Incidental Mutation 'R5620:Lig1'
| ID |
439786 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Lig1
|
| Ensembl Gene |
ENSMUSG00000056394 |
| Gene Name |
ligase I, DNA, ATP-dependent |
| Synonyms |
mLigI, LigI |
| MMRRC Submission |
043160-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R5620 (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 13020532 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Cysteine to Serine
at position 114
(C114S)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000138907
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000098814]
[ENSMUST00000123025]
[ENSMUST00000146998]
[ENSMUST00000165964]
[ENSMUST00000177588]
[ENSMUST00000185145]
|
| AlphaFold |
no structure available at present |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000098814
AA Change: C114S
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000096411
Gene: ENSMUSG00000056394
AA Change: C114S
| 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 |
possibly damaging
Transcript: ENSMUST00000123025
AA Change: C113S
PolyPhen 2
Score 0.663 (Sensitivity: 0.86; Specificity: 0.91)
|
| SMART Domains |
Protein: ENSMUSP00000114872
Gene: ENSMUSG00000056394
AA Change: C113S
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
96 |
111 |
N/A |
INTRINSIC |
|
low complexity region
|
159 |
177 |
N/A |
INTRINSIC |
|
| 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 |
probably benign
Transcript: ENSMUST00000146998
AA Change: C114S
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
| SMART Domains |
Protein: ENSMUSP00000121102
Gene: ENSMUSG00000056394
AA Change: C114S
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
99 |
111 |
N/A |
INTRINSIC |
|
low complexity region
|
160 |
178 |
N/A |
INTRINSIC |
|
| 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 benign
Transcript: ENSMUST00000165964
AA Change: C114S
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000126525
Gene: ENSMUSG00000056394
AA Change: C114S
| 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 benign
Transcript: ENSMUST00000177588
AA Change: C114S
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000136972
Gene: ENSMUSG00000056394
AA Change: C114S
| 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 |
possibly damaging
Transcript: ENSMUST00000185145
AA Change: C114S
PolyPhen 2
Score 0.663 (Sensitivity: 0.86; Specificity: 0.91)
|
| SMART Domains |
Protein: ENSMUSP00000138907
Gene: ENSMUSG00000056394
AA Change: C114S
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
99 |
111 |
N/A |
INTRINSIC |
|
coiled coil region
|
149 |
173 |
N/A |
INTRINSIC |
|
PDB:1X9N|A
|
247 |
313 |
3e-24 |
PDB |
|
| Coding Region Coverage |
- 1x: 99.3%
- 3x: 98.7%
- 10x: 97.3%
- 20x: 95.4%
|
| 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: 70 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Aaas |
A |
C |
15: 102,246,826 (GRCm39) |
S511A |
probably benign |
Het |
| Abca3 |
C |
T |
17: 24,615,444 (GRCm39) |
T845I |
probably benign |
Het |
| Acaa2 |
G |
A |
18: 74,938,945 (GRCm39) |
A377T |
possibly damaging |
Het |
| Adcy4 |
C |
A |
14: 56,009,824 (GRCm39) |
E743* |
probably null |
Het |
| Ahnak |
T |
A |
19: 8,990,458 (GRCm39) |
L3914* |
probably null |
Het |
| Akap1 |
G |
T |
11: 88,736,343 (GRCm39) |
N106K |
possibly damaging |
Het |
| Arid2 |
C |
T |
15: 96,270,387 (GRCm39) |
T1500I |
probably benign |
Het |
| Atp6v0a2 |
T |
A |
5: 124,783,909 (GRCm39) |
Y252* |
probably null |
Het |
| C4bp |
A |
G |
1: 130,581,090 (GRCm39) |
S140P |
probably damaging |
Het |
| Cald1 |
A |
G |
6: 34,739,047 (GRCm39) |
I384M |
probably damaging |
Het |
| Cdk12 |
A |
G |
11: 98,101,809 (GRCm39) |
I556V |
unknown |
Het |
| Chmp2a |
T |
C |
7: 12,766,237 (GRCm39) |
S174G |
probably benign |
Het |
| Clybl |
T |
A |
14: 122,548,755 (GRCm39) |
N52K |
probably damaging |
Het |
| Cyp4a29 |
C |
A |
4: 115,108,088 (GRCm39) |
S303R |
probably benign |
Het |
| Dab2 |
T |
A |
15: 6,447,796 (GRCm39) |
D59E |
probably damaging |
Het |
| Dag1 |
C |
A |
9: 108,086,214 (GRCm39) |
R309L |
probably damaging |
Het |
| Dync1i2 |
T |
A |
2: 71,088,483 (GRCm39) |
M505K |
probably benign |
Het |
| Eif2b1 |
A |
T |
5: 124,717,075 (GRCm39) |
M1K |
probably null |
Het |
| Epc1 |
A |
G |
18: 6,448,917 (GRCm39) |
S577P |
probably benign |
Het |
| Eps8l1 |
T |
A |
7: 4,463,945 (GRCm39) |
I23N |
possibly damaging |
Het |
| Etl4 |
A |
G |
2: 20,535,037 (GRCm39) |
E164G |
probably damaging |
Het |
| Firrm |
C |
A |
1: 163,789,613 (GRCm39) |
G641* |
probably null |
Het |
| Gadl1 |
A |
T |
9: 115,766,230 (GRCm39) |
M1L |
probably benign |
Het |
| Gda |
T |
C |
19: 21,374,908 (GRCm39) |
D336G |
probably damaging |
Het |
| Grm2 |
A |
T |
9: 106,527,645 (GRCm39) |
V413D |
probably damaging |
Het |
| Hnrnpll |
G |
T |
17: 80,346,051 (GRCm39) |
N403K |
probably damaging |
Het |
| Ifit1 |
T |
A |
19: 34,625,238 (GRCm39) |
F125I |
probably damaging |
Het |
| Igkv5-43 |
C |
T |
6: 69,800,892 (GRCm39) |
V2I |
probably benign |
Het |
| Kat5 |
A |
C |
19: 5,659,507 (GRCm39) |
Y44* |
probably null |
Het |
| Klc2 |
A |
G |
19: 5,162,884 (GRCm39) |
V205A |
probably damaging |
Het |
| Klrb1c |
T |
A |
6: 128,761,706 (GRCm39) |
T133S |
possibly damaging |
Het |
| Krt20 |
A |
G |
11: 99,326,283 (GRCm39) |
L157P |
probably damaging |
Het |
| Krt26 |
G |
T |
11: 99,228,597 (GRCm39) |
T45N |
possibly damaging |
Het |
| Lama2 |
C |
T |
10: 26,866,876 (GRCm39) |
D2873N |
probably damaging |
Het |
| Lonp1 |
G |
C |
17: 56,927,263 (GRCm39) |
A330G |
probably benign |
Het |
| Maml2 |
A |
T |
9: 13,608,616 (GRCm39) |
R21S |
probably damaging |
Het |
| Mrpl35 |
C |
T |
6: 71,794,720 (GRCm39) |
V83I |
probably benign |
Het |
| Myo3b |
A |
G |
2: 70,069,254 (GRCm39) |
R498G |
probably benign |
Het |
| Nup153 |
C |
A |
13: 46,837,482 (GRCm39) |
E1247* |
probably null |
Het |
| Or2t48 |
A |
T |
11: 58,420,557 (GRCm39) |
M85K |
probably damaging |
Het |
| Pcdhac2 |
A |
G |
18: 37,277,257 (GRCm39) |
N79S |
probably benign |
Het |
| Pcgf6 |
C |
T |
19: 47,036,406 (GRCm39) |
G221D |
probably damaging |
Het |
| Phf11b |
C |
T |
14: 59,558,953 (GRCm39) |
D260N |
probably benign |
Het |
| Pla2g5 |
T |
C |
4: 138,531,921 (GRCm39) |
M28V |
possibly damaging |
Het |
| Prpf8 |
T |
C |
11: 75,395,927 (GRCm39) |
S1934P |
possibly damaging |
Het |
| Prr5 |
A |
G |
15: 84,640,570 (GRCm39) |
S140G |
probably benign |
Het |
| Prrc2c |
T |
C |
1: 162,501,098 (GRCm39) |
D1235G |
probably damaging |
Het |
| Rasgrp2 |
T |
C |
19: 6,455,031 (GRCm39) |
S254P |
probably damaging |
Het |
| Rassf8 |
C |
T |
6: 145,765,907 (GRCm39) |
|
probably benign |
Het |
| Rgs20 |
T |
A |
1: 4,982,666 (GRCm39) |
E167D |
probably damaging |
Het |
| Rmnd1 |
G |
T |
10: 4,372,159 (GRCm39) |
A180E |
probably damaging |
Het |
| Rnf103 |
A |
G |
6: 71,486,992 (GRCm39) |
D541G |
probably benign |
Het |
| Rpl9 |
G |
T |
5: 65,546,468 (GRCm39) |
Q140K |
probably benign |
Het |
| Sfmbt1 |
T |
G |
14: 30,506,148 (GRCm39) |
|
probably null |
Het |
| Shank1 |
C |
A |
7: 43,962,160 (GRCm39) |
D10E |
unknown |
Het |
| Srrm4 |
G |
T |
5: 116,587,672 (GRCm39) |
|
probably benign |
Het |
| Sucla2 |
T |
A |
14: 73,832,836 (GRCm39) |
V447E |
probably damaging |
Het |
| Tbc1d1 |
A |
G |
5: 64,331,055 (GRCm39) |
D78G |
probably benign |
Het |
| Tcp1 |
T |
A |
17: 13,138,224 (GRCm39) |
|
probably null |
Het |
| Tctn3 |
C |
A |
19: 40,597,361 (GRCm39) |
E230* |
probably null |
Het |
| Thsd7b |
G |
A |
1: 130,090,673 (GRCm39) |
|
probably null |
Het |
| Tmem63a |
A |
G |
1: 180,797,811 (GRCm39) |
M621V |
probably benign |
Het |
| Tnxb |
A |
T |
17: 34,936,504 (GRCm39) |
K2756* |
probably null |
Het |
| Trpm8 |
G |
A |
1: 88,287,373 (GRCm39) |
|
probably null |
Het |
| Txndc16 |
C |
A |
14: 45,373,335 (GRCm39) |
V764F |
possibly damaging |
Het |
| Ush2a |
A |
T |
1: 188,492,020 (GRCm39) |
D3103V |
possibly damaging |
Het |
| Usp22 |
A |
T |
11: 61,049,206 (GRCm39) |
I381N |
probably damaging |
Het |
| Zfp462 |
T |
A |
4: 55,013,464 (GRCm39) |
M1810K |
probably benign |
Het |
| Zfp64 |
T |
A |
2: 168,741,888 (GRCm39) |
M347L |
possibly damaging |
Het |
| Zfp69 |
T |
C |
4: 120,787,719 (GRCm39) |
D532G |
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 |
|
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 |
|
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 |
|
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'- GGTGGATCTAATGATACCTAGGTG -3'
(R):5'- GAGACAGTTAACCATGCTCACC -3'
Sequencing Primer
(F):5'- TACCTAGGTGAGAGAAGGTGGCC -3'
(R):5'- CACCACAGTTCTACCATTGGAAGG -3'
|
| Posted On |
2016-11-08 |
Incidental Mutation