Mutagenetix > Incidental Mutation

Incidental Mutation 'R2512:Ythdf3'

253388

Institutional Source

Beutler Lab

Gene Symbol

Ythdf3

Ensembl Gene

ENSMUSG00000047213

Gene Name

YTH N6-methyladenosine RNA binding protein 3

Synonyms

9130022A11Rik

MMRRC Submission

040418-MU

Accession Numbers

Essential gene?

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

Stock #

R2512 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

16237376-16271201 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 16259059 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Serine at position 406 (N406S)

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: N402S

PolyPhen 2 Score 0.528 (Sensitivity: 0.88; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000103982
Gene: ENSMUSG00000047213
AA Change: N402S

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: N413S

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

SMART Domains

Protein: ENSMUSP00000103983
Gene: ENSMUSG00000047213
AA Change: N413S

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: N406S

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

SMART Domains

Protein: ENSMUSP00000141610
Gene: ENSMUSG00000047213
AA Change: N406S

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

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.4%
20x: 95.2%

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: 71 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2700049A03Rik	A	G	12: 71,219,945 (GRCm39)	T831A	possibly damaging	Het
Actg2	T	A	6: 83,503,829 (GRCm39)	I72F	probably damaging	Het
Add1	A	G	5: 34,774,030 (GRCm39)	T80A	probably benign	Het
Alpk2	G	A	18: 65,483,591 (GRCm39)	T139M	probably damaging	Het
Aplp2	C	T	9: 31,078,973 (GRCm39)	R325H	probably damaging	Het
Aptx	G	A	4: 40,694,917 (GRCm39)	P140S	probably benign	Het
Carm1	A	G	9: 21,486,708 (GRCm39)		probably null	Het
Carmil2	A	T	8: 106,424,025 (GRCm39)	I1293F	probably benign	Het
Cdh8	T	C	8: 100,127,495 (GRCm39)	T39A	probably benign	Het
Cimip3	T	C	17: 47,724,651 (GRCm39)	T60A	probably benign	Het
Col15a1	T	A	4: 47,245,868 (GRCm39)	N206K	possibly damaging	Het
Copg2	C	T	6: 30,873,591 (GRCm39)		probably null	Het
Ctr9	T	G	7: 110,646,078 (GRCm39)	I690S	probably damaging	Het
Dcaf8	T	G	1: 172,016,602 (GRCm39)	I463S	possibly damaging	Het
Dcp1b	G	T	6: 119,183,473 (GRCm39)	A187S	possibly damaging	Het
Ddo	T	A	10: 40,508,935 (GRCm39)	D58E	possibly damaging	Het
Dkkl1	G	T	7: 44,857,157 (GRCm39)	R137S	probably damaging	Het
Dxo	A	G	17: 35,056,718 (GRCm39)	N115S	probably benign	Het
Ep400	A	T	5: 110,856,781 (GRCm39)		probably benign	Het
F11	A	G	8: 45,714,098 (GRCm39)	V7A	probably benign	Het
Fermt1	G	T	2: 132,781,438 (GRCm39)		probably null	Het
Fign	A	T	2: 63,810,143 (GRCm39)	F376I	probably benign	Het
Flg2	G	T	3: 93,109,082 (GRCm39)	G370V	probably damaging	Het
Fndc3a	A	T	14: 72,793,715 (GRCm39)	D953E	probably benign	Het
Fsip2	A	T	2: 82,808,511 (GRCm39)	H1610L	probably benign	Het
Gfra3	T	C	18: 34,837,564 (GRCm39)	N145D	probably benign	Het
Inpp4b	G	T	8: 82,737,179 (GRCm39)	W525C	probably damaging	Het
Kremen1	CGGG	CGGGGGG	11: 5,151,791 (GRCm39)		probably benign	Het
Lgi2	A	G	5: 52,695,307 (GRCm39)	*543R	probably null	Het
Lyn	A	G	4: 3,745,542 (GRCm39)	T114A	probably benign	Het
Lynx1	A	G	15: 74,623,169 (GRCm39)	Y88H	probably damaging	Het
Map4	C	A	9: 109,863,770 (GRCm39)	P332T	possibly damaging	Het
Mapk8ip3	A	T	17: 25,133,677 (GRCm39)	C250*	probably null	Het
Metap1d	A	G	2: 71,352,954 (GRCm39)	H261R	probably damaging	Het
Mfrp	T	C	9: 44,013,835 (GRCm39)	V115A	probably benign	Het
Mtbp	A	G	15: 55,440,932 (GRCm39)	Y373C	probably damaging	Het
Mtor	C	A	4: 148,614,948 (GRCm39)	R1628S	possibly damaging	Het
Muc5b	A	G	7: 141,412,813 (GRCm39)	N1920D	unknown	Het
Myo1d	T	A	11: 80,670,543 (GRCm39)	M26L	probably benign	Het
Neb	A	C	2: 52,100,843 (GRCm39)	D643E	probably damaging	Het
Nme1	A	G	11: 93,851,513 (GRCm39)	F108L	possibly damaging	Het
Or2r11	A	G	6: 42,437,207 (GRCm39)	S249P	probably damaging	Het
Or8c15	G	T	9: 38,120,670 (GRCm39)	C54F	probably damaging	Het
Pan2	T	A	10: 128,140,326 (GRCm39)	D82E	probably damaging	Het
Pclo	A	G	5: 14,762,612 (GRCm39)	D3695G	unknown	Het
Pcnx4	A	T	12: 72,603,573 (GRCm39)		probably null	Het
Plg	A	G	17: 12,622,116 (GRCm39)	T479A	probably benign	Het
Plod3	G	C	5: 137,017,000 (GRCm39)	A50P	probably benign	Het
Pramel32	T	G	4: 88,547,195 (GRCm39)	M246L	probably damaging	Het
Ptgis	T	C	2: 167,049,196 (GRCm39)	D372G	probably damaging	Het
Ranbp3l	A	G	15: 8,997,949 (GRCm39)	T14A	probably benign	Het
Rcc1l	A	T	5: 134,195,508 (GRCm39)	V230D	probably damaging	Het
Reln	T	C	5: 22,184,688 (GRCm39)	D1609G	possibly damaging	Het
Rif1	GCCACCA	GCCA	2: 52,000,336 (GRCm39)		probably benign	Het
Ryr1	G	A	7: 28,802,967 (GRCm39)	L696F	possibly damaging	Het
Sacs	T	A	14: 61,440,529 (GRCm39)	D858E	probably benign	Het
Sec16a	C	T	2: 26,329,037 (GRCm39)	V993I	probably benign	Het
Skint5	T	A	4: 113,487,616 (GRCm39)	I901F	unknown	Het
Slc17a3	A	T	13: 24,030,230 (GRCm39)	I114F	probably benign	Het
Slc17a7	T	A	7: 44,818,288 (GRCm39)	L71Q	probably damaging	Het
Slc43a2	T	C	11: 75,461,403 (GRCm39)	S452P	probably damaging	Het
Smarca4	A	G	9: 21,546,994 (GRCm39)	N173S	possibly damaging	Het
Tbc1d21	T	C	9: 58,270,195 (GRCm39)	Y161C	probably damaging	Het
Tpsab1	C	A	17: 25,564,081 (GRCm39)	C94F	probably damaging	Het
Ubr5	G	A	15: 38,002,563 (GRCm39)	P1496L	probably damaging	Het
Unc80	G	T	1: 66,710,767 (GRCm39)	A2679S	possibly damaging	Het
Vdac1	T	A	11: 52,274,904 (GRCm39)	V184E	probably damaging	Het
Vmn2r24	T	A	6: 123,763,985 (GRCm39)	S287R	probably benign	Het
Vmn2r91	T	C	17: 18,356,048 (GRCm39)	F572L	probably benign	Het
Vps13b	G	A	15: 35,884,701 (GRCm39)	E3125K	probably benign	Het
Zfp708	T	C	13: 67,219,251 (GRCm39)	K158E	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
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
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'- ACAGCCACAGTTGCAGAATC -3'
(R):5'- ACAGACTTCATTTCAGCCACTC -3'

Sequencing Primer
(F):5'- CCACAGTTGCAGAATCGTTGG -3'
(R):5'- AGTAAATAGAGTGGGCCTTTCC -3'

Posted On

2014-12-04