Incidental Mutation 'R5212:Lig3'
| ID |
403196 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Lig3
|
| Ensembl Gene |
ENSMUSG00000020697 |
| Gene Name |
ligase III, DNA, ATP-dependent |
| Synonyms |
D11Wsu78e |
| MMRRC Submission |
042786-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R5212 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
11 |
| Chromosomal Location |
82671977-82695100 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 82678504 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Threonine to Alanine
at position 248
(T248A)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000133849
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000021039]
[ENSMUST00000080461]
[ENSMUST00000092849]
[ENSMUST00000131537]
[ENSMUST00000173009]
[ENSMUST00000173347]
[ENSMUST00000173722]
[ENSMUST00000173727]
|
| AlphaFold |
no structure available at present |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000021039
AA Change: T249A
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000021039
Gene: ENSMUSG00000020697
AA Change: T249A
| Domain | Start | End | E-Value | Type |
|---|
|
zf-PARP
|
97 |
183 |
8.89e-32 |
SMART |
|
low complexity region
|
188 |
202 |
N/A |
INTRINSIC |
|
Pfam:DNA_ligase_A_N
|
265 |
440 |
3.5e-34 |
PFAM |
|
Pfam:DNA_ligase_A_M
|
489 |
683 |
3.9e-65 |
PFAM |
|
Pfam:DNA_ligase_A_C
|
710 |
820 |
3.8e-21 |
PFAM |
|
low complexity region
|
855 |
885 |
N/A |
INTRINSIC |
|
BRCT
|
942 |
1010 |
9.77e-8 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000080461
AA Change: T249A
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000079317
Gene: ENSMUSG00000020697
AA Change: T249A
| Domain | Start | End | E-Value | Type |
|---|
|
zf-PARP
|
97 |
183 |
8.89e-32 |
SMART |
|
low complexity region
|
188 |
202 |
N/A |
INTRINSIC |
|
Pfam:DNA_ligase_A_N
|
263 |
437 |
6.8e-53 |
PFAM |
|
Pfam:DNA_ligase_A_M
|
485 |
679 |
1.3e-63 |
PFAM |
|
Pfam:DNA_ligase_A_C
|
706 |
816 |
3.2e-21 |
PFAM |
|
low complexity region
|
851 |
881 |
N/A |
INTRINSIC |
|
low complexity region
|
934 |
946 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000092849
AA Change: T249A
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000090525
Gene: ENSMUSG00000020697
AA Change: T249A
| Domain | Start | End | E-Value | Type |
|---|
|
zf-PARP
|
97 |
183 |
8.89e-32 |
SMART |
|
low complexity region
|
188 |
202 |
N/A |
INTRINSIC |
|
Pfam:DNA_ligase_A_N
|
263 |
437 |
1.4e-52 |
PFAM |
|
Pfam:DNA_ligase_A_M
|
485 |
679 |
7.2e-64 |
PFAM |
|
Pfam:DNA_ligase_A_C
|
706 |
816 |
2.2e-21 |
PFAM |
|
low complexity region
|
851 |
881 |
N/A |
INTRINSIC |
|
BRCT
|
938 |
1006 |
9.77e-8 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000131537
AA Change: T249A
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000133672
Gene: ENSMUSG00000020697
AA Change: T249A
| Domain | Start | End | E-Value | Type |
|---|
|
zf-PARP
|
97 |
183 |
8.89e-32 |
SMART |
|
low complexity region
|
188 |
202 |
N/A |
INTRINSIC |
|
Pfam:DNA_ligase_A_N
|
263 |
431 |
3.1e-50 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000172609
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000173009
AA Change: T249A
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000133348
Gene: ENSMUSG00000020697
AA Change: T249A
| Domain | Start | End | E-Value | Type |
|---|
|
zf-PARP
|
97 |
183 |
8.89e-32 |
SMART |
|
low complexity region
|
188 |
202 |
N/A |
INTRINSIC |
|
Pfam:DNA_ligase_A_N
|
263 |
431 |
3.1e-50 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000173347
AA Change: T248A
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000134300
Gene: ENSMUSG00000020697
AA Change: T248A
| Domain | Start | End | E-Value | Type |
|---|
|
zf-PARP
|
97 |
183 |
8.89e-32 |
SMART |
|
low complexity region
|
188 |
202 |
N/A |
INTRINSIC |
|
Pfam:DNA_ligase_A_N
|
262 |
436 |
1.4e-52 |
PFAM |
|
Pfam:DNA_ligase_A_M
|
484 |
678 |
7.2e-64 |
PFAM |
|
Pfam:DNA_ligase_A_C
|
705 |
815 |
2.2e-21 |
PFAM |
|
low complexity region
|
850 |
880 |
N/A |
INTRINSIC |
|
BRCT
|
937 |
1005 |
9.77e-8 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000173722
AA Change: T249A
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000133805
Gene: ENSMUSG00000020697
AA Change: T249A
| Domain | Start | End | E-Value | Type |
|---|
|
zf-PARP
|
97 |
183 |
8.89e-32 |
SMART |
|
low complexity region
|
188 |
202 |
N/A |
INTRINSIC |
|
Pfam:DNA_ligase_A_N
|
263 |
437 |
1.4e-52 |
PFAM |
|
Pfam:DNA_ligase_A_M
|
485 |
679 |
7.2e-64 |
PFAM |
|
Pfam:DNA_ligase_A_C
|
706 |
816 |
2.2e-21 |
PFAM |
|
low complexity region
|
851 |
881 |
N/A |
INTRINSIC |
|
BRCT
|
938 |
1006 |
9.77e-8 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000173727
AA Change: T248A
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000133849
Gene: ENSMUSG00000020697
AA Change: T248A
| Domain | Start | End | E-Value | Type |
|---|
|
zf-PARP
|
97 |
183 |
8.89e-32 |
SMART |
|
low complexity region
|
188 |
202 |
N/A |
INTRINSIC |
|
Pfam:DNA_ligase_A_N
|
262 |
436 |
1.4e-52 |
PFAM |
|
Pfam:DNA_ligase_A_M
|
484 |
678 |
7.2e-64 |
PFAM |
|
Pfam:DNA_ligase_A_C
|
705 |
815 |
2.2e-21 |
PFAM |
|
low complexity region
|
850 |
880 |
N/A |
INTRINSIC |
|
BRCT
|
937 |
1005 |
9.77e-8 |
SMART |
|
| Meta Mutation Damage Score |
0.0898 |
| Coding Region Coverage |
- 1x: 99.3%
- 3x: 98.7%
- 10x: 97.5%
- 20x: 95.7%
|
| Validation Efficiency |
97% (58/60) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene is a member of the DNA ligase family. Each member of this family encodes a protein that catalyzes the joining of DNA ends but they each have a distinct role in DNA metabolism. The protein encoded by this gene is involved in excision repair and is located in both the mitochondria and nucleus, with translation initiation from the upstream start codon allowing for transport to the mitochondria and translation initiation from a downstream start codon allowing for transport to the nucleus. Additionally, alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Jul 2008]
PHENOTYPE: Targeted inactivation of this gene causes embryonic growth arrest at 8.5 dpc, followed by excessive apoptosis at 9.5 dpc, and ultimately death, likely due to unrepaired DNA damage. Homozygous mutant cells display elevated sister chromatid exchange. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 55 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 1110002E22Rik |
T |
A |
3: 137,771,611 (GRCm39) |
S267T |
possibly damaging |
Het |
| Abca9 |
T |
C |
11: 109,998,052 (GRCm39) |
D1514G |
probably benign |
Het |
| Adamtsl4 |
T |
A |
3: 95,584,980 (GRCm39) |
D896V |
probably damaging |
Het |
| Amer2 |
A |
G |
14: 60,617,269 (GRCm39) |
Y362C |
probably damaging |
Het |
| Arglu1 |
T |
A |
8: 8,733,843 (GRCm39) |
R158W |
probably damaging |
Het |
| Arhgef7 |
A |
G |
8: 11,778,388 (GRCm39) |
E46G |
probably benign |
Het |
| Atg2b |
A |
G |
12: 105,613,055 (GRCm39) |
V1172A |
probably benign |
Het |
| Bhlhe23 |
T |
A |
2: 180,417,886 (GRCm39) |
K217N |
probably damaging |
Het |
| Birc6 |
A |
C |
17: 74,977,369 (GRCm39) |
N4388T |
probably damaging |
Het |
| Ccp110 |
C |
T |
7: 118,328,919 (GRCm39) |
A845V |
probably damaging |
Het |
| Cd63 |
A |
G |
10: 128,747,722 (GRCm39) |
Y105C |
probably damaging |
Het |
| Cdk11b |
T |
C |
4: 155,723,072 (GRCm39) |
|
probably null |
Het |
| Clip1 |
T |
A |
5: 123,768,744 (GRCm39) |
R618S |
probably benign |
Het |
| Crybg1 |
A |
T |
10: 43,843,739 (GRCm39) |
F1731L |
possibly damaging |
Het |
| Dock1 |
A |
C |
7: 134,390,923 (GRCm39) |
K728Q |
possibly damaging |
Het |
| Emc2 |
A |
G |
15: 43,374,240 (GRCm39) |
E180G |
probably damaging |
Het |
| F13b |
A |
T |
1: 139,440,725 (GRCm39) |
I394F |
probably benign |
Het |
| Fnta |
A |
G |
8: 26,499,735 (GRCm39) |
I155T |
probably benign |
Het |
| Fshr |
T |
A |
17: 89,293,685 (GRCm39) |
E331V |
probably benign |
Het |
| Fshr |
T |
A |
17: 89,293,684 (GRCm39) |
E331D |
probably benign |
Het |
| Gas2l1 |
A |
T |
11: 5,011,108 (GRCm39) |
C574S |
probably benign |
Het |
| Ggnbp2 |
T |
A |
11: 84,744,847 (GRCm39) |
|
probably benign |
Het |
| Gm3371 |
A |
C |
14: 44,641,111 (GRCm39) |
|
probably benign |
Het |
| Gm7489 |
T |
A |
15: 53,749,016 (GRCm39) |
|
probably benign |
Het |
| Hand1 |
A |
C |
11: 57,722,273 (GRCm39) |
F114V |
probably damaging |
Het |
| Itga4 |
A |
C |
2: 79,110,939 (GRCm39) |
H259P |
probably damaging |
Het |
| Jakmip1 |
A |
T |
5: 37,262,245 (GRCm39) |
H183L |
probably benign |
Het |
| Kifbp |
A |
T |
10: 62,398,908 (GRCm39) |
|
probably benign |
Het |
| Krt8 |
G |
T |
15: 101,906,402 (GRCm39) |
A369D |
possibly damaging |
Het |
| Krt82 |
T |
C |
15: 101,453,484 (GRCm39) |
S301G |
probably damaging |
Het |
| Madcam1 |
C |
G |
10: 79,504,179 (GRCm39) |
T255S |
probably benign |
Het |
| Med20 |
T |
C |
17: 47,929,775 (GRCm39) |
Y71H |
probably benign |
Het |
| Mtss2 |
A |
G |
8: 111,455,850 (GRCm39) |
I107V |
probably damaging |
Het |
| Nans |
T |
C |
4: 46,502,547 (GRCm39) |
F328S |
possibly damaging |
Het |
| Ncbp3 |
A |
G |
11: 72,944,373 (GRCm39) |
|
probably benign |
Het |
| Nek8 |
T |
C |
11: 78,063,342 (GRCm39) |
M1V |
probably null |
Het |
| Nufip1 |
A |
T |
14: 76,370,538 (GRCm39) |
N413I |
possibly damaging |
Het |
| Pbx3 |
T |
C |
2: 34,178,793 (GRCm39) |
|
probably benign |
Het |
| Plppr3 |
C |
T |
10: 79,698,279 (GRCm39) |
G419R |
probably benign |
Het |
| Rfx1 |
G |
T |
8: 84,793,221 (GRCm39) |
|
probably benign |
Het |
| Rnpepl1 |
C |
T |
1: 92,839,045 (GRCm39) |
A68V |
probably benign |
Het |
| Rsbn1l |
A |
T |
5: 21,101,212 (GRCm39) |
M776K |
probably benign |
Het |
| Setd7 |
A |
T |
3: 51,450,238 (GRCm39) |
Y63N |
probably damaging |
Het |
| Slc45a2 |
C |
T |
15: 11,027,871 (GRCm39) |
T480I |
probably damaging |
Het |
| Snap47 |
T |
C |
11: 59,319,178 (GRCm39) |
E320G |
probably damaging |
Het |
| Spaca6 |
C |
A |
17: 18,058,656 (GRCm39) |
P68Q |
probably benign |
Het |
| Tdrd3 |
G |
C |
14: 87,743,651 (GRCm39) |
R527P |
probably damaging |
Het |
| Tmprss2 |
G |
T |
16: 97,377,492 (GRCm39) |
Q202K |
probably benign |
Het |
| Tmprss6 |
A |
G |
15: 78,330,460 (GRCm39) |
V69A |
probably damaging |
Het |
| Trav6-1 |
A |
T |
14: 52,876,161 (GRCm39) |
Q27L |
probably benign |
Het |
| Ttn |
C |
T |
2: 76,731,957 (GRCm39) |
|
probably benign |
Het |
| Ttn |
T |
C |
2: 76,619,945 (GRCm39) |
I15908V |
probably benign |
Het |
| Ttn |
T |
A |
2: 76,628,019 (GRCm39) |
D12931V |
probably damaging |
Het |
| Ush2a |
T |
A |
1: 188,176,902 (GRCm39) |
|
probably null |
Het |
| Wls |
A |
G |
3: 159,578,645 (GRCm39) |
N69S |
probably benign |
Het |
|
| Other mutations in Lig3 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL01066:Lig3
|
APN |
11 |
82,688,141 (GRCm39) |
missense |
possibly damaging |
0.90 |
|
IGL01577:Lig3
|
APN |
11 |
82,674,303 (GRCm39) |
missense |
probably benign |
0.00 |
|
IGL01643:Lig3
|
APN |
11 |
82,689,118 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL01712:Lig3
|
APN |
11 |
82,680,367 (GRCm39) |
splice site |
probably benign |
|
|
IGL01724:Lig3
|
APN |
11 |
82,681,448 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
IGL01749:Lig3
|
APN |
11 |
82,680,693 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL01778:Lig3
|
APN |
11 |
82,685,367 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02798:Lig3
|
APN |
11 |
82,686,531 (GRCm39) |
splice site |
probably benign |
|
|
IGL03007:Lig3
|
APN |
11 |
82,680,401 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL03178:Lig3
|
APN |
11 |
82,680,548 (GRCm39) |
splice site |
probably benign |
|
|
R0001:Lig3
|
UTSW |
11 |
82,681,417 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0115:Lig3
|
UTSW |
11 |
82,684,761 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0834:Lig3
|
UTSW |
11 |
82,689,113 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R1460:Lig3
|
UTSW |
11 |
82,686,624 (GRCm39) |
splice site |
probably benign |
|
|
R1602:Lig3
|
UTSW |
11 |
82,683,020 (GRCm39) |
critical splice donor site |
probably null |
|
|
R1969:Lig3
|
UTSW |
11 |
82,686,544 (GRCm39) |
missense |
probably benign |
0.14 |
|
R1971:Lig3
|
UTSW |
11 |
82,686,544 (GRCm39) |
missense |
probably benign |
0.14 |
|
R1997:Lig3
|
UTSW |
11 |
82,678,492 (GRCm39) |
missense |
probably benign |
0.00 |
|
R3817:Lig3
|
UTSW |
11 |
82,686,941 (GRCm39) |
missense |
possibly damaging |
0.75 |
|
R4083:Lig3
|
UTSW |
11 |
82,681,320 (GRCm39) |
missense |
probably benign |
0.31 |
|
R4084:Lig3
|
UTSW |
11 |
82,686,250 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4665:Lig3
|
UTSW |
11 |
82,691,076 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R4737:Lig3
|
UTSW |
11 |
82,678,553 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5274:Lig3
|
UTSW |
11 |
82,688,118 (GRCm39) |
splice site |
probably null |
|
|
R6320:Lig3
|
UTSW |
11 |
82,684,833 (GRCm39) |
critical splice donor site |
probably null |
|
|
R6807:Lig3
|
UTSW |
11 |
82,674,577 (GRCm39) |
missense |
probably benign |
0.00 |
|
R7103:Lig3
|
UTSW |
11 |
82,688,138 (GRCm39) |
missense |
probably benign |
0.17 |
|
R7552:Lig3
|
UTSW |
11 |
82,679,717 (GRCm39) |
missense |
probably benign |
0.00 |
|
R7646:Lig3
|
UTSW |
11 |
82,674,304 (GRCm39) |
missense |
probably benign |
0.00 |
|
R7910:Lig3
|
UTSW |
11 |
82,688,601 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R7966:Lig3
|
UTSW |
11 |
82,681,342 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8001:Lig3
|
UTSW |
11 |
82,682,902 (GRCm39) |
missense |
probably benign |
0.18 |
|
R8436:Lig3
|
UTSW |
11 |
82,682,870 (GRCm39) |
missense |
possibly damaging |
0.82 |
|
R8699:Lig3
|
UTSW |
11 |
82,685,376 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9352:Lig3
|
UTSW |
11 |
82,686,971 (GRCm39) |
missense |
probably benign |
0.01 |
|
R9392:Lig3
|
UTSW |
11 |
82,680,666 (GRCm39) |
missense |
probably benign |
0.06 |
|
R9452:Lig3
|
UTSW |
11 |
82,681,448 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9469:Lig3
|
UTSW |
11 |
82,686,199 (GRCm39) |
missense |
probably benign |
0.01 |
|
R9726:Lig3
|
UTSW |
11 |
82,674,420 (GRCm39) |
missense |
possibly damaging |
0.89 |
|
| Predicted Primers |
PCR Primer
(F):5'- GTCTATACCTGATACACGGATCCG -3'
(R):5'- GCCATGGCTCTGAGCTTTTC -3'
Sequencing Primer
(F):5'- GGGACATCTCTCTCTAGGGACTC -3'
(R):5'- TCATGGATGATCTGGGTC -3'
|
| Posted On |
2016-07-22 |
Incidental Mutation