Incidental Mutation 'R1170:Lig1'
ID99300
Institutional Source Beutler Lab
Gene Symbol Lig1
Ensembl Gene ENSMUSG00000056394
Gene Nameligase I, DNA, ATP-dependent
SynonymsLigI, mLigI
MMRRC Submission 039243-MU
Accession Numbers
Is this an essential gene? Essential (E-score: 1.000) question?
Stock #R1170 (G1)
Quality Score225
Status Validated
Chromosome7
Chromosomal Location13277283-13311433 bp(+) (GRCm38)
Type of Mutationmissense
DNA Base Change (assembly) C to T at 13292153 bp
ZygosityHeterozygous
Amino Acid Change Alanine to Valine at position 278 (A278V)
Ref Sequence ENSEMBL: ENSMUSP00000138907 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000098814] [ENSMUST00000123025] [ENSMUST00000146998] [ENSMUST00000165964] [ENSMUST00000177588] [ENSMUST00000185145]
Predicted Effect probably benign
Transcript: ENSMUST00000098814
AA Change: A278V

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000096411
Gene: ENSMUSG00000056394
AA Change: A278V

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
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 benign
Transcript: ENSMUST00000146998
SMART Domains Protein: ENSMUSP00000121102
Gene: ENSMUSG00000056394

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
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 benign
Transcript: ENSMUST00000165964
AA Change: A278V

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000126525
Gene: ENSMUSG00000056394
AA Change: A278V

DomainStartEndE-ValueType
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: A278V

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000136972
Gene: ENSMUSG00000056394
AA Change: A278V

DomainStartEndE-ValueType
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: A278V

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000138907
Gene: ENSMUSG00000056394
AA Change: A278V

DomainStartEndE-ValueType
low complexity region 99 111 N/A INTRINSIC
coiled coil region 149 173 N/A INTRINSIC
PDB:1X9N|A 247 313 3e-24 PDB
Meta Mutation Damage Score 0.0898 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.3%
  • 10x: 96.4%
  • 20x: 93.0%
Validation Efficiency 100% (105/105)
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: 104 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700025G04Rik A G 1: 151,980,412 probably benign Het
4932438A13Rik T C 3: 37,044,631 S1136P probably damaging Het
Akap9 G A 5: 4,055,671 S2914N probably benign Het
Alk T C 17: 71,900,734 D1002G probably damaging Het
Ap3d1 A G 10: 80,732,840 probably benign Het
Asb15 T C 6: 24,562,487 probably benign Het
Asxl3 C A 18: 22,524,507 P1858Q probably benign Het
BC003331 T A 1: 150,386,391 E99D probably benign Het
Bud31 T A 5: 145,142,578 probably benign Het
C1qtnf1 G T 11: 118,448,269 R255L probably damaging Het
Cacna2d4 C T 6: 119,307,286 R745W probably damaging Het
Cage1 C T 13: 38,022,880 E330K probably damaging Het
Catsperz T A 19: 6,924,949 N59I probably benign Het
Ccdc110 G T 8: 45,941,885 S271I probably benign Het
Ccdc88b T A 19: 6,853,213 E787V probably damaging Het
Ccna2 A T 3: 36,568,970 probably benign Het
Cd36 T A 5: 17,813,088 D209V probably damaging Het
Cers4 T A 8: 4,519,475 W161R probably damaging Het
Ces2f T A 8: 104,953,546 H442Q probably damaging Het
Chchd6 A C 6: 89,384,687 C245G probably damaging Het
Cndp1 T G 18: 84,611,625 Q481P probably benign Het
Col3a1 A G 1: 45,327,601 R234G unknown Het
Col3a1 A T 1: 45,347,724 N232I probably damaging Het
Colgalt2 A T 1: 152,503,017 D398V probably damaging Het
Cxcl10 TACTCAC TACTCACTCAC 5: 92,348,082 probably null Het
Dcdc2a C A 13: 25,056,307 Q13K probably benign Het
Dzip3 A T 16: 48,961,208 I240N probably damaging Het
Epb41l3 T A 17: 69,259,180 L452* probably null Het
Fam193b C T 13: 55,541,705 A753T probably damaging Het
Fam35a A T 14: 34,268,491 S153T possibly damaging Het
Fam47e G C 5: 92,565,922 probably benign Het
Fastkd1 A G 2: 69,708,649 probably benign Het
Fmnl1 G A 11: 103,197,370 G69D probably benign Het
Foxn2 A G 17: 88,473,666 probably benign Het
Fsip2 A G 2: 82,991,500 E5859G possibly damaging Het
Gm9894 T A 13: 67,764,701 noncoding transcript Het
H2-Bl T C 17: 36,081,091 N44S possibly damaging Het
Helz2 T C 2: 181,229,815 Y2668C probably damaging Het
Hhipl1 T A 12: 108,311,693 C93* probably null Het
Lipn T A 19: 34,071,758 I108K probably benign Het
Lsamp A G 16: 42,151,229 probably benign Het
Map3k14 A G 11: 103,238,917 probably benign Het
Mdm4 A T 1: 132,991,820 C436S probably damaging Het
Mdm4 A G 1: 133,012,692 L33P probably damaging Het
Meiob T C 17: 24,836,484 W422R probably damaging Het
Mppe1 T C 18: 67,227,706 Y254C probably damaging Het
Mterf1a A T 5: 3,890,964 N301K probably benign Het
Muc6 C T 7: 141,644,233 S1210N probably damaging Het
Mycbp2 A T 14: 103,200,152 Y2091* probably null Het
Mylk G A 16: 34,874,039 R156H probably benign Het
Myo15 G T 11: 60,479,407 D998Y probably benign Het
Neb A T 2: 52,196,357 Y5235N probably damaging Het
Nop58 A G 1: 59,704,211 probably benign Het
Nr4a3 A G 4: 48,051,564 H135R probably damaging Het
Nr4a3 A G 4: 48,083,324 K619R probably benign Het
Nrg1 T C 8: 31,837,667 probably benign Het
Olfr1031 A T 2: 85,992,696 N293I probably damaging Het
Olfr1312 A T 2: 112,042,215 D272E probably benign Het
Olfr1484 T C 19: 13,586,213 V260A probably benign Het
Olfr938 T A 9: 39,078,229 D172V possibly damaging Het
Parp3 T C 9: 106,476,005 probably benign Het
Pde2a A G 7: 101,484,543 E103G probably benign Het
Pds5a A T 5: 65,635,302 probably benign Het
Pip4k2c A G 10: 127,211,393 V40A unknown Het
Pitrm1 T C 13: 6,552,744 probably benign Het
Plk4 A G 3: 40,801,847 I64M probably damaging Het
Ppp1r16a C T 15: 76,693,669 Q328* probably null Het
Ppp2r1a T C 17: 20,951,331 probably benign Het
Ppp4r3b T A 11: 29,209,426 N172K probably damaging Het
Prkcg G A 7: 3,319,661 R357Q probably damaging Het
Prmt3 T C 7: 49,848,547 probably null Het
Prx T A 7: 27,518,007 C644* probably null Het
Ptpru A G 4: 131,808,527 probably benign Het
Rbm5 A T 9: 107,742,497 D738E probably damaging Het
Recql5 A T 11: 115,897,234 Y420N probably damaging Het
Rnf17 T C 14: 56,425,631 I152T probably benign Het
Rnpepl1 A G 1: 92,919,195 S580G possibly damaging Het
Ryr3 C T 2: 112,946,987 G275D probably damaging Het
Serpinb9e T A 13: 33,257,752 Y222* probably null Het
Slc10a1 T A 12: 80,956,028 I279F probably damaging Het
Slc12a8 G T 16: 33,662,977 G584V probably damaging Het
Slc35b3 T A 13: 38,937,331 Y311F probably benign Het
Slc44a5 A G 3: 154,257,720 probably null Het
Slc6a9 A G 4: 117,864,806 E422G possibly damaging Het
Smpd2 A G 10: 41,488,732 probably null Het
Spast A G 17: 74,381,968 probably null Het
Spink5 A T 18: 43,983,563 E208V probably benign Het
Stag1 T C 9: 100,888,453 probably benign Het
Stambp A G 6: 83,563,821 probably null Het
Sult3a2 A T 10: 33,777,192 M184K possibly damaging Het
Tcp11 T C 17: 28,071,662 D162G probably damaging Het
Themis A C 10: 28,668,748 E30A possibly damaging Het
Tmc7 G A 7: 118,551,260 S350L probably benign Het
Tmem131 A T 1: 36,834,898 Y271* probably null Het
Trim35 T A 14: 66,308,799 S338R probably benign Het
Trim42 C A 9: 97,363,620 V376F probably benign Het
Tshr A T 12: 91,538,097 K11M probably damaging Het
Vps8 A G 16: 21,459,820 probably benign Het
Wdr11 T C 7: 129,607,107 probably benign Het
Wdr26 A T 1: 181,181,294 probably benign Het
Wdtc1 A G 4: 133,297,546 Y447H probably damaging Het
Zfp687 C T 3: 95,008,473 C996Y probably damaging Het
Zfp984 A T 4: 147,755,989 V135E probably benign Het
Zranb2 T C 3: 157,541,865 probably benign Het
Other mutations in Lig1
AlleleSourceChrCoordTypePredicted EffectPPH 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
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
R2343:Lig1 UTSW 7 13292195 splice site probably null
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
X0020:Lig1 UTSW 7 13296774 missense possibly damaging 0.48
Predicted Primers
Posted On2014-01-15