Incidental Mutation 'R7066:Tdp1'
| ID |
548588 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Tdp1
|
| Ensembl Gene |
ENSMUSG00000021177 |
| Gene Name |
tyrosyl-DNA phosphodiesterase 1 |
| Synonyms |
4921509N21Rik, SCAN1, 2810481F14Rik, E430034L06Rik, Gm40556 |
| MMRRC Submission |
045162-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.215)
|
| Stock # |
R7066 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
12 |
| Chromosomal Location |
99850776-99921478 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 99860991 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Aspartic acid to Glycine
at position 210
(D210G)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000118656
(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: D210G
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000021594
Gene: ENSMUSG00000021177
AA Change: D210G
| 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: D210G
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000118656
Gene: ENSMUSG00000021177
AA Change: D210G
| 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: 99.7%
- 20x: 99.0%
|
| Validation Efficiency |
98% (52/53) |
| 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: 52 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| A1cf |
T |
C |
19: 31,904,514 (GRCm39) |
V175A |
probably damaging |
Het |
| Adamts5 |
A |
T |
16: 85,659,652 (GRCm39) |
V880E |
probably damaging |
Het |
| Adgrf1 |
T |
A |
17: 43,621,151 (GRCm39) |
F463I |
probably benign |
Het |
| Ano1 |
T |
A |
7: 144,190,823 (GRCm39) |
E249D |
probably benign |
Het |
| Aoc1 |
A |
G |
6: 48,885,553 (GRCm39) |
D686G |
probably damaging |
Het |
| Cacna1d |
A |
T |
14: 30,074,935 (GRCm39) |
|
probably benign |
Het |
| Cdc42ep4 |
A |
G |
11: 113,620,044 (GRCm39) |
S116P |
probably damaging |
Het |
| Ces2a |
T |
C |
8: 105,466,880 (GRCm39) |
V463A |
probably damaging |
Het |
| Depdc5 |
A |
G |
5: 33,059,192 (GRCm39) |
D297G |
probably benign |
Het |
| Fsip2 |
T |
A |
2: 82,821,235 (GRCm39) |
V5656E |
possibly damaging |
Het |
| Gbp5 |
A |
G |
3: 142,213,490 (GRCm39) |
T469A |
probably benign |
Het |
| Gm21663 |
C |
G |
5: 26,146,259 (GRCm39) |
|
probably null |
Het |
| Iqch |
A |
G |
9: 63,432,027 (GRCm39) |
V456A |
probably benign |
Het |
| Lpcat1 |
A |
C |
13: 73,659,500 (GRCm39) |
I373L |
probably benign |
Het |
| Morc2b |
C |
T |
17: 33,355,610 (GRCm39) |
V721I |
probably benign |
Het |
| Mrgprb1 |
C |
T |
7: 48,097,424 (GRCm39) |
V163M |
probably benign |
Het |
| Mtfr2 |
A |
G |
10: 20,229,972 (GRCm39) |
I142V |
possibly damaging |
Het |
| Muc16 |
A |
T |
9: 18,569,317 (GRCm39) |
S1067R |
unknown |
Het |
| Myh14 |
T |
C |
7: 44,280,179 (GRCm39) |
S892G |
possibly damaging |
Het |
| Mylk2 |
C |
T |
2: 152,753,588 (GRCm39) |
|
probably null |
Het |
| Mzf1 |
A |
T |
7: 12,777,490 (GRCm39) |
V638E |
possibly damaging |
Het |
| Ncoa1 |
C |
T |
12: 4,372,934 (GRCm39) |
V156I |
possibly damaging |
Het |
| Nf1 |
A |
G |
11: 79,447,546 (GRCm39) |
E2450G |
probably damaging |
Het |
| Or14j3 |
T |
A |
17: 37,901,034 (GRCm39) |
D70V |
probably damaging |
Het |
| Or1e29 |
A |
G |
11: 73,668,018 (GRCm39) |
I45T |
probably damaging |
Het |
| Or4a72 |
T |
C |
2: 89,406,047 (GRCm39) |
T8A |
probably damaging |
Het |
| Or4f60 |
G |
A |
2: 111,902,541 (GRCm39) |
P129L |
probably damaging |
Het |
| Or5t7 |
T |
A |
2: 86,507,570 (GRCm39) |
T36S |
possibly damaging |
Het |
| Or6c88 |
T |
C |
10: 129,407,373 (GRCm39) |
L283S |
probably damaging |
Het |
| Or8g54 |
A |
G |
9: 39,707,420 (GRCm39) |
I250V |
probably benign |
Het |
| Or8k17 |
T |
C |
2: 86,067,002 (GRCm39) |
D52G |
probably damaging |
Het |
| P4htm |
T |
G |
9: 108,474,162 (GRCm39) |
K125N |
probably damaging |
Het |
| Patj |
A |
G |
4: 98,301,434 (GRCm39) |
T240A |
probably benign |
Het |
| Pcolce2 |
T |
C |
9: 95,563,674 (GRCm39) |
V220A |
probably benign |
Het |
| Pcyox1 |
A |
T |
6: 86,371,478 (GRCm39) |
I136N |
probably damaging |
Het |
| Pde4b |
A |
G |
4: 102,460,003 (GRCm39) |
S395G |
probably benign |
Het |
| Peg3 |
C |
A |
7: 6,711,856 (GRCm39) |
R1122L |
probably damaging |
Het |
| Plekhm1 |
A |
G |
11: 103,261,814 (GRCm39) |
V922A |
possibly damaging |
Het |
| Rad51c |
T |
C |
11: 87,293,502 (GRCm39) |
N118S |
possibly damaging |
Het |
| Rb1cc1 |
T |
A |
1: 6,320,229 (GRCm39) |
V1216D |
possibly damaging |
Het |
| Rictor |
C |
T |
15: 6,801,635 (GRCm39) |
S441L |
probably benign |
Het |
| Rlf |
T |
C |
4: 121,005,984 (GRCm39) |
M999V |
probably benign |
Het |
| Rsf1 |
GGCGGCGGC |
GGCGGCGGCCGCGGCGGC |
7: 97,229,125 (GRCm39) |
|
probably benign |
Het |
| Samd7 |
G |
C |
3: 30,805,272 (GRCm39) |
K18N |
probably benign |
Het |
| Sema5b |
A |
C |
16: 35,471,682 (GRCm39) |
D425A |
probably benign |
Het |
| Siglecg |
A |
G |
7: 43,061,166 (GRCm39) |
E413G |
probably benign |
Het |
| Tcaf1 |
A |
T |
6: 42,656,111 (GRCm39) |
N288K |
probably damaging |
Het |
| Umps |
A |
T |
16: 33,782,103 (GRCm39) |
L273* |
probably null |
Het |
| Vcan |
A |
T |
13: 89,853,805 (GRCm39) |
V385D |
probably damaging |
Het |
| Wdr59 |
T |
C |
8: 112,192,477 (GRCm39) |
T676A |
probably benign |
Het |
| Zdbf2 |
A |
G |
1: 63,346,718 (GRCm39) |
H1699R |
probably benign |
Het |
| Zfp27 |
AATCCGCTTGTGCA |
AA |
7: 29,594,446 (GRCm39) |
|
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 |
|
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'- TCCTTTAACCAGGTGTTCTTCAAG -3'
(R):5'- AAAACGTGTTGTTCTCAGCAG -3'
Sequencing Primer
(F):5'- CTTCAAGATGAAGTTTGGGTTGTC -3'
(R):5'- ACTTGTAATCCCAAGGCTGG -3'
|
| Posted On |
2019-05-13 |
Incidental Mutation