Mutagenetix > Incidental Mutations

Incidental Mutation 'R5141:Ythdc2'

396502

Institutional Source

Beutler Lab

Gene Symbol

Ythdc2

Ensembl Gene

ENSMUSG00000034653

Gene Name

YTH domain containing 2

Synonyms

3010002F02Rik

MMRRC Submission

042727-MU

Accession Numbers

Is this an essential gene?

Non essential (E-score: 0.000) question?

Stock #

R5141 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

44827746-44889724 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 44865047 bp

Zygosity

Heterozygous

Amino Acid Change

Serine to Threonine at position 1094 (S1094T)

Ref Sequence

ENSEMBL: ENSMUSP00000048340 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000037763] [ENSMUST00000201507]

Predicted Effect

probably benign
Transcript: ENSMUST00000037763
AA Change: S1094T

PolyPhen 2 Score 0.007 (Sensitivity: 0.96; Specificity: 0.75)

SMART Domains

Protein: ENSMUSP00000048340
Gene: ENSMUSG00000034653
AA Change: S1094T

Domain	Start	End	E-Value	Type
low complexity region	2	50	N/A	INTRINSIC
Pfam:R3H	59	119	1.7e-15	PFAM
DEXDc	206	393	4.95e-26	SMART
low complexity region	413	428	N/A	INTRINSIC
ANK	521	550	2.79e1	SMART
ANK	554	583	1.5e2	SMART
HELICc	648	759	5.31e-17	SMART
HA2	823	916	2.58e-22	SMART
Pfam:OB_NTP_bind	953	1082	1.3e-18	PFAM
low complexity region	1263	1299	N/A	INTRINSIC
Pfam:YTH	1303	1434	7.2e-50	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000201507
AA Change: S439T

PolyPhen 2 Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)

SMART Domains

Protein: ENSMUSP00000144479
Gene: ENSMUSG00000034653
AA Change: S439T

Domain	Start	End	E-Value	Type
HELICc	5	104	9.1e-19	SMART
HA2	168	261	2e-26	SMART
Pfam:OB_NTP_bind	298	427	6e-16	PFAM
low complexity region	570	582	N/A	INTRINSIC

Meta Mutation Damage Score

0.1018

Coding Region Coverage

1x: 99.3%
3x: 98.6%
10x: 97.1%
20x: 94.6%

Validation Efficiency

96% (76/79)

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 DEAH (Asp-Glu-Ala-His) subfamily of proteins, part of the DEAD (Asp-Glu-Ala-Asp) box family of RNA helicases. The encoded protein binds to N6-methyladenosine, a common modified RNA nucleotide that is enriched in the stop codons and 3' UTRs of eukaryotic messenger RNAs. Binding of proteins to this modified nucleotide may regulate mRNA translation and stability. This gene may be associated with susceptibility to pancreatic cancer in human patients, and knockdown of this gene resulted in reduced proliferation in a human liver cancer cell line. [provided by RefSeq, Sep 2016]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit female and male infertility with arrested meiosis and small gonads. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 75 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adamdec1	A	G	14: 68,573,128	V193A	probably benign	Het
Adamts18	T	A	8: 113,775,270	T320S	probably damaging	Het
Adamtsl1	G	T	4: 86,156,850	M151I	possibly damaging	Het
Adgrv1	A	T	13: 81,270,918	V5986E	probably damaging	Het
Aifm3	A	G	16: 17,499,722	E69G	probably damaging	Het
Akap13	C	A	7: 75,609,614	T662K	probably benign	Het
Alms1	A	G	6: 85,621,432	D1080G	probably benign	Het
Als2	T	C	1: 59,170,452	E1457G	possibly damaging	Het
Apobec4	A	G	1: 152,756,213		probably benign	Het
Apoo-ps	C	T	13: 107,414,395		noncoding transcript	Het
Aspscr1	G	A	11: 120,689,177	V181I	probably benign	Het
Atrn	T	C	2: 130,999,130		probably benign	Het
C3	T	A	17: 57,219,570	I804F	probably damaging	Het
Cbfa2t3	C	T	8: 122,635,021	G421R	probably benign	Het
Chmp4c	A	G	3: 10,367,153	E41G	probably damaging	Het
Clk4	T	A	11: 51,275,771	F96L	possibly damaging	Het
Ctsg	G	A	14: 56,101,727	R25*	probably null	Het
Cul1	A	G	6: 47,520,839	D618G	probably benign	Het
Cylc2	T	C	4: 51,228,587		probably benign	Het
Dip2a	G	A	10: 76,270,453	T1326I	probably damaging	Het
Etnk2	A	G	1: 133,368,862	I210V	probably benign	Het
Gm5773	T	A	3: 93,773,727	D235E	probably benign	Het
Gm7353	T	C	7: 3,111,001		noncoding transcript	Het
Gpi1	G	A	7: 34,227,096		probably benign	Het
Ing4	T	C	6: 125,039,874	M5T	probably benign	Het
Inpp4a	A	G	1: 37,380,087	I583V	probably benign	Het
Isyna1	T	C	8: 70,594,893	V64A	probably damaging	Het
Katnal2	T	A	18: 76,997,641	D310V	probably damaging	Het
Kbtbd8	A	G	6: 95,121,839	T126A	probably damaging	Het
Kif13a	T	C	13: 46,752,721	D582G	probably benign	Het
Lmf2	G	A	15: 89,351,607		probably null	Het
Lrp2	T	C	2: 69,552,349		probably null	Het
Lrp4	T	C	2: 91,478,678		probably benign	Het
Lyzl1	A	C	18: 4,169,209	D71A	possibly damaging	Het
Mak	C	T	13: 41,032,563	C543Y	possibly damaging	Het
Mapk8ip1	T	C	2: 92,386,765	D404G	probably damaging	Het
Mdga1	C	T	17: 29,852,493	E385K	probably benign	Het
Mst1r	T	A	9: 107,912,241	I573N	probably damaging	Het
Muc5ac	T	A	7: 141,814,742	N2365K	possibly damaging	Het
Ncan	T	C	8: 70,112,837	E179G	probably damaging	Het
Nlgn2	C	T	11: 69,825,390	R775H	probably damaging	Het
Olfr1228	A	C	2: 89,249,129	Y176*	probably null	Het
Olfr44	A	G	9: 39,484,531	F238L	probably damaging	Het
Olfr975	T	G	9: 39,949,874	K299T	probably benign	Het
Pcolce	G	T	5: 137,605,750	Q352K	probably benign	Het
Peg3	G	T	7: 6,709,382	T947N	probably benign	Het
Pld3	C	T	7: 27,533,795	D344N	probably damaging	Het
Plec	A	C	15: 76,190,533	D411E	probably damaging	Het
Pmp2	C	T	3: 10,182,414	D72N	probably benign	Het
Ptpn9	T	C	9: 57,036,676	V278A	possibly damaging	Het
Rbm33	A	G	5: 28,352,689	H300R	probably damaging	Het
Rpgrip1l	T	C	8: 91,260,918	Q837R	probably benign	Het
Rwdd4a	T	C	8: 47,550,674		probably benign	Het
Sema6a	T	C	18: 47,248,388	T1048A	probably damaging	Het
Senp1	G	A	15: 98,076,607	A108V	probably benign	Het
Serpine2	G	T	1: 79,802,863	Q290K	possibly damaging	Het
Sesn1	A	G	10: 41,811,101	N27S	probably benign	Het
Shroom1	T	A	11: 53,463,982	L243*	probably null	Het
Slc17a5	A	G	9: 78,540,988	Y395H	probably damaging	Het
Slc5a8	T	C	10: 88,919,560		probably null	Het
Sptbn5	G	A	2: 120,061,731	S1083F	probably benign	Het
Stx4a	T	A	7: 127,846,615	V231E	probably damaging	Het
Swt1	A	T	1: 151,411,394	S116T	probably benign	Het
Syt9	C	T	7: 107,504,219	T408I	probably damaging	Het
Tgm7	T	C	2: 121,100,999	T228A	probably benign	Het
Tmem115	A	G	9: 107,537,942	D310G	probably benign	Het
Trcg1	G	A	9: 57,241,304	G53D	probably damaging	Het
Tsfm	T	C	10: 127,029,613	K100E	probably damaging	Het
Usp1	A	G	4: 98,934,209	T587A	probably damaging	Het
Vcpip1	G	T	1: 9,748,077	A27E	unknown	Het
Vmn2r49	T	C	7: 9,986,373	N397S	probably benign	Het
Vmn2r8	A	G	5: 108,808,706	S17P	probably damaging	Het
Vwa3b	A	G	1: 37,187,021		probably benign	Het
Zbtb22	C	G	17: 33,918,636	S585C	possibly damaging	Het
Zhx2	A	G	15: 57,821,786	T184A	probably benign	Het

Other mutations in Ythdc2

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00321:Ythdc2	APN	18	44859973	missense	probably benign
IGL00341:Ythdc2	APN	18	44850397	missense	probably benign	0.00
IGL00502:Ythdc2	APN	18	44847812	missense	probably damaging	0.99
IGL00585:Ythdc2	APN	18	44864361	missense	probably damaging	1.00
IGL01081:Ythdc2	APN	18	44850659	missense	probably benign	0.19
IGL01569:Ythdc2	APN	18	44887651	missense	probably benign
IGL01577:Ythdc2	APN	18	44858282	missense	probably benign	0.00
IGL01617:Ythdc2	APN	18	44841415	missense	possibly damaging	0.53
IGL01674:Ythdc2	APN	18	44860404	missense	probably benign	0.04
IGL01736:Ythdc2	APN	18	44850668	missense	probably damaging	0.97
IGL02095:Ythdc2	APN	18	44873140	splice site	probably benign
IGL02245:Ythdc2	APN	18	44862684	missense	possibly damaging	0.74
IGL02524:Ythdc2	APN	18	44847854	missense	probably damaging	0.98
IGL02542:Ythdc2	APN	18	44840241	missense	probably damaging	1.00
IGL02622:Ythdc2	APN	18	44859934	missense	probably damaging	0.99
IGL02795:Ythdc2	APN	18	44837438	missense	possibly damaging	0.95
IGL02935:Ythdc2	APN	18	44855045	missense	probably damaging	1.00
PIT4618001:Ythdc2	UTSW	18	44834598	missense	probably benign	0.19
R0115:Ythdc2	UTSW	18	44841423	splice site	probably benign
R0329:Ythdc2	UTSW	18	44865060	splice site	probably benign
R0472:Ythdc2	UTSW	18	44864357	missense	probably benign	0.02
R0530:Ythdc2	UTSW	18	44850398	missense	probably damaging	0.99
R0547:Ythdc2	UTSW	18	44840264	missense	possibly damaging	0.92
R0563:Ythdc2	UTSW	18	44864848	splice site	probably benign
R0609:Ythdc2	UTSW	18	44864357	missense	probably benign	0.02
R1291:Ythdc2	UTSW	18	44855209	missense	probably benign	0.33
R1469:Ythdc2	UTSW	18	44864462	missense	probably benign	0.00
R1469:Ythdc2	UTSW	18	44864462	missense	probably benign	0.00
R1724:Ythdc2	UTSW	18	44828690	missense	probably benign	0.04
R1860:Ythdc2	UTSW	18	44872956	missense	possibly damaging	0.86
R2040:Ythdc2	UTSW	18	44855174	nonsense	probably null
R2308:Ythdc2	UTSW	18	44847748	missense	possibly damaging	0.95
R3711:Ythdc2	UTSW	18	44833173	missense	probably damaging	0.98
R4005:Ythdc2	UTSW	18	44833128	missense	probably benign	0.00
R4580:Ythdc2	UTSW	18	44858198	missense	possibly damaging	0.81
R4631:Ythdc2	UTSW	18	44887631	missense	probably benign	0.03
R4815:Ythdc2	UTSW	18	44885240	missense	probably benign	0.40
R4924:Ythdc2	UTSW	18	44847804	missense	probably damaging	1.00
R4982:Ythdc2	UTSW	18	44871465	missense	probably benign	0.01
R5011:Ythdc2	UTSW	18	44854742	missense	probably benign	0.38
R5147:Ythdc2	UTSW	18	44844292	missense	probably damaging	0.98
R5280:Ythdc2	UTSW	18	44860621	missense	probably damaging	1.00
R5388:Ythdc2	UTSW	18	44857025	missense	possibly damaging	0.65
R5928:Ythdc2	UTSW	18	44833205	missense	probably benign
R5931:Ythdc2	UTSW	18	44872956	missense	possibly damaging	0.86
R5995:Ythdc2	UTSW	18	44886253	missense	probably damaging	1.00
R6027:Ythdc2	UTSW	18	44860436	missense	probably benign	0.02
R6056:Ythdc2	UTSW	18	44840210	missense	probably damaging	0.98
R6318:Ythdc2	UTSW	18	44860377	missense	probably benign	0.04
R6399:Ythdc2	UTSW	18	44886402	missense	possibly damaging	0.93
R6586:Ythdc2	UTSW	18	44845788	missense	probably benign	0.00
R6684:Ythdc2	UTSW	18	44873069	missense	possibly damaging	0.47
R7040:Ythdc2	UTSW	18	44834462	missense	probably benign	0.02
R7071:Ythdc2	UTSW	18	44845788	missense	probably benign	0.00
R7105:Ythdc2	UTSW	18	44834563	missense	probably damaging	1.00
R7148:Ythdc2	UTSW	18	44833122	missense	probably benign	0.42
R7290:Ythdc2	UTSW	18	44837491	missense	possibly damaging	0.50
R7806:Ythdc2	UTSW	18	44844286	missense	possibly damaging	0.91
R7806:Ythdc2	UTSW	18	44850424	missense	probably benign	0.05
R8114:Ythdc2	UTSW	18	44877740	missense	probably benign	0.15

Predicted Primers

PCR Primer
(F):5'- AATAGATTCCTCCCGCCAATGG -3'
(R):5'- CCTGTCTCAGTATATCAAATATGCC -3'

Sequencing Primer
(F):5'- AATGGTCAGGCTGCAGC -3'
(R):5'- ATACACCTCAGTATTCCCTAACTATC -3'

Posted On

2016-06-21