Mutagenetix > Incidental Mutation

Incidental Mutation 'R7816:Ythdf3'

601512

Institutional Source

Beutler Lab

Gene Symbol

Ythdf3

Ensembl Gene

ENSMUSG00000047213

Gene Name

YTH N6-methyladenosine RNA binding protein 3

Synonyms

9130022A11Rik

MMRRC Submission

045870-MU

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.307) question?

Stock #

R7816 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

16237376-16271201 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 16243681 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 34 (V34A)

Ref Sequence

ENSEMBL: ENSMUSP00000141610 (fasta)

Gene Model

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

AlphaFold

Q8BYK6

Predicted Effect

possibly damaging
Transcript: ENSMUST00000108345
AA Change: V30A

PolyPhen 2 Score 0.942 (Sensitivity: 0.80; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000103982
Gene: ENSMUSG00000047213
AA Change: V30A

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: V30A

PolyPhen 2 Score 0.711 (Sensitivity: 0.86; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000103983
Gene: ENSMUSG00000047213
AA Change: V30A

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

probably damaging
Transcript: ENSMUST00000191774
AA Change: V34A

PolyPhen 2 Score 0.965 (Sensitivity: 0.78; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000141610
Gene: ENSMUSG00000047213
AA Change: V34A

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

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.9%

Validation Efficiency

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: 78 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca12	A	G	1: 71,331,588 (GRCm39)	S1321P	probably benign	Het
Abcb1a	T	C	5: 8,736,132 (GRCm39)	V175A	possibly damaging	Het
Adamts20	T	A	15: 94,220,725 (GRCm39)	M1403L	probably benign	Het
Akap13	G	A	7: 75,380,213 (GRCm39)	R462H	probably damaging	Het
Amotl2	T	A	9: 102,608,853 (GRCm39)	I789K	probably benign	Het
BC005537	C	T	13: 24,987,382 (GRCm39)	R7W	possibly damaging	Het
Bcar3	C	T	3: 122,220,343 (GRCm39)	T80I	probably benign	Het
Bcas1	G	T	2: 170,248,347 (GRCm39)	F181L	probably benign	Het
Cacnb1	T	C	11: 97,896,115 (GRCm39)	E389G	probably damaging	Het
Cd52	A	T	4: 133,821,199 (GRCm39)		probably benign	Het
Cmtm1	CGGCACGTACTGAAGGTCGCTGACTGGATGGTGTGGCACGTACTGAAGGTCGCTGACTGGATGGTGTGGCACGTACTGAAGGTCGCTGACTGGATGGT	CGGCACGTACTGAAGGTCGCTGACTGGATGGTGTGGCACGTACTGAAGGTCGCTGACTGGATGGT	8: 105,036,102 (GRCm39)		probably benign	Het
Coro2a	T	C	4: 46,546,809 (GRCm39)	D182G	probably benign	Het
Crp	T	C	1: 172,526,277 (GRCm39)	S121P	possibly damaging	Het
Csnka2ip	T	C	16: 64,299,852 (GRCm39)		probably benign	Het
Cttnbp2	T	C	6: 18,448,413 (GRCm39)	D82G	probably damaging	Het
Cyp2b9	A	G	7: 25,900,517 (GRCm39)	N385S	probably benign	Het
Dppa1	A	G	11: 46,507,003 (GRCm39)	S26P	possibly damaging	Het
Eif4e3	T	C	6: 99,617,599 (GRCm39)	R91G	probably damaging	Het
F13a1	A	T	13: 37,209,745 (GRCm39)	N73K	probably benign	Het
Fbxl13	T	C	5: 21,748,785 (GRCm39)	Y378C	probably benign	Het
Glis2	G	A	16: 4,431,328 (GRCm39)	R285H	probably damaging	Het
Gm17174	T	A	14: 51,829,569 (GRCm39)		probably benign	Het
Golga1	G	A	2: 38,942,110 (GRCm39)	S102F	probably damaging	Het
Hdac1	A	T	4: 129,411,888 (GRCm39)	Y336N	probably damaging	Het
Hfe	G	T	13: 23,888,382 (GRCm39)	T168K	possibly damaging	Het
Idh2	TCCCAGG	T	7: 79,748,079 (GRCm39)		probably benign	Het
Ighv1-56	T	C	12: 115,206,846 (GRCm39)	S4G	probably benign	Het
Ino80d	A	G	1: 63,125,556 (GRCm39)	Y74H	probably damaging	Het
Ints1	A	T	5: 139,757,134 (GRCm39)	H427Q	possibly damaging	Het
Itpkb	T	A	1: 180,241,454 (GRCm39)	V708E	probably damaging	Het
Jmjd4	G	T	11: 59,341,162 (GRCm39)	G31V	probably benign	Het
Kcnh5	C	T	12: 75,023,457 (GRCm39)	C537Y	probably damaging	Het
Kcnj11	A	T	7: 45,749,281 (GRCm39)	L14Q	probably damaging	Het
Lipo4	A	T	19: 33,491,642 (GRCm39)	W114R	probably damaging	Het
Lrrc9	T	A	12: 72,542,466 (GRCm39)	I1096N	probably damaging	Het
Lyzl6	C	T	11: 103,527,680 (GRCm39)	V15I	probably benign	Het
Map4k4	A	G	1: 40,053,368 (GRCm39)	T856A	possibly damaging	Het
Mks1	T	A	11: 87,751,542 (GRCm39)	W346R	probably damaging	Het
Mtmr14	T	C	6: 113,243,263 (GRCm39)	Y32H	probably damaging	Het
Muc13	A	G	16: 33,619,386 (GRCm39)	S45G	unknown	Het
Mx2	G	A	16: 97,346,812 (GRCm39)	G93D	probably damaging	Het
Noc4l	A	T	5: 110,797,539 (GRCm39)	V365E	probably benign	Het
Odf2l	T	C	3: 144,856,776 (GRCm39)	I577T	probably damaging	Het
Or4l1	T	C	14: 50,166,622 (GRCm39)	I126M	probably damaging	Het
Peg10	C	CTCT	6: 4,756,453 (GRCm39)		probably benign	Het
Pkd1l3	GACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCA	GACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCA	8: 110,350,827 (GRCm39)		probably benign	Het
Pnoc	A	T	14: 65,639,307 (GRCm39)	I186N	possibly damaging	Het
Pou4f3	A	G	18: 42,528,251 (GRCm39)	I65V	probably benign	Het
Pramel23	G	T	4: 143,424,764 (GRCm39)	N226K	probably benign	Het
Prss1l	T	C	6: 41,371,707 (GRCm39)	L51P	probably damaging	Het
Ptpn21	G	A	12: 98,648,791 (GRCm39)	A955V	probably damaging	Het
Rabgap1	G	T	2: 37,453,476 (GRCm39)	R968L	probably benign	Het
Rarres1	T	C	3: 67,386,677 (GRCm39)	N282S	probably damaging	Het
Rgs17	T	C	10: 5,791,501 (GRCm39)	N72S	probably benign	Het
Rp1	T	A	1: 4,417,926 (GRCm39)	N1062I	probably damaging	Het
Rpn1	T	A	6: 88,080,378 (GRCm39)	V559D	possibly damaging	Het
Rrbp1	A	T	2: 143,830,855 (GRCm39)	N437K	probably damaging	Het
Rtn4r	C	A	16: 17,969,399 (GRCm39)	Q276K	probably benign	Het
Rwdd4a	T	C	8: 47,990,335 (GRCm39)	S16P	probably damaging	Het
S1pr1	A	G	3: 115,505,947 (GRCm39)	S216P	possibly damaging	Het
Scn8a	C	A	15: 100,908,917 (GRCm39)	T795K	possibly damaging	Het
Spryd3	A	C	15: 102,026,141 (GRCm39)	F401C	probably damaging	Het
Stk36	G	T	1: 74,650,328 (GRCm39)	E287*	probably null	Het
Tbc1d1	G	T	5: 64,507,095 (GRCm39)	S1104I	probably damaging	Het
Tex15	A	G	8: 34,071,683 (GRCm39)	D2410G	probably benign	Het
Tmem92	T	A	11: 94,669,784 (GRCm39)	I116F	possibly damaging	Het
Trp53bp2	A	G	1: 182,276,260 (GRCm39)	E747G	probably damaging	Het
Trp63	A	T	16: 25,707,990 (GRCm39)	D562V	probably damaging	Het
Ttc21b	A	G	2: 66,077,705 (GRCm39)	Y167H	possibly damaging	Het
Ubr5	G	A	15: 37,980,076 (GRCm39)	A2434V	probably null	Het
Uggt1	G	A	1: 36,202,396 (GRCm39)	S1067F	possibly damaging	Het
Vmn2r103	T	A	17: 20,014,476 (GRCm39)	Y423N	probably benign	Het
Vmn2r111	A	G	17: 22,792,083 (GRCm39)	Y58H	probably damaging	Het
Ypel3	T	A	7: 126,377,013 (GRCm39)	V2E	probably damaging	Het
Zfp180	A	T	7: 23,804,570 (GRCm39)	S330C	probably damaging	Het
Zfp292	G	A	4: 34,809,865 (GRCm39)	P1060S	probably benign	Het
Zfp354c	TCACACTCGGCACA	TCACA	11: 50,706,067 (GRCm39)		probably benign	Het
Zfp981	C	T	4: 146,622,100 (GRCm39)	R342C	probably benign	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
R1940:Ythdf3	UTSW	3	16,259,256 (GRCm39)	missense	possibly damaging	0.71
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
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'- ACAGGATTTCTCAGTTTCCTGTGG -3'
(R):5'- ACCGTATGTAGGTACCCTAAATG -3'

Sequencing Primer
(F):5'- CCTGTGGCACACATTACT -3'
(R):5'- GGTACCCTAAATGAATTGACTCAC -3'

Posted On

2019-12-03