Incidental Mutation 'R2343:Lig1'
| ID |
245900 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Lig1
|
| Ensembl Gene |
ENSMUSG00000056394 |
| Gene Name |
ligase I, DNA, ATP-dependent |
| Synonyms |
LigI, mLigI |
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R2343 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
7 |
| Chromosomal Location |
13277283-13311433 bp(+) (GRCm38) |
| Type of Mutation |
splice site (678 bp from exon) |
| DNA Base Change (assembly) |
A to G
at 13292195 bp (GRCm38)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000121102
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000098814]
[ENSMUST00000123025]
[ENSMUST00000146998]
[ENSMUST00000165964]
[ENSMUST00000177588]
[ENSMUST00000185145]
|
| AlphaFold |
no structure available at present |
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000098814
AA Change: D292G
PolyPhen 2
Score 0.777 (Sensitivity: 0.85; Specificity: 0.92)
|
| SMART Domains |
Protein: ENSMUSP00000096411
Gene: ENSMUSG00000056394
AA Change: D292G
| 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 null
Transcript: ENSMUST00000123025
|
| SMART Domains |
Protein: ENSMUSP00000114872
Gene: ENSMUSG00000056394
| 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 null
Transcript: ENSMUST00000146998
|
| SMART Domains |
Protein: ENSMUSP00000121102
Gene: ENSMUSG00000056394
| 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 |
possibly damaging
Transcript: ENSMUST00000165964
AA Change: D292G
PolyPhen 2
Score 0.777 (Sensitivity: 0.85; Specificity: 0.92)
|
| SMART Domains |
Protein: ENSMUSP00000126525
Gene: ENSMUSG00000056394
AA Change: D292G
| 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 |
possibly damaging
Transcript: ENSMUST00000177588
AA Change: D292G
PolyPhen 2
Score 0.777 (Sensitivity: 0.85; Specificity: 0.92)
|
| SMART Domains |
Protein: ENSMUSP00000136972
Gene: ENSMUSG00000056394
AA Change: D292G
| 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: D292G
PolyPhen 2
Score 0.904 (Sensitivity: 0.82; Specificity: 0.94)
|
| SMART Domains |
Protein: ENSMUSP00000138907
Gene: ENSMUSG00000056394
AA Change: D292G
| 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: 97.4%
- 20x: 95.3%
|
| 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: 21 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Bcr |
T |
C |
10: 75,145,422 |
I691T |
probably benign |
Het |
| Col20a1 |
A |
G |
2: 181,001,331 |
T865A |
possibly damaging |
Het |
| Dmxl1 |
G |
A |
18: 49,890,678 |
R1676H |
probably damaging |
Het |
| Dsg2 |
T |
C |
18: 20,602,298 |
V1111A |
probably damaging |
Het |
| Eif3g |
T |
C |
9: 20,895,154 |
Y213C |
probably damaging |
Het |
| Fat4 |
C |
T |
3: 38,957,105 |
S2118F |
probably damaging |
Het |
| Gpr85 |
A |
G |
6: 13,836,696 |
S70P |
probably damaging |
Het |
| Krtap31-1 |
A |
C |
11: 99,908,021 |
T17P |
possibly damaging |
Het |
| Lman2l |
A |
T |
1: 36,428,109 |
D269E |
possibly damaging |
Het |
| Mcc |
A |
G |
18: 44,459,797 |
|
probably null |
Het |
| Nav2 |
T |
C |
7: 49,598,817 |
F2302L |
possibly damaging |
Het |
| Nsf |
C |
T |
11: 103,930,752 |
E26K |
possibly damaging |
Het |
| Olfr1282 |
A |
G |
2: 111,335,700 |
I126T |
probably damaging |
Het |
| Olfr1342 |
C |
A |
4: 118,690,187 |
M88I |
probably benign |
Het |
| Sema6c |
T |
C |
3: 95,167,083 |
F67L |
probably damaging |
Het |
| Sez6l |
A |
T |
5: 112,464,731 |
V448D |
probably damaging |
Het |
| Smoc2 |
A |
G |
17: 14,344,342 |
K160R |
probably benign |
Het |
| Spata2 |
A |
T |
2: 167,483,360 |
V513E |
probably damaging |
Het |
| Susd3 |
T |
A |
13: 49,238,859 |
M107L |
probably damaging |
Het |
| Tnni3k |
A |
G |
3: 154,938,829 |
I564T |
probably benign |
Het |
| Zfp971 |
A |
G |
2: 178,032,994 |
K129E |
possibly damaging |
Het |
|
| Other mutations in Lig1 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00093:Lig1
|
APN |
7 |
13301452 |
nonsense |
probably null |
|
|
IGL00499:Lig1
|
APN |
7 |
13298830 |
critical splice donor site |
probably null |
|
|
IGL01465:Lig1
|
APN |
7 |
13296391 |
missense |
probably benign |
0.19 |
|
IGL01804:Lig1
|
APN |
7 |
13309206 |
missense |
probably benign |
0.43 |
|
IGL02068:Lig1
|
APN |
7 |
13292451 |
splice site |
probably benign |
|
|
IGL02955:Lig1
|
APN |
7 |
13296347 |
missense |
probably damaging |
0.99 |
|
IGL03188:Lig1
|
APN |
7 |
13311107 |
splice site |
probably benign |
|
|
IGL03327:Lig1
|
APN |
7 |
13303855 |
missense |
probably damaging |
1.00 |
|
IGL03411:Lig1
|
APN |
7 |
13296768 |
missense |
probably damaging |
1.00 |
|
PIT4142001:Lig1
|
UTSW |
7 |
13305924 |
frame shift |
probably null |
|
|
R0085:Lig1
|
UTSW |
7 |
13307570 |
missense |
possibly damaging |
0.66 |
|
R0348:Lig1
|
UTSW |
7 |
13309197 |
missense |
probably damaging |
1.00 |
|
R0362:Lig1
|
UTSW |
7 |
13296804 |
unclassified |
probably benign |
|
|
R0787:Lig1
|
UTSW |
7 |
13299069 |
missense |
probably benign |
0.41 |
|
R1170:Lig1
|
UTSW |
7 |
13292153 |
missense |
probably benign |
0.00 |
|
R1371:Lig1
|
UTSW |
7 |
13288685 |
missense |
probably damaging |
1.00 |
|
R1610:Lig1
|
UTSW |
7 |
13285340 |
missense |
probably damaging |
1.00 |
|
R1809:Lig1
|
UTSW |
7 |
13300355 |
splice site |
probably benign |
|
|
R1986:Lig1
|
UTSW |
7 |
13309142 |
nonsense |
probably null |
|
|
R2106:Lig1
|
UTSW |
7 |
13305938 |
missense |
probably damaging |
1.00 |
|
R2380:Lig1
|
UTSW |
7 |
13303796 |
splice site |
probably benign |
|
|
R3545:Lig1
|
UTSW |
7 |
13292163 |
missense |
possibly damaging |
0.82 |
|
R4669:Lig1
|
UTSW |
7 |
13311028 |
missense |
probably damaging |
1.00 |
|
R4928:Lig1
|
UTSW |
7 |
13298738 |
missense |
probably damaging |
1.00 |
|
R5167:Lig1
|
UTSW |
7 |
13311058 |
missense |
probably damaging |
0.97 |
|
R5249:Lig1
|
UTSW |
7 |
13308507 |
missense |
possibly damaging |
0.60 |
|
R5351:Lig1
|
UTSW |
7 |
13300949 |
missense |
probably damaging |
1.00 |
|
R5373:Lig1
|
UTSW |
7 |
13305923 |
frame shift |
probably null |
|
|
R5607:Lig1
|
UTSW |
7 |
13306008 |
missense |
probably damaging |
0.97 |
|
R5608:Lig1
|
UTSW |
7 |
13306008 |
missense |
probably damaging |
0.97 |
|
R5620:Lig1
|
UTSW |
7 |
13286606 |
missense |
possibly damaging |
0.66 |
|
R5799:Lig1
|
UTSW |
7 |
13296258 |
missense |
possibly damaging |
0.67 |
|
R6057:Lig1
|
UTSW |
7 |
13288672 |
missense |
probably damaging |
0.99 |
|
R6897:Lig1
|
UTSW |
7 |
13305914 |
missense |
probably damaging |
1.00 |
|
R7202:Lig1
|
UTSW |
7 |
13291249 |
missense |
probably benign |
0.00 |
|
R7454:Lig1
|
UTSW |
7 |
13288721 |
missense |
probably damaging |
0.99 |
|
R7548:Lig1
|
UTSW |
7 |
13301418 |
missense |
possibly damaging |
0.79 |
|
R7596:Lig1
|
UTSW |
7 |
13305998 |
missense |
probably damaging |
1.00 |
|
R7597:Lig1
|
UTSW |
7 |
13296344 |
missense |
probably benign |
|
|
R7688:Lig1
|
UTSW |
7 |
13289463 |
missense |
probably benign |
|
|
R7733:Lig1
|
UTSW |
7 |
13296231 |
missense |
possibly damaging |
0.87 |
|
R8104:Lig1
|
UTSW |
7 |
13286565 |
missense |
possibly damaging |
0.46 |
|
R8887:Lig1
|
UTSW |
7 |
13296787 |
missense |
probably damaging |
1.00 |
|
R9025:Lig1
|
UTSW |
7 |
13303820 |
missense |
probably damaging |
1.00 |
|
R9321:Lig1
|
UTSW |
7 |
13301009 |
missense |
probably damaging |
1.00 |
|
R9555:Lig1
|
UTSW |
7 |
13291474 |
missense |
probably benign |
|
|
X0020:Lig1
|
UTSW |
7 |
13296774 |
missense |
possibly damaging |
0.48 |
|
| Predicted Primers |
PCR Primer
(F):5'- CTCTGTCAGCAGTGAGGAGATAG -3'
(R):5'- AACATCCTGTAGCCACCCTG -3'
Sequencing Primer
(F):5'- AGATAGGAATGTGTTAACCTTTGGC -3'
(R):5'- TTTCCTGAGATAAATGCAGAGGC -3'
|
| Posted On |
2014-10-30 |
Incidental Mutation