Mutagenetix > Incidental Mutation

Incidental Mutation 'R8284:Ythdc1'

638365

Institutional Source

Beutler Lab

Gene Symbol

Ythdc1

Ensembl Gene

ENSMUSG00000035851

Gene Name

YTH domain containing 1

Synonyms

A730098D12Rik

MMRRC Submission

067707-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.968) question?

Stock #

R8284 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

86952080-86984518 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to G at 86964325 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Alanine at position 45 (S45A)

Ref Sequence

ENSEMBL: ENSMUSP00000039133 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000038384] [ENSMUST00000119339] [ENSMUST00000120498] [ENSMUST00000156363]

AlphaFold

E9Q5K9

Predicted Effect

probably benign
Transcript: ENSMUST00000038384
AA Change: S45A

PolyPhen 2 Score 0.177 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000039133
Gene: ENSMUSG00000035851
AA Change: S45A

Domain	Start	End	E-Value	Type
SCOP:d1qbkb_	225	249	6e-3	SMART
low complexity region	269	280	N/A	INTRINSIC
low complexity region	316	330	N/A	INTRINSIC
Pfam:YTH	356	494	5e-42	PFAM
low complexity region	516	540	N/A	INTRINSIC
low complexity region	609	622	N/A	INTRINSIC
low complexity region	625	645	N/A	INTRINSIC
low complexity region	682	736	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000119339
AA Change: S45A

PolyPhen 2 Score 0.980 (Sensitivity: 0.75; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000113000
Gene: ENSMUSG00000035851
AA Change: S45A

Domain	Start	End	E-Value	Type
SCOP:d1qbkb_	225	249	6e-3	SMART
low complexity region	269	280	N/A	INTRINSIC
Pfam:YTH	337	478	4.4e-44	PFAM
low complexity region	498	522	N/A	INTRINSIC
low complexity region	583	596	N/A	INTRINSIC
low complexity region	599	619	N/A	INTRINSIC
low complexity region	656	710	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000120498
AA Change: S45A

PolyPhen 2 Score 0.980 (Sensitivity: 0.75; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000113951
Gene: ENSMUSG00000035851
AA Change: S45A

Domain	Start	End	E-Value	Type
SCOP:d1qbkb_	225	249	6e-3	SMART
low complexity region	269	280	N/A	INTRINSIC
low complexity region	316	330	N/A	INTRINSIC
Pfam:YTH	355	496	4.6e-44	PFAM
low complexity region	516	540	N/A	INTRINSIC
low complexity region	601	614	N/A	INTRINSIC
low complexity region	617	637	N/A	INTRINSIC
low complexity region	674	728	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000156363
AA Change: S57A

PolyPhen 2 Score 0.619 (Sensitivity: 0.87; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000122491
Gene: ENSMUSG00000035851
AA Change: S57A

Domain	Start	End	E-Value	Type
SCOP:d1qbkb_	237	261	8e-3	SMART
low complexity region	281	292	N/A	INTRINSIC
Pfam:YTH	350	488	3e-42	PFAM
low complexity region	510	525	N/A	INTRINSIC

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.6%

Validation Efficiency

100% (54/54)

Allele List at MGI

Other mutations in this stock

Total: 55 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adamts14	T	C	10: 61,034,438 (GRCm39)	Y1147C	possibly damaging	Het
Adgrf5	T	A	17: 43,766,161 (GRCm39)	S1328T	unknown	Het
Aff4	A	G	11: 53,295,379 (GRCm39)	K860E	probably damaging	Het
Aox1	A	C	1: 58,115,250 (GRCm39)	H745P	probably damaging	Het
Bpifc	T	C	10: 85,836,413 (GRCm39)	T31A	probably benign	Het
C3	C	A	17: 57,530,938 (GRCm39)	V388L	probably benign	Het
Celsr3	G	T	9: 108,723,612 (GRCm39)	M2874I	probably damaging	Het
Cnga4	T	A	7: 105,057,239 (GRCm39)	D550E	probably benign	Het
Dhx8	A	G	11: 101,648,455 (GRCm39)	T918A	probably damaging	Het
Dnah14	A	C	1: 181,601,376 (GRCm39)	E3670A	probably benign	Het
Fbxo31	T	C	8: 122,287,181 (GRCm39)	I131V	probably benign	Het
Ftcd	T	C	10: 76,413,893 (GRCm39)	V99A	probably benign	Het
Gucy2e	A	G	11: 69,123,177 (GRCm39)	V471A	probably benign	Het
H60b	T	A	10: 22,162,971 (GRCm39)	L182Q	probably benign	Het
Hbp1	G	A	12: 31,987,625 (GRCm39)	H188Y	probably damaging	Het
Itga4	C	T	2: 79,151,783 (GRCm39)	T862I	probably benign	Het
Kcnmb4	T	A	10: 116,254,158 (GRCm39)	K206N	probably damaging	Het
Klra4	A	G	6: 130,042,243 (GRCm39)	F8S	possibly damaging	Het
Mrpl2	C	A	17: 46,958,435 (GRCm39)	Y72*	probably null	Het
Nars2	C	A	7: 96,600,845 (GRCm39)		probably benign	Het
Nup214	T	C	2: 31,886,458 (GRCm39)	S607P	possibly damaging	Het
Oas1d	C	T	5: 121,057,221 (GRCm39)	R276*	probably null	Het
Or12d13	C	T	17: 37,647,587 (GRCm39)	V179I	probably benign	Het
Or1l8	T	A	2: 36,818,018 (GRCm39)	Y36F	probably damaging	Het
Or2t1	T	A	14: 14,329,011 (GRCm38)	L300Q	possibly damaging	Het
Or2y1b	A	G	11: 49,209,002 (GRCm39)	T210A	probably benign	Het
Pex13	A	G	11: 23,605,685 (GRCm39)	S182P	possibly damaging	Het
Piwil4	G	T	9: 14,638,774 (GRCm39)	N297K	probably benign	Het
Plxna4	T	C	6: 32,129,789 (GRCm39)	T1845A	probably benign	Het
Pml	T	C	9: 58,136,643 (GRCm39)	N579D	probably benign	Het
Ppl	A	G	16: 4,950,201 (GRCm39)	S3P	probably damaging	Het
Pramel16	G	T	4: 143,676,695 (GRCm39)	D136E	possibly damaging	Het
Prss54	G	A	8: 96,285,994 (GRCm39)	Q360*	probably null	Het
Ralgps2	A	G	1: 156,655,718 (GRCm39)	I402T	probably benign	Het
Rnf213	T	A	11: 119,318,909 (GRCm39)	D1123E		Het
Sdha	A	T	13: 74,479,416 (GRCm39)		probably null	Het
Senp8	G	A	9: 59,644,814 (GRCm39)	T114I		Het
Setx	C	T	2: 29,035,348 (GRCm39)	T611I	possibly damaging	Het
Shc1	T	G	3: 89,329,215 (GRCm39)	S20A	possibly damaging	Het
Slc15a1	T	C	14: 121,727,275 (GRCm39)	I98V	probably benign	Het
Snrk	A	G	9: 121,989,538 (GRCm39)	E294G	probably damaging	Het
Sox18	G	A	2: 181,312,751 (GRCm39)	P127S	probably damaging	Het
Spta1	A	G	1: 174,007,387 (GRCm39)	T206A	probably benign	Het
Tcfl5	A	G	2: 180,280,330 (GRCm39)	S358P	probably benign	Het
Tecta	T	A	9: 42,289,325 (GRCm39)	L413F	possibly damaging	Het
Tlk1	T	C	2: 70,544,365 (GRCm39)	T757A	probably benign	Het
Tmem232	T	A	17: 65,709,990 (GRCm39)	I433F	probably damaging	Het
Top1mt	T	A	15: 75,539,712 (GRCm39)	K300*	probably null	Het
Trbv20	C	T	6: 41,165,782 (GRCm39)	A69V	probably damaging	Het
Trim12a	A	T	7: 103,955,282 (GRCm39)	L147Q	probably damaging	Het
Tuba8	G	A	6: 121,199,736 (GRCm39)	S140N	probably damaging	Het
Vcan	A	T	13: 89,852,454 (GRCm39)	N835K	possibly damaging	Het
Xrcc1	G	A	7: 24,271,703 (GRCm39)	R562H	probably damaging	Het
Yipf7	C	T	5: 69,674,539 (GRCm39)	G202D	probably benign	Het
Zfp1002	T	C	2: 150,097,276 (GRCm39)		probably benign	Het

Other mutations in Ythdc1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00676:Ythdc1	APN	5	86,979,670 (GRCm39)	missense	probably damaging	1.00
IGL02222:Ythdc1	APN	5	86,975,902 (GRCm39)	missense	possibly damaging	0.72
R0091:Ythdc1	UTSW	5	86,968,560 (GRCm39)	intron	probably benign
R0311:Ythdc1	UTSW	5	86,983,564 (GRCm39)	missense	probably damaging	0.97
R0349:Ythdc1	UTSW	5	86,983,579 (GRCm39)	missense	probably damaging	1.00
R0630:Ythdc1	UTSW	5	86,957,207 (GRCm39)	splice site	probably benign
R1662:Ythdc1	UTSW	5	86,975,981 (GRCm39)	critical splice donor site	probably null
R1907:Ythdc1	UTSW	5	86,978,489 (GRCm39)	missense	probably damaging	1.00
R2100:Ythdc1	UTSW	5	86,964,544 (GRCm39)	missense	possibly damaging	0.62
R2911:Ythdc1	UTSW	5	86,964,418 (GRCm39)	missense	possibly damaging	0.95
R3692:Ythdc1	UTSW	5	86,970,526 (GRCm39)	missense	probably damaging	0.98
R4042:Ythdc1	UTSW	5	86,964,383 (GRCm39)	missense	probably benign	0.03
R4398:Ythdc1	UTSW	5	86,983,679 (GRCm39)	utr 3 prime	probably benign
R4398:Ythdc1	UTSW	5	86,963,513 (GRCm39)	missense	possibly damaging	0.95
R4608:Ythdc1	UTSW	5	86,970,667 (GRCm39)	missense	probably damaging	0.97
R4806:Ythdc1	UTSW	5	86,970,704 (GRCm39)	missense	probably damaging	0.99
R5291:Ythdc1	UTSW	5	86,983,547 (GRCm39)	missense	probably damaging	1.00
R5761:Ythdc1	UTSW	5	86,983,810 (GRCm39)	utr 3 prime	probably benign
R6180:Ythdc1	UTSW	5	86,975,953 (GRCm39)	missense	possibly damaging	0.91
R6249:Ythdc1	UTSW	5	86,979,815 (GRCm39)	missense	possibly damaging	0.94
R6560:Ythdc1	UTSW	5	86,964,467 (GRCm39)	missense	probably benign	0.06
R7145:Ythdc1	UTSW	5	86,964,467 (GRCm39)	missense	probably benign	0.06
R8072:Ythdc1	UTSW	5	86,969,133 (GRCm39)	nonsense	probably null
R8225:Ythdc1	UTSW	5	86,964,797 (GRCm39)	missense	possibly damaging	0.73
R8225:Ythdc1	UTSW	5	86,964,796 (GRCm39)	missense	possibly damaging	0.91
R8229:Ythdc1	UTSW	5	86,957,167 (GRCm39)	intron	probably benign
R8246:Ythdc1	UTSW	5	86,965,181 (GRCm39)	missense	possibly damaging	0.94
R8385:Ythdc1	UTSW	5	86,975,961 (GRCm39)	missense	possibly damaging	0.77
R8546:Ythdc1	UTSW	5	86,974,607 (GRCm39)	missense	possibly damaging	0.78

Predicted Primers

PCR Primer
(F):5'- CAGCAGTTGGGAAGCAGTTTTG -3'
(R):5'- AGGTTCTCTAGAGGAACTGCTTG -3'

Sequencing Primer
(F):5'- AGCAGTTGGGAAGCAGTTTTGTTTAC -3'
(R):5'- CGATCAGCATCTAGACGCTTG -3'

Posted On

2020-07-28