Incidental Mutation 'R7244:Tdp2'
ID |
563426 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Tdp2
|
Ensembl Gene |
ENSMUSG00000035958 |
Gene Name |
tyrosyl-DNA phosphodiesterase 2 |
Synonyms |
D13Ertd656e, Ttrap |
MMRRC Submission |
045308-MU
|
Accession Numbers |
|
Essential gene? |
Possibly essential
(E-score: 0.705)
|
Stock # |
R7244 (G1)
|
Quality Score |
225.009 |
Status
|
Validated
|
Chromosome |
13 |
Chromosomal Location |
25015662-25026136 bp(+) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
A to G
at 25025284 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Aspartic acid to Glycine
at position 351
(D351G)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000035660
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000006893]
[ENSMUST00000038039]
[ENSMUST00000141572]
[ENSMUST00000225138]
|
AlphaFold |
Q9JJX7 |
PDB Structure |
Mus Musculus Tdp2 Bound to dAMP and Mg2+ [X-RAY DIFFRACTION]
Mus Musculus Tdp2-DNA Substrate Analog (5'-6-aminohexanol) Complex [X-RAY DIFFRACTION]
Mus Musculus Tdp2 reaction product (5'-phosphorylated DNA)-Mg2+ complex at 1.5 Angstroms resolution [X-RAY DIFFRACTION]
Mus Musculus Tdp2 excluded ssDNA complex [X-RAY DIFFRACTION]
Mus Musculus Tdp2 reaction product complex with 5'-phosphorylated RNA/DNA, glycerol, and Mg2+ [X-RAY DIFFRACTION]
|
Predicted Effect |
probably benign
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: D351G
PolyPhen 2
Score 0.017 (Sensitivity: 0.95; Specificity: 0.80)
|
SMART Domains |
Protein: ENSMUSP00000035660 Gene: ENSMUSG00000035958 AA Change: D351G
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 |
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 |
probably benign
Transcript: ENSMUST00000225138
|
Coding Region Coverage |
- 1x: 100.0%
- 3x: 99.9%
- 10x: 99.7%
- 20x: 98.9%
|
Validation Efficiency |
96% (45/47) |
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: 46 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Adgrb3 |
A |
G |
1: 25,170,350 (GRCm39) |
F983L |
probably damaging |
Het |
Cc2d1b |
T |
A |
4: 108,486,799 (GRCm39) |
M632K |
probably benign |
Het |
Cdyl2 |
G |
A |
8: 117,301,999 (GRCm39) |
R461* |
probably null |
Het |
Cfap57 |
G |
A |
4: 118,411,997 (GRCm39) |
Q1216* |
probably null |
Het |
Chd1l |
A |
T |
3: 97,505,066 (GRCm39) |
V167E |
probably damaging |
Het |
Col6a1 |
C |
A |
10: 76,553,242 (GRCm39) |
G391* |
probably null |
Het |
Ctsc |
C |
A |
7: 87,951,430 (GRCm39) |
Q226K |
probably benign |
Het |
Cyp2c54 |
A |
G |
19: 40,035,953 (GRCm39) |
V319A |
probably damaging |
Het |
Dnah7b |
T |
C |
1: 46,316,303 (GRCm39) |
S3139P |
probably damaging |
Het |
Edrf1 |
T |
C |
7: 133,256,079 (GRCm39) |
S643P |
probably benign |
Het |
Fam186a |
A |
T |
15: 99,844,273 (GRCm39) |
V657D |
unknown |
Het |
Fkbp11 |
A |
G |
15: 98,626,073 (GRCm39) |
|
probably benign |
Het |
Fsip2 |
G |
A |
2: 82,823,607 (GRCm39) |
A6447T |
possibly damaging |
Het |
H2-T9 |
C |
A |
17: 36,438,496 (GRCm39) |
|
probably null |
Het |
Hydin |
A |
G |
8: 111,276,307 (GRCm39) |
D3017G |
probably damaging |
Het |
Ifi205 |
G |
A |
1: 173,845,210 (GRCm39) |
Q191* |
probably null |
Het |
Mbd4 |
C |
T |
6: 115,821,564 (GRCm39) |
D484N |
probably benign |
Het |
Med24 |
C |
T |
11: 98,605,223 (GRCm39) |
|
probably null |
Het |
Mis18bp1 |
T |
C |
12: 65,208,404 (GRCm39) |
N103S |
probably damaging |
Het |
Mmd2 |
T |
C |
5: 142,550,587 (GRCm39) |
H217R |
probably damaging |
Het |
Mn1 |
C |
T |
5: 111,566,699 (GRCm39) |
T223M |
possibly damaging |
Het |
Ms4a4a |
A |
G |
19: 11,358,794 (GRCm39) |
Y84C |
probably damaging |
Het |
Mup5 |
A |
T |
4: 61,749,818 (GRCm39) |
|
probably null |
Het |
Mybl2 |
C |
T |
2: 162,924,605 (GRCm39) |
P658S |
probably benign |
Het |
Mycbp2 |
C |
A |
14: 103,446,345 (GRCm39) |
V1828L |
probably damaging |
Het |
Myh15 |
T |
C |
16: 49,017,149 (GRCm39) |
Y1887H |
probably damaging |
Het |
Nadk2 |
A |
G |
15: 9,083,271 (GRCm39) |
|
probably null |
Het |
Nsd3 |
A |
G |
8: 26,156,055 (GRCm39) |
N541D |
probably damaging |
Het |
Or52e8b |
A |
G |
7: 104,674,148 (GRCm39) |
V13A |
probably benign |
Het |
Or52i2 |
G |
T |
7: 102,319,046 (GRCm39) |
|
probably benign |
Het |
Oxa1l |
A |
T |
14: 54,598,312 (GRCm39) |
M1L |
probably benign |
Het |
Pcdha11 |
A |
T |
18: 37,144,421 (GRCm39) |
R171* |
probably null |
Het |
Pkd1l1 |
A |
T |
11: 8,821,771 (GRCm39) |
V1641E |
|
Het |
Pramel28 |
A |
T |
4: 143,692,455 (GRCm39) |
M182K |
probably benign |
Het |
Prom1 |
T |
A |
5: 44,178,242 (GRCm39) |
I497L |
probably benign |
Het |
Rasgef1b |
T |
C |
5: 99,706,753 (GRCm39) |
K41E |
possibly damaging |
Het |
Rasgrf1 |
T |
C |
9: 89,876,810 (GRCm39) |
F725S |
probably damaging |
Het |
Ryr2 |
T |
A |
13: 11,612,032 (GRCm39) |
S3962C |
probably damaging |
Het |
Sema5b |
A |
T |
16: 35,480,915 (GRCm39) |
T829S |
probably benign |
Het |
Tet3 |
A |
T |
6: 83,347,603 (GRCm39) |
D1130E |
probably damaging |
Het |
Tg |
T |
C |
15: 66,612,563 (GRCm39) |
C1993R |
probably damaging |
Het |
Tll1 |
T |
C |
8: 64,478,222 (GRCm39) |
I844V |
probably benign |
Het |
Ttll13 |
A |
C |
7: 79,903,911 (GRCm39) |
K280Q |
probably damaging |
Het |
Vmn2r109 |
A |
G |
17: 20,760,945 (GRCm39) |
V804A |
possibly damaging |
Het |
Vps13c |
T |
C |
9: 67,797,086 (GRCm39) |
V491A |
probably benign |
Het |
Xpo5 |
G |
T |
17: 46,525,551 (GRCm39) |
G233C |
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 |
|
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 |
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'- GCCAGGTTATCAAATGTGGTGG -3'
(R):5'- GCTTTTGCTGTAGTAATCATCCAG -3'
Sequencing Primer
(F):5'- ACCTGACAACGTTTTTGATGC -3'
(R):5'- TCCTGAAAGGTTGAGACC -3'
|
Posted On |
2019-06-26 |