Incidental Mutation 'R4398:Ythdc1'
ID |
325580 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Ythdc1
|
Ensembl Gene |
ENSMUSG00000035851 |
Gene Name |
YTH domain containing 1 |
Synonyms |
A730098D12Rik |
MMRRC Submission |
041130-MU
|
Accession Numbers |
|
Essential gene? |
Probably essential
(E-score: 0.968)
|
Stock # |
R4398 (G1)
|
Quality Score |
225 |
Status
|
Validated
|
Chromosome |
5 |
Chromosomal Location |
86952080-86984518 bp(+) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
T to A
at 86963513 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Aspartic acid to Glutamic Acid
at position 30
(D30E)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000122491
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000038384]
[ENSMUST00000119339]
[ENSMUST00000120498]
[ENSMUST00000156363]
|
AlphaFold |
E9Q5K9 |
Predicted Effect |
possibly damaging
Transcript: ENSMUST00000038384
AA Change: D18E
PolyPhen 2
Score 0.705 (Sensitivity: 0.86; Specificity: 0.92)
|
SMART Domains |
Protein: ENSMUSP00000039133 Gene: ENSMUSG00000035851 AA Change: D18E
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 |
possibly damaging
Transcript: ENSMUST00000119339
AA Change: D18E
PolyPhen 2
Score 0.705 (Sensitivity: 0.86; Specificity: 0.92)
|
SMART Domains |
Protein: ENSMUSP00000113000 Gene: ENSMUSG00000035851 AA Change: D18E
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 |
possibly damaging
Transcript: ENSMUST00000120498
AA Change: D18E
PolyPhen 2
Score 0.705 (Sensitivity: 0.86; Specificity: 0.92)
|
SMART Domains |
Protein: ENSMUSP00000113951 Gene: ENSMUSG00000035851 AA Change: D18E
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 |
noncoding transcript
Transcript: ENSMUST00000151489
|
Predicted Effect |
possibly damaging
Transcript: ENSMUST00000156363
AA Change: D30E
PolyPhen 2
Score 0.948 (Sensitivity: 0.79; Specificity: 0.95)
|
SMART Domains |
Protein: ENSMUSP00000122491 Gene: ENSMUSG00000035851 AA Change: D30E
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 |
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000198859
|
Meta Mutation Damage Score |
0.0595 |
Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.1%
- 20x: 94.7%
|
Validation Efficiency |
96% (53/55) |
Allele List at MGI |
|
Other mutations in this stock |
Total: 46 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Adamts20 |
C |
A |
15: 94,231,576 (GRCm39) |
R871L |
possibly damaging |
Het |
Adcy5 |
G |
A |
16: 35,089,363 (GRCm39) |
C520Y |
probably damaging |
Het |
AI661453 |
G |
A |
17: 47,779,042 (GRCm39) |
|
probably benign |
Het |
Bptf |
T |
C |
11: 107,001,670 (GRCm39) |
K481E |
probably damaging |
Het |
Cnot10 |
T |
A |
9: 114,460,949 (GRCm39) |
K74* |
probably null |
Het |
Ctc1 |
C |
T |
11: 68,913,697 (GRCm39) |
P200S |
probably damaging |
Het |
Dact1 |
T |
C |
12: 71,363,959 (GRCm39) |
Y210H |
probably damaging |
Het |
Dbn1 |
T |
C |
13: 55,623,194 (GRCm39) |
T430A |
probably benign |
Het |
Dmd |
A |
C |
X: 82,765,624 (GRCm39) |
T657P |
probably benign |
Het |
Efnb2 |
C |
T |
8: 8,670,832 (GRCm39) |
R256H |
possibly damaging |
Het |
Eif4a1 |
T |
C |
11: 69,560,070 (GRCm39) |
I116M |
possibly damaging |
Het |
F730035P03Rik |
A |
T |
7: 99,429,475 (GRCm39) |
|
noncoding transcript |
Het |
Fbn1 |
C |
T |
2: 125,239,701 (GRCm39) |
V329I |
probably benign |
Het |
Gpr20 |
G |
A |
15: 73,568,125 (GRCm39) |
T88I |
probably benign |
Het |
Herc1 |
T |
G |
9: 66,386,735 (GRCm39) |
V3783G |
probably benign |
Het |
Khdc1a |
A |
G |
1: 21,420,617 (GRCm39) |
D79G |
possibly damaging |
Het |
Klk1b16 |
A |
T |
7: 43,790,851 (GRCm39) |
I218F |
probably damaging |
Het |
Malrd1 |
C |
T |
2: 16,155,594 (GRCm39) |
T2001I |
unknown |
Het |
Mia3 |
A |
G |
1: 183,111,733 (GRCm39) |
S556P |
probably damaging |
Het |
Myo3a |
T |
A |
2: 22,467,854 (GRCm39) |
D369E |
probably benign |
Het |
Nelfa |
T |
C |
5: 34,058,623 (GRCm39) |
D279G |
possibly damaging |
Het |
Ntrk3 |
A |
T |
7: 77,900,517 (GRCm39) |
C607* |
probably null |
Het |
Or13a20 |
T |
C |
7: 140,232,741 (GRCm39) |
V283A |
possibly damaging |
Het |
Pclo |
A |
T |
5: 14,825,380 (GRCm39) |
Q1371L |
probably damaging |
Het |
Pdzd2 |
A |
T |
15: 12,376,061 (GRCm39) |
V1358E |
probably benign |
Het |
Pgr |
T |
C |
9: 8,903,750 (GRCm39) |
|
probably null |
Het |
Prag1 |
A |
G |
8: 36,570,809 (GRCm39) |
D464G |
probably damaging |
Het |
Prickle4 |
A |
G |
17: 48,001,456 (GRCm39) |
|
probably benign |
Het |
Prim2 |
A |
G |
1: 33,551,192 (GRCm39) |
Y309H |
probably damaging |
Het |
Prkaa1 |
A |
G |
15: 5,206,642 (GRCm39) |
Q464R |
possibly damaging |
Het |
Rab36 |
G |
A |
10: 74,880,328 (GRCm39) |
V63I |
probably damaging |
Het |
Rint1 |
T |
A |
5: 23,999,445 (GRCm39) |
I78K |
possibly damaging |
Het |
Rnf130 |
T |
A |
11: 49,962,205 (GRCm39) |
F217Y |
probably benign |
Het |
Smad7 |
T |
C |
18: 75,527,234 (GRCm39) |
V360A |
probably damaging |
Het |
Sp110 |
A |
C |
1: 85,505,050 (GRCm39) |
F434C |
probably benign |
Het |
Stag1 |
A |
G |
9: 100,838,659 (GRCm39) |
|
probably benign |
Het |
Tlr12 |
T |
A |
4: 128,509,988 (GRCm39) |
D754V |
probably benign |
Het |
Tmf1 |
G |
A |
6: 97,155,857 (GRCm39) |
P43L |
probably damaging |
Het |
Togaram1 |
A |
G |
12: 65,027,630 (GRCm39) |
N873S |
probably benign |
Het |
Tsn |
C |
T |
1: 118,238,799 (GRCm39) |
|
probably benign |
Het |
Ubn1 |
A |
G |
16: 4,882,289 (GRCm39) |
K250R |
probably damaging |
Het |
Vmn1r25 |
A |
T |
6: 57,955,812 (GRCm39) |
V159D |
probably damaging |
Het |
Vmn2r89 |
T |
C |
14: 51,689,551 (GRCm39) |
L18P |
probably damaging |
Het |
Vps8 |
T |
G |
16: 21,323,216 (GRCm39) |
N689K |
probably damaging |
Het |
Zfp407 |
G |
A |
18: 84,580,856 (GRCm39) |
Q86* |
probably null |
Het |
Zfp521 |
C |
T |
18: 13,979,601 (GRCm39) |
E271K |
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 |
|
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 |
R8284:Ythdc1
|
UTSW |
5 |
86,964,325 (GRCm39) |
missense |
probably benign |
0.18 |
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'- ACTGTTTTAAGCAGGCCATATTTGG -3'
(R):5'- CCGGGTCTGTTATGCAAAATGG -3'
Sequencing Primer
(F):5'- AAGCAGGCCATATTTGGAGTTTTTG -3'
(R):5'- ATGCAAAATGGTTTATTGTGTGC -3'
|
Posted On |
2015-07-06 |