Mutagenetix > Incidental Mutation

Incidental Mutation 'R9537:Usp40'

719720

Institutional Source

Beutler Lab

Gene Symbol

Usp40

Ensembl Gene

ENSMUSG00000005501

Gene Name

ubiquitin specific peptidase 40

Synonyms

B230215L03Rik

MMRRC Submission

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R9537 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

87872841-87936273 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 87935117 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Cysteine at position 10 (Y10C)

Ref Sequence

ENSEMBL: ENSMUSP00000140107 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000040783] [ENSMUST00000187758] [ENSMUST00000188332]

AlphaFold

Q8BWR4

Predicted Effect

probably benign
Transcript: ENSMUST00000040783
AA Change: Y10C

PolyPhen 2 Score 0.015 (Sensitivity: 0.96; Specificity: 0.79)

SMART Domains

Protein: ENSMUSP00000038533
Gene: ENSMUSG00000005501
AA Change: Y10C

Domain	Start	End	E-Value	Type
Pfam:UCH	40	344	1.1e-31	PFAM
Pfam:UCH_1	41	320	1.2e-20	PFAM
low complexity region	641	650	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000187758
AA Change: Y10C

PolyPhen 2 Score 0.007 (Sensitivity: 0.96; Specificity: 0.75)

SMART Domains

Protein: ENSMUSP00000140107
Gene: ENSMUSG00000005501
AA Change: Y10C

Domain	Start	End	E-Value	Type
Pfam:UCH	40	346	8.7e-41	PFAM
Pfam:UCH_1	41	319	2.4e-22	PFAM
low complexity region	641	650	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000188332
AA Change: Y10C

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

SMART Domains

Protein: ENSMUSP00000140574
Gene: ENSMUSG00000005501
AA Change: Y10C

Domain	Start	End	E-Value	Type
Pfam:UCH	40	70	5.9e-6	PFAM

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 99.0%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] Modification of cellular proteins by ubiquitin is an essential regulatory mechanism controlled by the coordinated action of multiple ubiquitin-conjugating and deubiquitinating enzymes. USP40 belongs to a large family of cysteine proteases that function as deubiquitinating enzymes (Quesada et al., 2004 [PubMed 14715245]).[supplied by OMIM, Mar 2008]

Allele List at MGI

All alleles(4) : Targeted, other(2) Gene trapped(2)

Other mutations in this stock

Total: 41 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adgra3	A	G	5: 50,118,207 (GRCm39)	Y1114H	possibly damaging	Het
Atp5pf	A	G	16: 84,625,358 (GRCm39)	Y82H	probably damaging	Het
Bcl2a1d	T	G	9: 88,613,526 (GRCm39)	I83L	probably benign	Het
Bean1	CT	C	8: 104,908,664 (GRCm39)		probably null	Het
Bglap3	T	C	3: 88,276,139 (GRCm39)	D71G	probably benign	Het
Bnip3l	G	A	14: 67,246,214 (GRCm39)	P7L	possibly damaging	Het
Chmp2b	T	C	16: 65,347,932 (GRCm39)	K15E	probably benign	Het
Chrm3	A	T	13: 9,927,462 (GRCm39)	W525R	probably damaging	Het
Col7a1	A	T	9: 108,784,420 (GRCm39)	K143*	probably null	Het
D6Ertd527e	G	C	6: 87,088,839 (GRCm39)	S334T	unknown	Het
Dnai1	A	G	4: 41,629,790 (GRCm39)		probably null	Het
Dnhd1	G	A	7: 105,344,740 (GRCm39)	G2028D	probably damaging	Het
Esyt3	C	T	9: 99,199,292 (GRCm39)	R773Q	probably damaging	Het
Ffar1	T	C	7: 30,560,025 (GRCm39)	T291A	probably benign	Het
Golga2	G	T	2: 32,178,313 (GRCm39)		probably benign	Het
Hapln2	T	A	3: 87,931,780 (GRCm39)		probably null	Het
Ing1	T	C	8: 11,611,889 (GRCm39)	L203P	probably benign	Het
Litafd	G	T	16: 8,501,177 (GRCm39)	C11F		Het
Mab21l4	T	C	1: 93,080,884 (GRCm39)	K341E	possibly damaging	Het
Med1	T	C	11: 98,062,586 (GRCm39)	T171A	possibly damaging	Het
Mib2	A	T	4: 155,741,952 (GRCm39)	L387H	probably damaging	Het
Mier1	A	G	4: 103,019,758 (GRCm39)	N494S	probably benign	Het
Myof	A	G	19: 37,896,054 (GRCm39)	L1847P	probably damaging	Het
Ndst3	A	T	3: 123,465,162 (GRCm39)	V270D		Het
Nup160	T	C	2: 90,560,088 (GRCm39)	L1271S	possibly damaging	Het
Osgep	A	T	14: 51,162,119 (GRCm39)		probably null	Het
Ptgfr	G	T	3: 151,541,445 (GRCm39)	T21N	possibly damaging	Het
Ptgs1	T	C	2: 36,120,739 (GRCm39)	S23P	unknown	Het
Rsf1	CGGCGGCGG	CGGCGGCGGGGGCGGCGG	7: 97,229,121 (GRCm39)		probably benign	Het
Smu1	A	G	4: 40,755,671 (GRCm39)	S65P	probably benign	Het
Spef2	T	C	15: 9,601,885 (GRCm39)	Y1459C	unknown	Het
Spen	A	G	4: 141,199,015 (GRCm39)	V3204A	probably benign	Het
Spen	TTGCTGCTGCTGCTGCTGCTGCTGCTG	TTGCTGCTGCTGCTGCTGCTGCTG	4: 141,244,156 (GRCm39)		probably benign	Het
Timm44	G	A	8: 4,310,576 (GRCm39)	T392I	possibly damaging	Het
Tnc	A	T	4: 63,884,821 (GRCm39)	I1818N	probably damaging	Het
Trpm1	G	T	7: 63,803,616 (GRCm39)		probably benign	Het
Ttc14	A	G	3: 33,857,347 (GRCm39)	Y231C	probably damaging	Het
Ube3b	A	G	5: 114,525,245 (GRCm39)	R23G	probably damaging	Het
Vmn2r107	C	A	17: 20,595,149 (GRCm39)	S567R	probably benign	Het
Zfp112	T	C	7: 23,826,512 (GRCm39)	Y831H	probably damaging	Het
Zfy2	T	A	Y: 2,108,596 (GRCm39)	T355S		Het

Other mutations in Usp40

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00264:Usp40	APN	1	87,931,960 (GRCm39)	splice site	probably benign
IGL00828:Usp40	APN	1	87,906,028 (GRCm39)	unclassified	probably benign
IGL01090:Usp40	APN	1	87,890,187 (GRCm39)	missense	probably benign	0.01
IGL01123:Usp40	APN	1	87,913,845 (GRCm39)	missense	probably benign	0.01
IGL01401:Usp40	APN	1	87,921,920 (GRCm39)	missense	probably damaging	1.00
IGL02506:Usp40	APN	1	87,909,738 (GRCm39)	missense	probably damaging	0.98
IGL02580:Usp40	APN	1	87,908,688 (GRCm39)	splice site	probably null
IGL02625:Usp40	APN	1	87,877,739 (GRCm39)	missense	probably benign	0.19
IGL02811:Usp40	APN	1	87,923,458 (GRCm39)	missense	probably damaging	1.00
IGL02958:Usp40	APN	1	87,906,207 (GRCm39)	missense	probably damaging	0.99
Brink	UTSW	1	87,908,755 (GRCm39)	missense	probably benign	0.11
void	UTSW	1	87,923,435 (GRCm39)	nonsense	probably null
G5030:Usp40	UTSW	1	87,921,941 (GRCm39)	missense	probably damaging	1.00
R0019:Usp40	UTSW	1	87,906,133 (GRCm39)	missense	probably benign	0.00
R0282:Usp40	UTSW	1	87,908,680 (GRCm39)	splice site	probably benign
R0453:Usp40	UTSW	1	87,874,320 (GRCm39)	makesense	probably null
R0646:Usp40	UTSW	1	87,906,244 (GRCm39)	missense	probably benign	0.00
R1440:Usp40	UTSW	1	87,909,808 (GRCm39)	missense	probably benign	0.01
R1490:Usp40	UTSW	1	87,916,687 (GRCm39)	nonsense	probably null
R1620:Usp40	UTSW	1	87,921,947 (GRCm39)	missense	probably damaging	1.00
R1881:Usp40	UTSW	1	87,921,993 (GRCm39)	missense	probably benign	0.08
R1903:Usp40	UTSW	1	87,909,778 (GRCm39)	missense	probably benign	0.15
R1912:Usp40	UTSW	1	87,874,368 (GRCm39)	missense	probably benign	0.00
R1919:Usp40	UTSW	1	87,923,564 (GRCm39)	missense	possibly damaging	0.75
R1976:Usp40	UTSW	1	87,906,258 (GRCm39)	missense	probably benign	0.00
R2111:Usp40	UTSW	1	87,877,936 (GRCm39)	missense	probably benign	0.17
R2112:Usp40	UTSW	1	87,877,936 (GRCm39)	missense	probably benign	0.17
R2163:Usp40	UTSW	1	87,923,580 (GRCm39)	splice site	probably benign
R2432:Usp40	UTSW	1	87,909,804 (GRCm39)	missense	probably benign
R2865:Usp40	UTSW	1	87,877,701 (GRCm39)	nonsense	probably null
R3885:Usp40	UTSW	1	87,894,991 (GRCm39)	missense	probably damaging	1.00
R4360:Usp40	UTSW	1	87,880,083 (GRCm39)	missense	probably damaging	1.00
R4370:Usp40	UTSW	1	87,925,597 (GRCm39)	missense	probably benign
R4496:Usp40	UTSW	1	87,923,459 (GRCm39)	missense	possibly damaging	0.69
R4714:Usp40	UTSW	1	87,894,901 (GRCm39)	splice site	probably null
R4888:Usp40	UTSW	1	87,913,923 (GRCm39)	critical splice acceptor site	probably null
R4944:Usp40	UTSW	1	87,880,077 (GRCm39)	missense	probably benign	0.10
R5269:Usp40	UTSW	1	87,923,504 (GRCm39)	missense	probably benign	0.01
R5629:Usp40	UTSW	1	87,908,731 (GRCm39)	missense	probably benign
R5696:Usp40	UTSW	1	87,923,474 (GRCm39)	missense	probably benign	0.27
R5756:Usp40	UTSW	1	87,879,413 (GRCm39)	missense	possibly damaging	0.66
R5887:Usp40	UTSW	1	87,927,592 (GRCm39)	missense	probably damaging	1.00
R5910:Usp40	UTSW	1	87,896,122 (GRCm39)	nonsense	probably null
R6014:Usp40	UTSW	1	87,907,738 (GRCm39)	missense	probably damaging	1.00
R6044:Usp40	UTSW	1	87,917,872 (GRCm39)	missense	probably benign
R6083:Usp40	UTSW	1	87,906,281 (GRCm39)	missense	probably benign	0.01
R6299:Usp40	UTSW	1	87,925,649 (GRCm39)	missense	probably damaging	0.99
R6625:Usp40	UTSW	1	87,894,935 (GRCm39)	missense	probably benign	0.01
R6757:Usp40	UTSW	1	87,907,759 (GRCm39)	missense	probably damaging	0.99
R6810:Usp40	UTSW	1	87,908,755 (GRCm39)	missense	probably benign	0.11
R7110:Usp40	UTSW	1	87,913,884 (GRCm39)	missense	probably benign	0.11
R7573:Usp40	UTSW	1	87,913,794 (GRCm39)	missense	probably benign	0.09
R7575:Usp40	UTSW	1	87,877,682 (GRCm39)	missense	probably damaging	1.00
R7634:Usp40	UTSW	1	87,890,152 (GRCm39)	nonsense	probably null
R7756:Usp40	UTSW	1	87,894,922 (GRCm39)	missense	probably damaging	0.99
R7767:Usp40	UTSW	1	87,909,900 (GRCm39)	missense	probably benign	0.01
R7861:Usp40	UTSW	1	87,909,852 (GRCm39)	missense	probably damaging	0.99
R7881:Usp40	UTSW	1	87,923,435 (GRCm39)	nonsense	probably null
R7896:Usp40	UTSW	1	87,906,201 (GRCm39)	missense	possibly damaging	0.77
R8119:Usp40	UTSW	1	87,895,400 (GRCm39)	splice site	probably null
R8354:Usp40	UTSW	1	87,908,694 (GRCm39)	missense	probably benign	0.00
R8358:Usp40	UTSW	1	87,908,770 (GRCm39)	missense	possibly damaging	0.71
R8425:Usp40	UTSW	1	87,887,558 (GRCm39)	missense	probably benign
R8446:Usp40	UTSW	1	87,906,190 (GRCm39)	missense	probably benign
R8454:Usp40	UTSW	1	87,908,694 (GRCm39)	missense	probably benign	0.00
R8744:Usp40	UTSW	1	87,911,491 (GRCm39)	missense	probably benign
R9002:Usp40	UTSW	1	87,935,063 (GRCm39)	missense	probably benign
R9033:Usp40	UTSW	1	87,923,499 (GRCm39)	utr 3 prime	probably benign
R9210:Usp40	UTSW	1	87,885,035 (GRCm39)	missense	possibly damaging	0.90
R9245:Usp40	UTSW	1	87,878,009 (GRCm39)	missense	probably benign
R9331:Usp40	UTSW	1	87,901,828 (GRCm39)	missense	probably damaging	1.00
R9378:Usp40	UTSW	1	87,885,032 (GRCm39)	missense	probably damaging	1.00
R9379:Usp40	UTSW	1	87,881,889 (GRCm39)	missense	probably benign
R9501:Usp40	UTSW	1	87,925,557 (GRCm39)	missense	probably benign	0.01
R9535:Usp40	UTSW	1	87,935,161 (GRCm39)	start gained	probably benign
RF006:Usp40	UTSW	1	87,894,917 (GRCm39)	missense	possibly damaging	0.47
Z1177:Usp40	UTSW	1	87,896,136 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- TACCTCTGAATTCAGGTGTGAAATG -3'
(R):5'- AATCAGGACCCCGTGTAGGTAG -3'

Sequencing Primer
(F):5'- TTCAGGTGTGAAATGAAGCGTC -3'
(R):5'- GAAAGACAAGTCAGGTCTCGCTTTC -3'

Posted On

2022-07-18