Mutagenetix > Incidental Mutation

Incidental Mutation 'R4860:Usp53'

372383

Institutional Source

Beutler Lab

Gene Symbol

Usp53

Ensembl Gene

ENSMUSG00000039701

Gene Name

ubiquitin specific peptidase 53

Synonyms

Phxr3, Sp6

MMRRC Submission

042471-MU

Accession Numbers

Ncbi RefSeq: NM_133857.3; MGI: 2139607

Is this an essential gene?

Possibly non essential (E-score: 0.375) question?

Stock #

R4860 (G1)

Quality Score

172

Status

Not validated

Chromosome

Chromosomal Location

122931493-122984510 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 122961363 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Serine to Proline at position 32 (S32P)

Ref Sequence

ENSEMBL: ENSMUSP00000143460 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000090379] [ENSMUST00000197314] [ENSMUST00000197934] [ENSMUST00000199329] [ENSMUST00000199401]

AlphaFold

P15975

Predicted Effect

probably benign
Transcript: ENSMUST00000090379
AA Change: S148P

PolyPhen 2 Score 0.290 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000087857
Gene: ENSMUSG00000039701
AA Change: S148P

Domain	Start	End	E-Value	Type
Pfam:UCH	29	348	1.6e-20	PFAM
Pfam:UCH_1	30	322	9.6e-9	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000197314
AA Change: S148P

PolyPhen 2 Score 0.290 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000142600
Gene: ENSMUSG00000039701
AA Change: S148P

Domain	Start	End	E-Value	Type
Pfam:UCH	29	266	1.7e-15	PFAM
Pfam:UCH_1	30	266	2.3e-9	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000197358

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000197801

Predicted Effect

probably benign
Transcript: ENSMUST00000197934
AA Change: S148P

PolyPhen 2 Score 0.019 (Sensitivity: 0.95; Specificity: 0.80)

SMART Domains

Protein: ENSMUSP00000143412
Gene: ENSMUSG00000039701
AA Change: S148P

Domain	Start	End	E-Value	Type
Pfam:UCH	29	375	2.2e-21	PFAM
Pfam:UCH_1	30	349	5.1e-10	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000199329

SMART Domains

Protein: ENSMUSP00000143119
Gene: ENSMUSG00000039701

Domain	Start	End	E-Value	Type
Pfam:UCH	29	126	1.8e-6	PFAM

Predicted Effect

possibly damaging
Transcript: ENSMUST00000199401
AA Change: S32P

PolyPhen 2 Score 0.904 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000143460
Gene: ENSMUSG00000039701
AA Change: S32P

Domain	Start	End	E-Value	Type
low complexity region	76	87	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000199923

Meta Mutation Damage Score

0.2143

Coding Region Coverage

1x: 98.9%
3x: 97.9%
10x: 95.0%
20x: 87.3%

Validation Efficiency

MGI Phenotype

PHENOTYPE: Homozygotes for an ENU-induced allele show progressive hearing loss associated with altered cochlear outer hair cell (OHC) morphology, reduced endocochlear potential, and early OHC loss followed by IHC and spiral ganglion degeneration. Heterozygotes are susceptible to noise-induced hearing loss. [provided by MGI curators]

Allele List at MGI

All alleles(48) : Gene trapped(48)

Other mutations in this stock

Total: 92 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700030K09Rik	T	C	8: 72,455,423	S466P	possibly damaging	Het
1700061G19Rik	A	G	17: 56,888,655	N684S	probably benign	Het
4930435E12Rik	A	G	16: 38,828,145	S201P	probably damaging	Het
Ablim1	T	C	19: 57,079,866	T267A	probably damaging	Het
Acap2	A	T	16: 31,103,499	L724Q	possibly damaging	Het
Adcy4	T	C	14: 55,781,927	T89A	possibly damaging	Het
Agrp	T	C	8: 105,567,368	E41G	probably benign	Het
Akr1d1	G	A	6: 37,564,491	V308M	probably damaging	Het
Ap1m2	C	T	9: 21,309,674	R54Q	probably benign	Het
Arhgap45	T	A	10: 80,027,066	V692E	probably damaging	Het
Arid5b	G	T	10: 68,243,095	N137K	probably damaging	Het
Arsi	G	A	18: 60,916,651	G202E	probably benign	Het
BC048679	T	C	7: 81,495,720	N27D	probably benign	Het
Ccdc78	A	G	17: 25,788,700	N237S	probably benign	Het
Cd46	G	A	1: 195,062,396	L345F	possibly damaging	Het
Cngb3	A	T	4: 19,425,569	N459I	possibly damaging	Het
Ctnnd2	A	G	15: 30,881,167	E731G	probably damaging	Het
Ctsh	A	G	9: 90,054,548	E26G	probably benign	Het
Cul1	G	T	6: 47,517,146	K464N	probably benign	Het
Cul1	T	A	6: 47,517,191	S479R	probably damaging	Het
Dcaf5	A	T	12: 80,340,232	D373E	probably benign	Het
Ddx58	G	T	4: 40,210,000	S644R	probably damaging	Het
Dhcr7	A	G	7: 143,840,500	Q126R	probably benign	Het
Dok2	T	C	14: 70,777,516	F228L	probably damaging	Het
Dpep3	T	G	8: 105,976,189	I314L	probably benign	Het
Eps8	A	G	6: 137,514,295	F362L	probably damaging	Het
Espn	G	T	4: 152,138,846	R250S	probably damaging	Het
Faf1	A	C	4: 109,742,896	N163H	probably damaging	Het
Fam198b	C	A	3: 79,936,674	S36*	probably null	Het
Fam71e2	C	T	7: 4,757,469		probably null	Het
Fcho1	C	T	8: 71,710,481	V635I	probably benign	Het
Gm7579	G	A	7: 142,211,908	C17Y	unknown	Het
Gm996	T	C	2: 25,578,753	Y382C	probably damaging	Het
Gpx8	G	T	13: 113,045,508	Y130*	probably null	Het
Gvin1	A	T	7: 106,163,436	Y609N	possibly damaging	Het
Hectd4	T	A	5: 121,305,818	M30K	probably benign	Het
Iqub	T	C	6: 24,450,842	D586G	probably damaging	Het
Klhl25	T	C	7: 75,867,050	I568T	probably benign	Het
Larp6	A	G	9: 60,737,810	E411G	probably damaging	Het
Lepr	A	C	4: 101,789,337	I822L	probably benign	Het
Lrig3	C	A	10: 126,011,052	D896E	probably benign	Het
Lrp1	C	T	10: 127,553,824	G3114D	probably damaging	Het
Macf1	A	T	4: 123,486,750	Y1263N	probably damaging	Het
Mapk10	T	C	5: 102,990,619	D180G	probably damaging	Het
Matr3	T	A	18: 35,581,640	V113E	probably damaging	Het
Mbd4	A	T	6: 115,848,926	F368Y	possibly damaging	Het
Mcpt8	G	A	14: 56,082,280	R238W	probably benign	Het
Mcrip2	G	T	17: 25,864,647	T86N	possibly damaging	Het
Mink1	A	G	11: 70,611,592	N1043S	probably damaging	Het
Muc4	G	A	16: 32,754,616	G1497R	probably benign	Het
Muc4	T	A	16: 32,754,625	S1500T	probably benign	Het
Nbeal2	G	A	9: 110,635,194	T1128I	probably benign	Het
Nrg2	T	A	18: 36,196,547	Y205F	probably damaging	Het
Nubp2	A	G	17: 24,884,456	M149T	probably benign	Het
Olfr1062	T	C	2: 86,422,957	T240A	probably damaging	Het
Olfr462	T	A	11: 87,889,225	M224L	probably damaging	Het
Olfr974	G	T	9: 39,942,504	M81I	probably benign	Het
Pax3	A	G	1: 78,192,456	I191T	possibly damaging	Het
Pdcd5	T	C	7: 35,643,710	N137D	possibly damaging	Het
Pik3c2a	G	A	7: 116,340,156	A1649V	probably damaging	Het
Pkhd1l1	T	C	15: 44,537,378	S2183P	possibly damaging	Het
Plekho1	T	A	3: 95,988,993	Q388L	possibly damaging	Het
Ppfibp1	A	G	6: 146,990,514	T91A	probably benign	Het
Ptger4	G	T	15: 5,242,606	N177K	probably benign	Het
Reln	A	G	5: 21,901,751	F3207S	probably benign	Het
Ripk4	C	T	16: 97,751,536	R194H	probably damaging	Het
Rnf112	A	T	11: 61,452,744	C112S	possibly damaging	Het
Rprd1b	T	G	2: 158,074,935	Y278*	probably null	Het
Sel1l	A	G	12: 91,831,602	L140P	probably damaging	Het
Shroom3	G	T	5: 92,943,086	V1151F	probably damaging	Het
Slc38a3	A	G	9: 107,655,064	V423A	probably damaging	Het
Slitrk6	T	C	14: 110,751,883	T131A	probably damaging	Het
Slmap	A	T	14: 26,460,209	V323E	probably benign	Het
Smim6	T	C	11: 115,913,504	V39A	probably benign	Het
Sorbs1	T	C	19: 40,337,005	T382A	probably benign	Het
Sparc	G	A	11: 55,399,211	T218I	possibly damaging	Het
Steap1	A	T	5: 5,736,589	F283I	probably damaging	Het
Stil	A	G	4: 115,038,474	T586A	probably benign	Het
Tbce	T	A	13: 14,019,795	D93V	probably damaging	Het
Tcf12	C	T	9: 71,858,840	G504S	probably null	Het
Tle4	A	T	19: 14,464,345	I435K	probably benign	Het
Tmem245	A	G	4: 56,899,164	F254S	probably damaging	Het
Tmem251	A	T	12: 102,744,055		probably benign	Het
Tubgcp3	T	C	8: 12,649,722	K377R	probably benign	Het
Ush2a	A	T	1: 188,553,275	T2003S	probably benign	Het
Vmn1r78	T	A	7: 12,152,756	L98Q	probably damaging	Het
Vmn2r116	A	C	17: 23,401,803	Q837P	probably benign	Het
Vmn2r3	T	C	3: 64,275,601	I226V	probably benign	Het
Vmn2r84	T	A	10: 130,385,843	D836V	probably damaging	Het
Vps13d	A	G	4: 145,087,161	F165L	probably benign	Het
Vstm4	A	G	14: 32,863,785	E103G	possibly damaging	Het
Zfp870	A	T	17: 32,883,340	C339*	probably null	Het

Other mutations in Usp53

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01112:Usp53	APN	3	122957718	missense	probably damaging	0.99
IGL01965:Usp53	APN	3	122961153	critical splice donor site	probably null
IGL02115:Usp53	APN	3	122947390	missense	probably benign	0.25
IGL02993:Usp53	APN	3	122933843	missense	probably damaging	1.00
IGL03119:Usp53	APN	3	122961415	missense	possibly damaging	0.80
IGL03206:Usp53	APN	3	122953183	missense	probably benign
IGL03369:Usp53	APN	3	122933721	utr 3 prime	probably benign
R0066:Usp53	UTSW	3	122953307	nonsense	probably null
R0066:Usp53	UTSW	3	122953307	nonsense	probably null
R0366:Usp53	UTSW	3	122949201	missense	probably damaging	1.00
R1015:Usp53	UTSW	3	122933759	missense	probably benign	0.02
R1388:Usp53	UTSW	3	122957628	missense	probably damaging	0.96
R1592:Usp53	UTSW	3	122934050	nonsense	probably null
R1635:Usp53	UTSW	3	122934223	missense	probably benign	0.03
R1707:Usp53	UTSW	3	122947400	missense	probably benign
R2177:Usp53	UTSW	3	122936057	missense	probably damaging	0.99
R2848:Usp53	UTSW	3	122934491	missense	probably benign	0.00
R2898:Usp53	UTSW	3	122957574	nonsense	probably null
R3411:Usp53	UTSW	3	122949858	critical splice acceptor site	probably null
R3618:Usp53	UTSW	3	122934412	missense	probably benign	0.25
R3713:Usp53	UTSW	3	122949319	missense	probably benign	0.08
R3715:Usp53	UTSW	3	122949319	missense	probably benign	0.08
R3923:Usp53	UTSW	3	122934305	missense	probably benign	0.11
R4616:Usp53	UTSW	3	122959120	missense	probably damaging	1.00
R4718:Usp53	UTSW	3	122933982	missense	probably benign	0.22
R4730:Usp53	UTSW	3	122962933	missense	probably null	0.82
R4860:Usp53	UTSW	3	122961363	missense	possibly damaging	0.90
R5073:Usp53	UTSW	3	122933946	missense	probably benign	0.21
R5580:Usp53	UTSW	3	122934234	missense	probably benign	0.00
R5894:Usp53	UTSW	3	122959085	missense	probably damaging	0.96
R6176:Usp53	UTSW	3	122934003	nonsense	probably null
R6191:Usp53	UTSW	3	122949741	missense	probably damaging	0.96
R6634:Usp53	UTSW	3	122964286	missense	probably benign	0.00
R7179:Usp53	UTSW	3	122949710	missense	probably benign	0.01
R7211:Usp53	UTSW	3	122957650	missense	probably damaging	0.98
R7613:Usp53	UTSW	3	122949818	missense	probably benign	0.43
R7621:Usp53	UTSW	3	122961285	missense	probably benign	0.00
R7652:Usp53	UTSW	3	122953235	missense	possibly damaging	0.80
R7753:Usp53	UTSW	3	122949238	missense	probably damaging	1.00
R7859:Usp53	UTSW	3	122949766	missense	possibly damaging	0.91
R7861:Usp53	UTSW	3	122934463	missense	probably benign	0.26
R7911:Usp53	UTSW	3	122961267	missense	probably benign	0.00
R7962:Usp53	UTSW	3	122934351	missense	possibly damaging	0.90
R7965:Usp53	UTSW	3	122962882	critical splice donor site	probably null
R8193:Usp53	UTSW	3	122947363	missense	probably benign	0.02
R8210:Usp53	UTSW	3	122947396	missense	probably benign	0.27
R8848:Usp53	UTSW	3	122949176	missense	probably benign	0.16
R8848:Usp53	UTSW	3	122949586	missense	probably benign	0.01
R8966:Usp53	UTSW	3	122961332	missense	probably damaging	0.99
R9054:Usp53	UTSW	3	122934076	missense	probably benign	0.04
R9204:Usp53	UTSW	3	122947419	missense	probably benign	0.01
R9405:Usp53	UTSW	3	122953269	missense	probably damaging	1.00
X0025:Usp53	UTSW	3	122957583	critical splice donor site	probably null
Z1177:Usp53	UTSW	3	122953195	missense	probably benign	0.01

Predicted Primers

PCR Primer
(F):5'- CTCACGAGTTCGGTAAAGGG -3'
(R):5'- GCTAGCGGTTATGGCATTCC -3'

Sequencing Primer
(F):5'- TTCGGTAAAGGGCAGAGGGTC -3'
(R):5'- CCTGCATTTACACTTTGGAAAATG -3'

Posted On

2016-03-01