Mutagenetix > Incidental Mutation

Incidental Mutation 'R7479:Tdp1'

579691

Institutional Source

Beutler Lab

Gene Symbol

Tdp1

Ensembl Gene

ENSMUSG00000021177

Gene Name

tyrosyl-DNA phosphodiesterase 1

Synonyms

4921509N21Rik, SCAN1, 2810481F14Rik, E430034L06Rik, Gm40556

MMRRC Submission

045553-MU

Accession Numbers

Essential gene?

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

Stock #

R7479 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

99850776-99921478 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 99857654 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 71 (V71A)

Ref Sequence

ENSEMBL: ENSMUSP00000021594 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000021594] [ENSMUST00000137653] [ENSMUST00000153627]

AlphaFold

no structure available at present

Predicted Effect

probably benign
Transcript: ENSMUST00000021594
AA Change: V71A

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000021594
Gene: ENSMUSG00000021177
AA Change: V71A

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

probably benign
Transcript: ENSMUST00000137653

SMART Domains

Protein: ENSMUSP00000123269
Gene: ENSMUSG00000021177

Domain	Start	End	E-Value	Type
low complexity region	13	32	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000153627
AA Change: V71A

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000118656
Gene: ENSMUSG00000021177
AA Change: V71A

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: 100.0%
3x: 99.9%
10x: 99.5%
20x: 98.1%

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: 70 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700003H04Rik	T	A	3: 124,372,142 (GRCm39)	M81L	probably benign	Het
Ano9	T	C	7: 140,682,348 (GRCm39)	T667A	probably damaging	Het
Anpep	T	A	7: 79,485,118 (GRCm39)	I623F	probably benign	Het
Apba2	T	C	7: 64,389,607 (GRCm39)	I501T	possibly damaging	Het
Ascc3	T	A	10: 50,525,895 (GRCm39)	Y536N	probably damaging	Het
B4galt1	T	C	4: 40,823,587 (GRCm39)	Y168C	probably damaging	Het
C1ra	G	A	6: 124,494,684 (GRCm39)	E316K	probably benign	Het
C2	A	G	17: 35,082,441 (GRCm39)	C647R	probably damaging	Het
Cnot4	G	A	6: 35,001,083 (GRCm39)	T604I	probably benign	Het
Col11a1	C	T	3: 113,896,218 (GRCm39)	T506I	unknown	Het
Cr2	A	C	1: 194,840,718 (GRCm39)		probably null	Het
Ctsm	A	T	13: 61,685,569 (GRCm39)	V281D	probably damaging	Het
Cyp2c69	T	C	19: 39,870,001 (GRCm39)	I74V	probably benign	Het
Dennd4c	T	A	4: 86,717,590 (GRCm39)	V529D	probably damaging	Het
Dlgap3	C	A	4: 127,088,418 (GRCm39)	H5N	possibly damaging	Het
Dusp10	C	A	1: 183,769,617 (GRCm39)	H194Q	probably damaging	Het
Eln	C	G	5: 134,736,429 (GRCm39)	G753A	unknown	Het
Emb	T	A	13: 117,385,962 (GRCm39)	N118K	possibly damaging	Het
Fam184a	C	T	10: 53,531,110 (GRCm39)	V755I	probably benign	Het
Fryl	A	G	5: 73,254,904 (GRCm39)	I846T	possibly damaging	Het
Gabbr2	T	A	4: 46,681,166 (GRCm39)	I722F	probably damaging	Het
Gabrb3	T	A	7: 57,474,171 (GRCm39)	D362E	possibly damaging	Het
Galnt2	G	A	8: 125,061,077 (GRCm39)	G357D	probably damaging	Het
Gbx2	A	T	1: 89,858,373 (GRCm39)	S35R	probably benign	Het
Glg1	A	G	8: 111,924,367 (GRCm39)	I207T	possibly damaging	Het
Gm10192	A	T	4: 97,071,272 (GRCm39)	N44K	unknown	Het
Gpd1	A	G	15: 99,617,984 (GRCm39)	D123G	probably benign	Het
Grm2	A	T	9: 106,531,050 (GRCm39)	D146E	possibly damaging	Het
Gsg1l2	A	G	11: 67,676,032 (GRCm39)	D132G	probably benign	Het
Hecw1	C	T	13: 14,515,425 (GRCm39)	G236R	probably damaging	Het
Hif3a	G	A	7: 16,776,560 (GRCm39)	T462I	possibly damaging	Het
Hspg2	C	T	4: 137,266,714 (GRCm39)	A1934V	probably benign	Het
Il7r	C	T	15: 9,513,117 (GRCm39)	A131T	probably damaging	Het
Itga6	C	T	2: 71,668,680 (GRCm39)	R540*	probably null	Het
Kcnh2	A	G	5: 24,530,490 (GRCm39)		probably null	Het
Kcnq4	C	T	4: 120,573,022 (GRCm39)	A260T	probably damaging	Het
Lrp1b	T	C	2: 40,691,517 (GRCm39)	N3434S		Het
Lrrc41	C	T	4: 115,946,238 (GRCm39)	P318S	probably damaging	Het
Map4	G	A	9: 109,897,892 (GRCm39)	G873R	possibly damaging	Het
Med24	A	G	11: 98,595,787 (GRCm39)	I968T	possibly damaging	Het
Mfap5	T	C	6: 122,503,821 (GRCm39)		probably null	Het
Mtcl1	A	G	17: 66,686,485 (GRCm39)	V807A	probably benign	Het
Mug1	T	A	6: 121,855,467 (GRCm39)	S934T	possibly damaging	Het
Nckap5l	C	A	15: 99,321,127 (GRCm39)	V1218F	probably damaging	Het
Nek1	T	A	8: 61,583,179 (GRCm39)	D1272E	probably benign	Het
Nkx2-4	T	C	2: 146,926,088 (GRCm39)	E258G	probably benign	Het
Polr1a	T	A	6: 71,913,281 (GRCm39)	V545E	probably damaging	Het
Ppp1r9b	A	G	11: 94,882,858 (GRCm39)	D162G	possibly damaging	Het
Rhot2	A	G	17: 26,059,723 (GRCm39)	L367P	probably damaging	Het
Ripk2	A	G	4: 16,155,154 (GRCm39)	F122L	probably benign	Het
Scn11a	T	C	9: 119,588,941 (GRCm39)	T1322A	probably benign	Het
Scn8a	T	A	15: 100,853,358 (GRCm39)	L115Q	probably damaging	Het
Sel1l3	G	T	5: 53,274,462 (GRCm39)	P1006Q	probably damaging	Het
Septin11	A	T	5: 93,304,804 (GRCm39)	N207I	probably damaging	Het
Sez6l2	C	T	7: 126,562,831 (GRCm39)	T669I	probably damaging	Het
Sfxn4	T	A	19: 60,847,112 (GRCm39)	D57V	possibly damaging	Het
Smarca2	T	A	19: 26,617,887 (GRCm39)	V306D	probably benign	Het
Srgap3	C	T	6: 112,712,794 (GRCm39)		probably null	Het
Tas2r134	T	C	2: 51,517,541 (GRCm39)	F7L	not run	Het
Tbcd	T	C	11: 121,383,431 (GRCm39)		probably null	Het
Tcn2	G	A	11: 3,867,703 (GRCm39)	A413V	probably damaging	Het
Tjp1	T	C	7: 64,950,928 (GRCm39)	T1649A	probably damaging	Het
Tnc	T	C	4: 63,935,865 (GRCm39)	E357G	possibly damaging	Het
Tnrc6b	A	G	15: 80,773,327 (GRCm39)	T1158A	probably benign	Het
Ttn	C	A	2: 76,568,952 (GRCm39)	E27314*	probably null	Het
Vps35	G	T	8: 85,997,434 (GRCm39)	T512K	probably benign	Het
Zfp40	A	T	17: 23,396,292 (GRCm39)	S98R	probably benign	Het
Zfp764l1	C	T	7: 126,992,496 (GRCm39)	C38Y	probably null	Het
Zfp945	A	T	17: 23,070,340 (GRCm39)	C541S	possibly damaging	Het
Zfp976	T	A	7: 42,262,603 (GRCm39)	E412D	probably benign	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
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
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'- GTCCCAAGAAAGCAGCTACG -3'
(R):5'- CAGGAGGGCTTCTATCCACAAC -3'

Sequencing Primer
(F):5'- CAGCTACGGGAAGTGGACAATATC -3'
(R):5'- ATCCACAACTTTCTGGGCAGTAG -3'

Posted On

2019-10-07