Mutagenetix > Incidental Mutation

Incidental Mutation 'R1992:Usp1'

223585

Institutional Source

Beutler Lab

Gene Symbol

Usp1

Ensembl Gene

ENSMUSG00000028560

Gene Name

ubiquitin specific peptidase 1

Synonyms

MMRRC Submission

040003-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.901) question?

Stock #

R1992 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

98812047-98823780 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 98822531 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glycine at position 615 (D615G)

Ref Sequence

ENSEMBL: ENSMUSP00000088917 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000030286] [ENSMUST00000030289] [ENSMUST00000075836] [ENSMUST00000091358] [ENSMUST00000125104] [ENSMUST00000127417] [ENSMUST00000205650]

AlphaFold

Q8BJQ2

Predicted Effect

probably benign
Transcript: ENSMUST00000030286

SMART Domains

Protein: ENSMUSP00000030286
Gene: ENSMUSG00000028556

Domain	Start	End	E-Value	Type
Pfam:DUF3398	67	159	6.5e-30	PFAM
coiled coil region	367	394	N/A	INTRINSIC
low complexity region	493	504	N/A	INTRINSIC
Pfam:DOCK-C2	557	736	1.8e-51	PFAM
low complexity region	789	799	N/A	INTRINSIC
low complexity region	862	873	N/A	INTRINSIC
low complexity region	888	901	N/A	INTRINSIC
low complexity region	1135	1163	N/A	INTRINSIC
low complexity region	1350	1364	N/A	INTRINSIC
low complexity region	1543	1565	N/A	INTRINSIC
Pfam:DHR-2	1571	2095	1.4e-217	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000030289
AA Change: D615G

PolyPhen 2 Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)

SMART Domains

Protein: ENSMUSP00000030289
Gene: ENSMUSG00000028560
AA Change: D615G

Domain	Start	End	E-Value	Type
Pfam:UCH	80	616	9.2e-35	PFAM
Pfam:UCH_1	415	618	1.3e-11	PFAM
Pfam:UCH	723	781	3.9e-6	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000075836

SMART Domains

Protein: ENSMUSP00000075233
Gene: ENSMUSG00000028556

Domain	Start	End	E-Value	Type
Pfam:DUF3398	65	159	5.8e-34	PFAM
coiled coil region	367	394	N/A	INTRINSIC
low complexity region	493	504	N/A	INTRINSIC
Pfam:DOCK-C2	556	737	3.3e-58	PFAM
low complexity region	789	799	N/A	INTRINSIC
low complexity region	862	873	N/A	INTRINSIC
low complexity region	888	901	N/A	INTRINSIC
low complexity region	1105	1133	N/A	INTRINSIC
low complexity region	1320	1334	N/A	INTRINSIC
low complexity region	1513	1535	N/A	INTRINSIC
Pfam:Ded_cyto	1888	2065	6.5e-80	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000091358
AA Change: D615G

PolyPhen 2 Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)

SMART Domains

Protein: ENSMUSP00000088917
Gene: ENSMUSG00000028560
AA Change: D615G

Domain	Start	End	E-Value	Type
Pfam:UCH	80	622	5e-39	PFAM
Pfam:UCH_1	346	613	2.8e-11	PFAM
low complexity region	765	779	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000124466

Predicted Effect

probably benign
Transcript: ENSMUST00000125104

SMART Domains

Protein: ENSMUSP00000135496
Gene: ENSMUSG00000028560

Domain	Start	End	E-Value	Type
Pfam:UCH	37	150	4.1e-14	PFAM
Pfam:UCH_1	38	80	1.2e-7	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000127417

SMART Domains

Protein: ENSMUSP00000117797
Gene: ENSMUSG00000028556

Domain	Start	End	E-Value	Type
low complexity region	140	162	N/A	INTRINSIC
Pfam:Ded_cyto	517	694	3e-80	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000205650

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000206128

Meta Mutation Damage Score

0.0644

Coding Region Coverage

1x: 99.1%
3x: 98.4%
10x: 96.4%
20x: 92.5%

Validation Efficiency

MGI Phenotype

FUNCTION: This gene encodes a member of the ubiquitin-specific peptidase family. The encoded protein acts as a catalytic subunit in a heterodimeric deubiquitinating enzyme complex that deubiquitinates Fanconi anemia, complementation group D2, and plays a role in homologous recombination-mediated DNA repair. Disruption of this gene is associated with a Fanconi anemia-like phenotype and genomic instability. Alternative splicing results in multiple transcript variants. Pseudogenes of this gene have been defined on chromosomes 3, 12, and 15. [provided by RefSeq, Aug 2014]
PHENOTYPE: Homozygous null mice have a high rate of postnatal lethality related to cyanosis. Male survivors are infertile while female survivors have reduced fertility. Both sexes have reduced number of gametes, are sensitive to ionizing radiation, and have decreased numbers of bone marrow cells. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 123 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2310009B15Rik	T	C	1: 138,781,380 (GRCm39)	T90A	probably damaging	Het
A930011G23Rik	T	C	5: 99,381,784 (GRCm39)	D326G	possibly damaging	Het
Abcc2	A	T	19: 43,795,581 (GRCm39)	I446F	probably damaging	Het
Adam34l	T	C	8: 44,080,176 (GRCm39)	K16R	probably benign	Het
Adamts14	A	G	10: 61,034,439 (GRCm39)	Y1150H	probably benign	Het
Adgrl2	A	G	3: 148,522,880 (GRCm39)	I217T	possibly damaging	Het
Afap1l1	A	T	18: 61,874,842 (GRCm39)	Y446*	probably null	Het
Aimp2	G	A	5: 143,843,548 (GRCm39)	A14V	probably damaging	Het
Akap8	G	A	17: 32,535,586 (GRCm39)	H143Y	probably damaging	Het
Aldh2	A	T	5: 121,714,026 (GRCm39)	V207E	possibly damaging	Het
Aoc1l2	T	A	6: 48,907,703 (GRCm39)	H234Q	probably damaging	Het
Armc3	T	C	2: 19,297,953 (GRCm39)	Y575H	probably damaging	Het
Arpp21	T	C	9: 111,986,861 (GRCm39)	E230G	probably damaging	Het
Arrdc3	G	A	13: 81,031,808 (GRCm39)	D14N	probably damaging	Het
Atn1	A	G	6: 124,722,291 (GRCm39)		probably benign	Het
Atxn7l1	G	A	12: 33,408,743 (GRCm39)	D302N	probably damaging	Het
Bbs1	T	A	19: 4,941,736 (GRCm39)	H518L	probably benign	Het
Bltp1	A	T	3: 37,054,181 (GRCm39)	H3100L	probably benign	Het
Bmpr1a	C	A	14: 34,147,050 (GRCm39)	G241C	probably damaging	Het
Cacna1b	G	A	2: 24,622,318 (GRCm39)	P222L	probably damaging	Het
Calcrl	T	C	2: 84,200,855 (GRCm39)	Y63C	probably damaging	Het
Cand2	A	G	6: 115,762,093 (GRCm39)	H173R	possibly damaging	Het
Cap2	T	A	13: 46,791,357 (GRCm39)	Y175N	possibly damaging	Het
Card14	A	T	11: 119,212,647 (GRCm39)		probably null	Het
Cd3d	T	A	9: 44,896,299 (GRCm39)	Y29*	probably null	Het
Cd4	A	G	6: 124,844,651 (GRCm39)	V378A	possibly damaging	Het
Cluh	A	T	11: 74,550,828 (GRCm39)	H318L	probably damaging	Het
Clvs1	T	A	4: 9,281,899 (GRCm39)	D114E	probably benign	Het
Cnot4	T	A	6: 35,000,344 (GRCm39)	T548S	probably benign	Het
Col18a1	T	C	10: 76,916,988 (GRCm39)	I114V	unknown	Het
Cr2	G	A	1: 194,836,458 (GRCm39)	P1278S	possibly damaging	Het
Crebbp	A	T	16: 3,946,561 (GRCm39)		probably null	Het
Dnah7a	T	G	1: 53,621,835 (GRCm39)	K1097Q	possibly damaging	Het
Doc2a	T	A	7: 126,450,979 (GRCm39)		probably null	Het
Dpp10	A	T	1: 123,832,833 (GRCm39)	V48E	probably null	Het
Dsg2	A	G	18: 20,734,530 (GRCm39)	K836R	probably damaging	Het
Egr2	T	C	10: 67,375,857 (GRCm39)	V164A	probably damaging	Het
Erbin	A	T	13: 103,970,221 (GRCm39)	S1132T	probably benign	Het
Espn	T	A	4: 152,213,012 (GRCm39)		probably null	Het
Fam83b	A	G	9: 76,399,304 (GRCm39)	S600P	probably benign	Het
Fanca	A	T	8: 124,024,551 (GRCm39)	N425K	possibly damaging	Het
Flot2	C	T	11: 77,949,445 (GRCm39)	L294F	probably damaging	Het
Frs2	A	G	10: 116,910,459 (GRCm39)	V301A	probably benign	Het
Fv1	T	A	4: 147,953,618 (GRCm39)	N61K	possibly damaging	Het
Fxr2	A	G	11: 69,540,659 (GRCm39)	E339G	possibly damaging	Het
Gck	T	C	11: 5,856,515 (GRCm39)	Y214C	probably damaging	Het
Golga3	C	G	5: 110,340,839 (GRCm39)	T551R	probably damaging	Het
Gorab	A	G	1: 163,224,625 (GRCm39)	S59P	probably damaging	Het
Gsdme	C	T	6: 50,185,102 (GRCm39)	V451M	probably damaging	Het
H2-T13	A	C	17: 36,391,938 (GRCm39)	I216S	probably damaging	Het
Herc4	T	A	10: 63,081,743 (GRCm39)	V22E	possibly damaging	Het
Hjurp	GT	GTT	1: 88,194,246 (GRCm39)		probably null	Het
Hoxa2	A	T	6: 52,141,576 (GRCm39)	S17T	probably damaging	Het
Hs3st5	A	G	10: 36,708,882 (GRCm39)	Y139C	probably damaging	Het
Ism1	G	A	2: 139,587,937 (GRCm39)	V221I	probably benign	Het
Kalrn	T	G	16: 33,796,108 (GRCm39)	L1222F	probably damaging	Het
Katnip	A	G	7: 125,419,261 (GRCm39)	N476S	probably benign	Het
Kdm4c	A	G	4: 74,261,631 (GRCm39)	D602G	possibly damaging	Het
Ktn1	A	G	14: 47,932,978 (GRCm39)	K711E	probably damaging	Het
Lce1k	A	T	3: 92,714,125 (GRCm39)	C20S	unknown	Het
Macf1	A	G	4: 123,350,488 (GRCm39)	S3792P	probably damaging	Het
Maml3	C	T	3: 51,598,178 (GRCm39)	M189I	probably benign	Het
Mcc	C	A	18: 44,624,382 (GRCm39)	E213*	probably null	Het
Mep1a	T	G	17: 43,813,573 (GRCm39)	I13L	probably benign	Het
Mkrn2	G	T	6: 115,586,562 (GRCm39)	C16F	probably damaging	Het
Mlh1	C	T	9: 111,057,631 (GRCm39)	A727T	probably damaging	Het
Muc21	A	T	17: 35,929,600 (GRCm39)	S1529T	probably benign	Het
Naa16	T	C	14: 79,593,931 (GRCm39)	Y344C	probably damaging	Het
Nebl	T	A	2: 17,457,321 (GRCm39)	I80F	probably damaging	Het
Nlrc4	T	A	17: 74,752,628 (GRCm39)	Y585F	probably benign	Het
Nrcam	A	G	12: 44,587,753 (GRCm39)	K149R	probably damaging	Het
Nufip1	T	A	14: 76,372,287 (GRCm39)	I467N	probably damaging	Het
Nup133	A	G	8: 124,632,960 (GRCm39)	I1057T	possibly damaging	Het
Obscn	A	T	11: 58,886,653 (GRCm39)		probably benign	Het
Or10ag52	T	A	2: 87,043,588 (GRCm39)	C117*	probably null	Het
Or5k1	A	G	16: 58,617,309 (GRCm39)	V300A	probably benign	Het
Or5k14	A	C	16: 58,692,874 (GRCm39)	I213R	probably benign	Het
Pi4k2a	A	T	19: 42,104,377 (GRCm39)	I380F	probably damaging	Het
Piezo2	A	T	18: 63,207,733 (GRCm39)	L1426Q	probably null	Het
Pik3cg	A	T	12: 32,254,024 (GRCm39)	D654E	possibly damaging	Het
Poli	G	T	18: 70,642,058 (GRCm39)	P714Q	probably damaging	Het
Polr3f	A	G	2: 144,378,230 (GRCm39)	N201D	probably benign	Het
Prorp	A	G	12: 55,384,991 (GRCm39)	D89G	probably damaging	Het
Ptprz1	A	T	6: 22,959,747 (GRCm39)	K81N	probably benign	Het
Rbm19	T	C	5: 120,271,948 (GRCm39)		probably null	Het
Sec24a	C	T	11: 51,627,190 (GRCm39)	V241I	probably benign	Het
Sgk3	A	G	1: 9,950,567 (GRCm39)	T160A	possibly damaging	Het
Slc1a4	A	G	11: 20,254,375 (GRCm39)	I497T	probably benign	Het
Slc26a9	A	T	1: 131,690,532 (GRCm39)	D512V	probably damaging	Het
Slc43a3	C	T	2: 84,788,084 (GRCm39)	R489C	probably damaging	Het
Slc5a12	T	A	2: 110,452,089 (GRCm39)	F327L	probably benign	Het
Slitrk3	A	G	3: 72,957,104 (GRCm39)	V556A	possibly damaging	Het
Spata6l	A	G	19: 28,926,024 (GRCm39)	F130L	probably damaging	Het
Spib	T	C	7: 44,178,281 (GRCm39)	E180G	probably benign	Het
Spint2	T	A	7: 28,958,833 (GRCm39)	N128Y	probably damaging	Het
Spx	G	A	6: 142,364,245 (GRCm39)	G102E	probably benign	Het
Spz1	T	A	13: 92,712,166 (GRCm39)	E103D	possibly damaging	Het
Sstr2	T	C	11: 113,515,495 (GRCm39)	I138T	probably benign	Het
Sytl3	T	A	17: 7,000,448 (GRCm39)	I206N	possibly damaging	Het
Tcaf2	T	C	6: 42,606,791 (GRCm39)	T388A	probably benign	Het
Tdpoz8	G	T	3: 92,981,344 (GRCm39)	A121S	probably benign	Het
Thap12	T	C	7: 98,365,572 (GRCm39)	V580A	possibly damaging	Het
Tlr5	T	A	1: 182,801,912 (GRCm39)	D405E	probably damaging	Het
Tnxb	T	C	17: 34,890,878 (GRCm39)	V407A	probably damaging	Het
Tpx2	T	A	2: 152,732,544 (GRCm39)	M606K	probably benign	Het
Trim43a	T	G	9: 88,466,312 (GRCm39)	L211R	probably damaging	Het
Trim46	A	T	3: 89,145,008 (GRCm39)	Y489N	probably damaging	Het
Ttc28	C	T	5: 111,424,188 (GRCm39)	S1485L	probably benign	Het
Ttll8	T	C	15: 88,798,654 (GRCm39)	T694A	probably benign	Het
Txnl1	T	C	18: 63,812,585 (GRCm39)	T70A	probably benign	Het
Ube3a	C	T	7: 58,953,535 (GRCm39)	A823V	probably damaging	Het
Ubqln5	C	A	7: 103,778,741 (GRCm39)	V28F	probably damaging	Het
Ulk1	T	A	5: 110,935,017 (GRCm39)	Q972L	probably damaging	Het
Unc93b1	T	C	19: 3,994,062 (GRCm39)	Y398H	probably benign	Het
Utp15	A	G	13: 98,387,420 (GRCm39)	C385R	probably benign	Het
Vmn2r91	T	A	17: 18,356,142 (GRCm39)	V603D	probably damaging	Het
Whamm	C	T	7: 81,241,519 (GRCm39)	R277*	probably null	Het
Wnt8a	A	G	18: 34,677,937 (GRCm39)	D115G	probably damaging	Het
Yjefn3	A	T	8: 70,341,645 (GRCm39)		probably null	Het
Ywhab	A	T	2: 163,853,807 (GRCm39)	I95F	probably damaging	Het
Zfp143	C	T	7: 109,660,489 (GRCm39)		probably benign	Het
Zfp607b	C	G	7: 27,401,949 (GRCm39)	T135R	possibly damaging	Het
Zfp970	A	G	2: 177,166,663 (GRCm39)	Q79R	possibly damaging	Het

Other mutations in Usp1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00715:Usp1	APN	4	98,822,818 (GRCm39)	splice site	probably null
IGL02692:Usp1	APN	4	98,817,197 (GRCm39)	missense	probably benign	0.00
R1782:Usp1	UTSW	4	98,822,435 (GRCm39)	missense	probably damaging	1.00
R1991:Usp1	UTSW	4	98,822,531 (GRCm39)	missense	probably benign	0.00
R2273:Usp1	UTSW	4	98,818,079 (GRCm39)	missense	probably damaging	1.00
R2274:Usp1	UTSW	4	98,818,079 (GRCm39)	missense	probably damaging	1.00
R2275:Usp1	UTSW	4	98,818,079 (GRCm39)	missense	probably damaging	1.00
R3750:Usp1	UTSW	4	98,822,357 (GRCm39)	splice site	probably null
R3886:Usp1	UTSW	4	98,817,973 (GRCm39)	missense	probably damaging	1.00
R4014:Usp1	UTSW	4	98,822,939 (GRCm39)	missense	probably damaging	1.00
R5141:Usp1	UTSW	4	98,822,446 (GRCm39)	missense	probably damaging	1.00
R5304:Usp1	UTSW	4	98,822,855 (GRCm39)	missense	probably benign
R5388:Usp1	UTSW	4	98,819,294 (GRCm39)	missense	probably benign
R5709:Usp1	UTSW	4	98,819,360 (GRCm39)	missense	probably damaging	0.99
R6035:Usp1	UTSW	4	98,818,082 (GRCm39)	missense	probably damaging	1.00
R6035:Usp1	UTSW	4	98,818,082 (GRCm39)	missense	probably damaging	1.00
R6592:Usp1	UTSW	4	98,814,756 (GRCm39)	missense	possibly damaging	0.86
R6956:Usp1	UTSW	4	98,819,243 (GRCm39)	missense	probably damaging	0.96
R7117:Usp1	UTSW	4	98,817,127 (GRCm39)	missense	possibly damaging	0.59
R7396:Usp1	UTSW	4	98,814,688 (GRCm39)	intron	probably benign
R7516:Usp1	UTSW	4	98,822,356 (GRCm39)	missense	probably damaging	1.00
R7590:Usp1	UTSW	4	98,822,489 (GRCm39)	missense	possibly damaging	0.67
R7828:Usp1	UTSW	4	98,820,544 (GRCm39)	missense	probably damaging	1.00
R8050:Usp1	UTSW	4	98,817,150 (GRCm39)	missense	probably benign	0.10
R8085:Usp1	UTSW	4	98,816,578 (GRCm39)	missense	probably damaging	1.00
R8298:Usp1	UTSW	4	98,819,136 (GRCm39)	missense	probably damaging	1.00
R8736:Usp1	UTSW	4	98,821,105 (GRCm39)	missense	probably damaging	1.00
R8801:Usp1	UTSW	4	98,822,848 (GRCm39)	missense	probably benign
R8844:Usp1	UTSW	4	98,823,017 (GRCm39)	missense	probably damaging	1.00
R8887:Usp1	UTSW	4	98,819,185 (GRCm39)	missense	probably benign	0.43
R8899:Usp1	UTSW	4	98,819,347 (GRCm39)	missense	probably damaging	1.00
R9063:Usp1	UTSW	4	98,819,389 (GRCm39)	missense	probably benign	0.00
R9275:Usp1	UTSW	4	98,819,578 (GRCm39)	missense	probably damaging	0.98
R9738:Usp1	UTSW	4	98,819,672 (GRCm39)	missense	probably benign	0.01

Predicted Primers

PCR Primer
(F):5'- CCAAAGGTTTGACTGTTACGG -3'
(R):5'- CTTTTGTCCACCGAGAAGTCC -3'

Sequencing Primer
(F):5'- TCCAAGATCAACACTCCTTTATTGAC -3'
(R):5'- TTTTGTCCACCGAGAAGTCCAATAC -3'

Posted On

2014-08-25