Incidental Mutation 'R1610:Lig1'
| ID |
176732 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Lig1
|
| Ensembl Gene |
ENSMUSG00000056394 |
| Gene Name |
ligase I, DNA, ATP-dependent |
| Synonyms |
mLigI, LigI |
| MMRRC Submission |
039647-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R1610 (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 13019266 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Leucine to Glutamine
at position 80
(L80Q)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000121102
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000098814]
[ENSMUST00000123025]
[ENSMUST00000146998]
[ENSMUST00000165964]
[ENSMUST00000185145]
[ENSMUST00000177588]
|
| AlphaFold |
no structure available at present |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000098814
AA Change: L80Q
PolyPhen 2
Score 0.965 (Sensitivity: 0.78; Specificity: 0.95)
|
| SMART Domains |
Protein: ENSMUSP00000096411
Gene: ENSMUSG00000056394
AA Change: L80Q
| 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 |
probably damaging
Transcript: ENSMUST00000123025
AA Change: L80Q
PolyPhen 2
Score 0.974 (Sensitivity: 0.76; Specificity: 0.96)
|
| SMART Domains |
Protein: ENSMUSP00000114872
Gene: ENSMUSG00000056394
AA Change: L80Q
| 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 damaging
Transcript: ENSMUST00000146998
AA Change: L80Q
PolyPhen 2
Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
|
| SMART Domains |
Protein: ENSMUSP00000121102
Gene: ENSMUSG00000056394
AA Change: L80Q
| 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 damaging
Transcript: ENSMUST00000165964
AA Change: L80Q
PolyPhen 2
Score 0.965 (Sensitivity: 0.78; Specificity: 0.95)
|
| SMART Domains |
Protein: ENSMUSP00000126525
Gene: ENSMUSG00000056394
AA Change: L80Q
| 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: ENSMUST00000185145
AA Change: L80Q
PolyPhen 2
Score 0.974 (Sensitivity: 0.76; Specificity: 0.96)
|
| SMART Domains |
Protein: ENSMUSP00000138907
Gene: ENSMUSG00000056394
AA Change: L80Q
| 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 |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000177588
AA Change: L80Q
PolyPhen 2
Score 0.965 (Sensitivity: 0.78; Specificity: 0.95)
|
| SMART Domains |
Protein: ENSMUSP00000136972
Gene: ENSMUSG00000056394
AA Change: L80Q
| 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: 93.1%
|
| 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: 54 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Acbd5 |
G |
A |
2: 22,980,563 (GRCm39) |
C312Y |
probably damaging |
Het |
| Adgrl1 |
T |
A |
8: 84,659,002 (GRCm39) |
M601K |
probably benign |
Het |
| Agbl4 |
G |
A |
4: 111,514,365 (GRCm39) |
E459K |
probably benign |
Het |
| Anxa2 |
TCCC |
TCC |
9: 69,397,036 (GRCm39) |
|
probably null |
Het |
| Casz1 |
C |
T |
4: 149,013,544 (GRCm39) |
A36V |
possibly damaging |
Het |
| Cfap20dc |
G |
T |
14: 8,511,110 (GRCm38) |
H435N |
probably benign |
Het |
| Chpf |
A |
G |
1: 75,453,292 (GRCm39) |
V327A |
probably damaging |
Het |
| Cldn23 |
A |
G |
8: 36,293,084 (GRCm39) |
Y135H |
probably damaging |
Het |
| Cobll1 |
C |
T |
2: 64,963,986 (GRCm39) |
D211N |
probably damaging |
Het |
| Cramp1 |
A |
G |
17: 25,202,925 (GRCm39) |
V368A |
probably benign |
Het |
| Dnah6 |
T |
C |
6: 73,121,946 (GRCm39) |
T1374A |
probably benign |
Het |
| Dpyd |
A |
G |
3: 118,858,655 (GRCm39) |
H623R |
probably benign |
Het |
| Dyrk2 |
T |
C |
10: 118,695,830 (GRCm39) |
N476S |
probably benign |
Het |
| Endog |
A |
T |
2: 30,063,899 (GRCm39) |
I267F |
probably damaging |
Het |
| Ephb6 |
A |
T |
6: 41,591,307 (GRCm39) |
K155* |
probably null |
Het |
| Far2 |
T |
C |
6: 148,058,956 (GRCm39) |
V214A |
possibly damaging |
Het |
| Fat2 |
A |
G |
11: 55,169,750 (GRCm39) |
V3003A |
probably damaging |
Het |
| Frg2f1 |
T |
A |
4: 119,388,485 (GRCm39) |
T5S |
possibly damaging |
Het |
| Gm14496 |
A |
T |
2: 181,637,972 (GRCm39) |
T349S |
probably benign |
Het |
| Golgb1 |
A |
G |
16: 36,746,463 (GRCm39) |
T2951A |
probably benign |
Het |
| Hc |
G |
T |
2: 34,896,173 (GRCm39) |
D1203E |
probably benign |
Het |
| Isg20 |
C |
A |
7: 78,564,257 (GRCm39) |
Q55K |
possibly damaging |
Het |
| Jph4 |
G |
T |
14: 55,351,560 (GRCm39) |
A152E |
probably damaging |
Het |
| Kcnq3 |
T |
C |
15: 65,897,109 (GRCm39) |
T264A |
probably damaging |
Het |
| Kcnq5 |
T |
G |
1: 21,527,685 (GRCm39) |
T463P |
probably damaging |
Het |
| Klra8 |
A |
G |
6: 130,095,981 (GRCm39) |
S204P |
probably damaging |
Het |
| Ldlrad1 |
A |
G |
4: 107,072,072 (GRCm39) |
D98G |
probably damaging |
Het |
| Lhfpl4 |
T |
C |
6: 113,171,097 (GRCm39) |
T30A |
possibly damaging |
Het |
| Lmbrd2 |
A |
G |
15: 9,186,699 (GRCm39) |
Y558C |
probably benign |
Het |
| Lrrn3 |
G |
T |
12: 41,502,992 (GRCm39) |
L442I |
possibly damaging |
Het |
| Mc2r |
A |
G |
18: 68,540,519 (GRCm39) |
F258S |
probably damaging |
Het |
| Mmp16 |
A |
G |
4: 18,011,582 (GRCm39) |
T137A |
probably benign |
Het |
| Nfatc2ip |
A |
T |
7: 125,986,579 (GRCm39) |
S359T |
probably damaging |
Het |
| Nup214 |
C |
T |
2: 31,924,478 (GRCm39) |
S1669F |
probably damaging |
Het |
| Nup50l |
G |
T |
6: 96,142,270 (GRCm39) |
P258Q |
probably damaging |
Het |
| Or10a48 |
T |
A |
7: 108,425,131 (GRCm39) |
H25L |
probably benign |
Het |
| Or4c15b |
T |
C |
2: 89,113,165 (GRCm39) |
H104R |
probably damaging |
Het |
| Or4s2b |
A |
T |
2: 88,508,918 (GRCm39) |
K233* |
probably null |
Het |
| Or8b1b |
C |
T |
9: 38,375,927 (GRCm39) |
L197F |
probably damaging |
Het |
| Pacc1 |
A |
G |
1: 191,077,262 (GRCm39) |
D195G |
probably benign |
Het |
| Plagl1 |
C |
T |
10: 13,004,706 (GRCm39) |
|
probably benign |
Het |
| Plxnb2 |
A |
T |
15: 89,042,696 (GRCm39) |
S1531T |
probably damaging |
Het |
| Ptpn22 |
G |
A |
3: 103,809,512 (GRCm39) |
|
probably null |
Het |
| Rtn1 |
T |
A |
12: 72,266,053 (GRCm39) |
Q174L |
possibly damaging |
Het |
| Selenoo |
A |
G |
15: 88,984,119 (GRCm39) |
E645G |
probably benign |
Het |
| Serpina1a |
A |
C |
12: 103,820,096 (GRCm39) |
D383E |
possibly damaging |
Het |
| Slc6a18 |
T |
A |
13: 73,816,344 (GRCm39) |
Y345F |
probably benign |
Het |
| Smbd1 |
A |
G |
16: 32,627,135 (GRCm39) |
V51A |
possibly damaging |
Het |
| Tchh |
C |
T |
3: 93,352,146 (GRCm39) |
R529W |
unknown |
Het |
| Tonsl |
A |
T |
15: 76,522,757 (GRCm39) |
Y165N |
probably damaging |
Het |
| Trdmt1 |
G |
A |
2: 13,520,870 (GRCm39) |
T344I |
probably damaging |
Het |
| Ubash3b |
C |
A |
9: 40,954,796 (GRCm39) |
R116L |
probably damaging |
Het |
| Vmn2r94 |
A |
G |
17: 18,463,995 (GRCm39) |
V765A |
probably damaging |
Het |
| Zfp474 |
C |
T |
18: 52,771,437 (GRCm39) |
T30I |
probably benign |
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 |
|
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'- TGCTCACTGCTCACTGAAATGGAAG -3'
(R):5'- TGCCAATCTCCTGAACAATGTCCC -3'
Sequencing Primer
(F):5'- CTGCTCACTGAAATGGAAGAGAAG -3'
(R):5'- gctgcacaagcctagagac -3'
|
| Posted On |
2014-04-24 |
Incidental Mutation