	UTSW	14	20581455	critical splice donor site	probably null
R9139:Usp54	UTSW	14	20577094	missense	probably benign	0.00
R9433:Usp54	UTSW	14	20561610	missense	probably benign
RF004:Usp54	UTSW	14	20561300	missense	possibly damaging	0.90
X0024:Usp54	UTSW	14	20577251	small deletion	probably benign

Predicted Primers

PCR Primer
(F):5'- ATTCTTCGTGGACCAGGTGTTC -3'
(R):5'- TCAAGGAGTGTCCACCAGTTTC -3'

Sequencing Primer
(F):5'- CCAGAATTCCAAGTTGACCTAAGGG -3'
(R):5'- CCAGTTTCTGGCTATGTGTGACAG -3'

Posted On

2016-12-20