Mutagenetix > Incidental Mutation

Incidental Mutation 'R1789:Tyw1'

201606

Institutional Source

Beutler Lab

Gene Symbol

Tyw1

Ensembl Gene

ENSMUSG00000056310

Gene Name

tRNA-yW synthesizing protein 1 homolog (S. cerevisiae)

Synonyms

Rsafd1

MMRRC Submission

039820-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R1789 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

130255619-130341563 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to G at 130258993 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Arginine at position 22 (I22R)

Ref Sequence

ENSEMBL: ENSMUSP00000047318 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000026387] [ENSMUST00000040213] [ENSMUST00000044204] [ENSMUST00000100662] [ENSMUST00000125625] [ENSMUST00000139211] [ENSMUST00000147619]

AlphaFold

Q8BJM7

Predicted Effect

probably benign
Transcript: ENSMUST00000026387

SMART Domains

Protein: ENSMUSP00000026387
Gene: ENSMUSG00000025337

Domain	Start	End	E-Value	Type
Pfam:SBDS	14	101	1.2e-36	PFAM
Pfam:SBDS_C	107	225	2.1e-42	PFAM

Predicted Effect

possibly damaging
Transcript: ENSMUST00000040213
AA Change: I22R

PolyPhen 2 Score 0.938 (Sensitivity: 0.80; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000037173
Gene: ENSMUSG00000056310
AA Change: I22R

Domain	Start	End	E-Value	Type
transmembrane domain	20	39	N/A	INTRINSIC
Pfam:Flavodoxin_1	73	224	1.6e-27	PFAM
low complexity region	276	288	N/A	INTRINSIC
Pfam:Radical_SAM	399	581	1.1e-29	PFAM
Pfam:Wyosine_form	583	646	3.6e-29	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000044204
AA Change: I22R

PolyPhen 2 Score 0.992 (Sensitivity: 0.70; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000047318
Gene: ENSMUSG00000056310
AA Change: I22R

Domain	Start	End	E-Value	Type
transmembrane domain	20	39	N/A	INTRINSIC
Pfam:Flavodoxin_1	73	224	1.5e-27	PFAM
low complexity region	276	288	N/A	INTRINSIC
transmembrane domain	375	397	N/A	INTRINSIC
transmembrane domain	423	445	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000100662
AA Change: I22R

PolyPhen 2 Score 0.938 (Sensitivity: 0.80; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000098226
Gene: ENSMUSG00000056310
AA Change: I22R

Domain	Start	End	E-Value	Type
transmembrane domain	20	39	N/A	INTRINSIC
Pfam:Flavodoxin_1	73	224	4.9e-28	PFAM
low complexity region	276	288	N/A	INTRINSIC
low complexity region	319	332	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000125625

SMART Domains

Protein: ENSMUSP00000115494
Gene: ENSMUSG00000025337

Domain	Start	End	E-Value	Type
Pfam:SBDS	3	66	2.1e-25	PFAM
Pfam:SBDS_C	69	173	9.9e-40	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000139211

Predicted Effect

probably benign
Transcript: ENSMUST00000147619

SMART Domains

Protein: ENSMUSP00000123693
Gene: ENSMUSG00000056310

Domain	Start	End	E-Value	Type
Pfam:Flavodoxin_1	50	201	4.3e-28	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000173375

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000200815

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000201598

Coding Region Coverage

1x: 97.4%
3x: 96.8%
10x: 95.2%
20x: 92.1%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] Wybutosine (yW) is a hypermodified guanosine found in phenylalanine tRNA adjacent to the anticodon that stabilizes codon-anticodon interactions in the ribosome. In yeast, the homolog of this gene is essential for the synthesis of wybutosine. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2015]

Allele List at MGI

Other mutations in this stock

Total: 100 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcc5	G	A	16: 20,365,951	P986L	probably damaging	Het
Acad10	A	T	5: 121,631,393	Y667N	possibly damaging	Het
Ahi1	G	A	10: 20,963,115	G121D	probably benign	Het
Ampd1	T	A	3: 103,099,126	I690N	possibly damaging	Het
Amy1	C	A	3: 113,558,165	W425L	possibly damaging	Het
Arhgap27	A	T	11: 103,333,005	V823E	probably damaging	Het
Arhgef17	A	G	7: 100,929,870	S624P	probably damaging	Het
Arid5b	T	C	10: 68,186,067	H231R	probably damaging	Het
Aspscr1	C	A	11: 120,688,560	T78N	probably damaging	Het
Auts2	T	A	5: 131,472,450	T42S	probably damaging	Het
Ccdc171	A	G	4: 83,554,808	D158G	probably damaging	Het
Ces4a	G	A	8: 105,138,097	G69S	probably damaging	Het
Cfap61	T	C	2: 145,939,993		probably null	Het
Chrna5	T	C	9: 55,004,651	V245A	possibly damaging	Het
Cntnap5c	G	A	17: 58,013,921	G163R	probably damaging	Het
Col5a2	T	C	1: 45,394,776	Q759R	probably damaging	Het
Col5a2	A	G	1: 45,378,305		probably null	Het
Comp	A	G	8: 70,377,146	D340G	probably benign	Het
Cyfip1	T	A	7: 55,926,395	D1104E	probably damaging	Het
Dnah11	A	T	12: 118,038,780	S308T	probably damaging	Het
Dnah5	A	G	15: 28,270,426	H958R	probably benign	Het
Elp3	A	G	14: 65,547,919	Y478H	probably damaging	Het
Fat3	T	C	9: 16,376,985	Y414C	probably benign	Het
Fbxo10	C	A	4: 45,046,389	A574S	probably damaging	Het
Fsip2	G	T	2: 82,977,562	L1408F	probably benign	Het
Fubp3	T	C	2: 31,611,735	V425A	possibly damaging	Het
Gm7168	A	T	17: 13,949,584	R404S	probably benign	Het
Gm8773	A	T	5: 5,575,652	Q116L	possibly damaging	Het
Gpd1	T	G	15: 99,723,202	F299C	probably damaging	Het
Gpr137	C	T	19: 6,942,057		probably benign	Het
Grin3b	T	C	10: 79,973,408	S331P	probably benign	Het
Grk3	T	A	5: 112,941,718	I281F	probably damaging	Het
Hoxb7	T	A	11: 96,286,781	S18R	probably damaging	Het
Igf1r	C	T	7: 68,214,933	R1160*	probably null	Het
Itfg1	A	G	8: 85,725,512		probably null	Het
Itgb8	T	C	12: 119,202,455	I114V	probably benign	Het
Kcnk1	A	G	8: 126,025,384	E243G	possibly damaging	Het
Kif27	A	G	13: 58,344,008	L439P	probably damaging	Het
Kif2c	T	A	4: 117,167,361	Q279L	probably benign	Het
Kmt2d	A	T	15: 98,852,074		probably benign	Het
L3mbtl1	A	G	2: 162,974,502	T821A	probably benign	Het
Lrrc24	A	T	15: 76,722,578	M206K	probably benign	Het
Mamdc4	T	G	2: 25,567,622	K460Q	possibly damaging	Het
Maml2	C	G	9: 13,697,345	L30V	probably damaging	Het
Mc5r	C	G	18: 68,338,670		probably null	Het
Myo10	T	G	15: 25,726,525		probably null	Het
Myo1e	T	A	9: 70,338,784	L419Q	probably damaging	Het
Myo6	C	A	9: 80,300,572	H1115Q	probably damaging	Het
Myo7a	A	G	7: 98,107,095	V10A	probably damaging	Het
Myoz2	C	T	3: 123,026,127	R61H	probably damaging	Het
Ncdn	G	A	4: 126,752,003	R38C	probably damaging	Het
Nckap1	T	A	2: 80,520,556	T736S	probably benign	Het
Ncor2	G	A	5: 125,019,890	A2325V	probably damaging	Het
Nid2	T	A	14: 19,752,431	V140E	possibly damaging	Het
Nlrp9c	C	A	7: 26,380,490	D704Y	probably benign	Het
Notch3	T	A	17: 32,158,725	S126C	probably damaging	Het
Olfr1128	A	T	2: 87,544,983	L187H	probably damaging	Het
Olfr130	T	C	17: 38,067,948	I259T	probably damaging	Het
Olfr215	A	C	6: 116,582,697	F83C	probably damaging	Het
Olfr484	A	G	7: 108,124,915	F116S	probably benign	Het
Olfr804	T	C	10: 129,705,607	M243T	possibly damaging	Het
Olfr818	A	T	10: 129,945,582	L160*	probably null	Het
Pdzd7	A	G	19: 45,039,228	I269T	probably damaging	Het
Phf3	A	T	1: 30,806,206	D1299E	probably damaging	Het
Pitx2	T	A	3: 129,218,754	Y271N	probably damaging	Het
Polk	T	C	13: 96,496,632	E301G	probably damaging	Het
Prkdc	C	A	16: 15,739,524	N2230K	probably damaging	Het
Prlr	A	G	15: 10,322,536	E170G	probably benign	Het
Prss55	A	G	14: 64,075,730	I235T	probably damaging	Het
Psd3	T	C	8: 67,960,565	I724V	probably benign	Het
Rabep2	A	G	7: 126,438,799	T248A	possibly damaging	Het
Rbm26	T	A	14: 105,117,073	K949N	probably benign	Het
Rnf213	T	A	11: 119,440,221	D2085E	probably damaging	Het
Serpinb7	A	T	1: 107,450,273	H232L	possibly damaging	Het
Slu7	A	G	11: 43,445,242	Q484R	probably benign	Het
Smg1	A	G	7: 118,145,798	S3044P	possibly damaging	Het
Snrnp48	A	G	13: 38,221,360	D248G	possibly damaging	Het
Snrpc	C	A	17: 27,845,219	P66Q	unknown	Het
Snrpn	T	A	7: 59,983,459		probably benign	Het
Spag17	T	A	3: 99,939,356	S65R	possibly damaging	Het
Srsf6	C	A	2: 162,934,488		probably benign	Het
Stil	T	A	4: 115,041,782	M1203K	probably benign	Het
Syt17	T	C	7: 118,436,838	T106A	probably benign	Het
Tbx15	C	T	3: 99,352,246	Q478*	probably null	Het
Tg	A	T	15: 66,737,548	Q319L	probably benign	Het
Thada	A	G	17: 84,448,033	L243P	probably damaging	Het
Thada	G	T	17: 84,448,034	L243I	probably damaging	Het
Tnnt3	A	G	7: 142,512,364	R211G	probably damaging	Het
Togaram1	A	T	12: 65,002,635	Q1282L	possibly damaging	Het
Tpm3-rs7	T	G	14: 113,314,947	M91R	probably damaging	Het
Trappc9	G	A	15: 73,025,967	R377W	probably damaging	Het
Ttll7	T	G	3: 146,915,780	L378R	probably damaging	Het
Ubr3	T	C	2: 70,016,367	S1645P	possibly damaging	Het
Ubr4	T	C	4: 139,393,053	L263P	probably damaging	Het
Unc13c	T	C	9: 73,756,339	E1071G	possibly damaging	Het
Vmn2r44	G	T	7: 8,380,123	D157E	possibly damaging	Het
Vps16	C	T	2: 130,443,600	T821I	probably benign	Het
Washc4	T	C	10: 83,579,525	V793A	possibly damaging	Het
Wdr35	G	T	12: 8,977,435		probably null	Het
Zfp277	A	G	12: 40,364,085	F254L	probably benign	Het

Other mutations in Tyw1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL02329:Tyw1	APN	5	130267080	missense	probably benign	0.20
IGL02873:Tyw1	APN	5	130335330	missense	probably benign	0.00
IGL02879:Tyw1	APN	5	130296771	missense	probably damaging	1.00
IGL03080:Tyw1	APN	5	130267055	missense	probably damaging	1.00
IGL03291:Tyw1	APN	5	130299993	missense	probably damaging	1.00
IGL03297:Tyw1	APN	5	130340734	missense	probably damaging	1.00
remnant	UTSW	5	130262921	missense	probably damaging	0.99
schimmel	UTSW	5	130269224	missense	probably damaging	1.00
tyrone	UTSW	5	130296679	nonsense	probably null
yang	UTSW	5	130259035	missense	probably damaging	0.98
R1420:Tyw1	UTSW	5	130274745	critical splice donor site	probably null
R1650:Tyw1	UTSW	5	130288911	missense	possibly damaging	0.91
R1674:Tyw1	UTSW	5	130269328	missense	probably benign	0.01
R1996:Tyw1	UTSW	5	130262811	splice site	probably benign
R2421:Tyw1	UTSW	5	130269260	missense	probably damaging	1.00
R3913:Tyw1	UTSW	5	130259035	missense	probably damaging	0.98
R4412:Tyw1	UTSW	5	130335232	splice site	probably null
R4835:Tyw1	UTSW	5	130277058	missense	probably benign
R5058:Tyw1	UTSW	5	130277086	missense	probably benign	0.03
R5190:Tyw1	UTSW	5	130267915	nonsense	probably null
R5398:Tyw1	UTSW	5	130277157	intron	probably benign
R5459:Tyw1	UTSW	5	130274706	missense	probably damaging	1.00
R5597:Tyw1	UTSW	5	130274657	missense	probably benign	0.00
R5704:Tyw1	UTSW	5	130282022	nonsense	probably null
R5825:Tyw1	UTSW	5	130268088	missense	probably damaging	0.99
R5887:Tyw1	UTSW	5	130325699	missense	probably damaging	1.00
R6072:Tyw1	UTSW	5	130267911	missense	possibly damaging	0.92
R6349:Tyw1	UTSW	5	130277031	missense	possibly damaging	0.82
R6366:Tyw1	UTSW	5	130281951	unclassified	probably benign
R7012:Tyw1	UTSW	5	130277730	splice site	probably null
R7259:Tyw1	UTSW	5	130267872	splice site	probably null
R7328:Tyw1	UTSW	5	130262844	missense	probably benign	0.08
R7555:Tyw1	UTSW	5	130274706	missense	probably damaging	1.00
R8006:Tyw1	UTSW	5	130268072	missense	possibly damaging	0.87
R8171:Tyw1	UTSW	5	130300014	missense	probably benign	0.19
R8196:Tyw1	UTSW	5	130300021	missense	probably damaging	1.00
R8714:Tyw1	UTSW	5	130269224	missense	probably damaging	1.00
R8715:Tyw1	UTSW	5	130269224	missense	probably damaging	1.00
R8716:Tyw1	UTSW	5	130269224	missense	probably damaging	1.00
R8970:Tyw1	UTSW	5	130269224	missense	probably damaging	1.00
R8992:Tyw1	UTSW	5	130269224	missense	probably damaging	1.00
R9117:Tyw1	UTSW	5	130269224	missense	probably damaging	1.00
R9119:Tyw1	UTSW	5	130269224	missense	probably damaging	1.00
R9120:Tyw1	UTSW	5	130269224	missense	probably damaging	1.00
R9172:Tyw1	UTSW	5	130296679	nonsense	probably null
R9204:Tyw1	UTSW	5	130269224	missense	probably damaging	1.00
R9205:Tyw1	UTSW	5	130269224	missense	probably damaging	1.00
R9207:Tyw1	UTSW	5	130269224	missense	probably damaging	1.00
R9325:Tyw1	UTSW	5	130262921	missense	probably damaging	0.99
R9364:Tyw1	UTSW	5	130269224	missense	probably damaging	1.00
R9368:Tyw1	UTSW	5	130269224	missense	probably damaging	1.00
R9369:Tyw1	UTSW	5	130269224	missense	probably damaging	1.00
R9470:Tyw1	UTSW	5	130269224	missense	probably damaging	1.00
R9471:Tyw1	UTSW	5	130269224	missense	probably damaging	1.00
R9566:Tyw1	UTSW	5	130269224	missense	probably damaging	1.00
R9567:Tyw1	UTSW	5	130269224	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- TCATGACATTGGCTTATAATCCCC -3'
(R):5'- GCGAGCAAACGAACTGGTTC -3'

Sequencing Primer
(F):5'- CTGGAACTCACTCTGTAGATCAGG -3'
(R):5'- GCAAACGAACTGGTTCTTCACTGG -3'

Posted On

2014-06-23