Incidental Mutation 'R5373:Lig1'
ID |
428867 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Lig1
|
Ensembl Gene |
ENSMUSG00000056394 |
Gene Name |
ligase I, DNA, ATP-dependent |
Synonyms |
mLigI, LigI |
MMRRC Submission |
042949-MU
|
Accession Numbers |
|
Essential gene? |
Essential
(E-score: 1.000)
|
Stock # |
R5373 (G1)
|
Quality Score |
214 |
Status
|
Validated
|
Chromosome |
7 |
Chromosomal Location |
13011239-13045350 bp(+) (GRCm39) |
Type of Mutation |
frame shift |
DNA Base Change (assembly) |
AG to A
at 13039849 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
|
Ref Sequence |
ENSEMBL: ENSMUSP00000136972
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000098814]
[ENSMUST00000165964]
[ENSMUST00000177588]
|
AlphaFold |
no structure available at present |
Predicted Effect |
probably null
Transcript: ENSMUST00000098814
|
SMART Domains |
Protein: ENSMUSP00000096411 Gene: ENSMUSG00000056394
Domain | Start | End | E-Value | Type |
low complexity region
|
99 |
111 |
N/A |
INTRINSIC |
coiled coil region
|
149 |
173 |
N/A |
INTRINSIC |
Pfam:DNA_ligase_A_N
|
301 |
479 |
8.6e-50 |
PFAM |
Pfam:DNA_ligase_A_M
|
556 |
760 |
3.4e-67 |
PFAM |
Pfam:DNA_ligase_A_C
|
785 |
896 |
9.4e-28 |
PFAM |
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000123846
|
SMART Domains |
Protein: ENSMUSP00000119788 Gene: ENSMUSG00000056394
Domain | Start | End | E-Value | Type |
low complexity region
|
99 |
111 |
N/A |
INTRINSIC |
coiled coil region
|
149 |
173 |
N/A |
INTRINSIC |
Pfam:DNA_ligase_A_N
|
301 |
479 |
4e-47 |
PFAM |
Pfam:DNA_ligase_A_M
|
556 |
687 |
1e-38 |
PFAM |
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000131294
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000138453
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000147735
|
SMART Domains |
Protein: ENSMUSP00000115286 Gene: ENSMUSG00000056394
Domain | Start | End | E-Value | Type |
low complexity region
|
99 |
111 |
N/A |
INTRINSIC |
coiled coil region
|
149 |
173 |
N/A |
INTRINSIC |
Pfam:DNA_ligase_A_N
|
301 |
479 |
4e-47 |
PFAM |
Pfam:DNA_ligase_A_M
|
556 |
687 |
1e-38 |
PFAM |
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000148471
|
SMART Domains |
Protein: ENSMUSP00000114153 Gene: ENSMUSG00000056394
Domain | Start | End | E-Value | Type |
low complexity region
|
99 |
111 |
N/A |
INTRINSIC |
coiled coil region
|
149 |
173 |
N/A |
INTRINSIC |
Pfam:DNA_ligase_A_N
|
301 |
479 |
4e-47 |
PFAM |
Pfam:DNA_ligase_A_M
|
556 |
687 |
1e-38 |
PFAM |
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000156525
|
SMART Domains |
Protein: ENSMUSP00000118055 Gene: ENSMUSG00000056394
Domain | Start | End | E-Value | Type |
low complexity region
|
99 |
111 |
N/A |
INTRINSIC |
coiled coil region
|
149 |
173 |
N/A |
INTRINSIC |
Pfam:DNA_ligase_A_N
|
301 |
479 |
4e-47 |
PFAM |
Pfam:DNA_ligase_A_M
|
556 |
687 |
1e-38 |
PFAM |
|
Predicted Effect |
probably null
Transcript: ENSMUST00000165964
|
SMART Domains |
Protein: ENSMUSP00000126525 Gene: ENSMUSG00000056394
Domain | Start | End | E-Value | Type |
low complexity region
|
99 |
111 |
N/A |
INTRINSIC |
coiled coil region
|
149 |
173 |
N/A |
INTRINSIC |
Pfam:DNA_ligase_A_N
|
302 |
478 |
1.7e-40 |
PFAM |
Pfam:DNA_ligase_A_M
|
556 |
760 |
1.1e-69 |
PFAM |
Pfam:DNA_ligase_A_C
|
785 |
896 |
1.6e-27 |
PFAM |
|
Predicted Effect |
probably null
Transcript: ENSMUST00000177588
|
SMART Domains |
Protein: ENSMUSP00000136972 Gene: ENSMUSG00000056394
Domain | Start | End | E-Value | Type |
low complexity region
|
99 |
111 |
N/A |
INTRINSIC |
coiled coil region
|
149 |
173 |
N/A |
INTRINSIC |
Pfam:DNA_ligase_A_N
|
301 |
479 |
8.6e-50 |
PFAM |
Pfam:DNA_ligase_A_M
|
556 |
760 |
3.4e-67 |
PFAM |
Pfam:DNA_ligase_A_C
|
785 |
896 |
9.4e-28 |
PFAM |
|
Coding Region Coverage |
- 1x: 99.3%
- 3x: 98.6%
- 10x: 97.2%
- 20x: 95.2%
|
Validation Efficiency |
96% (74/77) |
MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the ATP-dependent DNA ligase protein family. The encoded protein functions in DNA replication, recombination, and the base excision repair process. Mutations in this gene that lead to DNA ligase I deficiency result in immunodeficiency and increased sensitivity to DNA-damaging agents. Disruption of this gene may also be associated with a variety of cancers. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2014] PHENOTYPE: Mice homozygous for a null allele exhibit impaired fetal hematopoiesis, develop anemia, and die by E16.5. [provided by MGI curators]
|
Allele List at MGI |
|
Other mutations in this stock |
Total: 68 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
1110002E22Rik |
A |
G |
3: 137,773,396 (GRCm39) |
S862G |
probably benign |
Het |
Abcb5 |
G |
T |
12: 118,850,912 (GRCm39) |
T887K |
probably damaging |
Het |
Adgrf1 |
G |
A |
17: 43,601,896 (GRCm39) |
|
probably benign |
Het |
Adss2 |
T |
G |
1: 177,623,954 (GRCm39) |
I3L |
probably benign |
Het |
Anapc7 |
T |
A |
5: 122,576,280 (GRCm39) |
D302E |
probably benign |
Het |
Ank3 |
A |
G |
10: 69,789,306 (GRCm39) |
|
probably null |
Het |
Arpp21 |
T |
G |
9: 111,896,336 (GRCm39) |
M687L |
probably benign |
Het |
Camkv |
T |
C |
9: 107,824,088 (GRCm39) |
S221P |
probably benign |
Het |
Ccdc88a |
C |
T |
11: 29,413,409 (GRCm39) |
T649M |
possibly damaging |
Het |
Cdh12 |
A |
C |
15: 21,583,998 (GRCm39) |
S613R |
probably damaging |
Het |
Chsy1 |
C |
T |
7: 65,759,824 (GRCm39) |
Q56* |
probably null |
Het |
Cisd2 |
A |
G |
3: 135,114,596 (GRCm39) |
V125A |
probably benign |
Het |
Cntnap2 |
T |
A |
6: 47,084,903 (GRCm39) |
H1121Q |
probably benign |
Het |
Corin |
A |
T |
5: 72,462,296 (GRCm39) |
C876S |
probably damaging |
Het |
Cplane1 |
T |
C |
15: 8,300,287 (GRCm39) |
V3198A |
unknown |
Het |
Cspp1 |
T |
G |
1: 10,204,351 (GRCm39) |
L1038R |
probably damaging |
Het |
Cwc15 |
A |
G |
9: 14,416,234 (GRCm39) |
K147E |
possibly damaging |
Het |
Dlgap2 |
A |
G |
8: 14,873,614 (GRCm39) |
D739G |
probably benign |
Het |
Dmxl2 |
A |
G |
9: 54,276,473 (GRCm39) |
|
probably benign |
Het |
Dnajc6 |
T |
C |
4: 101,472,824 (GRCm39) |
I317T |
probably damaging |
Het |
Dpysl3 |
T |
C |
18: 43,494,101 (GRCm39) |
Y193C |
probably damaging |
Het |
Dtna |
T |
C |
18: 23,784,670 (GRCm39) |
Y730H |
probably damaging |
Het |
Dusp3 |
A |
G |
11: 101,875,451 (GRCm39) |
Y38H |
possibly damaging |
Het |
Eif3m |
A |
T |
2: 104,843,277 (GRCm39) |
I151N |
probably damaging |
Het |
Eml2 |
A |
T |
7: 18,913,188 (GRCm39) |
D62V |
possibly damaging |
Het |
Epb41l3 |
C |
A |
17: 69,593,795 (GRCm39) |
H810N |
probably damaging |
Het |
Evc2 |
C |
T |
5: 37,535,554 (GRCm39) |
R410W |
probably damaging |
Het |
Fam169b |
T |
C |
7: 67,950,586 (GRCm39) |
Y13H |
probably damaging |
Het |
Fcrl5 |
A |
G |
3: 87,353,698 (GRCm39) |
T348A |
probably benign |
Het |
Fezf2 |
A |
T |
14: 12,344,803 (GRCm38) |
V128E |
possibly damaging |
Het |
Ighv3-5 |
A |
G |
12: 114,226,573 (GRCm39) |
S18P |
probably damaging |
Het |
Kcnq5 |
T |
A |
1: 22,031,795 (GRCm39) |
H4L |
unknown |
Het |
Kdm5d |
C |
T |
Y: 927,995 (GRCm39) |
P756S |
probably benign |
Het |
Ly75 |
A |
T |
2: 60,142,115 (GRCm39) |
L1332M |
possibly damaging |
Het |
Med1 |
T |
A |
11: 98,054,789 (GRCm39) |
K378N |
probably damaging |
Het |
Mn1 |
A |
G |
5: 111,569,752 (GRCm39) |
|
probably null |
Het |
Mpo |
T |
C |
11: 87,694,437 (GRCm39) |
|
probably null |
Het |
Mtfr2 |
G |
T |
10: 20,228,598 (GRCm39) |
C48F |
probably benign |
Het |
Nt5c |
G |
A |
11: 115,381,643 (GRCm39) |
|
probably null |
Het |
Pcdhga4 |
T |
C |
18: 37,818,649 (GRCm39) |
V66A |
probably damaging |
Het |
Pik3c3 |
T |
C |
18: 30,445,614 (GRCm39) |
S534P |
probably benign |
Het |
Pla2g4e |
A |
T |
2: 120,016,876 (GRCm39) |
C222S |
probably benign |
Het |
Plch1 |
A |
C |
3: 63,605,499 (GRCm39) |
H1468Q |
probably benign |
Het |
Psd2 |
T |
A |
18: 36,140,556 (GRCm39) |
W610R |
probably damaging |
Het |
Ptgs1 |
A |
T |
2: 36,141,198 (GRCm39) |
K548N |
probably damaging |
Het |
Ptpn14 |
T |
C |
1: 189,583,160 (GRCm39) |
M669T |
probably benign |
Het |
Ptprf |
G |
T |
4: 118,083,238 (GRCm39) |
T923K |
possibly damaging |
Het |
Ptprg |
A |
G |
14: 12,213,665 (GRCm38) |
N1011S |
probably benign |
Het |
Ptprz1 |
T |
A |
6: 23,007,354 (GRCm39) |
V1639E |
probably damaging |
Het |
Rgsl1 |
C |
T |
1: 153,666,053 (GRCm39) |
V986I |
probably benign |
Het |
Rufy4 |
T |
C |
1: 74,186,822 (GRCm39) |
C537R |
probably damaging |
Het |
Rxfp2 |
A |
G |
5: 149,993,725 (GRCm39) |
T596A |
probably benign |
Het |
Serpina3j |
A |
G |
12: 104,280,986 (GRCm39) |
D53G |
probably damaging |
Het |
Slc26a7 |
A |
T |
4: 14,546,447 (GRCm39) |
I294N |
probably damaging |
Het |
Slirp |
T |
C |
12: 87,496,192 (GRCm39) |
S96P |
possibly damaging |
Het |
Snx6 |
T |
C |
12: 54,817,513 (GRCm39) |
E128G |
probably damaging |
Het |
Spata6 |
T |
A |
4: 111,680,031 (GRCm39) |
|
probably null |
Het |
Stap1 |
A |
G |
5: 86,238,787 (GRCm39) |
T152A |
possibly damaging |
Het |
Susd5 |
G |
A |
9: 113,911,653 (GRCm39) |
G188R |
probably damaging |
Het |
Thap2 |
A |
T |
10: 115,208,744 (GRCm39) |
Y125* |
probably null |
Het |
Tnrc18 |
G |
A |
5: 142,725,911 (GRCm39) |
R1793C |
unknown |
Het |
Ugt1a10 |
T |
A |
1: 87,983,632 (GRCm39) |
D143E |
probably damaging |
Het |
Vmn1r85 |
A |
T |
7: 12,818,255 (GRCm39) |
Y296* |
probably null |
Het |
Vmn2r71 |
C |
T |
7: 85,267,750 (GRCm39) |
T68I |
possibly damaging |
Het |
Zc3h6 |
A |
T |
2: 128,844,076 (GRCm39) |
I207F |
possibly damaging |
Het |
Zfp518a |
T |
C |
19: 40,901,954 (GRCm39) |
S628P |
probably benign |
Het |
Zfp85 |
T |
C |
13: 67,897,577 (GRCm39) |
Y165C |
probably damaging |
Het |
Zup1 |
T |
C |
10: 33,803,462 (GRCm39) |
N541D |
possibly damaging |
Het |
|
Other mutations in Lig1 |
Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
IGL00093:Lig1
|
APN |
7 |
13,035,378 (GRCm39) |
nonsense |
probably null |
|
IGL00499:Lig1
|
APN |
7 |
13,032,756 (GRCm39) |
critical splice donor site |
probably null |
|
IGL01465:Lig1
|
APN |
7 |
13,030,317 (GRCm39) |
missense |
probably benign |
0.19 |
IGL01804:Lig1
|
APN |
7 |
13,043,131 (GRCm39) |
missense |
probably benign |
0.43 |
IGL02068:Lig1
|
APN |
7 |
13,026,377 (GRCm39) |
splice site |
probably benign |
|
IGL02955:Lig1
|
APN |
7 |
13,030,273 (GRCm39) |
missense |
probably damaging |
0.99 |
IGL03188:Lig1
|
APN |
7 |
13,045,032 (GRCm39) |
splice site |
probably benign |
|
IGL03327:Lig1
|
APN |
7 |
13,037,781 (GRCm39) |
missense |
probably damaging |
1.00 |
IGL03411:Lig1
|
APN |
7 |
13,030,694 (GRCm39) |
missense |
probably damaging |
1.00 |
PIT4142001:Lig1
|
UTSW |
7 |
13,039,850 (GRCm39) |
frame shift |
probably null |
|
R0085:Lig1
|
UTSW |
7 |
13,041,495 (GRCm39) |
missense |
possibly damaging |
0.66 |
R0348:Lig1
|
UTSW |
7 |
13,043,122 (GRCm39) |
missense |
probably damaging |
1.00 |
R0362:Lig1
|
UTSW |
7 |
13,030,730 (GRCm39) |
unclassified |
probably benign |
|
R0787:Lig1
|
UTSW |
7 |
13,032,995 (GRCm39) |
missense |
probably benign |
0.41 |
R1170:Lig1
|
UTSW |
7 |
13,026,079 (GRCm39) |
missense |
probably benign |
0.00 |
R1371:Lig1
|
UTSW |
7 |
13,022,611 (GRCm39) |
missense |
probably damaging |
1.00 |
R1610:Lig1
|
UTSW |
7 |
13,019,266 (GRCm39) |
missense |
probably damaging |
1.00 |
R1809:Lig1
|
UTSW |
7 |
13,034,281 (GRCm39) |
splice site |
probably benign |
|
R1986:Lig1
|
UTSW |
7 |
13,043,067 (GRCm39) |
nonsense |
probably null |
|
R2106:Lig1
|
UTSW |
7 |
13,039,863 (GRCm39) |
missense |
probably damaging |
1.00 |
R2343:Lig1
|
UTSW |
7 |
13,026,121 (GRCm39) |
splice site |
probably null |
|
R2380:Lig1
|
UTSW |
7 |
13,037,722 (GRCm39) |
splice site |
probably benign |
|
R3545:Lig1
|
UTSW |
7 |
13,026,089 (GRCm39) |
missense |
possibly damaging |
0.82 |
R4669:Lig1
|
UTSW |
7 |
13,044,953 (GRCm39) |
missense |
probably damaging |
1.00 |
R4928:Lig1
|
UTSW |
7 |
13,032,664 (GRCm39) |
missense |
probably damaging |
1.00 |
R5167:Lig1
|
UTSW |
7 |
13,044,983 (GRCm39) |
missense |
probably damaging |
0.97 |
R5249:Lig1
|
UTSW |
7 |
13,042,432 (GRCm39) |
missense |
possibly damaging |
0.60 |
R5351:Lig1
|
UTSW |
7 |
13,034,875 (GRCm39) |
missense |
probably damaging |
1.00 |
R5607:Lig1
|
UTSW |
7 |
13,039,933 (GRCm39) |
missense |
probably damaging |
0.97 |
R5608:Lig1
|
UTSW |
7 |
13,039,933 (GRCm39) |
missense |
probably damaging |
0.97 |
R5620:Lig1
|
UTSW |
7 |
13,020,532 (GRCm39) |
missense |
possibly damaging |
0.66 |
R5799:Lig1
|
UTSW |
7 |
13,030,184 (GRCm39) |
missense |
possibly damaging |
0.67 |
R6057:Lig1
|
UTSW |
7 |
13,022,598 (GRCm39) |
missense |
probably damaging |
0.99 |
R6897:Lig1
|
UTSW |
7 |
13,039,840 (GRCm39) |
missense |
probably damaging |
1.00 |
R7202:Lig1
|
UTSW |
7 |
13,025,175 (GRCm39) |
missense |
probably benign |
0.00 |
R7454:Lig1
|
UTSW |
7 |
13,022,647 (GRCm39) |
missense |
probably damaging |
0.99 |
R7548:Lig1
|
UTSW |
7 |
13,035,344 (GRCm39) |
missense |
possibly damaging |
0.79 |
R7596:Lig1
|
UTSW |
7 |
13,039,923 (GRCm39) |
missense |
probably damaging |
1.00 |
R7597:Lig1
|
UTSW |
7 |
13,030,270 (GRCm39) |
missense |
probably benign |
|
R7688:Lig1
|
UTSW |
7 |
13,023,389 (GRCm39) |
missense |
probably benign |
|
R7733:Lig1
|
UTSW |
7 |
13,030,157 (GRCm39) |
missense |
possibly damaging |
0.87 |
R8104:Lig1
|
UTSW |
7 |
13,020,491 (GRCm39) |
missense |
possibly damaging |
0.46 |
R8887:Lig1
|
UTSW |
7 |
13,030,713 (GRCm39) |
missense |
probably damaging |
1.00 |
R9025:Lig1
|
UTSW |
7 |
13,037,746 (GRCm39) |
missense |
probably damaging |
1.00 |
R9321:Lig1
|
UTSW |
7 |
13,034,935 (GRCm39) |
missense |
probably damaging |
1.00 |
R9555:Lig1
|
UTSW |
7 |
13,025,400 (GRCm39) |
missense |
probably benign |
|
X0020:Lig1
|
UTSW |
7 |
13,030,700 (GRCm39) |
missense |
possibly damaging |
0.48 |
|
Predicted Primers |
PCR Primer
(F):5'- CTGAGTTCAGCATGCTAGTGG -3'
(R):5'- AGCAAAGCTTCAAACCTTGGG -3'
Sequencing Primer
(F):5'- CAGCATGCTAGTGGGATCTGC -3'
(R):5'- GAGAGAAGAGTAGTTACACTCACCC -3'
|
Posted On |
2016-09-06 |