Mutagenetix > Incidental Mutation

Incidental Mutation 'R4616:Usp53'

351030

Institutional Source

Beutler Lab

Gene Symbol

Usp53

Ensembl Gene

ENSMUSG00000039701

Gene Name

ubiquitin specific peptidase 53

Synonyms

Phxr3, Sp6

MMRRC Submission

041827-MU

Accession Numbers

Ncbi RefSeq: NM_133857.3; MGI: 2139607

Essential gene?

Probably non essential (E-score: 0.221) question?

Stock #

R4616 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

122931493-122984510 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 122959120 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Methionine to Lysine at position 80 (M80K)

Ref Sequence

ENSEMBL: ENSMUSP00000143460 (fasta)

Gene Model

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

AlphaFold

P15975

Predicted Effect

possibly damaging
Transcript: ENSMUST00000090379
AA Change: M196K

PolyPhen 2 Score 0.787 (Sensitivity: 0.85; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000087857
Gene: ENSMUSG00000039701
AA Change: M196K

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

possibly damaging
Transcript: ENSMUST00000197314
AA Change: M196K

PolyPhen 2 Score 0.787 (Sensitivity: 0.85; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000142600
Gene: ENSMUSG00000039701
AA Change: M196K

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: M223K

PolyPhen 2 Score 0.329 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000143412
Gene: ENSMUSG00000039701
AA Change: M223K

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

probably damaging
Transcript: ENSMUST00000199401
AA Change: M80K

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000143460
Gene: ENSMUSG00000039701
AA Change: M80K

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000199923

Meta Mutation Damage Score

0.2216

Coding Region Coverage

1x: 99.4%
3x: 98.7%
10x: 97.4%
20x: 95.6%

Validation Efficiency

100% (64/64)

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: 60 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2010111I01Rik	G	A	13: 63,298,751	E123K	probably damaging	Het
4931417E11Rik	A	G	6: 73,469,269	V99A	probably benign	Het
Acod1	C	T	14: 103,055,345	T435M	probably benign	Het
Adgrf5	T	C	17: 43,452,440	F1078L	probably benign	Het
Adh6a	A	T	3: 138,324,947	N110I	probably damaging	Het
Aldh16a1	T	C	7: 45,148,788		probably benign	Het
Arhgef17	A	G	7: 100,882,485	F1302S	probably damaging	Het
Bcl2a1a	C	T	9: 88,957,453	R135W	probably damaging	Het
Bpifa6	T	C	2: 153,982,988	S28P	possibly damaging	Het
C9	A	G	15: 6,491,463	D51G	probably damaging	Het
Cfb	T	A	17: 34,859,068	H962L	probably benign	Het
Chn2	G	A	6: 54,290,403	M292I	probably damaging	Het
Clec16a	T	A	16: 10,644,883		probably null	Het
Cyp1a1	T	C	9: 57,701,756	S307P	probably benign	Het
Dsg3	T	C	18: 20,531,559	V538A	probably benign	Het
Erbb3	G	A	10: 128,572,770	Q815*	probably null	Het
Fam90a1a	C	A	8: 21,963,846	Q406K	possibly damaging	Het
Frmd3	T	C	4: 74,187,872	V585A	probably benign	Het
Gm7102	C	T	19: 61,175,926	G24R	unknown	Het
Gm8214	T	C	1: 183,681,897		noncoding transcript	Het
Gpld1	G	A	13: 24,984,816	G771D	probably damaging	Het
Gpr20	T	C	15: 73,695,736	N268S	probably benign	Het
Gria2	A	T	3: 80,706,897	I612N	probably damaging	Het
Ifit1bl1	T	C	19: 34,594,610	E149G	probably damaging	Het
Ighv1-82	T	C	12: 115,952,660	T77A	probably benign	Het
Ighv2-9	G	T	12: 113,879,219	T76K	probably damaging	Het
Igkv6-13	A	T	6: 70,458,035	M1K	probably null	Het
Igkv8-21	A	T	6: 70,315,157	S34T	probably benign	Het
Itpr1	A	G	6: 108,481,223	N1985D	probably damaging	Het
Lama3	T	C	18: 12,504,397		probably null	Het
Lamc2	T	C	1: 153,166,169	Y73C	probably damaging	Het
Maff	A	G	15: 79,357,698	D105G	probably damaging	Het
Mep1a	C	T	17: 43,486,241	V312M	possibly damaging	Het
Mfap4	C	A	11: 61,485,509		probably benign	Het
Mrgbp	A	T	2: 180,585,314		silent	Het
Mtmr4	T	C	11: 87,610,935	L548S	probably damaging	Het
Myo7b	T	C	18: 32,003,487		probably null	Het
Myo9a	T	C	9: 59,821,649	I596T	probably damaging	Het
Olfr38	G	T	6: 42,762,418	R122L	probably benign	Het
Olfr594	C	T	7: 103,220,422	R235*	probably null	Het
Pcsk5	T	G	19: 17,560,750	Q904H	probably benign	Het
Pdzrn3	G	T	6: 101,152,009	H565Q	probably damaging	Het
Phkg2	C	T	7: 127,577,620	R61W	probably damaging	Het
Pkd2l1	C	A	19: 44,154,134	A490S	probably damaging	Het
Pomgnt1	T	A	4: 116,154,890	I337N	probably damaging	Het
Psmd3	T	C	11: 98,682,926	V66A	probably benign	Het
Ptger3	T	C	3: 157,567,294	S93P	probably damaging	Het
Rbm27	T	A	18: 42,301,775	D301E	probably damaging	Het
Rdh16	A	T	10: 127,801,513		probably null	Het
Slc35a5	A	T	16: 45,144,292	F193I	probably benign	Het
Slc4a4	A	G	5: 89,038,561	K167R	probably damaging	Het
Sort1	A	T	3: 108,355,541	T772S	possibly damaging	Het
Sptbn5	T	A	2: 120,048,757		noncoding transcript	Het
Stard5	G	T	7: 83,633,281		probably benign	Het
Tbc1d22a	A	G	15: 86,235,685	T61A	probably damaging	Het
Tox2	T	C	2: 163,320,647	L479P	probably damaging	Het
Vmn1r209	A	T	13: 22,805,965	L185Q	probably damaging	Het
Vmn2r59	A	G	7: 42,012,438	I651T	probably benign	Het
Vsig1	G	T	X: 140,926,386	A95S	probably benign	Het
Zfhx4	T	C	3: 5,413,067	S3556P	possibly damaging	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
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
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'- TGCCCAATCAGTGCTTCCATG -3'
(R):5'- AGAACCTTTACCCTCATCCAGG -3'

Sequencing Primer
(F):5'- CTTCCATGATAATTTTTGGGTGCC -3'
(R):5'- AGTTCATAGGCGAGGCTAG -3'

Posted On

2015-10-08