Mutagenetix > Incidental Mutation

Incidental Mutation 'R1940:Ythdf3'

213899

Institutional Source

Beutler Lab

Gene Symbol

Ythdf3

Ensembl Gene

ENSMUSG00000047213

Gene Name

YTH N6-methyladenosine RNA binding protein 3

Synonyms

9130022A11Rik

MMRRC Submission

039958-MU

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.354) question?

Stock #

R1940 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

16237376-16271201 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 16259256 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Aspartic acid at position 468 (N468D)

Ref Sequence

ENSEMBL: ENSMUSP00000103982 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000108345] [ENSMUST00000108346] [ENSMUST00000191774]

AlphaFold

Q8BYK6

Predicted Effect

possibly damaging
Transcript: ENSMUST00000108345
AA Change: N468D

PolyPhen 2 Score 0.707 (Sensitivity: 0.86; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000103982
Gene: ENSMUSG00000047213
AA Change: N468D

Domain	Start	End	E-Value	Type
low complexity region	48	64	N/A	INTRINSIC
low complexity region	134	161	N/A	INTRINSIC
low complexity region	244	255	N/A	INTRINSIC
low complexity region	289	351	N/A	INTRINSIC
low complexity region	379	394	N/A	INTRINSIC
Pfam:YTH	415	553	1.5e-50	PFAM
low complexity region	567	582	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000108346
AA Change: N479D

PolyPhen 2 Score 0.659 (Sensitivity: 0.86; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000103983
Gene: ENSMUSG00000047213
AA Change: N479D

Domain	Start	End	E-Value	Type
low complexity region	59	75	N/A	INTRINSIC
low complexity region	145	172	N/A	INTRINSIC
low complexity region	255	266	N/A	INTRINSIC
low complexity region	300	362	N/A	INTRINSIC
low complexity region	390	405	N/A	INTRINSIC
Pfam:YTH	427	562	1.1e-44	PFAM
low complexity region	578	593	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000191774
AA Change: N472D

PolyPhen 2 Score 0.659 (Sensitivity: 0.86; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000141610
Gene: ENSMUSG00000047213
AA Change: N472D

Domain	Start	End	E-Value	Type
low complexity region	52	68	N/A	INTRINSIC
low complexity region	138	165	N/A	INTRINSIC
low complexity region	248	259	N/A	INTRINSIC
low complexity region	293	355	N/A	INTRINSIC
low complexity region	383	398	N/A	INTRINSIC
Pfam:YTH	419	557	1.6e-50	PFAM
low complexity region	571	586	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000193598

Meta Mutation Damage Score

0.1092

Coding Region Coverage

1x: 97.5%
3x: 97.0%
10x: 95.8%
20x: 93.7%

Validation Efficiency

98% (108/110)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the YTH (YT521-B homology) domain protein family. The YTH domain is common in eukaryotes, is often found in the middle of the protein sequence, and may function in binding to RNA. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2013]

Allele List at MGI

Other mutations in this stock

Total: 107 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca16	T	C	7: 120,032,832 (GRCm39)		probably benign	Het
Ace2	A	T	X: 162,939,524 (GRCm39)	M123L	possibly damaging	Het
Acvr1c	A	T	2: 58,173,517 (GRCm39)	N248K	probably damaging	Het
Adam24	A	T	8: 41,134,400 (GRCm39)	R623*	probably null	Het
Agbl2	T	A	2: 90,641,626 (GRCm39)	L752Q	probably damaging	Het
Ankrd26	A	T	6: 118,488,654 (GRCm39)	F1335Y	probably damaging	Het
Ankrd34a	A	G	3: 96,505,992 (GRCm39)	S399G	probably benign	Het
Aoc1l3	A	T	6: 48,967,007 (GRCm39)	K652*	probably null	Het
Ap3d1	G	A	10: 80,545,607 (GRCm39)	P1041S	probably benign	Het
Arid3b	A	T	9: 57,703,431 (GRCm39)	M466K	possibly damaging	Het
Arsj	T	C	3: 126,231,995 (GRCm39)	I247T	probably damaging	Het
AU016765	G	A	17: 64,826,873 (GRCm39)		noncoding transcript	Het
Azin2	C	T	4: 128,844,577 (GRCm39)		probably null	Het
Bcat2	T	C	7: 45,237,792 (GRCm39)	Y313H	possibly damaging	Het
Cables2	A	G	2: 179,901,873 (GRCm39)	V465A	probably damaging	Het
Ccdc60	G	A	5: 116,264,224 (GRCm39)	H517Y	probably damaging	Het
Cd55b	A	T	1: 130,345,843 (GRCm39)		probably null	Het
Cdc40	G	A	10: 40,759,067 (GRCm39)		probably benign	Het
Cdh20	G	A	1: 109,976,754 (GRCm39)	V140I	probably benign	Het
Cdhr18	A	T	14: 13,828,582 (GRCm38)	M726K	probably null	Het
Cfi	T	C	3: 129,652,477 (GRCm39)		probably benign	Het
Chit1	G	A	1: 134,073,156 (GRCm39)		probably null	Het
Chn1	A	G	2: 73,455,245 (GRCm39)	C39R	probably damaging	Het
Ciao1	A	G	2: 127,088,380 (GRCm39)	S148P	possibly damaging	Het
Clmn	G	A	12: 104,756,361 (GRCm39)	T163I	probably damaging	Het
Cngb1	C	A	8: 96,026,320 (GRCm39)	G154W	probably damaging	Het
Col19a1	A	T	1: 24,303,831 (GRCm39)	C1117*	probably null	Het
Cplane1	T	A	15: 8,263,336 (GRCm39)	S2496R	probably damaging	Het
Cyp2d10	T	A	15: 82,289,495 (GRCm39)	I206F	probably benign	Het
Ddrgk1	G	T	2: 130,505,480 (GRCm39)		probably benign	Het
Ddx18	A	T	1: 121,482,953 (GRCm39)	V611D	probably damaging	Het
Dnah8	A	T	17: 30,950,181 (GRCm39)	H2000L	probably damaging	Het
Duox1	T	C	2: 122,156,465 (GRCm39)	V464A	probably benign	Het
Dync2h1	A	G	9: 7,139,159 (GRCm39)		probably null	Het
Eif4enif1	A	G	11: 3,193,279 (GRCm39)	H857R	probably damaging	Het
Elmo2	A	G	2: 165,133,970 (GRCm39)		probably benign	Het
Fam171b	CCAGCAGCAGCAGCAGCAGCAGC	CCAGCAGCAGCAGCAGCAGC	2: 83,643,218 (GRCm39)		probably benign	Het
Glrx	A	G	13: 75,988,256 (GRCm39)	I57V	probably benign	Het
Golm1	A	T	13: 59,790,051 (GRCm39)		probably benign	Het
Grm3	G	A	5: 9,561,682 (GRCm39)	R723W	probably damaging	Het
Gsta3	G	A	1: 21,327,601 (GRCm39)	R45Q	probably benign	Het
Gtf3c3	A	C	1: 54,468,117 (GRCm39)		probably benign	Het
Hk3	C	T	13: 55,159,204 (GRCm39)	V451I	probably damaging	Het
Hoxa10	C	A	6: 52,211,350 (GRCm39)	G189C	possibly damaging	Het
Hs3st3b1	T	C	11: 63,780,569 (GRCm39)	D186G	probably benign	Het
Hscb	G	T	5: 110,983,926 (GRCm39)	H63N	probably benign	Het
Itpr3	A	G	17: 27,330,191 (GRCm39)	E1603G	probably damaging	Het
Ivl	T	A	3: 92,480,056 (GRCm39)	H3L	probably benign	Het
Klhl26	C	A	8: 70,904,911 (GRCm39)	R252L	probably damaging	Het
Krt31	T	A	11: 99,939,069 (GRCm39)	T251S	probably benign	Het
Lama5	T	C	2: 179,832,714 (GRCm39)	N1646S	probably benign	Het
Lhx3	T	C	2: 26,093,974 (GRCm39)	D83G	probably benign	Het
Lss	C	A	10: 76,381,296 (GRCm39)	N427K	possibly damaging	Het
Mettl24	G	A	10: 40,613,722 (GRCm39)	A154T	probably benign	Het
Mgat4a	A	T	1: 37,575,118 (GRCm39)		probably null	Het
Moxd2	C	T	6: 40,860,466 (GRCm39)	R326Q	probably damaging	Het
Mpdz	G	A	4: 81,279,680 (GRCm39)	A669V	probably benign	Het
Msra	G	A	14: 64,522,505 (GRCm39)		probably benign	Het
Muc13	A	T	16: 33,628,281 (GRCm39)	T344S	probably benign	Het
Myo3b	T	C	2: 70,088,419 (GRCm39)	I866T	probably benign	Het
Nbea	T	C	3: 55,860,521 (GRCm39)	S1852G	possibly damaging	Het
Ncf2	A	G	1: 152,709,815 (GRCm39)		probably benign	Het
Nfyc	C	A	4: 120,630,861 (GRCm39)		probably benign	Het
Nop2	T	C	6: 125,111,597 (GRCm39)	V110A	probably benign	Het
Nrg2	C	A	18: 36,329,897 (GRCm39)		probably benign	Het
Nrl	A	G	14: 55,759,892 (GRCm39)	Y12H	probably damaging	Het
Nrxn3	T	C	12: 89,227,151 (GRCm39)	V635A	probably damaging	Het
Or4d11	A	C	19: 12,013,275 (GRCm39)	V277G	probably benign	Het
Or6b2b	T	A	1: 92,419,457 (GRCm39)	T7S	probably benign	Het
Or8k41	T	A	2: 86,313,703 (GRCm39)	K128*	probably null	Het
Or9g8	T	A	2: 85,607,515 (GRCm39)	S196T	probably benign	Het
Papolg	A	T	11: 23,817,279 (GRCm39)	N639K	probably benign	Het
Paqr4	T	C	17: 23,956,638 (GRCm39)	I242V	probably damaging	Het
Pramel6	A	T	2: 87,339,076 (GRCm39)	K92M	probably damaging	Het
Prg4	T	C	1: 150,331,774 (GRCm39)	T300A	possibly damaging	Het
Ptprb	A	T	10: 116,155,515 (GRCm39)		probably benign	Het
Rab28	A	T	5: 41,783,133 (GRCm39)	S216T	probably benign	Het
Rrp1b	A	T	17: 32,275,819 (GRCm39)	R455S	possibly damaging	Het
Sash1	A	T	10: 8,605,696 (GRCm39)	M898K	probably benign	Het
Scn8a	C	T	15: 100,868,085 (GRCm39)	T310I	probably benign	Het
Secisbp2l	C	A	2: 125,582,259 (GRCm39)	D1066Y	probably damaging	Het
Sipa1l2	A	G	8: 126,206,887 (GRCm39)		probably benign	Het
Slc12a1	A	G	2: 125,036,113 (GRCm39)	T662A	probably benign	Het
Slc12a4	T	C	8: 106,672,669 (GRCm39)	I749V	probably benign	Het
Slc22a27	A	G	19: 7,887,092 (GRCm39)	S266P	probably damaging	Het
Slc25a14	G	A	X: 47,740,840 (GRCm39)	V210I	probably benign	Het
Slit1	T	A	19: 41,619,215 (GRCm39)	N762I	probably damaging	Het
Spata31d1b	C	A	13: 59,865,835 (GRCm39)	D994E	possibly damaging	Het
Sphk1	A	G	11: 116,426,676 (GRCm39)	I204V	probably benign	Het
Srsf6	C	T	2: 162,776,403 (GRCm39)		probably benign	Het
Tet2	T	C	3: 133,194,399 (GRCm39)	T12A	possibly damaging	Het
Tgfbi	A	T	13: 56,762,127 (GRCm39)	Q70L	possibly damaging	Het
Tlr9	T	C	9: 106,101,846 (GRCm39)	L379P	probably damaging	Het
Tnrc6c	A	G	11: 117,646,849 (GRCm39)	D1450G	possibly damaging	Het
Tra2b	A	G	16: 22,073,795 (GRCm39)		probably benign	Het
Trit1	T	C	4: 122,948,033 (GRCm39)	I451T	probably benign	Het
Trnau1ap	A	G	4: 132,049,114 (GRCm39)	Y30H	probably damaging	Het
Ttc34	G	A	4: 154,950,139 (GRCm39)	A1031T	possibly damaging	Het
Ubiad1	A	G	4: 148,528,468 (GRCm39)	L147P	probably damaging	Het
Ush2a	A	G	1: 188,683,758 (GRCm39)	D4979G	probably null	Het
Usp50	C	T	2: 126,619,943 (GRCm39)	R123Q	probably benign	Het
Vmn2r117	A	T	17: 23,696,454 (GRCm39)	Y318N	probably damaging	Het
Whamm	C	T	7: 81,228,047 (GRCm39)	T304I	probably null	Het
Wipf2	C	T	11: 98,783,236 (GRCm39)	R221*	probably null	Het
Zbtb17	T	C	4: 141,192,859 (GRCm39)	I486T	possibly damaging	Het
Zfp3	T	C	11: 70,662,202 (GRCm39)	S54P	probably benign	Het
Zscan10	A	T	17: 23,828,826 (GRCm39)	H379L	probably damaging	Het

Other mutations in Ythdf3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL02585:Ythdf3	APN	3	16,243,642 (GRCm39)	missense	probably benign	0.01
IGL03068:Ythdf3	APN	3	16,258,882 (GRCm39)	missense	possibly damaging	0.92
Disinclined	UTSW	3	16,257,356 (GRCm39)	nonsense	probably null
R0501:Ythdf3	UTSW	3	16,259,236 (GRCm39)	missense	probably damaging	0.98
R0644:Ythdf3	UTSW	3	16,259,056 (GRCm39)	missense	possibly damaging	0.46
R1667:Ythdf3	UTSW	3	16,259,056 (GRCm39)	missense	possibly damaging	0.46
R2121:Ythdf3	UTSW	3	16,259,356 (GRCm39)	missense	possibly damaging	0.71
R2191:Ythdf3	UTSW	3	16,257,375 (GRCm39)	intron	probably benign
R2341:Ythdf3	UTSW	3	16,257,379 (GRCm39)	intron	probably benign
R2512:Ythdf3	UTSW	3	16,259,059 (GRCm39)	missense	possibly damaging	0.66
R2850:Ythdf3	UTSW	3	16,257,982 (GRCm39)	splice site	probably benign
R3037:Ythdf3	UTSW	3	16,259,355 (GRCm39)	missense	probably benign	0.32
R4934:Ythdf3	UTSW	3	16,258,220 (GRCm39)	missense	probably damaging	0.97
R5007:Ythdf3	UTSW	3	16,259,362 (GRCm39)	missense	possibly damaging	0.51
R5164:Ythdf3	UTSW	3	16,237,677 (GRCm39)	missense	possibly damaging	0.67
R5172:Ythdf3	UTSW	3	16,258,198 (GRCm39)	missense	probably damaging	1.00
R5480:Ythdf3	UTSW	3	16,237,664 (GRCm39)	missense	possibly damaging	0.83
R5512:Ythdf3	UTSW	3	16,238,086 (GRCm39)	missense	probably damaging	0.98
R6059:Ythdf3	UTSW	3	16,257,356 (GRCm39)	nonsense	probably null
R6104:Ythdf3	UTSW	3	16,259,325 (GRCm39)	missense	possibly damaging	0.51
R6273:Ythdf3	UTSW	3	16,259,020 (GRCm39)	missense	possibly damaging	0.92
R6721:Ythdf3	UTSW	3	16,258,025 (GRCm39)	missense	possibly damaging	0.72
R7187:Ythdf3	UTSW	3	16,258,451 (GRCm39)	missense	probably benign	0.05
R7285:Ythdf3	UTSW	3	16,258,049 (GRCm39)	splice site	probably null
R7307:Ythdf3	UTSW	3	16,237,664 (GRCm39)	missense	possibly damaging	0.83
R7816:Ythdf3	UTSW	3	16,243,681 (GRCm39)	missense	probably damaging	0.96
R8499:Ythdf3	UTSW	3	16,259,179 (GRCm39)	missense	possibly damaging	0.85
R8754:Ythdf3	UTSW	3	16,258,138 (GRCm39)	missense	probably damaging	0.99
R9401:Ythdf3	UTSW	3	16,258,659 (GRCm39)	missense	probably damaging	0.99

Predicted Primers

PCR Primer
(F):5'- CAAAGACTTTGATTGGAACCTGAAG -3'
(R):5'- GGGTACTTCTTGAGTGTCCC -3'

Sequencing Primer
(F):5'- CTTTGATTGGAACCTGAAGAATGGAC -3'
(R):5'- ACTTCTTGAGTGTCCCTTGAATTG -3'

Posted On

2014-07-14