Mutagenetix > Incidental Mutation

Incidental Mutation 'R0179:Tdp2'

23064

Institutional Source

Beutler Lab

Gene Symbol

Tdp2

Ensembl Gene

ENSMUSG00000035958

Gene Name

tyrosyl-DNA phosphodiesterase 2

Synonyms

D13Ertd656e, Ttrap

MMRRC Submission

038447-MU

Accession Numbers

Essential gene?

Possibly essential (E-score: 0.674) question?

Stock #

R0179 (G1)

Quality Score

225

Status

Validated (trace)

Chromosome

Chromosomal Location

25015662-25026136 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 25024431 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Histidine to Tyrosine at position 243 (H243Y)

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

possibly damaging
Transcript: ENSMUST00000038039
AA Change: H243Y

PolyPhen 2 Score 0.461 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000035660
Gene: ENSMUSG00000035958
AA Change: H243Y

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

0.1265

Coding Region Coverage

1x: 99.1%
3x: 98.4%
10x: 96.8%
20x: 94.1%

Validation Efficiency

98% (81/83)

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: 80 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adamts1	C	T	16: 85,592,353 (GRCm39)	S948N	probably benign	Het
Adck1	A	T	12: 88,425,942 (GRCm39)	M457L	possibly damaging	Het
Adprm	A	T	11: 66,929,051 (GRCm39)	H313Q	possibly damaging	Het
Adss1	T	C	12: 112,598,703 (GRCm39)	I104T	probably benign	Het
Agxt2	A	C	15: 10,399,134 (GRCm39)	Q435P	possibly damaging	Het
Amotl1	G	A	9: 14,460,069 (GRCm39)	A890V	probably benign	Het
Ankrd50	A	G	3: 38,509,463 (GRCm39)	V968A	possibly damaging	Het
Brf2	T	C	8: 27,615,896 (GRCm39)	D163G	possibly damaging	Het
Cd226	C	A	18: 89,225,263 (GRCm39)	N53K	probably benign	Het
Cdc42ep2	T	C	19: 5,968,636 (GRCm39)	D23G	probably benign	Het
Cdc7	T	C	5: 107,112,905 (GRCm39)	S8P	probably benign	Het
Cdh8	C	T	8: 99,838,344 (GRCm39)	E499K	possibly damaging	Het
Chd7	T	A	4: 8,862,516 (GRCm39)	F2534L	probably benign	Het
Ckb	T	C	12: 111,636,610 (GRCm39)	T255A	probably benign	Het
Cntnap5c	G	T	17: 58,076,620 (GRCm39)	W19L	probably benign	Het
Cntrl	A	G	2: 35,057,871 (GRCm39)	E1854G	probably benign	Het
Colec12	C	T	18: 9,858,921 (GRCm39)	P568L	unknown	Het
Cop1	A	G	1: 159,077,636 (GRCm39)	D157G	probably benign	Het
Csf2rb	A	C	15: 78,220,572 (GRCm39)	Q38P	possibly damaging	Het
Ctla2b	T	C	13: 61,044,107 (GRCm39)	D52G	possibly damaging	Het
Dcaf7	A	T	11: 105,942,623 (GRCm39)	D190V	probably damaging	Het
Depdc5	T	A	5: 33,058,918 (GRCm39)		probably benign	Het
Dgkq	A	G	5: 108,806,066 (GRCm39)		probably benign	Het
Dhrs2	A	G	14: 55,477,933 (GRCm39)	T222A	probably damaging	Het
Dock1	G	A	7: 134,700,566 (GRCm39)	D1109N	probably damaging	Het
E4f1	G	C	17: 24,670,411 (GRCm39)	T92S	possibly damaging	Het
Ep400	A	T	5: 110,816,515 (GRCm39)	S2669T	probably damaging	Het
Eprs1	T	G	1: 185,145,744 (GRCm39)	D1184E	probably benign	Het
Fpr-rs4	A	T	17: 18,242,289 (GRCm39)	K99*	probably null	Het
Fzr1	A	T	10: 81,204,904 (GRCm39)		probably benign	Het
Gcc2	C	T	10: 58,112,472 (GRCm39)	R1001C	probably benign	Het
Gm4884	A	G	7: 40,693,252 (GRCm39)	D407G	probably benign	Het
Golga4	A	T	9: 118,389,808 (GRCm39)		probably null	Het
Gp2	T	G	7: 119,051,540 (GRCm39)	D225A	possibly damaging	Het
Gramd1a	T	A	7: 30,841,843 (GRCm39)	T120S	probably damaging	Het
Hbb-bh2	T	A	7: 103,488,434 (GRCm39)	N121I	probably benign	Het
Htr6	A	T	4: 138,789,437 (GRCm39)	L276Q	probably damaging	Het
Itga9	A	T	9: 118,490,454 (GRCm39)	I262F	probably benign	Het
Lamc3	A	G	2: 31,805,096 (GRCm39)		probably benign	Het
Large1	T	C	8: 73,825,474 (GRCm39)	N200S	probably benign	Het
Lct	C	T	1: 128,255,422 (GRCm39)	V207I	probably benign	Het
Marf1	C	A	16: 13,969,040 (GRCm39)	L144F	probably damaging	Het
Morc2b	A	T	17: 33,355,956 (GRCm39)	Y605*	probably null	Het
Mtus1	G	T	8: 41,455,398 (GRCm39)	L87I	possibly damaging	Het
Muc2	A	G	7: 141,302,708 (GRCm39)	Y17C	probably damaging	Het
Myf5	T	C	10: 107,321,779 (GRCm39)	D5G	possibly damaging	Het
Nasp	C	T	4: 116,459,354 (GRCm39)	V375M	probably damaging	Het
Nr1h2	A	T	7: 44,201,689 (GRCm39)		probably null	Het
Nrg2	T	C	18: 36,155,468 (GRCm39)	Q447R	probably benign	Het
Ntn5	G	A	7: 45,335,737 (GRCm39)	G56D	probably damaging	Het
Oasl2	A	G	5: 115,048,973 (GRCm39)	R138G	probably benign	Het
Or4c29	A	T	2: 88,740,237 (GRCm39)	C167S	possibly damaging	Het
Or5b124	T	A	19: 13,610,504 (GRCm39)	F10I	probably damaging	Het
Or9k7	T	C	10: 130,046,207 (GRCm39)	Y264C	probably damaging	Het
Pcdhb5	G	A	18: 37,455,612 (GRCm39)	G664D	probably damaging	Het
Ppp1r15a	T	C	7: 45,174,424 (GRCm39)	E128G	probably damaging	Het
Prpf19	T	C	19: 10,875,172 (GRCm39)		probably benign	Het
Ptpn3	T	A	4: 57,270,118 (GRCm39)	T15S	probably benign	Het
R3hdm2	G	A	10: 127,330,975 (GRCm39)	C818Y	probably damaging	Het
Rad51d	A	G	11: 82,780,824 (GRCm39)	V39A	possibly damaging	Het
Rptor	A	T	11: 119,763,193 (GRCm39)	T926S	probably benign	Het
Rwdd4a	G	A	8: 47,995,742 (GRCm39)	D41N	probably damaging	Het
Sephs1	A	G	2: 4,904,371 (GRCm39)	T250A	probably benign	Het
Spata31g1	T	C	4: 42,972,214 (GRCm39)	S516P	probably benign	Het
Ssbp3	T	C	4: 106,903,585 (GRCm39)	S334P	probably damaging	Het
Suco	A	G	1: 161,703,874 (GRCm39)		probably benign	Het
Synj1	T	C	16: 90,761,519 (GRCm39)	K649R	possibly damaging	Het
Tinag	A	G	9: 76,904,164 (GRCm39)		probably benign	Het
Trerf1	T	C	17: 47,627,588 (GRCm39)		noncoding transcript	Het
Trip10	T	C	17: 57,569,349 (GRCm39)		probably benign	Het
Tsen54	A	T	11: 115,712,856 (GRCm39)	S131C	probably damaging	Het
Unc5c	A	T	3: 141,523,828 (GRCm39)	R794*	probably null	Het
Vmn2r59	A	T	7: 41,696,432 (GRCm39)	Y103*	probably null	Het
Washc5	A	G	15: 59,224,379 (GRCm39)	V460A	probably benign	Het
Wdr87-ps	A	G	7: 29,235,365 (GRCm39)		noncoding transcript	Het
Whamm	A	G	7: 81,243,763 (GRCm39)	T358A	probably benign	Het
Xlr4b	C	T	X: 72,262,277 (GRCm39)		probably benign	Het
Zbbx	C	T	3: 74,992,869 (GRCm39)		probably benign	Het
Zdhhc23	G	A	16: 43,794,066 (GRCm39)	P203S	probably benign	Het
Zfp27	T	A	7: 29,595,850 (GRCm39)	E38D	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
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

Predicted Primers

PCR Primer
(F):5'- GCACCTTCTGCTCTTCATTTAGGAACA -3'
(R):5'- CAGGGATGCTACAAATACCCTCAACTTT -3'

Sequencing Primer
(F):5'- TTAGTGGTCAGTGGCCAGTT -3'
(R):5'- AGGATTTCTCCTAATAGCTTTTGTGC -3'

Posted On

2013-04-16