Mutagenetix > Incidental Mutation

Incidental Mutation 'R8714:Tyw1'

669762

Institutional Source

Beutler Lab

Gene Symbol

Tyw1

Ensembl Gene

ENSMUSG00000056310

Gene Name

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

Synonyms

Rsafd1

MMRRC Submission

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R8714 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

130255619-130341563 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 130269224 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Arginine to Glutamine at position 202 (R202Q)

Ref Sequence

ENSEMBL: ENSMUSP00000037173 (fasta)

Gene Model

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

AlphaFold

Q8BJM7

Predicted Effect

probably damaging
Transcript: ENSMUST00000040213
AA Change: R202Q

PolyPhen 2 Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000037173
Gene: ENSMUSG00000056310
AA Change: R202Q

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: R202Q

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000047318
Gene: ENSMUSG00000056310
AA Change: R202Q

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

probably damaging
Transcript: ENSMUST00000100662
AA Change: R202Q

PolyPhen 2 Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000098226
Gene: ENSMUSG00000056310
AA Change: R202Q

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 damaging
Transcript: ENSMUST00000147619
AA Change: R179Q

PolyPhen 2 Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000123693
Gene: ENSMUSG00000056310
AA Change: R179Q

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

Meta Mutation Damage Score

0.3244

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.7%

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: 53 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4921539E11Rik	C	T	4: 103,242,896	A137T	probably benign	Het
4930474N05Rik	T	A	14: 36,096,499	C151*	probably null	Het
Abca4	A	G	3: 122,148,879	T1674A	probably benign	Het
Acat3	A	T	17: 12,928,629	V167E	probably benign	Het
Alb	T	C	5: 90,461,015		probably null	Het
Apol9a	T	C	15: 77,404,742	T142A	probably benign	Het
Asb14	C	T	14: 26,901,075	P135S	possibly damaging	Het
Asb17	A	G	3: 153,850,676	Y140C	probably damaging	Het
Atp4a	T	A	7: 30,720,588	I750N	probably damaging	Het
Bard1	T	C	1: 71,030,827	Y664C	probably damaging	Het
Cacnb3	G	A	15: 98,632,381		probably benign	Het
Card11	T	A	5: 140,913,392	D9V	possibly damaging	Het
Casp8	A	T	1: 58,833,653	Q229H	possibly damaging	Het
Ccdc88b	T	C	19: 6,855,845	E278G	probably damaging	Het
Cd209d	CAT	C	8: 3,873,772		probably null	Het
Cep350	T	C	1: 155,860,731	D2853G	probably damaging	Het
Cfap161	T	C	7: 83,793,274	I110M	probably benign	Het
Chid1	T	A	7: 141,513,765	K313*	probably null	Het
Col16a1	T	A	4: 130,054,168	I227N	unknown	Het
D3Ertd751e	G	T	3: 41,746,563	E6*	probably null	Het
Ddx41	T	C	13: 55,534,437	Q208R	probably damaging	Het
Dhrs13	G	C	11: 78,032,666	R70P	possibly damaging	Het
Dmrta1	A	T	4: 89,691,445	Q214L	probably benign	Het
Eif2ak4	T	C	2: 118,462,284	F1330L	possibly damaging	Het
Fbxw13	C	T	9: 109,194,764	V71I	probably benign	Het
Gm8882	G	A	6: 132,364,088	T7I	unknown	Het
H2-Q2	T	C	17: 35,343,362	L195P	possibly damaging	Het
Hemgn	C	T	4: 46,395,904	G444D	probably damaging	Het
Lmtk2	A	G	5: 144,176,058	T1199A	probably damaging	Het
Ly75	T	C	2: 60,334,485	D783G	probably damaging	Het
Micall1	G	A	15: 79,127,310	A627T	probably benign	Het
Morc2a	C	T	11: 3,675,877	T159I	probably benign	Het
Mthfr	C	A	4: 148,041,818	N115K	probably damaging	Het
Muc1	G	A	3: 89,231,514	V477M	possibly damaging	Het
Mug1	C	T	6: 121,882,722	P1227S	probably benign	Het
Ogfod3	T	A	11: 121,196,782	D163V	possibly damaging	Het
Olfr644	T	A	7: 104,068,276	I252F	probably damaging	Het
Pcnx2	C	T	8: 125,773,807	V1515I	probably benign	Het
Plat	G	T	8: 22,772,232	G91W	probably damaging	Het
Plscr3	G	T	11: 69,848,012	G167C	probably benign	Het
Plxna4	T	A	6: 32,163,444	K1670*	probably null	Het
Rab7	T	C	6: 88,012,387	S34G	probably damaging	Het
Rnf157	C	A	11: 116,347,065	A577S	probably benign	Het
Rnf213	C	T	11: 119,468,894	S4371L		Het
S1pr1	A	T	3: 115,711,821	S375T	probably benign	Het
Spen	T	C	4: 141,488,003	N506S	unknown	Het
Sulf1	T	A	1: 12,807,917	Y210N	probably benign	Het
Tenm4	C	T	7: 96,905,941	P2618S	probably benign	Het
Tg	A	G	15: 66,684,042	N861S	probably damaging	Het
Ttc29	A	G	8: 78,333,702	E417G	possibly damaging	Het
Ubxn7	T	A	16: 32,367,411		probably benign	Het
Vmn1r62	C	A	7: 5,675,630	Y103*	probably null	Het
Zfp804b	A	T	5: 6,772,378	Y228*	probably null	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
R1789:Tyw1	UTSW	5	130258993	missense	probably damaging	0.99
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
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'- AGCCTGGAAGCCTGCTTTAG -3'
(R):5'- ATCCCCAGGATGCAATTCG -3'

Sequencing Primer
(F):5'- CTGGAAGCCTGCTTTAGAGGAC -3'
(R):5'- CAGGATGCAATTCGCCTTG -3'

Posted On

2021-04-30