Incidental Mutation 'R7597:Lig1'
ID 587783
Institutional Source Beutler Lab
Gene Symbol Lig1
Ensembl Gene ENSMUSG00000056394
Gene Name ligase I, DNA, ATP-dependent
Synonyms mLigI, LigI
MMRRC Submission 045672-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R7597 (G1)
Quality Score 225.009
Status Not validated
Chromosome 7
Chromosomal Location 13011239-13045350 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to G at 13030270 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Alanine at position 416 (S416A)
Ref Sequence ENSEMBL: ENSMUSP00000096411 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000098814] [ENSMUST00000146998] [ENSMUST00000165964] [ENSMUST00000177588] [ENSMUST00000185145]
AlphaFold no structure available at present
Predicted Effect probably benign
Transcript: ENSMUST00000098814
AA Change: S416A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000096411
Gene: ENSMUSG00000056394
AA Change: S416A

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: 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 probably benign
Transcript: ENSMUST00000165964
AA Change: S416A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000126525
Gene: ENSMUSG00000056394
AA Change: S416A

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: S416A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000136972
Gene: ENSMUSG00000056394
AA Change: S416A

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
SMART Domains Protein: ENSMUSP00000138907
Gene: ENSMUSG00000056394

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
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.7%
  • 20x: 98.9%
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: 59 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcc6 A G 7: 45,644,661 (GRCm39) L838P probably damaging Het
Adam34l T G 8: 44,078,281 (GRCm39) N648H probably damaging Het
Adgrl4 T A 3: 151,248,895 (GRCm39) F728I probably damaging Het
Asap1 A G 15: 64,184,304 (GRCm39) V7A probably benign Het
B230104I21Rik A G 4: 154,434,050 (GRCm39) probably benign Het
C4b A T 17: 34,958,649 (GRCm39) S562T probably benign Het
Carmil2 A G 8: 106,422,121 (GRCm39) Y1130C probably damaging Het
Cit A T 5: 116,024,740 (GRCm39) K328* probably null Het
Col18a1 T C 10: 76,949,137 (GRCm39) D125G unknown Het
Cxadr T C 16: 78,125,996 (GRCm39) V122A probably damaging Het
Cyp2d22 G A 15: 82,260,053 (GRCm39) P44S probably damaging Het
Elapor1 A G 3: 108,378,745 (GRCm39) V351A possibly damaging Het
Gabrr1 A G 4: 33,148,964 (GRCm39) T74A probably benign Het
Gfm2 C A 13: 97,309,086 (GRCm39) A597E probably benign Het
H2-T22 T C 17: 36,351,408 (GRCm39) Y274C probably damaging Het
Has2 C A 15: 56,531,817 (GRCm39) W299C probably damaging Het
Hsd17b6 A G 10: 127,827,227 (GRCm39) S282P probably benign Het
Itga1 T C 13: 115,110,676 (GRCm39) I972V probably benign Het
Itih5 T A 2: 10,254,187 (GRCm39) Y813N probably damaging Het
Kctd16 A G 18: 40,663,848 (GRCm39) T326A possibly damaging Het
Klhdc1 T C 12: 69,316,642 (GRCm39) S342P probably damaging Het
Kmt2a T C 9: 44,742,650 (GRCm39) I1682M unknown Het
Lamc1 T C 1: 153,116,200 (GRCm39) K994E possibly damaging Het
Lims1 A G 10: 58,248,263 (GRCm39) E240G probably damaging Het
Lnpk T C 2: 74,399,316 (GRCm39) M76V probably benign Het
Lrrtm4 T A 6: 79,999,428 (GRCm39) L280* probably null Het
Mfap3l A T 8: 61,124,315 (GRCm39) I186F possibly damaging Het
Mta3 T C 17: 84,083,011 (GRCm39) F234L probably benign Het
Muc4 C G 16: 32,575,221 (GRCm39) Q1269E probably benign Het
Mybpc2 C T 7: 44,159,223 (GRCm39) G609D probably damaging Het
Naga A T 15: 82,219,035 (GRCm39) D237E probably benign Het
Naip6 C T 13: 100,437,108 (GRCm39) A472T probably benign Het
Nbn G A 4: 15,963,911 (GRCm39) S104N probably damaging Het
Nipsnap2 T C 5: 129,816,637 (GRCm39) L60P probably damaging Het
Or4f47 T A 2: 111,972,925 (GRCm39) F212I probably benign Het
Or8b1b G A 9: 38,375,802 (GRCm39) G155D probably benign Het
Pclo C T 5: 14,727,601 (GRCm39) T2153I unknown Het
Pclo A C 5: 14,908,869 (GRCm39) K5059T unknown Het
Pdlim2 C A 14: 70,403,645 (GRCm39) A256S possibly damaging Het
Pira2 T C 7: 3,845,460 (GRCm39) D308G probably damaging Het
Proc G T 18: 32,256,689 (GRCm39) A326E probably damaging Het
Rab40b T C 11: 121,248,709 (GRCm39) D182G probably benign Het
Rai14 A G 15: 10,574,937 (GRCm39) S703P possibly damaging Het
Rdx C T 9: 51,972,196 (GRCm39) P2L possibly damaging Het
Recql5 T C 11: 115,819,207 (GRCm39) K120E probably benign Het
Rev3l C T 10: 39,698,880 (GRCm39) R1126C probably damaging Het
Slc2a6 G T 2: 26,917,195 (GRCm39) D70E possibly damaging Het
Slc6a17 A T 3: 107,378,668 (GRCm39) D671E possibly damaging Het
Slc7a8 G A 14: 55,018,857 (GRCm39) probably benign Het
Srpk2 A G 5: 23,753,517 (GRCm39) Y79H possibly damaging Het
Traf3ip1 T A 1: 91,439,167 (GRCm39) I361K probably damaging Het
Trpm8 A G 1: 88,255,918 (GRCm39) Y191C probably damaging Het
Ubr3 T C 2: 69,803,812 (GRCm39) V1135A possibly damaging Het
Usp12 C A 5: 146,691,179 (GRCm39) probably null Het
Vmn1r44 C A 6: 89,870,818 (GRCm39) P188Q probably benign Het
Xirp2 T A 2: 67,356,099 (GRCm39) V3620D possibly damaging Het
Zcchc14 A T 8: 122,335,239 (GRCm39) S294T unknown Het
Zfp800 T C 6: 28,260,764 (GRCm39) D5G probably damaging Het
Zfp87 C T 13: 67,665,412 (GRCm39) R350Q probably benign Het
Other mutations in Lig1
AlleleSourceChrCoordTypePredicted EffectPPH 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
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
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'- AGGTTACTGCAGTGTCGTCTTC -3'
(R):5'- AACAAGCATTAACAAGTGTCCTGAC -3'

Sequencing Primer
(F):5'- ACTGCAGTGTCGTCTTCTACTTTC -3'
(R):5'- CCAAGAGATGCTAGGTTCTCCAG -3'
Posted On 2019-10-24