Mutagenetix > Incidental Mutation

Incidental Mutation 'R0008:Tdp1'

58248

Institutional Source

Beutler Lab

Gene Symbol

Tdp1

Ensembl Gene

ENSMUSG00000021177

Gene Name

tyrosyl-DNA phosphodiesterase 1

Synonyms

4921509N21Rik, SCAN1, 2810481F14Rik, E430034L06Rik, Gm40556

MMRRC Submission

038303-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.215) question?

Stock #

R0008 (G1)

Quality Score

200

Status

Validated

Chromosome

Chromosomal Location

99850776-99921478 bp(+) (GRCm39)

Type of Mutation

splice site

DNA Base Change (assembly)

C to T at 99921217 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000118656 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000021594] [ENSMUST00000153627]

AlphaFold

no structure available at present

Predicted Effect

probably benign
Transcript: ENSMUST00000021594

SMART Domains

Protein: ENSMUSP00000021594
Gene: ENSMUSG00000021177

Domain	Start	End	E-Value	Type
low complexity region	13	32	N/A	INTRINSIC
Pfam:Tyr-DNA_phospho	164	583	2.7e-142	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000128739

Predicted Effect

probably benign
Transcript: ENSMUST00000153627

SMART Domains

Protein: ENSMUSP00000118656
Gene: ENSMUSG00000021177

Domain	Start	End	E-Value	Type
low complexity region	13	32	N/A	INTRINSIC
Pfam:Tyr-DNA_phospho	166	583	2.4e-142	PFAM

Coding Region Coverage

1x: 99.4%
3x: 98.8%
10x: 97.4%
20x: 94.8%

Validation Efficiency

98% (109/111)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is involved in repairing stalled topoisomerase I-DNA complexes by catalyzing the hydrolysis of the phosphodiester bond between the tyrosine residue of topoisomerase I and the 3-prime phosphate of DNA. This protein may also remove glycolate from single-stranded DNA containing 3-prime phosphoglycolate, suggesting a role in repair of free-radical mediated DNA double-strand breaks. This gene is a member of the phospholipase D family and contains two PLD phosphodiesterase domains. Mutations in this gene are associated with the disease spinocerebellar ataxia with axonal neuropathy (SCAN1). [provided by RefSeq, Aug 2016]
PHENOTYPE: Mice homozygous for a null allele exhibit defective single strand DNA repair in neurons, decreased cerebellum size and increased sensitivity to topotecan. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 98 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930579F01Rik	T	C	3: 137,882,346 (GRCm39)	K118R	possibly damaging	Het
Adtrp	T	C	13: 41,920,941 (GRCm39)	T88A	probably 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
Apoe	G	A	7: 19,431,005 (GRCm39)	T79M	probably damaging	Het
Arrdc3	T	A	13: 81,032,011 (GRCm39)	Y81*	probably null	Het
Arrdc3	T	A	13: 81,039,194 (GRCm39)	I75N	probably damaging	Het
Asah2	T	A	19: 31,981,131 (GRCm39)	K629*	probably null	Het
Ass1	A	T	2: 31,404,831 (GRCm39)	N371Y	probably damaging	Het
C130074G19Rik	A	G	1: 184,615,119 (GRCm39)	S24P	probably benign	Het
C87436	A	G	6: 86,423,265 (GRCm39)		probably benign	Het
Calcrl	T	C	2: 84,203,618 (GRCm39)	D54G	probably benign	Het
Clcn2	T	C	16: 20,529,140 (GRCm39)	N367S	probably null	Het
Cnot1	G	T	8: 96,487,969 (GRCm39)	D562E	probably damaging	Het
Commd6	G	A	14: 101,877,709 (GRCm39)		probably benign	Het
Cox6a2	G	A	7: 127,805,212 (GRCm39)		probably benign	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
Eng	T	C	2: 32,567,692 (GRCm39)	V110A	probably damaging	Het
Esyt3	T	C	9: 99,220,860 (GRCm39)	I114M	possibly damaging	Het
Fam83h	A	T	15: 75,875,811 (GRCm39)	Y509N	probably damaging	Het
Fat2	A	T	11: 55,202,075 (GRCm39)	L333H	probably damaging	Het
Fbxo21	A	G	5: 118,146,078 (GRCm39)	N567S	possibly damaging	Het
Fcsk	T	C	8: 111,610,865 (GRCm39)		probably benign	Het
Fn1	A	T	1: 71,634,879 (GRCm39)	L1964Q	probably damaging	Het
Gorasp1	G	T	9: 119,757,312 (GRCm39)	S353R	possibly damaging	Het
Grk2	C	T	19: 4,337,262 (GRCm39)	E646K	probably damaging	Het
Hoxc11	T	C	15: 102,863,397 (GRCm39)	V146A	probably damaging	Het
Igf2bp2	T	C	16: 21,894,841 (GRCm39)	T301A	probably benign	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
Kdm2b	G	A	5: 123,019,806 (GRCm39)	S738L	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
Mapk15	G	A	15: 75,870,103 (GRCm39)	E408K	probably benign	Het
Mdn1	T	A	4: 32,718,317 (GRCm39)	F2191I	possibly damaging	Het
Metrn	C	A	17: 26,015,479 (GRCm39)	V79F	possibly damaging	Het
Mtbp	T	A	15: 55,449,889 (GRCm39)		probably benign	Het
Myh11	C	A	16: 14,041,883 (GRCm39)	Q720H	probably damaging	Het
Myo3a	T	A	2: 22,469,753 (GRCm39)	I508N	probably damaging	Het
Nat9	A	T	11: 115,075,941 (GRCm39)	Y27N	probably damaging	Het
Ncapg2	T	C	12: 116,393,455 (GRCm39)	F553S	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
Or2d3b	A	G	7: 106,514,226 (GRCm39)	I274V	probably benign	Het
Or2t6	T	A	14: 14,176,092 (GRCm38)		probably benign	Het
Or4a78	T	A	2: 89,497,428 (GRCm39)	K267N	probably damaging	Het
Or52e3	A	T	7: 102,869,558 (GRCm39)	D211V	probably damaging	Het
Or52e3	G	A	7: 102,869,584 (GRCm39)	A220T	probably benign	Het
Or5b122	A	G	19: 13,563,240 (GRCm39)	I191V	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
Pdlim4	C	T	11: 53,945,875 (GRCm39)	V327M	probably 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
Prdm1	C	T	10: 44,317,675 (GRCm39)	E398K	probably damaging	Het
Prep	T	C	10: 44,991,174 (GRCm39)	V280A	probably benign	Het
Prkdc	T	A	16: 15,526,565 (GRCm39)		probably benign	Het
Proser3	G	A	7: 30,239,563 (GRCm39)	R514C	probably damaging	Het
Ptk7	G	A	17: 46,883,688 (GRCm39)		probably benign	Het
Rbm45	T	C	2: 76,208,742 (GRCm39)	Y293H	probably damaging	Het
Rnf213	A	C	11: 119,355,878 (GRCm39)	E4108A	possibly damaging	Het
Sdk2	A	G	11: 113,747,581 (GRCm39)	L643P	probably damaging	Het
Sec24d	C	A	3: 123,144,525 (GRCm39)		probably benign	Het
Sh2d3c	C	G	2: 32,643,033 (GRCm39)	H587D	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
Slc46a2	T	A	4: 59,914,544 (GRCm39)	L126F	probably damaging	Het
Slc4a8	T	C	15: 100,698,374 (GRCm39)	M621T	possibly damaging	Het
Slc9b2	T	A	3: 135,042,269 (GRCm39)	V516D	possibly damaging	Het
Slco1a6	T	A	6: 142,102,948 (GRCm39)		probably benign	Het
Sncg	C	T	14: 34,096,495 (GRCm39)	V15I	probably benign	Het
Srgap2	T	C	1: 131,283,302 (GRCm39)	T260A	probably damaging	Het
Stk10	T	A	11: 32,537,305 (GRCm39)		probably benign	Het
Taf5	A	G	19: 47,064,301 (GRCm39)	S415G	possibly damaging	Het
Tdp2	T	G	13: 25,025,333 (GRCm39)		probably null	Het
Tgfbi	T	A	13: 56,777,587 (GRCm39)	I357N	probably benign	Het
Tmem116	A	G	5: 121,633,159 (GRCm39)	T178A	probably damaging	Het
Tnrc6a	G	A	7: 122,769,617 (GRCm39)	R469H	probably benign	Het
Top2a	A	T	11: 98,893,729 (GRCm39)	L1055*	probably null	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
Trpv2	A	G	11: 62,481,086 (GRCm39)	Y395C	probably damaging	Het
Ubn2	T	A	6: 38,411,535 (GRCm39)		probably null	Het
Ubr4	C	T	4: 139,157,487 (GRCm39)	T2348M	probably damaging	Het
Ubxn4	G	A	1: 128,190,641 (GRCm39)	E256K	probably benign	Het
Vmn1r33	C	A	6: 66,589,510 (GRCm39)	G15*	probably null	Het
Vmn1r37	T	A	6: 66,708,769 (GRCm39)	S95T	probably benign	Het
Vmn2r57	A	G	7: 41,050,076 (GRCm39)	C558R	probably damaging	Het
Vnn1	T	C	10: 23,774,500 (GRCm39)		probably null	Het
Vps13c	T	C	9: 67,826,544 (GRCm39)	V1395A	probably benign	Het
Vwa7	A	G	17: 35,238,781 (GRCm39)	I290V	probably benign	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
Zfp942	A	T	17: 22,147,319 (GRCm39)	C437S	probably damaging	Het
Zfyve9	T	A	4: 108,575,902 (GRCm39)	E393V	possibly damaging	Het

Other mutations in Tdp1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00780:Tdp1	APN	12	99,859,907 (GRCm39)	missense	possibly damaging	0.79
IGL01099:Tdp1	APN	12	99,881,704 (GRCm39)	splice site	probably benign
IGL01295:Tdp1	APN	12	99,857,929 (GRCm39)	missense	probably benign	0.00
IGL01409:Tdp1	APN	12	99,875,940 (GRCm39)	missense	possibly damaging	0.83
IGL01482:Tdp1	APN	12	99,857,639 (GRCm39)	missense	probably benign
IGL03116:Tdp1	APN	12	99,921,290 (GRCm39)	missense	probably benign	0.27
BB004:Tdp1	UTSW	12	99,878,555 (GRCm39)	missense	probably damaging	1.00
BB014:Tdp1	UTSW	12	99,878,555 (GRCm39)	missense	probably damaging	1.00
R0033:Tdp1	UTSW	12	99,901,311 (GRCm39)	missense	probably benign	0.30
R0092:Tdp1	UTSW	12	99,921,248 (GRCm39)	missense	probably damaging	1.00
R0485:Tdp1	UTSW	12	99,876,101 (GRCm39)	missense	probably benign	0.30
R0611:Tdp1	UTSW	12	99,875,970 (GRCm39)	missense	probably benign
R0853:Tdp1	UTSW	12	99,901,326 (GRCm39)	missense	probably damaging	0.96
R1539:Tdp1	UTSW	12	99,878,571 (GRCm39)	missense	probably damaging	1.00
R1692:Tdp1	UTSW	12	99,921,260 (GRCm39)	missense	probably damaging	1.00
R1751:Tdp1	UTSW	12	99,857,602 (GRCm39)	splice site	probably null
R1767:Tdp1	UTSW	12	99,857,602 (GRCm39)	splice site	probably null
R3788:Tdp1	UTSW	12	99,858,011 (GRCm39)	splice site	probably benign
R3790:Tdp1	UTSW	12	99,858,011 (GRCm39)	splice site	probably benign
R3837:Tdp1	UTSW	12	99,860,967 (GRCm39)	critical splice acceptor site	probably null
R3917:Tdp1	UTSW	12	99,860,976 (GRCm39)	missense	probably damaging	1.00
R4209:Tdp1	UTSW	12	99,864,588 (GRCm39)	missense	probably damaging	1.00
R4211:Tdp1	UTSW	12	99,864,588 (GRCm39)	missense	probably damaging	1.00
R4509:Tdp1	UTSW	12	99,921,324 (GRCm39)	utr 3 prime	probably benign
R4774:Tdp1	UTSW	12	99,868,623 (GRCm39)	missense	possibly damaging	0.56
R4859:Tdp1	UTSW	12	99,876,070 (GRCm39)	missense	probably benign	0.20
R5229:Tdp1	UTSW	12	99,859,919 (GRCm39)	missense	probably damaging	1.00
R5348:Tdp1	UTSW	12	99,881,765 (GRCm39)	missense	probably damaging	1.00
R5441:Tdp1	UTSW	12	99,876,544 (GRCm39)	missense	probably damaging	1.00
R5457:Tdp1	UTSW	12	99,861,005 (GRCm39)	nonsense	probably null
R5685:Tdp1	UTSW	12	99,868,611 (GRCm39)	missense	possibly damaging	0.51
R6329:Tdp1	UTSW	12	99,880,331 (GRCm39)	missense	probably benign	0.02
R6329:Tdp1	UTSW	12	99,880,330 (GRCm39)	missense	probably damaging	0.99
R7060:Tdp1	UTSW	12	99,877,947 (GRCm39)	missense	probably benign	0.02
R7066:Tdp1	UTSW	12	99,860,991 (GRCm39)	missense	probably benign
R7479:Tdp1	UTSW	12	99,857,654 (GRCm39)	missense	probably benign	0.00
R7927:Tdp1	UTSW	12	99,878,555 (GRCm39)	missense	probably damaging	1.00
R8556:Tdp1	UTSW	12	99,857,527 (GRCm39)	missense	probably benign	0.07
R8774:Tdp1	UTSW	12	99,877,917 (GRCm39)	missense	probably damaging	1.00
R8774-TAIL:Tdp1	UTSW	12	99,877,917 (GRCm39)	missense	probably damaging	1.00
R9521:Tdp1	UTSW	12	99,877,906 (GRCm39)	missense	probably damaging	0.98
Z1177:Tdp1	UTSW	12	99,877,892 (GRCm39)	missense	probably benign

Predicted Primers

PCR Primer
(F):5'- GCACTATGTCTTACACGCTACGGG -3'
(R):5'- AGGAATGGTCTGATCTGGCTCTCTC -3'

Sequencing Primer
(F):5'- TTACACGCTACGGGGCTTG -3'
(R):5'- GTACGGGTGCAGGACTTTAA -3'

Posted On

2013-07-11