Mutagenetix > Incidental Mutation

Incidental Mutation 'R1674:Tyw1'

254703

Institutional Source

Beutler Lab

Gene Symbol

Tyw1

Ensembl Gene

ENSMUSG00000056310

Gene Name

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

Synonyms

Rsafd1

MMRRC Submission

039710-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R1674 (G1)

Quality Score

Status

Validated

Chromosome

Chromosomal Location

130284460-130370404 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 130298169 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Arginine to Glycine at position 237 (R237G)

Ref Sequence

ENSEMBL: ENSMUSP00000047318 (fasta)

Gene Model

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

AlphaFold

Q8BJM7

Predicted Effect

probably benign
Transcript: ENSMUST00000040213
AA Change: R237G

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000037173
Gene: ENSMUSG00000056310
AA Change: R237G

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 benign
Transcript: ENSMUST00000044204
AA Change: R237G

PolyPhen 2 Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)

SMART Domains

Protein: ENSMUSP00000047318
Gene: ENSMUSG00000056310
AA Change: R237G

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 benign
Transcript: ENSMUST00000100662
AA Change: R237G

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000098226
Gene: ENSMUSG00000056310
AA Change: R237G

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: ENSMUST00000147619
AA Change: R214G

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000123693
Gene: ENSMUSG00000056310
AA Change: R214G

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000173375

Meta Mutation Damage Score

0.0898

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 96.8%
20x: 94.1%

Validation Efficiency

100% (91/91)

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: 89 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930579G24Rik	A	G	3: 79,538,451 (GRCm39)	T66A	probably benign	Het
5430401F13Rik	A	T	6: 131,529,766 (GRCm39)	Q120L	unknown	Het
Akirin1	A	G	4: 123,637,256 (GRCm39)	S110P	possibly damaging	Het
Ankmy2	T	A	12: 36,237,668 (GRCm39)	S256T	probably benign	Het
Areg	T	C	5: 91,291,485 (GRCm39)	F143L	probably damaging	Het
Arhgap42	A	G	9: 9,006,585 (GRCm39)	S604P	probably damaging	Het
Arid1a	A	G	4: 133,416,571 (GRCm39)	V1068A	unknown	Het
Arid4a	G	A	12: 71,122,112 (GRCm39)	S509N	probably benign	Het
Atoh1	T	G	6: 64,706,914 (GRCm39)	I203S	possibly damaging	Het
Atp5mg	T	C	9: 44,825,957 (GRCm39)	T69A	possibly damaging	Het
Baz1b	A	G	5: 135,233,965 (GRCm39)	E164G	probably damaging	Het
Baz2b	A	T	2: 59,743,336 (GRCm39)	V1545E	possibly damaging	Het
Best1	A	G	19: 9,970,590 (GRCm39)		probably null	Het
Casp8	T	A	1: 58,883,575 (GRCm39)	I314N	probably damaging	Het
Ccdc13	T	C	9: 121,638,208 (GRCm39)	T26A	probably damaging	Het
Ccr6	A	T	17: 8,475,049 (GRCm39)	I85L	probably damaging	Het
Cdh10	A	T	15: 18,985,152 (GRCm39)	N272I	probably benign	Het
Cdh10	T	A	15: 19,013,416 (GRCm39)	I672K	probably damaging	Het
Cdk17	A	T	10: 93,057,492 (GRCm39)	E163V	probably benign	Het
Chsy1	T	C	7: 65,821,411 (GRCm39)	F549L	probably damaging	Het
CN725425	T	C	15: 91,131,124 (GRCm39)	Y420H	possibly damaging	Het
Cpt1b	A	T	15: 89,306,535 (GRCm39)	M281K	possibly damaging	Het
Crlf2	A	G	5: 109,706,669 (GRCm39)		probably null	Het
Ctif	T	C	18: 75,770,251 (GRCm39)	T45A	probably benign	Het
Ddx31	T	C	2: 28,748,828 (GRCm39)	F252S	probably damaging	Het
Dennd2d	T	C	3: 106,399,833 (GRCm39)	I242T	probably benign	Het
Dennd5b	A	G	6: 148,899,782 (GRCm39)	F1205S	probably damaging	Het
Dop1a	T	C	9: 86,418,213 (GRCm39)	S1981P	probably damaging	Het
Dsg1b	A	T	18: 20,532,578 (GRCm39)	T541S	probably benign	Het
Dst	T	A	1: 34,262,876 (GRCm39)		probably null	Het
Dysf	T	C	6: 84,156,697 (GRCm39)	V1508A	probably benign	Het
Erf	A	T	7: 24,944,731 (GRCm39)	L200Q	possibly damaging	Het
Erich3	A	G	3: 154,468,260 (GRCm39)		probably benign	Het
Esrrb	C	T	12: 86,561,225 (GRCm39)	L320F	probably damaging	Het
Fap	T	A	2: 62,349,349 (GRCm39)	D508V	probably benign	Het
Fdft1	A	C	14: 63,402,034 (GRCm39)	N48K	probably benign	Het
Fdps	A	G	3: 89,008,037 (GRCm39)	V94A	probably benign	Het
Fes	A	T	7: 80,027,686 (GRCm39)	H819Q	probably benign	Het
Foxd1	G	T	13: 98,491,347 (GRCm39)	D74Y	unknown	Het
Gm136	A	T	4: 34,746,662 (GRCm39)		probably benign	Het
Gm5919	T	A	9: 83,765,338 (GRCm39)	L58*	probably null	Het
Gm6871	C	T	7: 41,223,059 (GRCm39)	V10I	possibly damaging	Het
Isy1	T	C	6: 87,811,469 (GRCm39)	R29G	probably damaging	Het
Kif16b	T	A	2: 142,554,873 (GRCm39)	K653*	probably null	Het
Kif17	A	G	4: 138,028,569 (GRCm39)	T706A	probably benign	Het
Kif18b	G	T	11: 102,803,886 (GRCm39)	P425T	probably benign	Het
Lama1	T	A	17: 68,098,239 (GRCm39)	V1812E	probably benign	Het
Lama5	A	G	2: 179,843,780 (GRCm39)	V430A	probably benign	Het
Lclat1	A	G	17: 73,546,776 (GRCm39)	E231G	probably damaging	Het
Lig4	T	C	8: 10,021,692 (GRCm39)	D696G	probably benign	Het
Mylpf	T	A	7: 126,813,309 (GRCm39)	V151E	probably damaging	Het
Naa16	A	T	14: 79,624,497 (GRCm39)	M1K	probably null	Het
Ndufaf6	T	C	4: 11,070,264 (GRCm39)	K119R	probably benign	Het
Nt5c1b	T	C	12: 10,420,055 (GRCm39)		probably benign	Het
Or14a260	G	A	7: 85,984,765 (GRCm39)	P280S	probably damaging	Het
Or4a27	A	G	2: 88,559,601 (GRCm39)	V114A	probably damaging	Het
Or5t17	T	C	2: 86,832,577 (GRCm39)	V88A	probably benign	Het
Or8k33	T	A	2: 86,384,204 (GRCm39)	D88V	probably damaging	Het
Or9i16	T	A	19: 13,864,954 (GRCm39)	I207L	probably benign	Het
Otud4	A	G	8: 80,399,776 (GRCm39)	N830S	probably benign	Het
Pdcd10	A	C	3: 75,448,486 (GRCm39)	M26R	probably damaging	Het
Pitpnc1	A	G	11: 107,117,071 (GRCm39)	V223A	possibly damaging	Het
Pkp2	A	G	16: 16,058,422 (GRCm39)	D368G	possibly damaging	Het
Pla1a	A	T	16: 38,235,172 (GRCm39)	M174K	probably benign	Het
Polr2b	A	G	5: 77,474,470 (GRCm39)	K436E	possibly damaging	Het
Pwwp4a	G	T	X: 72,171,261 (GRCm39)	G218C	probably damaging	Het
Rdh16	A	G	10: 127,637,226 (GRCm39)	M54V	probably benign	Het
Sall2	C	A	14: 52,551,293 (GRCm39)	C632F	probably damaging	Het
Sart1	T	A	19: 5,435,853 (GRCm39)	I120F	probably damaging	Het
Slco1a1	A	T	6: 141,881,661 (GRCm39)	M157K	probably damaging	Het
Snapc4	T	C	2: 26,266,209 (GRCm39)	T178A	probably benign	Het
Sox6	T	C	7: 115,400,654 (GRCm39)	I63V	probably benign	Het
Spin1	T	A	13: 51,303,135 (GRCm39)	Y243N	probably damaging	Het
Stmnd1	T	C	13: 46,453,097 (GRCm39)	Y258H	possibly damaging	Het
Tex13b	A	T	X: 139,710,819 (GRCm39)	N184K	probably benign	Het
Tgm5	T	C	2: 120,902,025 (GRCm39)	T215A	possibly damaging	Het
Tnks2	A	G	19: 36,849,022 (GRCm39)	T165A	probably benign	Het
Top2a	A	T	11: 98,900,099 (GRCm39)	F667Y	probably damaging	Het
Tpo	T	C	12: 30,150,567 (GRCm39)	M438V	probably benign	Het
Unc5c	G	A	3: 141,463,598 (GRCm39)	V240I	possibly damaging	Het
Unc80	A	C	1: 66,548,467 (GRCm39)	T580P	probably damaging	Het
Upp2	G	A	2: 58,680,076 (GRCm39)	E301K	probably benign	Het
Utp18	A	G	11: 93,766,879 (GRCm39)		probably null	Het
Vmn1r23	T	C	6: 57,903,046 (GRCm39)	D244G	possibly damaging	Het
Vps13c	T	A	9: 67,760,985 (GRCm39)	L51*	probably null	Het
Xpnpep3	A	G	15: 81,314,968 (GRCm39)	T223A	probably benign	Het
Zfp28	T	A	7: 6,397,942 (GRCm39)	H792Q	possibly damaging	Het
Zfp804a	A	G	2: 82,089,168 (GRCm39)	K999R	probably benign	Het
Zkscan16	G	A	4: 58,948,918 (GRCm39)	V158M	possibly damaging	Het

Other mutations in Tyw1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL02329:Tyw1	APN	5	130,295,921 (GRCm39)	missense	probably benign	0.20
IGL02873:Tyw1	APN	5	130,364,171 (GRCm39)	missense	probably benign	0.00
IGL02879:Tyw1	APN	5	130,325,612 (GRCm39)	missense	probably damaging	1.00
IGL03080:Tyw1	APN	5	130,295,896 (GRCm39)	missense	probably damaging	1.00
IGL03291:Tyw1	APN	5	130,328,834 (GRCm39)	missense	probably damaging	1.00
IGL03297:Tyw1	APN	5	130,369,575 (GRCm39)	missense	probably damaging	1.00
remnant	UTSW	5	130,291,762 (GRCm39)	missense	probably damaging	0.99
schimmel	UTSW	5	130,298,065 (GRCm39)	missense	probably damaging	1.00
tyrone	UTSW	5	130,325,520 (GRCm39)	nonsense	probably null
yang	UTSW	5	130,287,876 (GRCm39)	missense	probably damaging	0.98
R1420:Tyw1	UTSW	5	130,303,586 (GRCm39)	critical splice donor site	probably null
R1650:Tyw1	UTSW	5	130,317,752 (GRCm39)	missense	possibly damaging	0.91
R1789:Tyw1	UTSW	5	130,287,834 (GRCm39)	missense	probably damaging	0.99
R1996:Tyw1	UTSW	5	130,291,652 (GRCm39)	splice site	probably benign
R2421:Tyw1	UTSW	5	130,298,101 (GRCm39)	missense	probably damaging	1.00
R3913:Tyw1	UTSW	5	130,287,876 (GRCm39)	missense	probably damaging	0.98
R4412:Tyw1	UTSW	5	130,364,073 (GRCm39)	splice site	probably null
R4835:Tyw1	UTSW	5	130,305,899 (GRCm39)	missense	probably benign
R5058:Tyw1	UTSW	5	130,305,927 (GRCm39)	missense	probably benign	0.03
R5190:Tyw1	UTSW	5	130,296,756 (GRCm39)	nonsense	probably null
R5398:Tyw1	UTSW	5	130,305,998 (GRCm39)	intron	probably benign
R5459:Tyw1	UTSW	5	130,303,547 (GRCm39)	missense	probably damaging	1.00
R5597:Tyw1	UTSW	5	130,303,498 (GRCm39)	missense	probably benign	0.00
R5704:Tyw1	UTSW	5	130,310,863 (GRCm39)	nonsense	probably null
R5825:Tyw1	UTSW	5	130,296,929 (GRCm39)	missense	probably damaging	0.99
R5887:Tyw1	UTSW	5	130,354,540 (GRCm39)	missense	probably damaging	1.00
R6072:Tyw1	UTSW	5	130,296,752 (GRCm39)	missense	possibly damaging	0.92
R6349:Tyw1	UTSW	5	130,305,872 (GRCm39)	missense	possibly damaging	0.82
R6366:Tyw1	UTSW	5	130,310,792 (GRCm39)	unclassified	probably benign
R7012:Tyw1	UTSW	5	130,306,571 (GRCm39)	splice site	probably null
R7259:Tyw1	UTSW	5	130,296,713 (GRCm39)	splice site	probably null
R7328:Tyw1	UTSW	5	130,291,685 (GRCm39)	missense	probably benign	0.08
R7555:Tyw1	UTSW	5	130,303,547 (GRCm39)	missense	probably damaging	1.00
R8006:Tyw1	UTSW	5	130,296,913 (GRCm39)	missense	possibly damaging	0.87
R8171:Tyw1	UTSW	5	130,328,855 (GRCm39)	missense	probably benign	0.19
R8196:Tyw1	UTSW	5	130,328,862 (GRCm39)	missense	probably damaging	1.00
R8714:Tyw1	UTSW	5	130,298,065 (GRCm39)	missense	probably damaging	1.00
R8715:Tyw1	UTSW	5	130,298,065 (GRCm39)	missense	probably damaging	1.00
R8716:Tyw1	UTSW	5	130,298,065 (GRCm39)	missense	probably damaging	1.00
R8970:Tyw1	UTSW	5	130,298,065 (GRCm39)	missense	probably damaging	1.00
R8992:Tyw1	UTSW	5	130,298,065 (GRCm39)	missense	probably damaging	1.00
R9117:Tyw1	UTSW	5	130,298,065 (GRCm39)	missense	probably damaging	1.00
R9119:Tyw1	UTSW	5	130,298,065 (GRCm39)	missense	probably damaging	1.00
R9120:Tyw1	UTSW	5	130,298,065 (GRCm39)	missense	probably damaging	1.00
R9172:Tyw1	UTSW	5	130,325,520 (GRCm39)	nonsense	probably null
R9204:Tyw1	UTSW	5	130,298,065 (GRCm39)	missense	probably damaging	1.00
R9205:Tyw1	UTSW	5	130,298,065 (GRCm39)	missense	probably damaging	1.00
R9207:Tyw1	UTSW	5	130,298,065 (GRCm39)	missense	probably damaging	1.00
R9325:Tyw1	UTSW	5	130,291,762 (GRCm39)	missense	probably damaging	0.99
R9364:Tyw1	UTSW	5	130,298,065 (GRCm39)	missense	probably damaging	1.00
R9368:Tyw1	UTSW	5	130,298,065 (GRCm39)	missense	probably damaging	1.00
R9369:Tyw1	UTSW	5	130,298,065 (GRCm39)	missense	probably damaging	1.00
R9470:Tyw1	UTSW	5	130,298,065 (GRCm39)	missense	probably damaging	1.00
R9471:Tyw1	UTSW	5	130,298,065 (GRCm39)	missense	probably damaging	1.00
R9566:Tyw1	UTSW	5	130,298,065 (GRCm39)	missense	probably damaging	1.00
R9567:Tyw1	UTSW	5	130,298,065 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- AGCACGAACGTTGACAAATGGC -3'
(R):5'- TCAGATCATCTAACCGGGACAGAGG -3'

Sequencing Primer
(F):5'- ACAAATGGCTCTGGATGCTC -3'
(R):5'- cctctctccctccctccc -3'

Posted On

2014-12-16