Incidental Mutation 'R5351:Lig1'
| ID |
423799 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Lig1
|
| Ensembl Gene |
ENSMUSG00000056394 |
| Gene Name |
ligase I, DNA, ATP-dependent |
| Synonyms |
mLigI, LigI |
| MMRRC Submission |
042930-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R5351 (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 C
at 13034875 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Methionine to Threonine
at position 557
(M557T)
|
| 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: M557T
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000096411
Gene: ENSMUSG00000056394
AA Change: M557T
| 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 damaging
Transcript: ENSMUST00000165964
AA Change: M557T
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000126525
Gene: ENSMUSG00000056394
AA Change: M557T
| 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: M557T
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000136972
Gene: ENSMUSG00000056394
AA Change: M557T
| 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: 99.4%
- 3x: 98.8%
- 10x: 97.7%
- 20x: 96.2%
|
| 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: 28 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Alpk1 |
T |
A |
3: 127,522,941 (GRCm39) |
S34C |
probably damaging |
Het |
| Apol7e |
T |
G |
15: 77,602,511 (GRCm39) |
*370G |
probably null |
Het |
| Cacna2d4 |
T |
C |
6: 119,245,162 (GRCm39) |
I290T |
probably damaging |
Het |
| Ceacam12 |
T |
A |
7: 17,801,159 (GRCm39) |
V46D |
probably damaging |
Het |
| Ces1d |
A |
G |
8: 93,904,706 (GRCm39) |
Y345H |
probably damaging |
Het |
| Cirbp |
T |
C |
10: 80,006,136 (GRCm39) |
|
probably benign |
Het |
| Cnot8 |
T |
A |
11: 58,006,147 (GRCm39) |
H225Q |
probably damaging |
Het |
| Fstl1 |
T |
C |
16: 37,649,542 (GRCm39) |
V252A |
probably damaging |
Het |
| H2-T3 |
T |
C |
17: 36,500,965 (GRCm39) |
Q17R |
probably benign |
Het |
| Htt |
A |
G |
5: 34,961,177 (GRCm39) |
Y268C |
probably damaging |
Het |
| Ildr2 |
T |
C |
1: 166,136,478 (GRCm39) |
V439A |
possibly damaging |
Het |
| Ltbp2 |
T |
C |
12: 84,837,132 (GRCm39) |
E1229G |
possibly damaging |
Het |
| Mynn |
C |
T |
3: 30,661,691 (GRCm39) |
R258W |
probably benign |
Het |
| Nbas |
T |
A |
12: 13,610,850 (GRCm39) |
N2180K |
probably damaging |
Het |
| Or8j3c |
A |
G |
2: 86,253,610 (GRCm39) |
S137P |
probably damaging |
Het |
| Pcdh1 |
C |
T |
18: 38,330,819 (GRCm39) |
G728D |
probably damaging |
Het |
| Pfas |
T |
C |
11: 68,882,217 (GRCm39) |
D882G |
probably damaging |
Het |
| Prkar2b |
C |
T |
12: 32,022,126 (GRCm39) |
G60R |
probably damaging |
Het |
| Prkdc |
G |
C |
16: 15,649,176 (GRCm39) |
V3717L |
probably benign |
Het |
| Prom1 |
A |
T |
5: 44,201,697 (GRCm39) |
V250E |
probably damaging |
Het |
| Slc35d1 |
A |
G |
4: 103,047,036 (GRCm39) |
L254P |
probably damaging |
Het |
| Srrt |
T |
C |
5: 137,296,546 (GRCm39) |
*239W |
probably null |
Het |
| Tns2 |
C |
T |
15: 102,017,369 (GRCm39) |
R281C |
probably damaging |
Het |
| Ttn |
T |
A |
2: 76,585,168 (GRCm39) |
I22042F |
probably damaging |
Het |
| Ttn |
A |
G |
2: 76,773,385 (GRCm39) |
V2339A |
probably damaging |
Het |
| Unc80 |
T |
A |
1: 66,645,672 (GRCm39) |
S1449R |
possibly damaging |
Het |
| Vmn2r24 |
A |
T |
6: 123,793,223 (GRCm39) |
K850M |
possibly damaging |
Het |
| Zfp516 |
A |
G |
18: 82,974,876 (GRCm39) |
E358G |
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 |
|
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 |
|
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'- GACCTTTATTAGCTTCCAGGGAG -3'
(R):5'- TGTGTCTGGCATTCACCATC -3'
Sequencing Primer
(F):5'- AGGCTGGTATGAGGACCC -3'
(R):5'- TGTGTGCACGCACTCAC -3'
|
| Posted On |
2016-08-04 |
Incidental Mutation