Incidental Mutation 'R0348:Lig1'
| ID |
35988 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Lig1
|
| Ensembl Gene |
ENSMUSG00000056394 |
| Gene Name |
ligase I, DNA, ATP-dependent |
| Synonyms |
mLigI, LigI |
| MMRRC Submission |
038555-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R0348 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
7 |
| Chromosomal Location |
13011239-13045350 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to A
at 13043122 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Tryptophan to Arginine
at position 856
(W856R)
|
| 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 damaging
Transcript: ENSMUST00000098814
AA Change: W856R
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000096411
Gene: ENSMUSG00000056394
AA Change: W856R
| 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 damaging
Transcript: ENSMUST00000165964
AA Change: W856R
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000126525
Gene: ENSMUSG00000056394
AA Change: W856R
| 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 damaging
Transcript: ENSMUST00000177588
AA Change: W856R
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000136972
Gene: ENSMUSG00000056394
AA Change: W856R
| 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: 99.2%
- 3x: 98.4%
- 10x: 96.5%
- 20x: 93.5%
|
| Validation Efficiency |
|
| 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: 66 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 4921536K21Rik |
T |
C |
11: 3,844,987 (GRCm39) |
D34G |
probably benign |
Het |
| Adam6a |
T |
C |
12: 113,508,337 (GRCm39) |
S237P |
probably damaging |
Het |
| Adamts13 |
A |
C |
2: 26,871,092 (GRCm39) |
D235A |
probably benign |
Het |
| Adgb |
T |
A |
10: 10,233,623 (GRCm39) |
M1259L |
probably benign |
Het |
| Apbb1 |
T |
C |
7: 105,214,510 (GRCm39) |
Q529R |
probably damaging |
Het |
| Bcl2 |
G |
A |
1: 106,640,292 (GRCm39) |
R107C |
probably damaging |
Het |
| Camta1 |
T |
C |
4: 151,670,888 (GRCm39) |
T96A |
possibly damaging |
Het |
| Ccdc148 |
A |
T |
2: 58,894,084 (GRCm39) |
|
probably null |
Het |
| Cep170b |
T |
C |
12: 112,703,240 (GRCm39) |
Y568H |
probably damaging |
Het |
| Clca4b |
A |
T |
3: 144,627,741 (GRCm39) |
I410N |
probably damaging |
Het |
| Cnot10 |
G |
A |
9: 114,427,838 (GRCm39) |
T592I |
probably benign |
Het |
| Col6a3 |
C |
T |
1: 90,755,771 (GRCm39) |
A173T |
probably damaging |
Het |
| Ctcf |
T |
A |
8: 106,402,789 (GRCm39) |
C560* |
probably null |
Het |
| Daglb |
G |
A |
5: 143,472,951 (GRCm39) |
V369I |
probably benign |
Het |
| Defb19 |
G |
A |
2: 152,422,146 (GRCm39) |
L8F |
unknown |
Het |
| Emcn |
G |
T |
3: 137,078,608 (GRCm39) |
E65* |
probably null |
Het |
| Etl4 |
G |
T |
2: 20,782,940 (GRCm39) |
R753L |
probably damaging |
Het |
| Fam151b |
T |
C |
13: 92,586,689 (GRCm39) |
Y248C |
probably benign |
Het |
| Fmo1 |
T |
C |
1: 162,663,704 (GRCm39) |
D275G |
probably benign |
Het |
| Gjd4 |
A |
G |
18: 9,280,964 (GRCm39) |
V38A |
possibly damaging |
Het |
| Hivep1 |
T |
C |
13: 42,311,855 (GRCm39) |
V1365A |
possibly damaging |
Het |
| Hivep2 |
T |
C |
10: 14,005,702 (GRCm39) |
S767P |
possibly damaging |
Het |
| Hoxa6 |
T |
C |
6: 52,183,548 (GRCm39) |
T166A |
possibly damaging |
Het |
| Ift80 |
G |
T |
3: 68,843,232 (GRCm39) |
L367I |
probably benign |
Het |
| Igf2bp1 |
T |
C |
11: 95,859,719 (GRCm39) |
N369S |
possibly damaging |
Het |
| Igsf11 |
C |
A |
16: 38,829,179 (GRCm39) |
D24E |
probably benign |
Het |
| Ints5 |
C |
T |
19: 8,873,114 (GRCm39) |
L358F |
probably damaging |
Het |
| Kbtbd3 |
A |
G |
9: 4,330,519 (GRCm39) |
T298A |
possibly damaging |
Het |
| Kif28 |
C |
A |
1: 179,558,818 (GRCm39) |
V297F |
probably damaging |
Het |
| Krt12 |
T |
C |
11: 99,308,771 (GRCm39) |
Y422C |
probably damaging |
Het |
| Liph |
C |
T |
16: 21,786,730 (GRCm39) |
|
probably null |
Het |
| Lrig3 |
T |
A |
10: 125,849,317 (GRCm39) |
C1012* |
probably null |
Het |
| Lrit1 |
A |
G |
14: 36,782,182 (GRCm39) |
E285G |
probably damaging |
Het |
| Lrrc31 |
A |
G |
3: 30,743,377 (GRCm39) |
V196A |
probably benign |
Het |
| Lrrn4 |
T |
C |
2: 132,712,363 (GRCm39) |
T487A |
probably benign |
Het |
| Mllt10 |
T |
C |
2: 18,167,424 (GRCm39) |
Y372H |
probably damaging |
Het |
| Mrpl50 |
A |
T |
4: 49,514,515 (GRCm39) |
V52E |
probably damaging |
Het |
| Mthfd1l |
T |
C |
10: 4,006,766 (GRCm39) |
V676A |
probably damaging |
Het |
| Ncl |
C |
T |
1: 86,284,362 (GRCm39) |
D245N |
possibly damaging |
Het |
| Neil1 |
A |
T |
9: 57,054,065 (GRCm39) |
|
probably null |
Het |
| Nfatc3 |
A |
G |
8: 106,818,827 (GRCm39) |
E515G |
probably damaging |
Het |
| Nlrp4b |
A |
G |
7: 10,449,108 (GRCm39) |
E70G |
possibly damaging |
Het |
| Nme3 |
A |
T |
17: 25,115,491 (GRCm39) |
I2F |
possibly damaging |
Het |
| Nup210 |
G |
A |
6: 91,051,292 (GRCm39) |
H364Y |
probably benign |
Het |
| Nxpe3 |
T |
A |
16: 55,686,898 (GRCm39) |
T37S |
probably benign |
Het |
| Olfm1 |
T |
A |
2: 28,102,554 (GRCm39) |
M76K |
probably benign |
Het |
| Pgbd5 |
A |
T |
8: 125,160,771 (GRCm39) |
V32E |
probably damaging |
Het |
| Plcb4 |
T |
C |
2: 135,810,339 (GRCm39) |
M646T |
probably damaging |
Het |
| Plekha7 |
G |
A |
7: 115,757,255 (GRCm39) |
P565L |
probably damaging |
Het |
| Poc5 |
A |
G |
13: 96,535,374 (GRCm39) |
D213G |
probably null |
Het |
| Poli |
A |
G |
18: 70,656,452 (GRCm39) |
I125T |
probably benign |
Het |
| Ppm1f |
T |
C |
16: 16,721,254 (GRCm39) |
M1T |
probably null |
Het |
| Psmd7 |
T |
C |
8: 108,307,523 (GRCm39) |
K320R |
unknown |
Het |
| Rabggtb |
A |
G |
3: 153,615,954 (GRCm39) |
V128A |
probably damaging |
Het |
| Rasa2 |
A |
T |
9: 96,454,012 (GRCm39) |
L308H |
probably damaging |
Het |
| Serpina1d |
C |
T |
12: 103,730,034 (GRCm39) |
V383M |
probably benign |
Het |
| Sipa1l1 |
T |
C |
12: 82,431,530 (GRCm39) |
|
probably null |
Het |
| Sos1 |
T |
C |
17: 80,715,740 (GRCm39) |
T1006A |
probably benign |
Het |
| Sugp1 |
T |
A |
8: 70,522,658 (GRCm39) |
Y453N |
probably damaging |
Het |
| Taf3 |
A |
T |
2: 10,047,455 (GRCm39) |
D64E |
probably benign |
Het |
| Tcf19 |
A |
T |
17: 35,826,801 (GRCm39) |
|
probably null |
Het |
| Trim60 |
T |
A |
8: 65,453,868 (GRCm39) |
H127L |
probably damaging |
Het |
| Tubb4a |
C |
T |
17: 57,387,770 (GRCm39) |
V419M |
probably damaging |
Het |
| Vmn2r22 |
G |
T |
6: 123,614,684 (GRCm39) |
T302K |
probably damaging |
Het |
| Vmn2r68 |
T |
G |
7: 84,870,884 (GRCm39) |
T800P |
possibly damaging |
Het |
| Zfhx2 |
A |
C |
14: 55,300,965 (GRCm39) |
V2262G |
probably 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 |
|
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 |
|
R5373:Lig1
|
UTSW |
7 |
13,039,849 (GRCm39) |
frame shift |
probably null |
|
|
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'- TTTCCCTGAGAAGTGCCATGAGCC -3'
(R):5'- TCAAAGGGAGCAATGCCACTGTC -3'
Sequencing Primer
(F):5'- AGTGCCATGAGCCTCTAAAG -3'
(R):5'- TGAGAATGATGTCTGACACCC -3'
|
| Posted On |
2013-05-09 |
Incidental Mutation