Incidental Mutation 'R5167:Lig1'
| ID |
397346 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Lig1
|
| Ensembl Gene |
ENSMUSG00000056394 |
| Gene Name |
ligase I, DNA, ATP-dependent |
| Synonyms |
mLigI, LigI |
| MMRRC Submission |
042747-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R5167 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
7 |
| Chromosomal Location |
13011239-13045350 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to A
at 13044983 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Valine to Aspartic acid
at position 892
(V892D)
|
| 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: V892D
PolyPhen 2
Score 0.970 (Sensitivity: 0.77; Specificity: 0.96)
|
| SMART Domains |
Protein: ENSMUSP00000096411
Gene: ENSMUSG00000056394
AA Change: V892D
| 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: 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: V892D
PolyPhen 2
Score 0.970 (Sensitivity: 0.77; Specificity: 0.96)
|
| SMART Domains |
Protein: ENSMUSP00000126525
Gene: ENSMUSG00000056394
AA Change: V892D
| 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: V892D
PolyPhen 2
Score 0.970 (Sensitivity: 0.77; Specificity: 0.96)
|
| SMART Domains |
Protein: ENSMUSP00000136972
Gene: ENSMUSG00000056394
AA Change: V892D
| 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 |
0.8034 |
| Coding Region Coverage |
- 1x: 99.3%
- 3x: 98.7%
- 10x: 97.4%
- 20x: 95.7%
|
| Validation Efficiency |
97% (38/39) |
| 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: 35 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abcb1b |
T |
A |
5: 8,862,656 (GRCm39) |
Y113N |
probably damaging |
Het |
| Bcan |
G |
T |
3: 87,901,514 (GRCm39) |
S396Y |
probably damaging |
Het |
| Calm3 |
T |
C |
7: 16,651,626 (GRCm39) |
D21G |
probably damaging |
Het |
| Cldn23 |
C |
T |
8: 36,293,474 (GRCm39) |
V5M |
possibly damaging |
Het |
| D630003M21Rik |
A |
G |
2: 158,047,665 (GRCm39) |
S735P |
probably damaging |
Het |
| Dscaml1 |
T |
C |
9: 45,628,730 (GRCm39) |
Y1095H |
probably damaging |
Het |
| Esr2 |
T |
C |
12: 76,170,048 (GRCm39) |
T427A |
probably benign |
Het |
| Fbxo28 |
T |
C |
1: 182,145,558 (GRCm39) |
I177V |
possibly damaging |
Het |
| Fubp1 |
T |
C |
3: 151,926,989 (GRCm39) |
L372P |
possibly damaging |
Het |
| Glis1 |
G |
A |
4: 107,491,891 (GRCm39) |
G585E |
probably damaging |
Het |
| Gm7258 |
T |
C |
7: 128,197,791 (GRCm39) |
|
noncoding transcript |
Het |
| Hecw1 |
C |
T |
13: 14,460,242 (GRCm39) |
R613Q |
probably damaging |
Het |
| Kif13b |
T |
C |
14: 65,010,384 (GRCm39) |
S1228P |
probably damaging |
Het |
| Knl1 |
A |
G |
2: 118,900,512 (GRCm39) |
I738V |
probably damaging |
Het |
| Lvrn |
T |
A |
18: 47,013,814 (GRCm39) |
Y499N |
probably damaging |
Het |
| Ly9 |
C |
A |
1: 171,432,773 (GRCm39) |
W80L |
probably damaging |
Het |
| Lypd5 |
T |
C |
7: 24,051,889 (GRCm39) |
V68A |
possibly damaging |
Het |
| Ngdn |
C |
T |
14: 55,259,656 (GRCm39) |
Q236* |
probably null |
Het |
| Nudt7 |
C |
A |
8: 114,878,567 (GRCm39) |
C154* |
probably null |
Het |
| Obi1 |
A |
G |
14: 104,716,223 (GRCm39) |
S717P |
probably damaging |
Het |
| Or14j10 |
C |
A |
17: 37,934,642 (GRCm39) |
E295* |
probably null |
Het |
| Or4f14b |
A |
T |
2: 111,775,447 (GRCm39) |
M118K |
probably damaging |
Het |
| Or5b117 |
T |
A |
19: 13,431,741 (GRCm39) |
I47F |
probably damaging |
Het |
| Paxbp1 |
A |
G |
16: 90,819,555 (GRCm39) |
|
probably null |
Het |
| Pcnt |
G |
T |
10: 76,256,258 (GRCm39) |
Q661K |
probably damaging |
Het |
| Plekha1 |
G |
A |
7: 130,487,179 (GRCm39) |
|
probably null |
Het |
| Polr1c |
G |
T |
17: 46,558,635 (GRCm39) |
|
probably benign |
Het |
| Rac3 |
A |
G |
11: 120,613,421 (GRCm39) |
D58G |
probably null |
Het |
| Rgl2 |
C |
T |
17: 34,154,948 (GRCm39) |
R203* |
probably null |
Het |
| Ryr1 |
T |
C |
7: 28,767,118 (GRCm39) |
D2948G |
probably damaging |
Het |
| Serpina12 |
A |
T |
12: 104,004,179 (GRCm39) |
L151Q |
probably damaging |
Het |
| Sf3a1 |
T |
C |
11: 4,127,456 (GRCm39) |
V594A |
possibly damaging |
Het |
| Spdl1 |
G |
T |
11: 34,704,187 (GRCm39) |
H549N |
possibly damaging |
Het |
| Srp68 |
C |
A |
11: 116,156,300 (GRCm39) |
E147D |
probably damaging |
Het |
| Zfp352 |
A |
G |
4: 90,112,453 (GRCm39) |
T198A |
possibly 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 |
|
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'- GATTTCAAACATGCTGACACCC -3'
(R):5'- CAACAGTGCCCATGTTCTCG -3'
Sequencing Primer
(F):5'- TGCTGACACCCCCATTGAGTTAAG -3'
(R):5'- TAGTCTTCAACGTCGGAGTCCAAG -3'
|
| Posted On |
2016-07-06 |
Incidental Mutation