Incidental Mutation 'R7202:Lig1'
ID |
560369 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Lig1
|
Ensembl Gene |
ENSMUSG00000056394 |
Gene Name |
ligase I, DNA, ATP-dependent |
Synonyms |
mLigI, LigI |
MMRRC Submission |
045280-MU
|
Accession Numbers |
|
Essential gene? |
Essential
(E-score: 1.000)
|
Stock # |
R7202 (G1)
|
Quality Score |
225.009 |
Status
|
Validated
|
Chromosome |
7 |
Chromosomal Location |
13011239-13045350 bp(+) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
C to T
at 13025175 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Proline to Serine
at position 227
(P227S)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000096411
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000098814]
[ENSMUST00000123025]
[ENSMUST00000146998]
[ENSMUST00000165964]
[ENSMUST00000177588]
[ENSMUST00000185145]
|
AlphaFold |
no structure available at present |
Predicted Effect |
probably benign
Transcript: ENSMUST00000098814
AA Change: P227S
PolyPhen 2
Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)
|
SMART Domains |
Protein: ENSMUSP00000096411 Gene: ENSMUSG00000056394 AA Change: P227S
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 benign
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 |
probably damaging
Transcript: ENSMUST00000146998
AA Change: P229S
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
SMART Domains |
Protein: ENSMUSP00000121102 Gene: ENSMUSG00000056394 AA Change: P229S
Domain | Start | End | E-Value | Type |
low complexity region
|
99 |
111 |
N/A |
INTRINSIC |
low complexity region
|
160 |
178 |
N/A |
INTRINSIC |
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000165964
AA Change: P227S
PolyPhen 2
Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)
|
SMART Domains |
Protein: ENSMUSP00000126525 Gene: ENSMUSG00000056394 AA Change: P227S
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: P227S
PolyPhen 2
Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)
|
SMART Domains |
Protein: ENSMUSP00000136972 Gene: ENSMUSG00000056394 AA Change: P227S
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 benign
Transcript: ENSMUST00000185145
AA Change: P227S
PolyPhen 2
Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)
|
SMART Domains |
Protein: ENSMUSP00000138907 Gene: ENSMUSG00000056394 AA Change: P227S
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: 100.0%
- 3x: 100.0%
- 10x: 99.7%
- 20x: 99.0%
|
Validation Efficiency |
99% (74/75) |
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: 74 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Abca14 |
T |
C |
7: 119,917,236 (GRCm39) |
I1467T |
probably damaging |
Het |
Abtb3 |
A |
G |
10: 85,223,629 (GRCm39) |
E146G |
unknown |
Het |
Adgrf3 |
T |
A |
5: 30,409,378 (GRCm39) |
K38* |
probably null |
Het |
Ahdc1 |
T |
A |
4: 132,789,198 (GRCm39) |
C146* |
probably null |
Het |
Ahnak |
A |
T |
19: 8,995,163 (GRCm39) |
K5482N |
probably damaging |
Het |
Arhgap23 |
C |
T |
11: 97,342,819 (GRCm39) |
A367V |
possibly damaging |
Het |
Arvcf |
T |
C |
16: 18,223,948 (GRCm39) |
S960P |
probably damaging |
Het |
Asb14 |
C |
A |
14: 26,622,394 (GRCm39) |
P74Q |
probably benign |
Het |
Atad5 |
T |
C |
11: 79,980,601 (GRCm39) |
V2A |
probably damaging |
Het |
Baz2a |
A |
G |
10: 127,954,428 (GRCm39) |
I691M |
possibly damaging |
Het |
Brca2 |
A |
G |
5: 150,455,819 (GRCm39) |
T187A |
probably benign |
Het |
Calr4 |
T |
A |
4: 109,101,254 (GRCm39) |
N152K |
possibly damaging |
Het |
Ccnb2 |
C |
T |
9: 70,318,128 (GRCm39) |
A215T |
probably damaging |
Het |
Cdh16 |
C |
T |
8: 105,340,780 (GRCm39) |
D140N |
unknown |
Het |
Ces1g |
T |
C |
8: 94,029,595 (GRCm39) |
T546A |
probably benign |
Het |
Cfap74 |
G |
T |
4: 155,510,654 (GRCm39) |
|
probably null |
Het |
Cfap91 |
T |
C |
16: 38,155,959 (GRCm39) |
Y88C |
probably benign |
Het |
Col5a1 |
G |
T |
2: 27,842,390 (GRCm39) |
D422Y |
unknown |
Het |
Cyp2c66 |
A |
T |
19: 39,130,348 (GRCm39) |
Y61F |
probably damaging |
Het |
Dnah12 |
G |
A |
14: 26,500,869 (GRCm39) |
|
probably null |
Het |
Dnah6 |
A |
G |
6: 73,158,688 (GRCm39) |
|
probably null |
Het |
Dop1a |
T |
G |
9: 86,386,220 (GRCm39) |
|
probably null |
Het |
Fam163a |
A |
G |
1: 155,954,834 (GRCm39) |
F106L |
probably damaging |
Het |
Gfy |
T |
C |
7: 44,827,596 (GRCm39) |
T167A |
probably benign |
Het |
Gm6525 |
A |
T |
3: 84,082,341 (GRCm39) |
R87S |
probably benign |
Het |
Gramd1c |
C |
A |
16: 43,879,584 (GRCm39) |
A19S |
possibly damaging |
Het |
Herc2 |
T |
C |
7: 55,781,034 (GRCm39) |
V1233A |
probably damaging |
Het |
Hibch |
G |
A |
1: 52,892,874 (GRCm39) |
|
probably null |
Het |
Ibsp |
A |
T |
5: 104,450,027 (GRCm39) |
S9C |
probably benign |
Het |
Il17ra |
A |
G |
6: 120,452,572 (GRCm39) |
I252V |
probably benign |
Het |
Ino80 |
A |
T |
2: 119,204,918 (GRCm39) |
M1536K |
probably benign |
Het |
Ipo11 |
A |
T |
13: 107,012,078 (GRCm39) |
L568Q |
probably damaging |
Het |
Kcnu1 |
T |
G |
8: 26,409,609 (GRCm39) |
|
probably null |
Het |
Kdm5b |
T |
G |
1: 134,552,497 (GRCm39) |
S1158A |
probably benign |
Het |
Kmt2a |
T |
C |
9: 44,759,012 (GRCm39) |
T946A |
probably benign |
Het |
Kmt2e |
A |
T |
5: 23,697,292 (GRCm39) |
|
probably benign |
Het |
Krba1 |
G |
A |
6: 48,389,261 (GRCm39) |
V594M |
probably damaging |
Het |
Lamb1 |
T |
C |
12: 31,374,314 (GRCm39) |
L1559P |
probably damaging |
Het |
Lims2 |
T |
A |
18: 32,090,017 (GRCm39) |
D255E |
probably benign |
Het |
Marchf3 |
C |
T |
18: 56,909,161 (GRCm39) |
C208Y |
probably benign |
Het |
Mei1 |
A |
G |
15: 81,976,843 (GRCm39) |
E142G |
|
Het |
Melk |
G |
T |
4: 44,351,106 (GRCm39) |
R549L |
probably benign |
Het |
Muc6 |
AGGCGCAGAAACCCTGGC |
AGGC |
7: 141,214,363 (GRCm39) |
|
probably null |
Het |
Myorg |
T |
C |
4: 41,498,268 (GRCm39) |
Y454C |
probably damaging |
Het |
Nae1 |
T |
C |
8: 105,250,215 (GRCm39) |
Y226C |
possibly damaging |
Het |
Nap1l1 |
T |
C |
10: 111,326,964 (GRCm39) |
F175S |
probably damaging |
Het |
Ndn |
T |
C |
7: 61,998,709 (GRCm39) |
L185P |
probably damaging |
Het |
Ndst3 |
T |
A |
3: 123,465,388 (GRCm39) |
I195F |
possibly damaging |
Het |
Ndufaf1 |
A |
T |
2: 119,488,907 (GRCm39) |
S206T |
probably benign |
Het |
Nek10 |
C |
A |
14: 14,836,171 (GRCm38) |
H131N |
probably benign |
Het |
Obsl1 |
T |
A |
1: 75,466,360 (GRCm39) |
D1456V |
possibly damaging |
Het |
Or10a2 |
A |
G |
7: 106,673,448 (GRCm39) |
N138D |
probably benign |
Het |
Or10ak7 |
C |
T |
4: 118,791,215 (GRCm39) |
V277I |
probably benign |
Het |
Or52s6 |
T |
A |
7: 103,092,292 (GRCm39) |
T13S |
probably benign |
Het |
Otog |
C |
T |
7: 45,937,474 (GRCm39) |
L1728F |
probably damaging |
Het |
Pcx |
A |
T |
19: 4,652,361 (GRCm39) |
M150L |
possibly damaging |
Het |
Pole |
A |
G |
5: 110,444,973 (GRCm39) |
D443G |
possibly damaging |
Het |
Prr14 |
G |
T |
7: 127,075,648 (GRCm39) |
R552L |
probably damaging |
Het |
Rasgrf1 |
T |
G |
9: 89,899,125 (GRCm39) |
S1156A |
possibly damaging |
Het |
Rfc4 |
T |
A |
16: 22,946,359 (GRCm39) |
|
probably benign |
Het |
Rfx5 |
G |
T |
3: 94,866,272 (GRCm39) |
A524S |
unknown |
Het |
Ryr3 |
G |
A |
2: 112,596,664 (GRCm39) |
P2497S |
probably damaging |
Het |
Scg3 |
T |
C |
9: 75,590,992 (GRCm39) |
T6A |
probably benign |
Het |
Slc26a9 |
A |
T |
1: 131,690,526 (GRCm39) |
D510V |
possibly damaging |
Het |
Stpg3 |
A |
G |
2: 25,104,586 (GRCm39) |
F10L |
probably damaging |
Het |
Tmc5 |
T |
A |
7: 118,239,179 (GRCm39) |
H357Q |
possibly damaging |
Het |
Tmem40 |
A |
T |
6: 115,707,420 (GRCm39) |
L253H |
probably damaging |
Het |
Tmie |
A |
G |
9: 110,696,632 (GRCm39) |
V83A |
probably damaging |
Het |
Uck2 |
A |
T |
1: 167,054,084 (GRCm39) |
I218N |
probably damaging |
Het |
Vtn |
A |
G |
11: 78,391,626 (GRCm39) |
D310G |
possibly damaging |
Het |
Wdr49 |
A |
T |
3: 75,240,580 (GRCm39) |
S430T |
probably benign |
Het |
Wtip |
A |
G |
7: 33,832,087 (GRCm39) |
V133A |
probably benign |
Het |
Zbtb9 |
T |
A |
17: 27,193,666 (GRCm39) |
V357E |
probably damaging |
Het |
Zfp953 |
G |
A |
13: 67,491,706 (GRCm39) |
T82M |
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 |
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 |
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'- TAGTGCTAGAAACTTTATAGTGAGTGG -3'
(R):5'- ACAGGAAGTAGAAGGCCCCT -3'
Sequencing Primer
(F):5'- TGGGGAACATTCTTCACAGC -3'
(R):5'- GTAGAAGGCCCCTACTCCTCATAG -3'
|
Posted On |
2019-06-26 |