Incidental Mutation 'R5827:Tdp2'
| ID |
450226 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Tdp2
|
| Ensembl Gene |
ENSMUSG00000035958 |
| Gene Name |
tyrosyl-DNA phosphodiesterase 2 |
| Synonyms |
D13Ertd656e, Ttrap |
| MMRRC Submission |
043218-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly essential
(E-score: 0.674)
|
| Stock # |
R5827 (G1)
|
| Quality Score |
165 |
|
Status
|
Not validated
|
| Chromosome |
13 |
| Chromosomal Location |
25015662-25026136 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 25015836 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Leucine to Proline
at position 41
(L41P)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000153301
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000006900]
[ENSMUST00000038039]
[ENSMUST00000223804]
[ENSMUST00000225138]
|
| AlphaFold |
Q9JJX7 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000006900
|
| SMART Domains |
Protein: ENSMUSP00000006900
Gene: ENSMUSG00000006717
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:4HBT
|
52 |
129 |
1.1e-19 |
PFAM |
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000038039
AA Change: L41P
PolyPhen 2
Score 0.777 (Sensitivity: 0.85; Specificity: 0.92)
|
| SMART Domains |
Protein: ENSMUSP00000035660
Gene: ENSMUSG00000035958
AA Change: L41P
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
9 |
30 |
N/A |
INTRINSIC |
|
Pfam:Exo_endo_phos
|
127 |
359 |
3.9e-20 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000130788
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000223804
AA Change: L41P
PolyPhen 2
Score 0.993 (Sensitivity: 0.70; Specificity: 0.97)
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000224542
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000224839
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000225138
AA Change: L41P
PolyPhen 2
Score 0.993 (Sensitivity: 0.70; Specificity: 0.97)
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000225490
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000226055
|
| Coding Region Coverage |
- 1x: 99.9%
- 3x: 99.6%
- 10x: 98.3%
- 20x: 95.2%
|
| Validation Efficiency |
|
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of a superfamily of divalent cation-dependent phosphodiesterases. The encoded protein associates with CD40, tumor necrosis factor (TNF) receptor-75 and TNF receptor associated factors (TRAFs), and inhibits nuclear factor-kappa-B activation. This protein has sequence and structural similarities with APE1 endonuclease, which is involved in both DNA repair and the activation of transcription factors. [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygous mutant mice carrying a gene trap insertion into intron 5 but subsequently shown to harbor a partial duplication of the wild-type allele at the ES cell level are born with a normal Mendelian distribution. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 38 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abca8b |
C |
A |
11: 109,868,639 (GRCm39) |
G175V |
probably damaging |
Het |
| Agl |
T |
C |
3: 116,574,703 (GRCm39) |
I34V |
probably damaging |
Het |
| Cavin4 |
A |
T |
4: 48,672,074 (GRCm39) |
D173V |
probably damaging |
Het |
| Chd9 |
A |
G |
8: 91,716,078 (GRCm39) |
D884G |
probably damaging |
Het |
| Col6a5 |
G |
A |
9: 105,805,319 (GRCm39) |
R1196* |
probably null |
Het |
| Disc1 |
T |
C |
8: 125,862,104 (GRCm39) |
L492P |
probably damaging |
Het |
| Dscam |
A |
G |
16: 96,451,191 (GRCm39) |
|
probably null |
Het |
| Fbxw4 |
T |
C |
19: 45,568,096 (GRCm39) |
T26A |
probably benign |
Het |
| H1f6 |
A |
G |
13: 23,880,185 (GRCm39) |
K113E |
possibly damaging |
Het |
| Klhl24 |
T |
A |
16: 19,938,871 (GRCm39) |
Y475* |
probably null |
Het |
| Map4k3 |
C |
T |
17: 80,900,712 (GRCm39) |
|
probably null |
Het |
| Mfsd6 |
T |
C |
1: 52,701,551 (GRCm39) |
E633G |
probably damaging |
Het |
| Mycn |
G |
A |
12: 12,989,794 (GRCm39) |
R201* |
probably null |
Het |
| Nek11 |
T |
C |
9: 105,191,944 (GRCm39) |
I155M |
probably damaging |
Het |
| Notch2 |
G |
A |
3: 97,980,178 (GRCm39) |
V231I |
possibly damaging |
Het |
| Npnt |
A |
C |
3: 132,612,536 (GRCm39) |
V187G |
possibly damaging |
Het |
| Nr1d2 |
C |
A |
14: 18,222,248 (GRCm38) |
V8L |
possibly damaging |
Het |
| Nup188 |
C |
T |
2: 30,229,859 (GRCm39) |
T1359I |
probably damaging |
Het |
| Or2m12 |
T |
A |
16: 19,105,182 (GRCm39) |
I104L |
probably benign |
Het |
| Or4k35 |
A |
T |
2: 111,100,266 (GRCm39) |
W149R |
probably damaging |
Het |
| Or5m11b |
C |
A |
2: 85,805,650 (GRCm39) |
P21Q |
probably benign |
Het |
| Or8g36 |
T |
A |
9: 39,422,354 (GRCm39) |
I221F |
probably damaging |
Het |
| P2rx2 |
C |
T |
5: 110,488,195 (GRCm39) |
R453Q |
probably benign |
Het |
| Pcdhb7 |
A |
G |
18: 37,475,077 (GRCm39) |
E71G |
probably benign |
Het |
| Pcdhb9 |
A |
T |
18: 37,535,011 (GRCm39) |
D335V |
possibly damaging |
Het |
| Pcsk9 |
C |
T |
4: 106,306,144 (GRCm39) |
G368R |
probably damaging |
Het |
| Ptgr2 |
G |
A |
12: 84,342,110 (GRCm39) |
|
probably null |
Het |
| Rhebl1 |
T |
A |
15: 98,776,151 (GRCm39) |
I168F |
probably damaging |
Het |
| Serpina3b |
A |
G |
12: 104,097,036 (GRCm39) |
T106A |
probably benign |
Het |
| Sh3pxd2b |
A |
G |
11: 32,372,422 (GRCm39) |
I530V |
probably benign |
Het |
| Skint10 |
T |
C |
4: 112,603,972 (GRCm39) |
T72A |
probably benign |
Het |
| Slx4 |
G |
T |
16: 3,819,148 (GRCm39) |
F8L |
possibly damaging |
Het |
| Tiam2 |
A |
G |
17: 3,498,764 (GRCm39) |
I847V |
probably benign |
Het |
| Tmem200c |
A |
G |
17: 69,149,004 (GRCm39) |
E529G |
probably benign |
Het |
| Tnpo1 |
T |
C |
13: 98,993,416 (GRCm39) |
D590G |
probably damaging |
Het |
| Ube3d |
T |
C |
9: 86,254,489 (GRCm39) |
T331A |
possibly damaging |
Het |
| Ugt1a2 |
T |
A |
1: 88,128,787 (GRCm39) |
S143R |
probably damaging |
Het |
| Zfp58 |
A |
T |
13: 67,639,412 (GRCm39) |
C360S |
probably damaging |
Het |
|
| Other mutations in Tdp2 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00775:Tdp2
|
APN |
13 |
25,024,521 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL01376:Tdp2
|
APN |
13 |
25,020,932 (GRCm39) |
splice site |
probably null |
|
|
IGL02346:Tdp2
|
APN |
13 |
25,025,335 (GRCm39) |
missense |
possibly damaging |
0.86 |
|
IGL02455:Tdp2
|
APN |
13 |
25,025,245 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R0008:Tdp2
|
UTSW |
13 |
25,025,333 (GRCm39) |
splice site |
probably null |
|
|
R0008:Tdp2
|
UTSW |
13 |
25,025,333 (GRCm39) |
splice site |
probably null |
|
|
R0164:Tdp2
|
UTSW |
13 |
25,022,222 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0164:Tdp2
|
UTSW |
13 |
25,022,222 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0179:Tdp2
|
UTSW |
13 |
25,024,431 (GRCm39) |
missense |
possibly damaging |
0.46 |
|
R1939:Tdp2
|
UTSW |
13 |
25,025,260 (GRCm39) |
missense |
probably benign |
0.07 |
|
R3807:Tdp2
|
UTSW |
13 |
25,015,776 (GRCm39) |
nonsense |
probably null |
|
|
R3955:Tdp2
|
UTSW |
13 |
25,020,082 (GRCm39) |
missense |
probably benign |
0.00 |
|
R4943:Tdp2
|
UTSW |
13 |
25,022,248 (GRCm39) |
missense |
probably benign |
0.02 |
|
R5044:Tdp2
|
UTSW |
13 |
25,015,809 (GRCm39) |
missense |
probably benign |
0.00 |
|
R5529:Tdp2
|
UTSW |
13 |
25,022,219 (GRCm39) |
nonsense |
probably null |
|
|
R6235:Tdp2
|
UTSW |
13 |
25,024,378 (GRCm39) |
nonsense |
probably null |
|
|
R6326:Tdp2
|
UTSW |
13 |
25,024,540 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7091:Tdp2
|
UTSW |
13 |
25,022,207 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7244:Tdp2
|
UTSW |
13 |
25,025,284 (GRCm39) |
missense |
probably benign |
0.02 |
|
R7341:Tdp2
|
UTSW |
13 |
25,016,059 (GRCm39) |
missense |
probably benign |
0.00 |
|
R8010:Tdp2
|
UTSW |
13 |
25,020,010 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9203:Tdp2
|
UTSW |
13 |
25,020,916 (GRCm39) |
nonsense |
probably null |
|
|
Z1177:Tdp2
|
UTSW |
13 |
25,025,234 (GRCm39) |
missense |
probably benign |
0.00 |
|
| Predicted Primers |
PCR Primer
(F):5'- ACGGGTTACCTTCACTCTTTAG -3'
(R):5'- CGCTCAGGGCTTTCTGAAAAG -3'
Sequencing Primer
(F):5'- CGGTCTTCTTGCCGGAAG -3'
(R):5'- CTTTCTGAAAAGCAAAGGCACAAG -3'
|
| Posted On |
2016-12-20 |
Incidental Mutation