Incidental Mutation 'R5388:Ythdc2'
| ID |
425438 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Ythdc2
|
| Ensembl Gene |
ENSMUSG00000034653 |
| Gene Name |
YTH domain containing 2 |
| Synonyms |
3010002F02Rik |
| MMRRC Submission |
042960-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R5388 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
18 |
| Chromosomal Location |
44961521-45022787 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to A
at 44990092 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Leucine to Glutamine
at position 732
(L732Q)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000048340
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000037763]
[ENSMUST00000201507]
|
| AlphaFold |
B2RR83 |
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000037763
AA Change: L732Q
PolyPhen 2
Score 0.654 (Sensitivity: 0.87; Specificity: 0.91)
|
| SMART Domains |
Protein: ENSMUSP00000048340
Gene: ENSMUSG00000034653
AA Change: L732Q
| 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: L77Q
PolyPhen 2
Score 0.047 (Sensitivity: 0.94; Specificity: 0.83)
|
| SMART Domains |
Protein: ENSMUSP00000144479
Gene: ENSMUSG00000034653
AA Change: L77Q
| 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 |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000202176
|
| Meta Mutation Damage Score |
0.1899 |
| Coding Region Coverage |
- 1x: 99.3%
- 3x: 98.8%
- 10x: 97.5%
- 20x: 95.9%
|
| Validation Efficiency |
98% (57/58) |
| 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: 54 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abca16 |
T |
C |
7: 120,139,969 (GRCm39) |
|
probably null |
Het |
| Acap2 |
C |
A |
16: 30,928,543 (GRCm39) |
C475F |
probably damaging |
Het |
| Ace |
C |
A |
11: 105,879,284 (GRCm39) |
P603Q |
possibly damaging |
Het |
| Adamts20 |
C |
G |
15: 94,243,659 (GRCm39) |
V657L |
possibly damaging |
Het |
| Antxr2 |
A |
G |
5: 98,125,458 (GRCm39) |
|
probably null |
Het |
| Atp6v1b2 |
G |
A |
8: 69,554,089 (GRCm39) |
V89I |
probably benign |
Het |
| Cacna1e |
G |
A |
1: 154,353,542 (GRCm39) |
P676L |
probably damaging |
Het |
| Camsap3 |
A |
T |
8: 3,654,276 (GRCm39) |
I649F |
probably damaging |
Het |
| Camta1 |
G |
T |
4: 151,159,695 (GRCm39) |
S490R |
probably damaging |
Het |
| Celsr1 |
A |
G |
15: 85,809,719 (GRCm39) |
I2221T |
probably damaging |
Het |
| Cfd |
A |
T |
10: 79,727,959 (GRCm39) |
D164V |
probably damaging |
Het |
| Cfdp1 |
T |
C |
8: 112,495,384 (GRCm39) |
D278G |
probably damaging |
Het |
| Cntn6 |
A |
T |
6: 104,809,523 (GRCm39) |
L519F |
probably damaging |
Het |
| Col4a4 |
C |
T |
1: 82,471,312 (GRCm39) |
G681E |
unknown |
Het |
| Cybrd1 |
T |
C |
2: 70,967,989 (GRCm39) |
|
probably null |
Het |
| Cyp2e1 |
T |
C |
7: 140,343,906 (GRCm39) |
L48P |
probably damaging |
Het |
| Eddm13 |
T |
C |
7: 6,269,346 (GRCm39) |
|
probably null |
Het |
| Ep400 |
G |
A |
5: 110,849,594 (GRCm39) |
T1409I |
unknown |
Het |
| Exosc7 |
A |
T |
9: 122,947,972 (GRCm39) |
D47V |
probably damaging |
Het |
| Fgr |
T |
C |
4: 132,722,342 (GRCm39) |
F204L |
probably damaging |
Het |
| Gm10100 |
G |
A |
10: 77,562,560 (GRCm39) |
V81M |
probably benign |
Het |
| Gm12367 |
T |
C |
4: 35,235,690 (GRCm39) |
|
noncoding transcript |
Het |
| Grxcr1 |
C |
A |
5: 68,323,538 (GRCm39) |
T272K |
probably damaging |
Het |
| Kcna5 |
C |
T |
6: 126,511,859 (GRCm39) |
D90N |
probably benign |
Het |
| Kdm5b |
T |
A |
1: 134,536,635 (GRCm39) |
Y618* |
probably null |
Het |
| Lama5 |
T |
A |
2: 179,832,539 (GRCm39) |
H1670L |
possibly damaging |
Het |
| Mtus2 |
C |
T |
5: 148,243,518 (GRCm39) |
Q113* |
probably null |
Het |
| Ncam1 |
A |
C |
9: 49,456,054 (GRCm39) |
D521E |
probably benign |
Het |
| Nkapl |
T |
C |
13: 21,651,740 (GRCm39) |
H291R |
possibly damaging |
Het |
| Nlrp1b |
T |
G |
11: 71,062,967 (GRCm39) |
N695H |
probably damaging |
Het |
| Npc1l1 |
T |
A |
11: 6,164,733 (GRCm39) |
Q1105H |
probably damaging |
Het |
| Paxip1 |
C |
G |
5: 27,986,453 (GRCm39) |
|
probably benign |
Het |
| Pign |
A |
T |
1: 105,583,695 (GRCm39) |
W136R |
probably damaging |
Het |
| Pira1 |
T |
C |
7: 3,741,856 (GRCm39) |
T175A |
possibly damaging |
Het |
| Pkn3 |
T |
A |
2: 29,971,086 (GRCm39) |
S222T |
probably damaging |
Het |
| Polr3a |
T |
C |
14: 24,505,009 (GRCm39) |
I1084V |
possibly damaging |
Het |
| Ppfibp1 |
T |
A |
6: 146,898,338 (GRCm39) |
I98N |
probably damaging |
Het |
| Ppfibp1 |
T |
G |
6: 146,917,828 (GRCm39) |
S484A |
probably damaging |
Het |
| Ppp1r7 |
T |
C |
1: 93,280,312 (GRCm39) |
F127L |
probably damaging |
Het |
| Pramel1 |
T |
C |
4: 143,123,954 (GRCm39) |
Y210H |
probably benign |
Het |
| Rad21l |
C |
T |
2: 151,495,403 (GRCm39) |
V427I |
probably benign |
Het |
| Ripply1 |
TTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCT |
TTCCTCCTCCTCCTCCTCCTCCTCCTCCT |
X: 138,680,599 (GRCm39) |
|
probably benign |
Het |
| Rnf225 |
A |
G |
7: 12,661,932 (GRCm39) |
D37G |
probably damaging |
Het |
| Smpd2 |
A |
G |
10: 41,363,967 (GRCm39) |
|
probably null |
Het |
| Spata31h1 |
T |
C |
10: 82,119,561 (GRCm39) |
Q4483R |
probably damaging |
Het |
| Tmem38b |
C |
T |
4: 53,859,945 (GRCm39) |
R242W |
probably benign |
Het |
| Topaz1 |
A |
T |
9: 122,603,158 (GRCm39) |
K1035I |
possibly damaging |
Het |
| Trhr |
T |
C |
15: 44,060,873 (GRCm39) |
I131T |
possibly damaging |
Het |
| Usp1 |
A |
G |
4: 98,819,294 (GRCm39) |
D252G |
probably benign |
Het |
| Usp14 |
C |
T |
18: 10,018,023 (GRCm39) |
E90K |
probably damaging |
Het |
| Yme1l1 |
T |
G |
2: 23,052,569 (GRCm39) |
D74E |
probably benign |
Het |
| Zbbx |
G |
T |
3: 74,990,977 (GRCm39) |
A289D |
probably damaging |
Het |
| Zfhx3 |
G |
A |
8: 109,673,446 (GRCm39) |
V1499I |
possibly damaging |
Het |
| Zfp622 |
T |
C |
15: 25,996,285 (GRCm39) |
V184A |
possibly damaging |
Het |
|
| Other mutations in Ythdc2 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00321:Ythdc2
|
APN |
18 |
44,993,040 (GRCm39) |
missense |
probably benign |
|
|
IGL00341:Ythdc2
|
APN |
18 |
44,983,464 (GRCm39) |
missense |
probably benign |
0.00 |
|
IGL00502:Ythdc2
|
APN |
18 |
44,980,879 (GRCm39) |
missense |
probably damaging |
0.99 |
|
IGL00585:Ythdc2
|
APN |
18 |
44,997,428 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL01081:Ythdc2
|
APN |
18 |
44,983,726 (GRCm39) |
missense |
probably benign |
0.19 |
|
IGL01569:Ythdc2
|
APN |
18 |
45,020,718 (GRCm39) |
missense |
probably benign |
|
|
IGL01577:Ythdc2
|
APN |
18 |
44,991,349 (GRCm39) |
missense |
probably benign |
0.00 |
|
IGL01617:Ythdc2
|
APN |
18 |
44,974,482 (GRCm39) |
missense |
possibly damaging |
0.53 |
|
IGL01674:Ythdc2
|
APN |
18 |
44,993,471 (GRCm39) |
missense |
probably benign |
0.04 |
|
IGL01736:Ythdc2
|
APN |
18 |
44,983,735 (GRCm39) |
missense |
probably damaging |
0.97 |
|
IGL02095:Ythdc2
|
APN |
18 |
45,006,207 (GRCm39) |
splice site |
probably benign |
|
|
IGL02245:Ythdc2
|
APN |
18 |
44,995,751 (GRCm39) |
missense |
possibly damaging |
0.74 |
|
IGL02524:Ythdc2
|
APN |
18 |
44,980,921 (GRCm39) |
missense |
probably damaging |
0.98 |
|
IGL02542:Ythdc2
|
APN |
18 |
44,973,308 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02622:Ythdc2
|
APN |
18 |
44,993,001 (GRCm39) |
missense |
probably damaging |
0.99 |
|
IGL02795:Ythdc2
|
APN |
18 |
44,970,505 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
IGL02935:Ythdc2
|
APN |
18 |
44,988,112 (GRCm39) |
missense |
probably damaging |
1.00 |
|
PIT4618001:Ythdc2
|
UTSW |
18 |
44,967,665 (GRCm39) |
missense |
probably benign |
0.19 |
|
R0115:Ythdc2
|
UTSW |
18 |
44,974,490 (GRCm39) |
splice site |
probably benign |
|
|
R0329:Ythdc2
|
UTSW |
18 |
44,998,127 (GRCm39) |
splice site |
probably benign |
|
|
R0472:Ythdc2
|
UTSW |
18 |
44,997,424 (GRCm39) |
missense |
probably benign |
0.02 |
|
R0530:Ythdc2
|
UTSW |
18 |
44,983,465 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R0547:Ythdc2
|
UTSW |
18 |
44,973,331 (GRCm39) |
missense |
possibly damaging |
0.92 |
|
R0563:Ythdc2
|
UTSW |
18 |
44,997,915 (GRCm39) |
splice site |
probably benign |
|
|
R0609:Ythdc2
|
UTSW |
18 |
44,997,424 (GRCm39) |
missense |
probably benign |
0.02 |
|
R1291:Ythdc2
|
UTSW |
18 |
44,988,276 (GRCm39) |
missense |
probably benign |
0.33 |
|
R1469:Ythdc2
|
UTSW |
18 |
44,997,529 (GRCm39) |
missense |
probably benign |
0.00 |
|
R1469:Ythdc2
|
UTSW |
18 |
44,997,529 (GRCm39) |
missense |
probably benign |
0.00 |
|
R1724:Ythdc2
|
UTSW |
18 |
44,961,757 (GRCm39) |
missense |
probably benign |
0.04 |
|
R1860:Ythdc2
|
UTSW |
18 |
45,006,023 (GRCm39) |
missense |
possibly damaging |
0.86 |
|
R2040:Ythdc2
|
UTSW |
18 |
44,988,241 (GRCm39) |
nonsense |
probably null |
|
|
R2308:Ythdc2
|
UTSW |
18 |
44,980,815 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
R3711:Ythdc2
|
UTSW |
18 |
44,966,240 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R4005:Ythdc2
|
UTSW |
18 |
44,966,195 (GRCm39) |
missense |
probably benign |
0.00 |
|
R4580:Ythdc2
|
UTSW |
18 |
44,991,265 (GRCm39) |
missense |
possibly damaging |
0.81 |
|
R4631:Ythdc2
|
UTSW |
18 |
45,020,698 (GRCm39) |
missense |
probably benign |
0.03 |
|
R4815:Ythdc2
|
UTSW |
18 |
45,018,307 (GRCm39) |
missense |
probably benign |
0.40 |
|
R4924:Ythdc2
|
UTSW |
18 |
44,980,871 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4982:Ythdc2
|
UTSW |
18 |
45,004,532 (GRCm39) |
missense |
probably benign |
0.01 |
|
R5011:Ythdc2
|
UTSW |
18 |
44,987,809 (GRCm39) |
missense |
probably benign |
0.38 |
|
R5141:Ythdc2
|
UTSW |
18 |
44,998,114 (GRCm39) |
missense |
probably benign |
0.01 |
|
R5147:Ythdc2
|
UTSW |
18 |
44,977,359 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R5280:Ythdc2
|
UTSW |
18 |
44,993,688 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5928:Ythdc2
|
UTSW |
18 |
44,966,272 (GRCm39) |
missense |
probably benign |
|
|
R5931:Ythdc2
|
UTSW |
18 |
45,006,023 (GRCm39) |
missense |
possibly damaging |
0.86 |
|
R5995:Ythdc2
|
UTSW |
18 |
45,019,320 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6027:Ythdc2
|
UTSW |
18 |
44,993,503 (GRCm39) |
missense |
probably benign |
0.02 |
|
R6056:Ythdc2
|
UTSW |
18 |
44,973,277 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R6318:Ythdc2
|
UTSW |
18 |
44,993,444 (GRCm39) |
missense |
probably benign |
0.04 |
|
R6399:Ythdc2
|
UTSW |
18 |
45,019,469 (GRCm39) |
missense |
possibly damaging |
0.93 |
|
R6586:Ythdc2
|
UTSW |
18 |
44,978,855 (GRCm39) |
missense |
probably benign |
0.00 |
|
R6684:Ythdc2
|
UTSW |
18 |
45,006,136 (GRCm39) |
missense |
possibly damaging |
0.47 |
|
R7040:Ythdc2
|
UTSW |
18 |
44,967,529 (GRCm39) |
missense |
probably benign |
0.02 |
|
R7071:Ythdc2
|
UTSW |
18 |
44,978,855 (GRCm39) |
missense |
probably benign |
0.00 |
|
R7105:Ythdc2
|
UTSW |
18 |
44,967,630 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7148:Ythdc2
|
UTSW |
18 |
44,966,189 (GRCm39) |
missense |
probably benign |
0.42 |
|
R7290:Ythdc2
|
UTSW |
18 |
44,970,558 (GRCm39) |
missense |
possibly damaging |
0.50 |
|
R7806:Ythdc2
|
UTSW |
18 |
44,983,491 (GRCm39) |
missense |
probably benign |
0.05 |
|
R7806:Ythdc2
|
UTSW |
18 |
44,977,353 (GRCm39) |
missense |
possibly damaging |
0.91 |
|
R8114:Ythdc2
|
UTSW |
18 |
45,010,807 (GRCm39) |
missense |
probably benign |
0.15 |
|
R8820:Ythdc2
|
UTSW |
18 |
44,967,531 (GRCm39) |
nonsense |
probably null |
|
|
R8840:Ythdc2
|
UTSW |
18 |
44,993,691 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8998:Ythdc2
|
UTSW |
18 |
44,997,371 (GRCm39) |
missense |
probably benign |
0.31 |
|
R9065:Ythdc2
|
UTSW |
18 |
44,977,418 (GRCm39) |
missense |
probably benign |
0.00 |
|
R9196:Ythdc2
|
UTSW |
18 |
44,988,464 (GRCm39) |
missense |
probably damaging |
0.96 |
|
R9251:Ythdc2
|
UTSW |
18 |
44,974,442 (GRCm39) |
missense |
probably benign |
0.00 |
|
R9331:Ythdc2
|
UTSW |
18 |
44,970,499 (GRCm39) |
missense |
possibly damaging |
0.87 |
|
R9469:Ythdc2
|
UTSW |
18 |
45,019,383 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9634:Ythdc2
|
UTSW |
18 |
45,006,037 (GRCm39) |
missense |
probably benign |
|
|
| Predicted Primers |
PCR Primer
(F):5'- CAGTTTCTTCTAATTAGTCAAGAGGGG -3'
(R):5'- GCCTGTGACACACATTCAAAATAAAGG -3'
Sequencing Primer
(F):5'- TCAAGAGGGGGCTTTAAGTTTAAC -3'
(R):5'- AGAGTTTGCTTGGAAAAAGTCAC -3'
|
| Posted On |
2016-08-04 |
Incidental Mutation