Mutagenetix > Incidental Mutations

Incidental Mutation 'R6329:Tdp1'

509416

Institutional Source

Beutler Lab

Gene Symbol

Tdp1

Ensembl Gene

ENSMUSG00000021177

Gene Name

tyrosyl-DNA phosphodiesterase 1

Synonyms

E430034L06Rik, 2810481F14Rik, SCAN1, 4921509N21Rik

MMRRC Submission

Accession Numbers

Is this an essential gene?

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

Stock #

R6329 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

99884517-99955219 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 99914071 bp

Zygosity

Heterozygous

Amino Acid Change

Serine to Cysteine at position 464 (S464C)

Ref Sequence

ENSEMBL: ENSMUSP00000118656 (fasta)

Gene Model

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

Predicted Effect

probably damaging
Transcript: ENSMUST00000021594
AA Change: S464C

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000021594
Gene: ENSMUSG00000021177
AA Change: S464C

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 damaging
Transcript: ENSMUST00000153627
AA Change: S464C

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000118656
Gene: ENSMUSG00000021177
AA Change: S464C

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: ENSMUST00000220685

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.3%
20x: 97.6%

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: 76 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930579F01Rik	T	C	3: 138,173,696	H72R	probably damaging	Het
Abca13	A	T	11: 9,277,937	N660I	probably damaging	Het
Actr8	C	T	14: 29,993,084	R619*	probably null	Het
Adam18	C	A	8: 24,614,827	G657V	probably damaging	Het
Adcyap1	A	G	17: 93,202,799	E85G	probably benign	Het
Akr1c14	A	G	13: 4,087,302	Y305C	probably damaging	Het
Ankdd1b	T	A	13: 96,454,880	H37L	possibly damaging	Het
Ap4e1	T	C	2: 127,061,716	L846P	probably benign	Het
Aqp9	A	T	9: 71,132,684	Y105*	probably null	Het
Arid1b	C	T	17: 5,337,263	Q1664*	probably null	Het
Aup1	A	G	6: 83,054,607		probably benign	Het
Bnip1	C	A	17: 26,786,710	S64*	probably null	Het
Calcr	T	A	6: 3,687,621	Q422L	probably damaging	Het
Ccdc162	T	A	10: 41,663,151	D407V	possibly damaging	Het
Ccdc66	G	T	14: 27,486,484	S760R	probably benign	Het
Cd22	T	A	7: 30,877,768	E38V	probably damaging	Het
Cggbp1	T	C	16: 64,856,020	Y150H	probably damaging	Het
Chd3	T	C	11: 69,361,684	K263R	possibly damaging	Het
Col4a2	T	A	8: 11,446,238	F1620I	probably damaging	Het
Col6a2	T	C	10: 76,599,828	T858A	probably benign	Het
Dnah7a	T	A	1: 53,541,114	D1554V	probably damaging	Het
Dnajc25	A	T	4: 59,013,678	Q132L	probably benign	Het
Dnase1l1	C	T	X: 74,277,038		probably null	Homo
Ehbp1l1	A	C	19: 5,718,767	I836S	possibly damaging	Het
Elf1	A	G	14: 79,573,339	Q288R	possibly damaging	Het
Fbn1	C	A	2: 125,308,473	V2608L	possibly damaging	Het
Frmpd1	T	C	4: 45,268,551	I232T	possibly damaging	Het
Fuca1	T	A	4: 135,934,826	I355N	probably damaging	Het
Gcnt4	A	G	13: 96,947,273	D359G	probably damaging	Het
Gm15448	T	C	7: 3,822,851	T340A	probably damaging	Het
Gm5134	T	C	10: 75,954,660	M30T	possibly damaging	Het
Grk1	T	G	8: 13,405,704	L196R	probably damaging	Het
Igkv14-126	A	C	6: 67,896,564	D92A	probably damaging	Het
Kmt2c	A	G	5: 25,315,602	S1837P	probably benign	Het
Lhx4	T	A	1: 155,702,554	T281S	probably benign	Het
Lrrc55	G	T	2: 85,196,309	H124N	probably benign	Het
March8	T	A	6: 116,406,316	I566N	possibly damaging	Het
Mycbp2	G	A	14: 103,155,852	A3091V	probably benign	Het
Nlrp4b	A	G	7: 10,724,920	N355S	probably benign	Het
Nmur2	A	G	11: 56,029,585	V278A	probably benign	Het
Nod1	T	C	6: 54,944,704	M210V	probably benign	Het
Nt5c1b	T	A	12: 10,372,138	C63*	probably null	Het
Olfr1164	G	A	2: 88,093,664	P91S	probably damaging	Het
Olfr1288	C	T	2: 111,479,228	A148V	possibly damaging	Het
Olfr346	A	T	2: 36,688,682	K227*	probably null	Het
Olfr397	A	G	11: 73,964,742	I45V	possibly damaging	Het
Olfr836	A	C	9: 19,120,957	M1L	probably benign	Het
Olfr884	T	C	9: 38,047,825	V201A	probably benign	Het
Olfr938	C	T	9: 39,077,903	V281I	probably benign	Het
Osbp2	T	A	11: 3,715,153	S517C	probably damaging	Het
Pcdha1	C	T	18: 36,932,248	P655L	probably damaging	Het
Pdcd6	A	G	13: 74,303,979	Y181H	probably damaging	Het
Perp	G	A	10: 18,855,754	G154S	probably damaging	Het
Perp	G	T	10: 18,855,755	G154V	probably damaging	Het
Prokr1	T	G	6: 87,581,792	T204P	possibly damaging	Het
Prpf3	A	T	3: 95,832,578	C630S	probably damaging	Het
Pter	C	A	2: 12,980,548	H230N	probably damaging	Het
Ptprs	A	T	17: 56,417,427	Y1167*	probably null	Het
Rad54l2	T	C	9: 106,717,922	I279V	possibly damaging	Het
Rora	T	A	9: 69,373,186	L347Q	probably damaging	Het
Runx1t1	T	G	4: 13,785,136	M1R	probably null	Het
Sdcbp	A	G	4: 6,381,064	S70G	probably benign	Het
Serpinb12	A	G	1: 106,953,763	Y210C	probably damaging	Het
Sipa1	T	C	19: 5,651,489	E1015G	probably damaging	Het
Slc15a2	A	C	16: 36,751,782	L740R	possibly damaging	Het
Specc1	A	G	11: 62,156,553	E916G	probably damaging	Het
Spta1	T	C	1: 174,214,177	I1371T	possibly damaging	Het
Tagln3	T	C	16: 45,713,002	M130V	probably benign	Het
Tchh	A	T	3: 93,446,445	E1064V	unknown	Het
Tenm3	T	C	8: 48,276,849	Y1374C	probably damaging	Het
Tmprss3	A	T	17: 31,183,859	Y455*	probably null	Het
Ttc5	A	G	14: 50,765,928	V433A	possibly damaging	Het
Wnt5a	A	T	14: 28,518,492	R180*	probably null	Het
Zfp53	A	G	17: 21,508,110	D135G	probably benign	Het
Zfp619	T	A	7: 39,537,545	C1000S	probably damaging	Het
Zfp647	G	A	15: 76,912,085	P125L	probably damaging	Het

Other mutations in Tdp1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00780:Tdp1	APN	12	99893648	missense	possibly damaging	0.79
IGL01099:Tdp1	APN	12	99915445	splice site	probably benign
IGL01295:Tdp1	APN	12	99891670	missense	probably benign	0.00
IGL01409:Tdp1	APN	12	99909681	missense	possibly damaging	0.83
IGL01482:Tdp1	APN	12	99891380	missense	probably benign
IGL03116:Tdp1	APN	12	99955031	missense	probably benign	0.27
R0008:Tdp1	UTSW	12	99954958	splice site	probably benign
R0033:Tdp1	UTSW	12	99935052	missense	probably benign	0.30
R0092:Tdp1	UTSW	12	99954989	missense	probably damaging	1.00
R0485:Tdp1	UTSW	12	99909842	missense	probably benign	0.30
R0611:Tdp1	UTSW	12	99909711	missense	probably benign
R0853:Tdp1	UTSW	12	99935067	missense	probably damaging	0.96
R1539:Tdp1	UTSW	12	99912312	missense	probably damaging	1.00
R1692:Tdp1	UTSW	12	99955001	missense	probably damaging	1.00
R1751:Tdp1	UTSW	12	99891343	unclassified	probably null
R1767:Tdp1	UTSW	12	99891343	unclassified	probably null
R3788:Tdp1	UTSW	12	99891752	splice site	probably benign
R3790:Tdp1	UTSW	12	99891752	splice site	probably benign
R3837:Tdp1	UTSW	12	99894708	critical splice acceptor site	probably null
R3917:Tdp1	UTSW	12	99894717	missense	probably damaging	1.00
R4209:Tdp1	UTSW	12	99898329	missense	probably damaging	1.00
R4211:Tdp1	UTSW	12	99898329	missense	probably damaging	1.00
R4509:Tdp1	UTSW	12	99955065	utr 3 prime	probably benign
R4774:Tdp1	UTSW	12	99902364	missense	possibly damaging	0.56
R4859:Tdp1	UTSW	12	99909811	missense	probably benign	0.20
R5229:Tdp1	UTSW	12	99893660	missense	probably damaging	1.00
R5348:Tdp1	UTSW	12	99915506	missense	probably damaging	1.00
R5441:Tdp1	UTSW	12	99910285	missense	probably damaging	1.00
R5457:Tdp1	UTSW	12	99894746	nonsense	probably null
R5685:Tdp1	UTSW	12	99902352	missense	possibly damaging	0.51
R6329:Tdp1	UTSW	12	99914072	missense	probably benign	0.02
R7060:Tdp1	UTSW	12	99911688	missense	probably benign	0.02
R7066:Tdp1	UTSW	12	99894732	missense	probably benign
R7479:Tdp1	UTSW	12	99891395	missense	probably benign	0.00

Predicted Primers

PCR Primer
(F):5'- GCCTAACGTAAGCATAGGTGG -3'
(R):5'- GCCAACAGAGATAAATTTTACTCCG -3'

Sequencing Primer
(F):5'- ACGTAAGCATAGGTGGATTTTTCAG -3'
(R):5'- TTACTCCGGTACTAAAAACCTATTCC -3'

Posted On

2018-04-02