Mutagenetix > Incidental Mutation

Incidental Mutation 'IGL02455:Tdp2'

293812

Institutional Source

Australian Phenomics Network (link to record)

Gene Symbol

Tdp2

Ensembl Gene

ENSMUSG00000035958

Gene Name

tyrosyl-DNA phosphodiesterase 2

Synonyms

D13Ertd656e, Ttrap

Accession Numbers

Essential gene?

Possibly essential (E-score: 0.705) question?

Stock #

IGL02455

Quality Score

Status

Chromosome

Chromosomal Location

25015662-25026136 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 25025245 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Asparagine at position 338 (I338N)

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: I338N

PolyPhen 2 Score 0.973 (Sensitivity: 0.76; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000035660
Gene: ENSMUSG00000035958
AA Change: I338N

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

Coding Region Coverage

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: 49 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcf1	A	G	17: 36,271,021 (GRCm39)	V479A	probably damaging	Het
Adam18	T	C	8: 25,141,864 (GRCm39)	D235G	probably damaging	Het
Cdh22	T	C	2: 164,984,175 (GRCm39)	N359S	possibly damaging	Het
Cebpz	G	T	17: 79,242,465 (GRCm39)	N396K	probably benign	Het
Celsr3	T	A	9: 108,720,092 (GRCm39)	W2493R	probably benign	Het
Clca3a2	C	T	3: 144,787,172 (GRCm39)	V500M	probably benign	Het
Clec4a4	A	C	6: 122,990,739 (GRCm39)	N160H	possibly damaging	Het
Crb2	T	C	2: 37,684,576 (GRCm39)	S1139P	possibly damaging	Het
Dnah8	T	C	17: 30,891,308 (GRCm39)	I771T	probably damaging	Het
Etfbkmt	C	T	6: 149,048,724 (GRCm39)	A121V	probably damaging	Het
Fat4	T	A	3: 39,005,280 (GRCm39)	L1893Q	possibly damaging	Het
Fbxw13	A	T	9: 109,012,255 (GRCm39)	S188T	probably benign	Het
Fign	T	C	2: 63,810,841 (GRCm39)	D143G	probably benign	Het
Foxj3	C	A	4: 119,477,434 (GRCm39)	H381N	unknown	Het
Gpr158	A	T	2: 21,373,511 (GRCm39)	T149S	probably benign	Het
Ift74	C	T	4: 94,524,068 (GRCm39)	Q195*	probably null	Het
Kif2c	C	A	4: 117,029,551 (GRCm39)	M143I	probably benign	Het
Kmt2b	A	G	7: 30,278,303 (GRCm39)		probably null	Het
Krt84	C	T	15: 101,434,170 (GRCm39)	R599H	unknown	Het
Ly6g6f	C	T	17: 35,301,866 (GRCm39)	R196H	possibly damaging	Het
Map4	C	A	9: 109,828,901 (GRCm39)	N95K	probably benign	Het
Mrgprx3-ps	T	A	7: 46,959,263 (GRCm39)		noncoding transcript	Het
Mroh9	T	C	1: 162,903,149 (GRCm39)	M85V	probably benign	Het
Npffr2	T	C	5: 89,715,994 (GRCm39)	I107T	probably damaging	Het
Nrcam	T	C	12: 44,617,313 (GRCm39)	V737A	probably damaging	Het
Oprm1	A	G	10: 6,780,219 (GRCm39)	T294A	probably damaging	Het
Or10d5j	T	C	9: 39,868,198 (GRCm39)	E11G	probably damaging	Het
Or5w17	A	T	2: 87,583,927 (GRCm39)	S137T	possibly damaging	Het
Or7g32	C	T	9: 19,408,559 (GRCm39)	Q172*	probably null	Het
Parvg	A	G	15: 84,214,283 (GRCm39)	R156G	possibly damaging	Het
Pclo	T	C	5: 14,590,189 (GRCm39)	S830P	unknown	Het
Pde11a	T	C	2: 75,988,737 (GRCm39)	D468G	possibly damaging	Het
Peak1	A	T	9: 56,134,757 (GRCm39)	S195T	possibly damaging	Het
Pkhd1	A	G	1: 20,434,425 (GRCm39)	Y2338H	probably damaging	Het
Ppp1r1b	A	T	11: 98,241,395 (GRCm39)	I28F	probably damaging	Het
Prpf8	A	G	11: 75,400,084 (GRCm39)	Y2326C	probably benign	Het
Psmd1	T	A	1: 86,006,302 (GRCm39)	L223I	probably damaging	Het
Runx3	T	A	4: 134,902,841 (GRCm39)	Y310N	probably damaging	Het
Secisbp2l	C	T	2: 125,615,398 (GRCm39)	D76N	possibly damaging	Het
Slfn4	A	T	11: 83,077,584 (GRCm39)	N124I	probably damaging	Het
Spata13	G	A	14: 60,944,163 (GRCm39)	V519I	probably benign	Het
Ssh3	C	T	19: 4,314,460 (GRCm39)	E365K	probably damaging	Het
Strc	A	G	2: 121,206,272 (GRCm39)		probably benign	Het
Vmn1r13	A	T	6: 57,187,457 (GRCm39)	R205S	probably damaging	Het
Wdr19	G	T	5: 65,382,102 (GRCm39)	A441S	probably benign	Het
Ylpm1	A	G	12: 85,077,037 (GRCm39)	D796G	probably damaging	Het
Zbtb11	T	C	16: 55,821,038 (GRCm39)	S712P	probably damaging	Het
Zcchc14	A	G	8: 122,333,009 (GRCm39)		probably benign	Het
Zfp608	T	G	18: 55,032,405 (GRCm39)	S512R	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
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
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

2015-04-16