Mutagenetix > Incidental Mutation

Incidental Mutation 'R6729:Yod1'

529963

Institutional Source

Beutler Lab

Gene Symbol

Yod1

Ensembl Gene

ENSMUSG00000046404

Gene Name

YOD1 deubiquitinase

Synonyms

9930028C20Rik

MMRRC Submission

044847-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R6729 (G1)

Quality Score

189.009

Status

Validated

Chromosome

Chromosomal Location

130645064-130652093 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 130645275 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glycine to Serine at position 19 (G19S)

Ref Sequence

ENSEMBL: ENSMUSP00000055318 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000049813] [ENSMUST00000050406] [ENSMUST00000066863] [ENSMUST00000169659] [ENSMUST00000171479] [ENSMUST00000185233] [ENSMUST00000186777] [ENSMUST00000189534] [ENSMUST00000186867] [ENSMUST00000188520] [ENSMUST00000191301] [ENSMUST00000187089] [ENSMUST00000189167] [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 damaging
Transcript: ENSMUST00000049813
AA Change: G19S

PolyPhen 2 Score 0.963 (Sensitivity: 0.78; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000055318
Gene: ENSMUSG00000046404
AA Change: G19S

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: 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: ENSMUST00000186867

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: 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: 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: 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: 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

Meta Mutation Damage Score

0.0977

Coding Region Coverage

1x: 99.9%
3x: 99.6%
10x: 98.4%
20x: 95.5%

Validation Efficiency

100% (34/34)

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: 33 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acad12	A	T	5: 121,745,998 (GRCm39)	H230Q	probably damaging	Het
AI182371	G	T	2: 34,974,717 (GRCm39)		probably benign	Het
Ank3	T	C	10: 69,644,755 (GRCm39)	V73A	probably damaging	Het
Apbb1	A	T	7: 105,214,588 (GRCm39)	M28K	probably damaging	Het
Atp6v1f	A	G	6: 29,467,964 (GRCm39)	D50G	probably benign	Het
Bltp3b	T	A	10: 89,641,546 (GRCm39)	S906T	probably benign	Het
Cdkal1	G	A	13: 29,658,678 (GRCm39)	T356M	probably damaging	Het
Clca3a1	A	G	3: 144,711,727 (GRCm39)	I756T	probably damaging	Het
Cplane1	T	C	15: 8,218,085 (GRCm39)		probably null	Het
Cyp17a1	A	G	19: 46,659,020 (GRCm39)	V207A	probably benign	Het
Dnah7c	A	G	1: 46,711,681 (GRCm39)	E2636G	possibly damaging	Het
Gm13090	A	T	4: 151,174,085 (GRCm39)		probably benign	Het
Nceh1	T	A	3: 27,295,420 (GRCm39)	L227*	probably null	Het
Nedd9	A	G	13: 41,469,278 (GRCm39)	M625T	probably damaging	Het
Or10n1	A	T	9: 39,525,069 (GRCm39)	M69L	probably benign	Het
Or4d1	G	A	11: 87,805,676 (GRCm39)	Q19*	probably null	Het
Or4d10c	T	A	19: 12,065,860 (GRCm39)	M99L	probably benign	Het
Or8b53	A	G	9: 38,667,124 (GRCm39)	I47V	probably benign	Het
Pcsk4	T	C	10: 80,160,935 (GRCm39)	N297S	probably damaging	Het
Psg21	T	A	7: 18,386,516 (GRCm39)	I157F	probably damaging	Het
Rabep2	T	C	7: 126,039,369 (GRCm39)	V294A	probably benign	Het
Rsph1	A	G	17: 31,496,226 (GRCm39)	S2P	unknown	Het
Sacs	A	G	14: 61,447,967 (GRCm39)	K3338E	probably damaging	Het
Slc35f4	T	G	14: 49,556,417 (GRCm39)	N112T	probably benign	Het
Slc43a3	T	C	2: 84,768,629 (GRCm39)	F83L	probably damaging	Het
Slc6a15	T	C	10: 103,229,775 (GRCm39)	V154A	probably damaging	Het
Synj2	T	A	17: 6,036,289 (GRCm39)	M1K	probably null	Het
Tcp1	G	A	17: 13,142,140 (GRCm39)	R378Q	probably damaging	Het
Tead2	A	G	7: 44,866,658 (GRCm39)	T6A	probably benign	Het
Tpte	G	T	8: 22,845,491 (GRCm39)	V514L	probably damaging	Het
Trpm6	A	G	19: 18,807,661 (GRCm39)	N1069D	probably damaging	Het
Vmn2r105	C	A	17: 20,428,605 (GRCm39)	G824C	probably damaging	Het
Zfp934	A	T	13: 62,640,746 (GRCm39)	N2K	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
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
R8058:Yod1	UTSW	1	130,646,806 (GRCm39)	nonsense	probably null
R8369:Yod1	UTSW	1	130,645,360 (GRCm39)	missense	probably benign	0.31

Predicted Primers

PCR Primer
(F):5'- TGCTAGACTCGGGAACTCCTTC -3'
(R):5'- AGGTCCCCAAGAGTGATGTC -3'

Sequencing Primer
(F):5'- ATAAATGCTGCCGACGCG -3'
(R):5'- AAGAGTGATGTCCCGGTCG -3'

Posted On

2018-08-01