Mutagenetix > Incidental Mutation

Incidental Mutation 'R0611:Tdp1'

54744

Institutional Source

Beutler Lab

Gene Symbol

Tdp1

Ensembl Gene

ENSMUSG00000021177

Gene Name

tyrosyl-DNA phosphodiesterase 1

Synonyms

4921509N21Rik, SCAN1, 2810481F14Rik, E430034L06Rik, Gm40556

MMRRC Submission

038800-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.220) question?

Stock #

R0611 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

99850776-99921478 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to C at 99875970 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Alanine at position 307 (D307A)

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
AA Change: D307A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000021594
Gene: ENSMUSG00000021177
AA Change: D307A

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: ENSMUST00000126424

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000128739

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000151019

Predicted Effect

probably benign
Transcript: ENSMUST00000153627
AA Change: D307A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000118656
Gene: ENSMUSG00000021177
AA Change: D307A

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000221445

Coding Region Coverage

1x: 99.4%
3x: 98.9%
10x: 97.5%
20x: 94.9%

Validation Efficiency

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: 82 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca14	T	A	7: 119,851,479 (GRCm39)	M819K	possibly damaging	Het
Adamtsl3	T	G	7: 82,178,120 (GRCm39)	C528G	probably damaging	Het
Akap9	A	G	5: 4,004,870 (GRCm39)	K148E	probably benign	Het
Akr1b1	A	T	6: 34,286,577 (GRCm39)	D225E	probably benign	Het
Alms1	C	A	6: 85,655,653 (GRCm39)	Q2931K	possibly damaging	Het
Ano3	T	C	2: 110,715,346 (GRCm39)	K31E	possibly damaging	Het
Cdc37	A	G	9: 21,053,537 (GRCm39)	I242T	probably damaging	Het
Celsr1	T	A	15: 85,816,524 (GRCm39)	K1806N	possibly damaging	Het
Clpb	T	A	7: 101,436,956 (GRCm39)	I707N	possibly damaging	Het
Cntnap2	A	T	6: 47,072,483 (GRCm39)	Y1017F	possibly damaging	Het
Creb3l2	A	T	6: 37,311,416 (GRCm39)	S458T	probably benign	Het
Ctnnd2	C	A	15: 31,009,230 (GRCm39)	T1109K	possibly damaging	Het
Dcaf10	T	A	4: 45,373,011 (GRCm39)	L425Q	probably damaging	Het
Dlec1	A	G	9: 118,941,167 (GRCm39)	E239G	probably benign	Het
Dnah2	T	C	11: 69,390,020 (GRCm39)	K742E	probably damaging	Het
Dsp	A	T	13: 38,371,717 (GRCm39)	R889S	probably damaging	Het
Dync1h1	T	A	12: 110,599,222 (GRCm39)	M1859K	probably damaging	Het
Efcab7	T	A	4: 99,758,886 (GRCm39)	N361K	probably damaging	Het
Eps8l2	T	C	7: 140,935,646 (GRCm39)	V139A	probably damaging	Het
Fads3	T	G	19: 10,019,200 (GRCm39)	H35Q	probably damaging	Het
Fam163b	C	A	2: 27,003,583 (GRCm39)	V24F	probably damaging	Het
Gm14496	A	T	2: 181,636,904 (GRCm39)	T121S	probably benign	Het
Gm4799	C	T	10: 82,790,563 (GRCm39)		noncoding transcript	Het
Gm7168	A	T	17: 14,169,797 (GRCm39)	D388V	probably benign	Het
Gmeb1	A	T	4: 131,953,386 (GRCm39)	L460*	probably null	Het
Gpc6	T	G	14: 118,212,430 (GRCm39)	F534V	probably null	Het
Hectd3	A	G	4: 116,853,241 (GRCm39)	D156G	possibly damaging	Het
Itga6	T	C	2: 71,650,404 (GRCm39)	I150T	possibly damaging	Het
Kansl1	A	G	11: 104,229,012 (GRCm39)	M863T	probably benign	Het
Kcnb2	A	T	1: 15,780,664 (GRCm39)	Y512F	probably benign	Het
Klhdc2	A	T	12: 69,347,053 (GRCm39)	M73L	probably benign	Het
Ktn1	A	G	14: 47,932,073 (GRCm39)	T667A	probably benign	Het
Lgsn	A	C	1: 31,242,736 (GRCm39)	I273L	probably benign	Het
Lilra5	A	G	7: 4,245,232 (GRCm39)	D292G	probably benign	Het
Mrps27	C	T	13: 99,541,582 (GRCm39)	R229C	probably damaging	Het
Muc5b	T	G	7: 141,416,173 (GRCm39)	S3040A	probably benign	Het
Nat14	T	C	7: 4,926,275 (GRCm39)	S7P	probably damaging	Het
Nfia	A	G	4: 97,671,694 (GRCm39)	I135V	possibly damaging	Het
Nkd1	G	A	8: 89,248,944 (GRCm39)	A30T	probably damaging	Het
Nup205	A	G	6: 35,202,903 (GRCm39)	D1370G	probably null	Het
Or1j15	C	G	2: 36,459,568 (GRCm39)		probably null	Het
Or4k15c	G	A	14: 50,321,310 (GRCm39)	T276I	probably damaging	Het
Or51k2	T	C	7: 103,596,400 (GRCm39)	L209P	probably damaging	Het
Or5p79	T	A	7: 108,221,494 (GRCm39)	N158K	possibly damaging	Het
Or8s10	T	C	15: 98,336,168 (GRCm39)	S273P	possibly damaging	Het
Orc1	C	T	4: 108,459,229 (GRCm39)	A466V	probably benign	Het
Otud7a	T	A	7: 63,385,638 (GRCm39)	D367E	possibly damaging	Het
Pcdhb4	A	G	18: 37,441,263 (GRCm39)	Y191C	probably damaging	Het
Pclo	T	C	5: 14,762,828 (GRCm39)	V3767A	unknown	Het
Pclo	T	C	5: 14,728,789 (GRCm39)		probably benign	Het
Prmt1	A	T	7: 44,628,225 (GRCm39)		probably null	Het
Ralgapa1	A	G	12: 55,842,483 (GRCm39)	F62S	probably damaging	Het
Rangrf	T	C	11: 68,863,518 (GRCm39)	S163G	probably benign	Het
Rgs12	C	A	5: 35,176,804 (GRCm39)	A65E	probably damaging	Het
Rrbp1	T	C	2: 143,830,436 (GRCm39)	N577S	probably damaging	Het
Septin11	A	G	5: 93,315,393 (GRCm39)	H374R	probably damaging	Het
Serpina5	T	G	12: 104,070,046 (GRCm39)	N314K	probably benign	Het
Sgce	T	C	6: 4,689,621 (GRCm39)	D395G	probably damaging	Het
Slc26a9	A	T	1: 131,690,499 (GRCm39)	N501I	probably damaging	Het
Slc9c1	A	G	16: 45,401,965 (GRCm39)	D784G	possibly damaging	Het
Snapc2	A	G	8: 4,305,676 (GRCm39)	D207G	probably benign	Het
Stard9	G	T	2: 120,529,738 (GRCm39)	M1998I	probably benign	Het
Stk38	A	C	17: 29,194,907 (GRCm39)	F280V	possibly damaging	Het
Tas2r126	A	G	6: 42,412,025 (GRCm39)	K186R	probably damaging	Het
Tead2	A	G	7: 44,866,674 (GRCm39)	D11G	probably damaging	Het
Tmco4	C	A	4: 138,747,383 (GRCm39)	L211I	probably damaging	Het
Tmem183a	A	G	1: 134,280,115 (GRCm39)	F255S	probably damaging	Het
Tmem87a	C	T	2: 120,205,929 (GRCm39)	G349S	possibly damaging	Het
Tpte	G	A	8: 22,826,549 (GRCm39)	E377K	possibly damaging	Het
Trim32	T	C	4: 65,531,893 (GRCm39)	F150S	possibly damaging	Het
Trpc7	T	A	13: 57,035,636 (GRCm39)	K99M	probably damaging	Het
Ttc22	A	G	4: 106,491,381 (GRCm39)	K195E	probably damaging	Het
Txn2	G	A	15: 77,811,917 (GRCm39)	P7S	probably damaging	Het
Ubxn2a	G	A	12: 4,930,700 (GRCm39)	T220I	probably damaging	Het
Ufd1	A	G	16: 18,633,626 (GRCm39)	N17S	possibly damaging	Het
Unc13a	A	G	8: 72,102,509 (GRCm39)	S958P	probably damaging	Het
Vmn1r202	T	A	13: 22,685,824 (GRCm39)	M198L	probably damaging	Het
Vmn2r84	G	A	10: 130,221,991 (GRCm39)	A743V	probably damaging	Het
Washc5	A	G	15: 59,213,007 (GRCm39)	F891S	probably damaging	Het
Zfp708	T	C	13: 67,218,375 (GRCm39)	T495A	probably benign	Het
Zfp81	A	G	17: 33,553,593 (GRCm39)	I407T	probably benign	Het
Zswim5	T	C	4: 116,843,874 (GRCm39)		probably null	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
R0008:Tdp1	UTSW	12	99,921,217 (GRCm39)	splice site	probably benign
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
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'- GGGCATGGTTTTGCATAAAGAGATAGC -3'
(R):5'- AGGAGTCCCTTTTGGGCCTCATAC -3'

Sequencing Primer
(F):5'- GCATTCAGAAATAATTCCGTGATG -3'
(R):5'- TCATACTGGAAGGGGCCAC -3'

Posted On

2013-07-11