Incidental Mutation 'R0787:Lig1'
| ID |
76901 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Lig1
|
| Ensembl Gene |
ENSMUSG00000056394 |
| Gene Name |
ligase I, DNA, ATP-dependent |
| Synonyms |
LigI, mLigI |
| MMRRC Submission |
038967-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R0787 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
7 |
| Chromosomal Location |
13277283-13311433 bp(+) (GRCm38) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to C
at 13299069 bp (GRCm38)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Lysine to Glutamine
at position 499
(K499Q)
|
| 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 benign
Transcript: ENSMUST00000098814
AA Change: K499Q
PolyPhen 2
Score 0.412 (Sensitivity: 0.89; Specificity: 0.90)
|
| SMART Domains |
Protein: ENSMUSP00000096411
Gene: ENSMUSG00000056394
AA Change: K499Q
| 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: 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 benign
Transcript: ENSMUST00000165964
AA Change: K499Q
PolyPhen 2
Score 0.412 (Sensitivity: 0.89; Specificity: 0.90)
|
| SMART Domains |
Protein: ENSMUSP00000126525
Gene: ENSMUSG00000056394
AA Change: K499Q
| 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: K499Q
PolyPhen 2
Score 0.412 (Sensitivity: 0.89; Specificity: 0.90)
|
| SMART Domains |
Protein: ENSMUSP00000136972
Gene: ENSMUSG00000056394
AA Change: K499Q
| 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 |
|
| Meta Mutation Damage Score |
0.1017 |
| Coding Region Coverage |
- 1x: 99.3%
- 3x: 98.7%
- 10x: 96.9%
- 20x: 93.4%
|
| Validation Efficiency |
100% (56/56) |
| 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 |
|---|
| 0610037L13Rik |
T |
A |
4: 107,890,129 (GRCm38) |
L6Q |
probably damaging |
Het |
| 1700001F09Rik |
A |
T |
14: 43,345,493 (GRCm38) |
|
probably null |
Het |
| Abca8a |
T |
A |
11: 110,042,988 (GRCm38) |
Y1197F |
possibly damaging |
Het |
| Abcc2 |
T |
C |
19: 43,798,516 (GRCm38) |
|
probably null |
Het |
| Adamts16 |
A |
T |
13: 70,738,829 (GRCm38) |
C979S |
probably damaging |
Het |
| Agap2 |
T |
A |
10: 127,085,150 (GRCm38) |
D523E |
unknown |
Het |
| Ankfy1 |
T |
A |
11: 72,760,296 (GRCm38) |
I1024N |
probably damaging |
Het |
| Ankrd13c |
A |
G |
3: 157,994,678 (GRCm38) |
S379G |
probably null |
Het |
| Arhgap40 |
T |
C |
2: 158,547,790 (GRCm38) |
S625P |
probably benign |
Het |
| Armc12 |
G |
C |
17: 28,538,766 (GRCm38) |
A291P |
probably damaging |
Het |
| Armc9 |
A |
G |
1: 86,202,505 (GRCm38) |
N524D |
probably damaging |
Het |
| Col12a1 |
G |
T |
9: 79,638,485 (GRCm38) |
T2305K |
probably damaging |
Het |
| Cyp2c54 |
T |
C |
19: 40,047,635 (GRCm38) |
N277S |
probably benign |
Het |
| E130311K13Rik |
A |
T |
3: 63,920,298 (GRCm38) |
V129E |
probably benign |
Het |
| Ehbp1l1 |
T |
C |
19: 5,722,668 (GRCm38) |
D79G |
possibly damaging |
Het |
| Epb41l1 |
A |
G |
2: 156,494,090 (GRCm38) |
E58G |
probably damaging |
Het |
| Fam217b |
T |
A |
2: 178,420,909 (GRCm38) |
V222E |
probably benign |
Het |
| Fat1 |
T |
A |
8: 45,040,555 (GRCm38) |
Y3913N |
probably damaging |
Het |
| Fgd4 |
A |
G |
16: 16,423,901 (GRCm38) |
|
probably benign |
Het |
| Hltf |
A |
T |
3: 20,106,446 (GRCm38) |
D759V |
probably damaging |
Het |
| Hsp90ab1 |
ACTTCTT |
ACTT |
17: 45,569,499 (GRCm38) |
|
probably benign |
Het |
| Isg15 |
C |
T |
4: 156,199,939 (GRCm38) |
R44H |
probably benign |
Het |
| Itga4 |
C |
T |
2: 79,279,153 (GRCm38) |
T232I |
probably benign |
Het |
| Kntc1 |
C |
A |
5: 123,796,104 (GRCm38) |
H1399Q |
probably benign |
Het |
| Lrrn3 |
C |
A |
12: 41,454,231 (GRCm38) |
C29F |
probably damaging |
Het |
| Mtmr10 |
T |
C |
7: 64,300,615 (GRCm38) |
I136T |
possibly damaging |
Het |
| Naip1 |
A |
G |
13: 100,426,096 (GRCm38) |
Y854H |
probably benign |
Het |
| Olfr770 |
T |
C |
10: 129,133,526 (GRCm38) |
N81D |
possibly damaging |
Het |
| Pcdh9 |
G |
A |
14: 93,886,757 (GRCm38) |
A659V |
possibly damaging |
Het |
| Phf20l1 |
T |
A |
15: 66,615,630 (GRCm38) |
|
probably benign |
Het |
| Phgdh |
A |
G |
3: 98,334,549 (GRCm38) |
V83A |
probably damaging |
Het |
| Pik3r1 |
A |
T |
13: 101,690,523 (GRCm38) |
M326K |
probably benign |
Het |
| Pirb |
A |
T |
7: 3,717,638 (GRCm38) |
L287Q |
probably benign |
Het |
| Pkd1l2 |
T |
C |
8: 117,076,177 (GRCm38) |
D235G |
possibly damaging |
Het |
| Pkhd1l1 |
C |
A |
15: 44,529,264 (GRCm38) |
P1665Q |
probably damaging |
Het |
| Ppp1r7 |
A |
G |
1: 93,364,956 (GRCm38) |
T326A |
probably damaging |
Het |
| Prr22 |
A |
T |
17: 56,771,072 (GRCm38) |
Y75F |
possibly damaging |
Het |
| Ptov1 |
A |
C |
7: 44,865,470 (GRCm38) |
|
probably null |
Het |
| Rasal2 |
A |
G |
1: 157,158,696 (GRCm38) |
S766P |
probably damaging |
Het |
| Shmt1 |
T |
C |
11: 60,792,976 (GRCm38) |
T337A |
probably benign |
Het |
| St5 |
G |
T |
7: 109,525,620 (GRCm38) |
R1068S |
possibly damaging |
Het |
| Tbc1d4 |
A |
T |
14: 101,449,209 (GRCm38) |
I1168N |
probably damaging |
Het |
| Tecpr2 |
T |
C |
12: 110,946,343 (GRCm38) |
V1126A |
probably benign |
Het |
| Tep1 |
A |
T |
14: 50,829,230 (GRCm38) |
S2304T |
possibly damaging |
Het |
| Tiam1 |
C |
A |
16: 89,789,561 (GRCm38) |
R1446M |
probably damaging |
Het |
| Tmem87a |
T |
C |
2: 120,370,484 (GRCm38) |
I425V |
probably benign |
Het |
| Ubr3 |
T |
C |
2: 69,951,421 (GRCm38) |
|
probably benign |
Het |
| Ubxn7 |
T |
A |
16: 32,381,763 (GRCm38) |
|
probably benign |
Het |
| Vmn2r13 |
A |
G |
5: 109,156,847 (GRCm38) |
S573P |
probably damaging |
Het |
| Wdfy3 |
A |
T |
5: 101,957,388 (GRCm38) |
V191E |
probably damaging |
Het |
| Zdhhc3 |
A |
T |
9: 123,083,623 (GRCm38) |
C153* |
probably null |
Het |
| Zfp407 |
A |
T |
18: 84,209,022 (GRCm38) |
V2154D |
probably damaging |
Het |
| Zfp407 |
A |
G |
18: 84,209,346 (GRCm38) |
V2046A |
probably benign |
Het |
| Zfr |
T |
A |
15: 12,140,548 (GRCm38) |
I227N |
unknown |
Het |
|
| Other mutations in Lig1 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00093:Lig1
|
APN |
7 |
13,301,452 (GRCm38) |
nonsense |
probably null |
|
|
IGL00499:Lig1
|
APN |
7 |
13,298,830 (GRCm38) |
critical splice donor site |
probably null |
|
|
IGL01465:Lig1
|
APN |
7 |
13,296,391 (GRCm38) |
missense |
probably benign |
0.19 |
|
IGL01804:Lig1
|
APN |
7 |
13,309,206 (GRCm38) |
missense |
probably benign |
0.43 |
|
IGL02068:Lig1
|
APN |
7 |
13,292,451 (GRCm38) |
splice site |
probably benign |
|
|
IGL02955:Lig1
|
APN |
7 |
13,296,347 (GRCm38) |
missense |
probably damaging |
0.99 |
|
IGL03188:Lig1
|
APN |
7 |
13,311,107 (GRCm38) |
splice site |
probably benign |
|
|
IGL03327:Lig1
|
APN |
7 |
13,303,855 (GRCm38) |
missense |
probably damaging |
1.00 |
|
IGL03411:Lig1
|
APN |
7 |
13,296,768 (GRCm38) |
missense |
probably damaging |
1.00 |
|
PIT4142001:Lig1
|
UTSW |
7 |
13,305,924 (GRCm38) |
frame shift |
probably null |
|
|
R0085:Lig1
|
UTSW |
7 |
13,307,570 (GRCm38) |
missense |
possibly damaging |
0.66 |
|
R0348:Lig1
|
UTSW |
7 |
13,309,197 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R0362:Lig1
|
UTSW |
7 |
13,296,804 (GRCm38) |
unclassified |
probably benign |
|
|
R1170:Lig1
|
UTSW |
7 |
13,292,153 (GRCm38) |
missense |
probably benign |
0.00 |
|
R1371:Lig1
|
UTSW |
7 |
13,288,685 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R1610:Lig1
|
UTSW |
7 |
13,285,340 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R1809:Lig1
|
UTSW |
7 |
13,300,355 (GRCm38) |
splice site |
probably benign |
|
|
R1986:Lig1
|
UTSW |
7 |
13,309,142 (GRCm38) |
nonsense |
probably null |
|
|
R2106:Lig1
|
UTSW |
7 |
13,305,938 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R2343:Lig1
|
UTSW |
7 |
13,292,195 (GRCm38) |
splice site |
probably null |
|
|
R2380:Lig1
|
UTSW |
7 |
13,303,796 (GRCm38) |
splice site |
probably benign |
|
|
R3545:Lig1
|
UTSW |
7 |
13,292,163 (GRCm38) |
missense |
possibly damaging |
0.82 |
|
R4669:Lig1
|
UTSW |
7 |
13,311,028 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R4928:Lig1
|
UTSW |
7 |
13,298,738 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R5167:Lig1
|
UTSW |
7 |
13,311,058 (GRCm38) |
missense |
probably damaging |
0.97 |
|
R5249:Lig1
|
UTSW |
7 |
13,308,507 (GRCm38) |
missense |
possibly damaging |
0.60 |
|
R5351:Lig1
|
UTSW |
7 |
13,300,949 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R5373:Lig1
|
UTSW |
7 |
13,305,923 (GRCm38) |
frame shift |
probably null |
|
|
R5607:Lig1
|
UTSW |
7 |
13,306,008 (GRCm38) |
missense |
probably damaging |
0.97 |
|
R5608:Lig1
|
UTSW |
7 |
13,306,008 (GRCm38) |
missense |
probably damaging |
0.97 |
|
R5620:Lig1
|
UTSW |
7 |
13,286,606 (GRCm38) |
missense |
possibly damaging |
0.66 |
|
R5799:Lig1
|
UTSW |
7 |
13,296,258 (GRCm38) |
missense |
possibly damaging |
0.67 |
|
R6057:Lig1
|
UTSW |
7 |
13,288,672 (GRCm38) |
missense |
probably damaging |
0.99 |
|
R6897:Lig1
|
UTSW |
7 |
13,305,914 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R7202:Lig1
|
UTSW |
7 |
13,291,249 (GRCm38) |
missense |
probably benign |
0.00 |
|
R7454:Lig1
|
UTSW |
7 |
13,288,721 (GRCm38) |
missense |
probably damaging |
0.99 |
|
R7548:Lig1
|
UTSW |
7 |
13,301,418 (GRCm38) |
missense |
possibly damaging |
0.79 |
|
R7596:Lig1
|
UTSW |
7 |
13,305,998 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R7597:Lig1
|
UTSW |
7 |
13,296,344 (GRCm38) |
missense |
probably benign |
|
|
R7688:Lig1
|
UTSW |
7 |
13,289,463 (GRCm38) |
missense |
probably benign |
|
|
R7733:Lig1
|
UTSW |
7 |
13,296,231 (GRCm38) |
missense |
possibly damaging |
0.87 |
|
R8104:Lig1
|
UTSW |
7 |
13,286,565 (GRCm38) |
missense |
possibly damaging |
0.46 |
|
R8887:Lig1
|
UTSW |
7 |
13,296,787 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R9025:Lig1
|
UTSW |
7 |
13,303,820 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R9321:Lig1
|
UTSW |
7 |
13,301,009 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R9555:Lig1
|
UTSW |
7 |
13,291,474 (GRCm38) |
missense |
probably benign |
|
|
X0020:Lig1
|
UTSW |
7 |
13,296,774 (GRCm38) |
missense |
possibly damaging |
0.48 |
|
| Predicted Primers |
PCR Primer
(F):5'- AGAATGCACTTGGGCAGCCTAC -3'
(R):5'- AAGCCCTAATCCTCTCTGTGCTGG -3'
Sequencing Primer
(F):5'- GGGCAGCCTACCTCATTC -3'
(R):5'- ATTATGAGTAGTCACCAGCCTC -3'
|
| Posted On |
2013-10-16 |
Incidental Mutation