Mutagenetix > Incidental Mutation

Incidental Mutation 'R8058:Yod1'

619499

Institutional Source

Beutler Lab

Gene Symbol

Yod1

Ensembl Gene

ENSMUSG00000046404

Gene Name

YOD1 deubiquitinase

Synonyms

9930028C20Rik

MMRRC Submission

067495-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R8058 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

130645064-130652093 bp(+) (GRCm39)

Type of Mutation

nonsense

DNA Base Change (assembly)

C to T at 130646806 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glutamine to Stop codon at position 228 (Q228*)

Ref Sequence

ENSEMBL: ENSMUSP00000055318 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000049813] [ENSMUST00000050406] [ENSMUST00000066863] [ENSMUST00000169659] [ENSMUST00000171479] [ENSMUST00000185233] [ENSMUST00000186777] [ENSMUST00000186867] [ENSMUST00000187089] [ENSMUST00000188520] [ENSMUST00000189167] [ENSMUST00000189534] [ENSMUST00000191301] [ENSMUST00000191347]

AlphaFold

Q8CB27

PDB Structure

Solution NMR Structure of Ubiquitin thioesterase OTU1 (EC 3.1.2.-) from Mus musculus, Northeast Structural Genomics Consortium Target MmT2A [SOLUTION NMR]

Predicted Effect

probably null
Transcript: ENSMUST00000049813
AA Change: Q228*

SMART Domains

Protein: ENSMUSP00000055318
Gene: ENSMUSG00000046404
AA Change: Q228*

Domain	Start	End	E-Value	Type
PDB:2KZR\|A	42	127	3e-54	PDB
Blast:UBQ	43	118	2e-20	BLAST
Pfam:OTU	150	268	3.4e-8	PFAM
ZnF_C2H2	313	337	2.12e1	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000050406

SMART Domains

Protein: ENSMUSP00000133073
Gene: ENSMUSG00000026409

Domain	Start	End	E-Value	Type
Pfam:6PF2K	28	251	8.1e-107	PFAM
Pfam:KTI12	40	206	9.6e-8	PFAM
Pfam:AAA_33	42	198	3.1e-9	PFAM
PGAM	253	400	3.82e-16	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000066863

SMART Domains

Protein: ENSMUSP00000066426
Gene: ENSMUSG00000026409

Domain	Start	End	E-Value	Type
Pfam:6PF2K	28	251	1.2e-106	PFAM
Pfam:KTI12	41	207	3.5e-8	PFAM
Pfam:AAA_33	42	199	1.2e-10	PFAM
PGAM	253	400	3.82e-16	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000169659

SMART Domains

Protein: ENSMUSP00000127587
Gene: ENSMUSG00000026409

Domain	Start	End	E-Value	Type
Pfam:6PF2K	28	251	1.3e-106	PFAM
Pfam:KTI12	41	207	4.3e-8	PFAM
Pfam:AAA_33	42	199	1.2e-10	PFAM
PGAM	253	400	3.82e-16	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000171479

SMART Domains

Protein: ENSMUSP00000129747
Gene: ENSMUSG00000026409

Domain	Start	End	E-Value	Type
Pfam:6PF2K	28	251	1.2e-106	PFAM
Pfam:KTI12	41	208	3.7e-8	PFAM
Pfam:AAA_33	42	199	1.1e-10	PFAM
PGAM	253	400	3.82e-16	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000185233

SMART Domains

Protein: ENSMUSP00000140551
Gene: ENSMUSG00000026409

Domain	Start	End	E-Value	Type
Pfam:6PF2K	28	251	1.2e-106	PFAM
Pfam:KTI12	41	207	3.5e-8	PFAM
Pfam:AAA_33	42	199	1.2e-10	PFAM
PGAM	253	400	3.82e-16	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000186777

Predicted Effect

probably benign
Transcript: ENSMUST00000186867

Predicted Effect

probably benign
Transcript: ENSMUST00000187089

SMART Domains

Protein: ENSMUSP00000140612
Gene: ENSMUSG00000026409

Domain	Start	End	E-Value	Type
Pfam:6PF2K	28	251	1e-103	PFAM
Pfam:KTI12	41	207	2.3e-5	PFAM
Pfam:AAA_33	42	199	1.4e-8	PFAM
PGAM	253	400	2.9e-20	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000188520

SMART Domains

Protein: ENSMUSP00000140786
Gene: ENSMUSG00000101904

Domain	Start	End	E-Value	Type
Pfam:6PF2K	28	251	6.3e-107	PFAM
Pfam:KTI12	41	209	2.3e-8	PFAM
Pfam:AAA_33	42	199	6.4e-11	PFAM
PGAM	253	342	1.31e-5	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000189167

SMART Domains

Protein: ENSMUSP00000140984
Gene: ENSMUSG00000026409

Domain	Start	End	E-Value	Type
Pfam:6PF2K	28	251	6.3e-107	PFAM
Pfam:KTI12	41	209	2.3e-8	PFAM
Pfam:AAA_33	42	199	6.4e-11	PFAM
PGAM	253	342	1.31e-5	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000189534

SMART Domains

Protein: ENSMUSP00000140355
Gene: ENSMUSG00000026409

Domain	Start	End	E-Value	Type
Pfam:6PF2K	28	251	1.2e-106	PFAM
Pfam:KTI12	41	208	3.7e-8	PFAM
Pfam:AAA_33	42	199	1.1e-10	PFAM
PGAM	253	400	3.82e-16	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000191301

SMART Domains

Protein: ENSMUSP00000140995
Gene: ENSMUSG00000026409

Domain	Start	End	E-Value	Type
Pfam:6PF2K	28	181	9.5e-70	PFAM
Pfam:KTI12	41	183	3.2e-8	PFAM
Pfam:AAA_33	42	184	1.1e-10	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000191347

SMART Domains

Protein: ENSMUSP00000140698
Gene: ENSMUSG00000026409

Domain	Start	End	E-Value	Type
Pfam:6PF2K	28	251	1.2e-103	PFAM
Pfam:KTI12	41	207	2.4e-5	PFAM
Pfam:AAA_33	42	199	1.6e-8	PFAM
PGAM	253	400	2.9e-20	SMART

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.8%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] Protein ubiquitination controls many intracellular processes, including cell cycle progression, transcriptional activation, and signal transduction. This dynamic process, involving ubiquitin conjugating enzymes and deubiquitinating enzymes, adds and removes ubiquitin. Deubiquitinating enzymes are cysteine proteases that specifically cleave ubiquitin from ubiquitin-conjugated protein substrates. The protein encoded by this gene belongs to a DUB subfamily characterized by an ovarian tumor (OTU) domain. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2013]

Allele List at MGI

Other mutations in this stock

Total: 78 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca1	C	T	4: 53,081,954 (GRCm39)	D769N	possibly damaging	Het
Abcb6	A	G	1: 75,156,653 (GRCm39)	L37P	possibly damaging	Het
Abcg1	G	T	17: 31,324,504 (GRCm39)	A250S	probably benign	Het
Acsf3	C	T	8: 123,540,373 (GRCm39)	H524Y	possibly damaging	Het
Agbl4	A	G	4: 110,518,039 (GRCm39)	K110R	unknown	Het
Arfgap2	G	A	2: 91,096,644 (GRCm39)		probably null	Het
B4galt4	T	C	16: 38,586,383 (GRCm39)		probably null	Het
Bex6	G	T	16: 32,005,224 (GRCm39)	D11Y	probably damaging	Het
Bhlhe40	TG	TGG	6: 108,641,818 (GRCm39)	254	probably null	Het
C8b	A	T	4: 104,647,811 (GRCm39)	D334V	probably damaging	Het
Capn11	T	C	17: 45,954,681 (GRCm39)	Q152R	probably null	Het
Ccdc171	C	A	4: 83,499,003 (GRCm39)	Q234K	probably damaging	Het
Cemip2	C	A	19: 21,829,695 (GRCm39)	A1268E	probably benign	Het
Clec2h	A	G	6: 128,650,966 (GRCm39)	D82G	probably benign	Het
Creld2	A	G	15: 88,710,632 (GRCm39)	D349G	probably damaging	Het
D430041D05Rik	A	G	2: 103,979,128 (GRCm39)	*1415Q	probably null	Het
Dnmt3a	T	C	12: 3,952,768 (GRCm39)	V755A	possibly damaging	Het
Doc2a	G	T	7: 126,450,164 (GRCm39)	V201L	probably benign	Het
Fan1	T	A	7: 64,022,234 (GRCm39)	N340Y	probably damaging	Het
Fbn1	G	T	2: 125,193,889 (GRCm39)	D1359E	possibly damaging	Het
Fcnb	T	C	2: 27,969,707 (GRCm39)	Y120C	probably damaging	Het
Fras1	T	A	5: 96,842,778 (GRCm39)	D1665E	probably benign	Het
Fry	A	T	5: 150,419,232 (GRCm39)	D524V		Het
Garem1	A	G	18: 21,281,621 (GRCm39)	L245P	probably damaging	Het
Gdf6	A	G	4: 9,859,712 (GRCm39)	S265G	probably benign	Het
Gm5591	T	C	7: 38,218,363 (GRCm39)	I837V	probably benign	Het
Gpr61	T	C	3: 108,058,211 (GRCm39)	Y150C	probably damaging	Het
Grin2b	A	T	6: 135,710,225 (GRCm39)	L1107Q	probably damaging	Het
Helb	A	G	10: 119,941,483 (GRCm39)	S402P	probably benign	Het
Htt	A	G	5: 34,977,444 (GRCm39)	T777A	probably benign	Het
Iffo2	A	G	4: 139,341,164 (GRCm39)	D383G	probably benign	Het
Ikzf3	G	T	11: 98,407,753 (GRCm39)	Y29*	probably null	Het
Ints2	A	T	11: 86,146,179 (GRCm39)	M143K	probably benign	Het
Jmjd1c	T	C	10: 67,090,274 (GRCm39)	V2292A	not run	Het
Katnip	A	G	7: 125,442,188 (GRCm39)	E725G	probably benign	Het
Lamb1	C	A	12: 31,353,046 (GRCm39)	Q916K	probably benign	Het
Lrrtm4	G	A	6: 79,999,528 (GRCm39)	M313I	probably benign	Het
Lum	A	G	10: 97,404,425 (GRCm39)	I107V	probably benign	Het
Ly6h	T	C	15: 75,437,061 (GRCm39)	E126G	probably benign	Het
Map3k5	G	A	10: 20,007,860 (GRCm39)	V1230M	probably damaging	Het
Mcoln1	T	C	8: 3,558,378 (GRCm39)	F211L	probably benign	Het
Mink1	G	A	11: 70,494,594 (GRCm39)	W258*	probably null	Het
Muc16	G	T	9: 18,571,298 (GRCm39)	S407*	probably null	Het
Ngef	G	A	1: 87,473,744 (GRCm39)	Q13*	probably null	Het
Nxpe5	T	A	5: 138,237,573 (GRCm39)	Y44*	probably null	Het
Or13d1	T	A	4: 52,971,106 (GRCm39)	L162M	probably benign	Het
Or4a77	A	G	2: 89,487,671 (GRCm39)	V38A	probably benign	Het
Or5t9	A	G	2: 86,660,052 (GRCm39)	R319G	probably benign	Het
Or7e178	T	A	9: 20,225,476 (GRCm39)	I247F	probably damaging	Het
Or8g24	A	T	9: 38,989,862 (GRCm39)	Y60N	probably damaging	Het
Or8h8	C	A	2: 86,753,151 (GRCm39)	A242S	probably benign	Het
Orc3	C	A	4: 34,595,223 (GRCm39)	E249*	probably null	Het
Otogl	A	T	10: 107,598,287 (GRCm39)	C2288S	probably damaging	Het
Pde1b	A	G	15: 103,433,238 (GRCm39)	E249G	probably damaging	Het
Phf2	T	C	13: 48,976,558 (GRCm39)	E219G	unknown	Het
Rbm19	T	A	5: 120,278,440 (GRCm39)		probably null	Het
Rcc2	G	A	4: 140,429,586 (GRCm39)	C40Y	probably benign	Het
Sbk2	A	G	7: 4,960,289 (GRCm39)	Y294H	possibly damaging	Het
Selenoo	T	C	15: 88,976,942 (GRCm39)	I198T	possibly damaging	Het
Sema3f	T	C	9: 107,559,800 (GRCm39)	E729G	probably benign	Het
Serpinb1b	A	T	13: 33,269,293 (GRCm39)	T9S	probably benign	Het
Sfxn4	T	C	19: 60,832,690 (GRCm39)	T235A	probably damaging	Het
Shc4	A	T	2: 125,491,154 (GRCm39)	Y461*	probably null	Het
Slc22a15	T	C	3: 101,771,926 (GRCm39)	D391G	probably benign	Het
Slc22a23	G	T	13: 34,489,167 (GRCm39)	Y239*	probably null	Het
Slc24a2	G	A	4: 86,909,750 (GRCm39)	A656V	probably damaging	Het
Slc2a5	A	T	4: 150,227,590 (GRCm39)	I470F	probably damaging	Het
Sptbn4	T	C	7: 27,063,694 (GRCm39)	E2249G	possibly damaging	Het
Tas2r139	A	T	6: 42,118,753 (GRCm39)	Q295L	probably benign	Het
Tdrd7	C	A	4: 46,034,309 (GRCm39)	S1051R	probably benign	Het
Tnfrsf18	G	A	4: 156,112,802 (GRCm39)	A163T	probably benign	Het
Ube3b	T	C	5: 114,544,846 (GRCm39)	V596A	possibly damaging	Het
Vmn2r10	T	A	5: 109,149,955 (GRCm39)	N363I	probably benign	Het
Vmn2r15	T	A	5: 109,440,956 (GRCm39)	I301F	probably damaging	Het
Zfp433	A	T	10: 81,556,124 (GRCm39)	K209*	probably null	Het
Zfp865	G	A	7: 5,033,445 (GRCm39)	V477I	probably benign	Het
Zfp937	T	A	2: 150,081,421 (GRCm39)	Y484N	probably benign	Het
Zfp951	T	G	5: 104,962,312 (GRCm39)	H418P	probably damaging	Het

Other mutations in Yod1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00585:Yod1	APN	1	130,646,870 (GRCm39)	missense	probably damaging	1.00
IGL02321:Yod1	APN	1	130,646,688 (GRCm39)	missense	probably damaging	1.00
IGL03018:Yod1	APN	1	130,646,695 (GRCm39)	missense	probably benign	0.08
R1310:Yod1	UTSW	1	130,646,567 (GRCm39)	missense	probably benign
R5825:Yod1	UTSW	1	130,646,743 (GRCm39)	missense	probably damaging	1.00
R6115:Yod1	UTSW	1	130,646,800 (GRCm39)	missense	possibly damaging	0.48
R6367:Yod1	UTSW	1	130,645,275 (GRCm39)	missense	probably damaging	0.96
R6437:Yod1	UTSW	1	130,646,885 (GRCm39)	missense	probably damaging	1.00
R6489:Yod1	UTSW	1	130,645,275 (GRCm39)	missense	probably damaging	0.96
R6491:Yod1	UTSW	1	130,645,275 (GRCm39)	missense	probably damaging	0.96
R6729:Yod1	UTSW	1	130,645,275 (GRCm39)	missense	probably damaging	0.96
R6731:Yod1	UTSW	1	130,645,275 (GRCm39)	missense	probably damaging	0.96
R6732:Yod1	UTSW	1	130,645,275 (GRCm39)	missense	probably damaging	0.96
R6742:Yod1	UTSW	1	130,645,275 (GRCm39)	missense	probably damaging	0.96
R6743:Yod1	UTSW	1	130,645,275 (GRCm39)	missense	probably damaging	0.96
R6766:Yod1	UTSW	1	130,647,008 (GRCm39)	nonsense	probably null
R6781:Yod1	UTSW	1	130,645,275 (GRCm39)	missense	probably damaging	0.96
R7831:Yod1	UTSW	1	130,646,986 (GRCm39)	missense	probably damaging	0.99
R8369:Yod1	UTSW	1	130,645,360 (GRCm39)	missense	probably benign	0.31

Predicted Primers

PCR Primer
(F):5'- TGGAAGGAGGAGTCTTGAATCC -3'
(R):5'- GCTTCATCAGCTAATTCCAGTGC -3'

Sequencing Primer
(F):5'- GAGTCTTGAATCCAGCTTGTGCC -3'
(R):5'- CAGCTAATTCCAGTGCTTGTACAAG -3'

Posted On

2020-01-23