Mutagenetix > Incidental Mutation

Incidental Mutation 'R6326:Tdp2'

510437

Institutional Source

Beutler Lab

Gene Symbol

Tdp2

Ensembl Gene

ENSMUSG00000035958

Gene Name

tyrosyl-DNA phosphodiesterase 2

Synonyms

D13Ertd656e, Ttrap

MMRRC Submission

044480-MU

Accession Numbers

Essential gene?

Possibly essential (E-score: 0.705) question?

Stock #

R6326 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

25015662-25026136 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 25024540 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glutamic Acid to Glycine at position 279 (E279G)

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 damaging
Transcript: ENSMUST00000038039
AA Change: E279G

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000035660
Gene: ENSMUSG00000035958
AA Change: E279G

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

0.5394

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.5%
20x: 98.3%

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: 79 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adamts17	A	T	7: 66,770,636 (GRCm39)	Y915F	probably benign	Het
Adap2	T	A	11: 80,045,848 (GRCm39)	F43I	probably damaging	Het
Adprs	A	T	4: 126,210,406 (GRCm39)	L358Q	possibly damaging	Het
Akap9	A	C	5: 4,012,061 (GRCm39)	Q921H	probably damaging	Het
Amigo2	A	G	15: 97,143,256 (GRCm39)	S389P	probably benign	Het
Atg2b	A	T	12: 105,627,351 (GRCm39)	C545*	probably null	Het
C2cd3	A	G	7: 100,065,635 (GRCm39)	E807G	probably benign	Het
Ccdc110	A	G	8: 46,395,078 (GRCm39)	E323G	probably damaging	Het
Cdk5rap2	T	A	4: 70,153,691 (GRCm39)	S1711C	probably damaging	Het
Cebpzos	T	G	17: 79,226,486 (GRCm39)	D39E	probably damaging	Het
Cenpe	A	G	3: 134,945,539 (GRCm39)	N1018D	probably benign	Het
Cfap68	T	G	9: 50,676,057 (GRCm39)	N87T	probably damaging	Het
Clspn	C	A	4: 126,459,532 (GRCm39)	H141Q	probably damaging	Het
Cluh	C	T	11: 74,557,068 (GRCm39)	A1010V	probably benign	Het
Col27a1	G	T	4: 63,242,678 (GRCm39)		probably benign	Het
Cpt2	T	C	4: 107,771,513 (GRCm39)	M61V	probably benign	Het
Ddr2	T	A	1: 169,814,709 (GRCm39)	H578L	probably damaging	Het
Dnah14	T	A	1: 181,611,121 (GRCm39)	I3749N	probably damaging	Het
Dnajc18	T	C	18: 35,813,978 (GRCm39)	T264A	possibly damaging	Het
Ecpas	T	A	4: 58,827,068 (GRCm39)	T1022S	probably benign	Het
Eml6	T	C	11: 29,769,066 (GRCm39)	N693S	probably damaging	Het
Ephx4	A	G	5: 107,553,977 (GRCm39)	E9G	probably damaging	Het
Eps15l1	G	A	8: 73,095,278 (GRCm39)	Q747*	probably null	Het
Flrt1	C	T	19: 7,073,974 (GRCm39)	S191N	probably damaging	Het
Gm5114	C	T	7: 39,057,579 (GRCm39)	R680H	probably benign	Het
Gm5431	T	C	11: 48,780,172 (GRCm39)	H250R	probably damaging	Het
Gm7233	T	C	14: 43,040,342 (GRCm39)	C198R	possibly damaging	Het
Herc2	C	G	7: 55,872,682 (GRCm39)	Q4407E	probably damaging	Het
Hmx3	C	G	7: 131,144,734 (GRCm39)		probably benign	Het
Hoxb7	C	A	11: 96,177,909 (GRCm39)	A119E	probably benign	Het
Ifi207	A	T	1: 173,557,532 (GRCm39)	M402K	probably benign	Het
Ints14	T	C	9: 64,871,719 (GRCm39)	V19A	probably benign	Het
Itgae	T	A	11: 73,022,519 (GRCm39)	N911K	possibly damaging	Het
Kif1a	T	C	1: 93,004,048 (GRCm39)	S145G	probably damaging	Het
Klhdc4	A	G	8: 122,531,793 (GRCm39)	W187R	probably damaging	Het
Krt1	A	T	15: 101,758,684 (GRCm39)	I160N	probably damaging	Het
Krt12	T	C	11: 99,307,745 (GRCm39)	T448A	probably benign	Het
Lcmt2	G	A	2: 120,969,938 (GRCm39)	R382*	probably null	Het
Map3k8	C	T	18: 4,340,651 (GRCm39)	S221N	probably damaging	Het
Med17	T	C	9: 15,190,854 (GRCm39)	D79G	probably benign	Het
Mlf1	A	T	3: 67,307,060 (GRCm39)	I257F	probably damaging	Het
Mov10l1	T	A	15: 88,879,098 (GRCm39)	F153I	probably damaging	Het
Msto1	A	C	3: 88,819,405 (GRCm39)	V149G	probably damaging	Het
Mybl1	T	C	1: 9,748,732 (GRCm39)		probably null	Het
Myoc	A	G	1: 162,476,580 (GRCm39)	Y428C	probably damaging	Het
Nin	A	G	12: 70,091,955 (GRCm39)	S785P	possibly damaging	Het
Oit3	A	T	10: 59,264,061 (GRCm39)	F358I	probably damaging	Het
Or5t15	C	T	2: 86,681,338 (GRCm39)	V235I	probably benign	Het
Or6c88	A	G	10: 129,406,571 (GRCm39)	T16A	possibly damaging	Het
Paip1	A	G	13: 119,566,753 (GRCm39)	N29S	probably benign	Het
Pcdhgb4	T	C	18: 37,855,509 (GRCm39)	S635P	probably benign	Het
Pcsk1	A	G	13: 75,280,298 (GRCm39)	N708D	possibly damaging	Het
Plch1	C	T	3: 63,688,811 (GRCm39)	W131*	probably null	Het
Prag1	A	T	8: 36,569,860 (GRCm39)	M148L	possibly damaging	Het
Ptch1	A	G	13: 63,691,359 (GRCm39)	L176P	probably damaging	Het
Ralgapa1	A	T	12: 55,793,931 (GRCm39)	V568D	probably damaging	Het
Rb1	A	T	14: 73,435,974 (GRCm39)	M897K	probably benign	Het
Resf1	T	A	6: 149,230,493 (GRCm39)	Y1180N	probably damaging	Het
Robo3	T	A	9: 37,338,323 (GRCm39)	Q386L	probably damaging	Het
Rtn4rl1	T	C	11: 75,156,828 (GRCm39)	V420A	possibly damaging	Het
Sall1	A	T	8: 89,756,896 (GRCm39)	N1069K	probably benign	Het
Sipa1l1	A	G	12: 82,419,242 (GRCm39)	E640G	probably damaging	Het
Slc22a2	C	A	17: 12,831,297 (GRCm39)	Y362*	probably null	Het
Slc5a9	T	C	4: 111,737,450 (GRCm39)	E603G	probably benign	Het
Slc6a17	A	T	3: 107,407,722 (GRCm39)	I83N	probably damaging	Het
Snx29	G	T	16: 11,221,430 (GRCm39)	M285I	probably benign	Het
Spata2	T	C	2: 167,326,094 (GRCm39)	T242A	possibly damaging	Het
Stard13	A	G	5: 150,970,384 (GRCm39)	L733P	possibly damaging	Het
Svep1	A	G	4: 58,073,045 (GRCm39)	V2088A	possibly damaging	Het
Tnfrsf8	T	G	4: 144,995,794 (GRCm39)	I422L	probably damaging	Het
Tpk1	T	A	6: 43,323,736 (GRCm39)	T189S	possibly damaging	Het
Trhde	A	T	10: 114,403,129 (GRCm39)	M498K	probably damaging	Het
Trim35	T	A	14: 66,540,653 (GRCm39)	H168Q	possibly damaging	Het
Tubb5	T	C	17: 36,147,347 (GRCm39)		probably benign	Het
Tut4	C	T	4: 108,336,177 (GRCm39)	T6I	probably benign	Het
Vmn1r181	G	A	7: 23,684,183 (GRCm39)	R216Q	probably benign	Het
Vmn2r77	G	A	7: 86,451,031 (GRCm39)	G306R	probably benign	Het
Xkr4	C	T	1: 3,741,261 (GRCm39)	R104H	possibly damaging	Het
Zfp398	T	C	6: 47,843,355 (GRCm39)	I337T	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
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
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'- GTCAGTGGCCAGTTCAACTG -3'
(R):5'- CAGGGATGCTACAAATACCCTC -3'

Sequencing Primer
(F):5'- CAGTGGCCAGTTCAACTGTAATTTC -3'
(R):5'- GAGGATTTCTCCTAATAGCTT -3'

Posted On

2018-04-02