Incidental Mutation 'R0008:Tdp2'
| ID |
7999 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Tdp2
|
| Ensembl Gene |
ENSMUSG00000035958 |
| Gene Name |
tyrosyl-DNA phosphodiesterase 2 |
| Synonyms |
D13Ertd656e, Ttrap |
| MMRRC Submission |
038303-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly essential
(E-score: 0.705)
|
| Stock # |
R0008 (G1)
|
| Quality Score |
|
|
Status
|
Validated
|
| Chromosome |
13 |
| Chromosomal Location |
25015662-25026136 bp(+) (GRCm39) |
| Type of Mutation |
splice site |
| DNA Base Change (assembly) |
T to G
at 25025333 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000006893
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000006893]
[ENSMUST00000038039]
[ENSMUST00000141572]
[ENSMUST00000225138]
|
| AlphaFold |
Q9JJX7 |
| Predicted Effect |
probably null
Transcript: ENSMUST00000006893
|
| SMART Domains |
Protein: ENSMUSP00000006893
Gene: ENSMUSG00000006711
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
22 |
N/A |
INTRINSIC |
|
Blast:MANEC
|
23 |
102 |
3e-44 |
BLAST |
|
low complexity region
|
236 |
270 |
N/A |
INTRINSIC |
|
FN3
|
332 |
427 |
3.43e1 |
SMART |
|
PKD
|
345 |
436 |
3.96e0 |
SMART |
|
FN3
|
435 |
521 |
3.08e1 |
SMART |
|
PKD
|
444 |
533 |
7.12e-10 |
SMART |
|
PKD
|
539 |
629 |
1.46e-6 |
SMART |
|
PKD
|
630 |
723 |
6.75e-11 |
SMART |
|
FN3
|
634 |
711 |
5.1e1 |
SMART |
|
FN3
|
728 |
808 |
9.15e1 |
SMART |
|
PKD
|
729 |
820 |
4.38e-10 |
SMART |
|
transmembrane domain
|
965 |
987 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000038039
AA Change: N367K
PolyPhen 2
Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)
|
| SMART Domains |
Protein: ENSMUSP00000035660
Gene: ENSMUSG00000035958
AA Change: N367K
| 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 benign
Transcript: ENSMUST00000141572
|
| SMART Domains |
Protein: ENSMUSP00000116004
Gene: ENSMUSG00000006711
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
22 |
N/A |
INTRINSIC |
|
Blast:MANEC
|
23 |
102 |
2e-44 |
BLAST |
|
low complexity region
|
236 |
270 |
N/A |
INTRINSIC |
|
FN3
|
332 |
427 |
3.43e1 |
SMART |
|
PKD
|
345 |
436 |
3.96e0 |
SMART |
|
FN3
|
435 |
521 |
3.08e1 |
SMART |
|
PKD
|
444 |
533 |
7.12e-10 |
SMART |
|
PKD
|
539 |
629 |
1.46e-6 |
SMART |
|
PKD
|
630 |
723 |
6.75e-11 |
SMART |
|
FN3
|
634 |
711 |
5.1e1 |
SMART |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000224542
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000225138
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000225490
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000226055
|
| Meta Mutation Damage Score |
0.3537 |
| Coding Region Coverage |
- 1x: 81.0%
- 3x: 72.4%
- 10x: 49.2%
- 20x: 28.4%
|
| Validation Efficiency |
90% (82/91) |
| 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 |
|---|
| 4930579F01Rik |
T |
C |
3: 137,882,346 (GRCm39) |
K118R |
possibly damaging |
Het |
| Afap1l1 |
A |
G |
18: 61,889,976 (GRCm39) |
S87P |
probably benign |
Het |
| Ankrd27 |
A |
G |
7: 35,303,125 (GRCm39) |
K196R |
probably benign |
Het |
| Arrdc3 |
T |
A |
13: 81,039,194 (GRCm39) |
I75N |
probably damaging |
Het |
| Calcrl |
T |
C |
2: 84,203,618 (GRCm39) |
D54G |
probably benign |
Het |
| Cnot1 |
G |
T |
8: 96,487,969 (GRCm39) |
D562E |
probably damaging |
Het |
| Cp |
T |
A |
3: 20,022,287 (GRCm39) |
Y230N |
probably damaging |
Het |
| Dclre1c |
T |
C |
2: 3,439,032 (GRCm39) |
V64A |
probably damaging |
Het |
| Fat2 |
A |
T |
11: 55,202,075 (GRCm39) |
L333H |
probably damaging |
Het |
| Hoxc11 |
T |
C |
15: 102,863,397 (GRCm39) |
V146A |
probably damaging |
Het |
| Il11 |
T |
C |
7: 4,776,658 (GRCm39) |
S111G |
probably benign |
Het |
| Ist1 |
A |
T |
8: 110,403,418 (GRCm39) |
I273K |
probably benign |
Het |
| Lrp2 |
T |
A |
2: 69,346,895 (GRCm39) |
N784Y |
probably benign |
Het |
| Lrp6 |
T |
C |
6: 134,462,716 (GRCm39) |
E648G |
probably damaging |
Het |
| Mtbp |
T |
A |
15: 55,449,889 (GRCm39) |
|
probably benign |
Het |
| Nat9 |
A |
T |
11: 115,075,941 (GRCm39) |
Y27N |
probably damaging |
Het |
| Nipsnap3b |
T |
A |
4: 53,015,112 (GRCm39) |
L53Q |
probably damaging |
Het |
| Nlrp3 |
A |
T |
11: 59,449,274 (GRCm39) |
H852L |
probably benign |
Het |
| Pax9 |
A |
G |
12: 56,756,528 (GRCm39) |
T289A |
probably benign |
Het |
| Pcyt2 |
A |
T |
11: 120,506,695 (GRCm39) |
I53N |
possibly damaging |
Het |
| Pdzph1 |
T |
A |
17: 59,229,756 (GRCm39) |
|
probably benign |
Het |
| Plekhm2 |
C |
T |
4: 141,369,704 (GRCm39) |
|
probably benign |
Het |
| Ppt1 |
T |
C |
4: 122,742,216 (GRCm39) |
|
probably benign |
Het |
| Prep |
T |
C |
10: 44,991,174 (GRCm39) |
V280A |
probably benign |
Het |
| Proser3 |
G |
A |
7: 30,239,563 (GRCm39) |
R514C |
probably damaging |
Het |
| Rbm45 |
T |
C |
2: 76,208,742 (GRCm39) |
Y293H |
probably damaging |
Het |
| Sdk2 |
A |
G |
11: 113,747,581 (GRCm39) |
L643P |
probably damaging |
Het |
| Slc1a1 |
G |
A |
19: 28,878,884 (GRCm39) |
G208S |
probably benign |
Het |
| Slc35b4 |
A |
T |
6: 34,135,452 (GRCm39) |
Y287N |
probably damaging |
Het |
| Srgap2 |
T |
C |
1: 131,283,302 (GRCm39) |
T260A |
probably damaging |
Het |
| Taf5 |
A |
G |
19: 47,064,301 (GRCm39) |
S415G |
possibly damaging |
Het |
| Tnrc6a |
G |
A |
7: 122,769,617 (GRCm39) |
R469H |
probably benign |
Het |
| Tox |
T |
A |
4: 6,842,411 (GRCm39) |
M40L |
probably benign |
Het |
| Trib2 |
A |
T |
12: 15,859,930 (GRCm39) |
H110Q |
probably benign |
Het |
| Trpa1 |
A |
G |
1: 14,973,439 (GRCm39) |
I293T |
possibly damaging |
Het |
| Wdr93 |
A |
G |
7: 79,408,221 (GRCm39) |
E234G |
probably damaging |
Het |
| Zfp385b |
A |
T |
2: 77,246,291 (GRCm39) |
S245R |
probably benign |
Het |
| Zfyve9 |
T |
A |
4: 108,575,902 (GRCm39) |
E393V |
possibly 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 |
|
|
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 |
|
|
R5827:Tdp2
|
UTSW |
13 |
25,015,836 (GRCm39) |
missense |
probably damaging |
0.99 |
|
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 |
|
| Posted On |
2012-11-20 |
Incidental Mutation