Incidental Mutation 'R4042:Ythdc1'
| ID |
315768 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Ythdc1
|
| Ensembl Gene |
ENSMUSG00000035851 |
| Gene Name |
YTH domain containing 1 |
| Synonyms |
A730098D12Rik |
| MMRRC Submission |
040851-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.968)
|
| Stock # |
R4042 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
5 |
| Chromosomal Location |
86952080-86984518 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 86964383 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Isoleucine to Threonine
at position 76
(I76T)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000122491
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000038384]
[ENSMUST00000119339]
[ENSMUST00000120498]
[ENSMUST00000156363]
|
| AlphaFold |
E9Q5K9 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000038384
AA Change: I64T
PolyPhen 2
Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)
|
| SMART Domains |
Protein: ENSMUSP00000039133
Gene: ENSMUSG00000035851
AA Change: I64T
| 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 benign
Transcript: ENSMUST00000119339
AA Change: I64T
PolyPhen 2
Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)
|
| SMART Domains |
Protein: ENSMUSP00000113000
Gene: ENSMUSG00000035851
AA Change: I64T
| 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 benign
Transcript: ENSMUST00000120498
AA Change: I64T
PolyPhen 2
Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)
|
| SMART Domains |
Protein: ENSMUSP00000113951
Gene: ENSMUSG00000035851
AA Change: I64T
| 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 |
probably benign
Transcript: ENSMUST00000156363
AA Change: I76T
PolyPhen 2
Score 0.026 (Sensitivity: 0.95; Specificity: 0.81)
|
| SMART Domains |
Protein: ENSMUSP00000122491
Gene: ENSMUSG00000035851
AA Change: I76T
| 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
|
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.7%
- 10x: 97.5%
- 20x: 95.9%
|
| Validation Efficiency |
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 38 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Adamts10 |
A |
G |
17: 33,768,514 (GRCm39) |
H864R |
possibly damaging |
Het |
| Akap6 |
A |
T |
12: 53,186,162 (GRCm39) |
|
probably null |
Het |
| Alox5 |
A |
G |
6: 116,437,979 (GRCm39) |
S3P |
possibly damaging |
Het |
| Bcl2l2 |
G |
A |
14: 55,122,091 (GRCm39) |
E85K |
possibly damaging |
Het |
| Chd6 |
A |
T |
2: 160,830,253 (GRCm39) |
I1014N |
probably damaging |
Het |
| Cog1 |
A |
T |
11: 113,551,836 (GRCm39) |
Q156L |
probably damaging |
Het |
| Col28a1 |
G |
A |
6: 8,014,678 (GRCm39) |
S909F |
probably damaging |
Het |
| Csmd3 |
C |
T |
15: 47,477,480 (GRCm39) |
G3339D |
probably damaging |
Het |
| Cst11 |
A |
G |
2: 148,613,200 (GRCm39) |
S42P |
probably benign |
Het |
| Cyp2d10 |
C |
T |
15: 82,290,269 (GRCm39) |
R67H |
probably benign |
Het |
| Fsip2 |
G |
T |
2: 82,813,896 (GRCm39) |
R3405L |
probably benign |
Het |
| H2-Ab1 |
T |
C |
17: 34,483,834 (GRCm39) |
V65A |
probably benign |
Het |
| Hdac6 |
T |
C |
X: 7,797,731 (GRCm39) |
T993A |
probably benign |
Het |
| Insrr |
T |
A |
3: 87,721,134 (GRCm39) |
M1095K |
probably damaging |
Het |
| Itih4 |
A |
T |
14: 30,616,995 (GRCm39) |
N517I |
probably damaging |
Het |
| Krt10 |
C |
T |
11: 99,277,819 (GRCm39) |
|
probably null |
Het |
| Mettl16 |
T |
A |
11: 74,683,118 (GRCm39) |
F187I |
probably damaging |
Het |
| Miga2 |
T |
C |
2: 30,257,738 (GRCm39) |
I12T |
possibly damaging |
Het |
| Muc5b |
T |
C |
7: 141,418,624 (GRCm39) |
Y3857H |
possibly damaging |
Het |
| Ncoa1 |
A |
G |
12: 4,317,871 (GRCm39) |
S165P |
probably damaging |
Het |
| Or5bb10 |
A |
T |
19: 12,206,676 (GRCm39) |
I83N |
probably benign |
Het |
| Otol1 |
A |
G |
3: 69,935,112 (GRCm39) |
D368G |
probably damaging |
Het |
| Pdlim2 |
C |
T |
14: 70,402,228 (GRCm39) |
R296H |
probably damaging |
Het |
| Plxnb1 |
A |
G |
9: 108,934,241 (GRCm39) |
D823G |
probably benign |
Het |
| Ppme1 |
A |
G |
7: 99,990,272 (GRCm39) |
S226P |
probably damaging |
Het |
| Ppp4r3c1 |
A |
G |
X: 88,975,909 (GRCm39) |
F96S |
probably damaging |
Het |
| Prss40 |
G |
T |
1: 34,599,960 (GRCm39) |
S9* |
probably null |
Het |
| Prune2 |
T |
C |
19: 16,981,190 (GRCm39) |
|
probably null |
Het |
| Radx |
C |
T |
X: 138,407,752 (GRCm39) |
S364L |
probably damaging |
Homo |
| Rgl2 |
C |
T |
17: 34,156,236 (GRCm39) |
R775W |
probably damaging |
Het |
| Rpp40 |
A |
G |
13: 36,082,549 (GRCm39) |
C275R |
probably benign |
Het |
| Rrm2 |
T |
C |
12: 24,761,450 (GRCm39) |
Y162H |
probably benign |
Het |
| Spata6l |
A |
T |
19: 28,923,183 (GRCm39) |
C80S |
possibly damaging |
Het |
| Syne1 |
T |
C |
10: 4,991,584 (GRCm39) |
M8377V |
probably benign |
Het |
| Uchl4 |
A |
C |
9: 64,142,839 (GRCm39) |
I107L |
probably benign |
Het |
| Ush1c |
T |
C |
7: 45,870,952 (GRCm39) |
E276G |
probably damaging |
Het |
| Usp34 |
C |
T |
11: 23,439,033 (GRCm39) |
P3532S |
possibly damaging |
Het |
| Vcan |
T |
A |
13: 89,840,662 (GRCm39) |
L1627F |
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 |
|
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 |
|
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'- CAGCAGTTGGGAAGCAGTTTTG -3'
(R):5'- GGTTCTCTAGAGGAACTGCTTGAC -3'
Sequencing Primer
(F):5'- AGCAGTTGGGAAGCAGTTTTGTTTAC -3'
(R):5'- CAGCATCTAGACGCTTGT -3'
|
| Posted On |
2015-05-15 |
Incidental Mutation