Incidental Mutation 'R2106:Lig1'
ID 230974
Institutional Source Beutler Lab
Gene Symbol Lig1
Ensembl Gene ENSMUSG00000056394
Gene Name ligase I, DNA, ATP-dependent
Synonyms mLigI, LigI
MMRRC Submission 040110-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R2106 (G1)
Quality Score 225
Status Not validated
Chromosome 7
Chromosomal Location 13011239-13045350 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to A at 13039863 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Arginine to Serine at position 692 (R692S)
Ref Sequence ENSEMBL: ENSMUSP00000136972 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000098814] [ENSMUST00000165964] [ENSMUST00000177588]
AlphaFold no structure available at present
Predicted Effect probably damaging
Transcript: ENSMUST00000098814
AA Change: R692S

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000096411
Gene: ENSMUSG00000056394
AA Change: R692S

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 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 noncoding transcript
Transcript: ENSMUST00000131294
Predicted Effect noncoding transcript
Transcript: ENSMUST00000138453
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 damaging
Transcript: ENSMUST00000165964
AA Change: R692S

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000126525
Gene: ENSMUSG00000056394
AA Change: R692S

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 damaging
Transcript: ENSMUST00000177588
AA Change: R692S

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000136972
Gene: ENSMUSG00000056394
AA Change: R692S

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
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.7%
  • 10x: 97.7%
  • 20x: 96.2%
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: 74 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adamtsl2 T C 2: 26,992,837 (GRCm39) F650S probably benign Het
Agrp G T 8: 106,293,467 (GRCm39) T106K probably damaging Het
Akr1c13 T A 13: 4,248,593 (GRCm39) V266E probably damaging Het
Ankrd61 A T 5: 143,828,564 (GRCm39) L95Q probably damaging Het
Atp11a A G 8: 12,885,228 (GRCm39) T22A probably benign Het
Brca1 A G 11: 101,415,803 (GRCm39) V777A possibly damaging Het
Ccdc40 G T 11: 119,155,123 (GRCm39) R1121L probably damaging Het
Cdhr4 A C 9: 107,874,693 (GRCm39) S588R possibly damaging Het
Cfap69 T C 5: 5,645,979 (GRCm39) N517D probably benign Het
Chrm2 T C 6: 36,500,382 (GRCm39) Y80H probably damaging Het
Cimip2a A G 2: 25,110,663 (GRCm39) Y157C probably damaging Het
Csgalnact2 G T 6: 118,086,090 (GRCm39) Y534* probably null Het
Defb35 A G 8: 22,430,809 (GRCm39) E61G unknown Het
Dhx15 A T 5: 52,327,428 (GRCm39) D95E probably benign Het
Dhx57 A G 17: 80,582,792 (GRCm39) V271A probably damaging Het
Dlg1 T C 16: 31,631,574 (GRCm39) S444P probably damaging Het
Edem1 T A 6: 108,825,686 (GRCm39) N406K probably damaging Het
Eif4g3 A T 4: 137,810,230 (GRCm39) probably benign Het
Epb41 A G 4: 131,717,152 (GRCm39) I56T probably damaging Het
Epg5 T A 18: 78,034,578 (GRCm39) Y1442* probably null Het
Fat2 T C 11: 55,147,390 (GRCm39) T3951A probably benign Het
Fryl A G 5: 73,255,674 (GRCm39) S786P probably damaging Het
Fyb2 A G 4: 104,802,769 (GRCm39) T224A probably benign Het
Ginm1 A T 10: 7,651,090 (GRCm39) F105L probably damaging Het
Heatr1 T C 13: 12,426,939 (GRCm39) V688A probably benign Het
Hnmt T G 2: 23,909,130 (GRCm39) Q94H probably benign Het
Ice1 A G 13: 70,753,741 (GRCm39) Y782H probably benign Het
Immt T C 6: 71,848,499 (GRCm39) V418A possibly damaging Het
Kcnd3 C T 3: 105,566,082 (GRCm39) A421V probably damaging Het
Kif1b G A 4: 149,272,097 (GRCm39) S1568L possibly damaging Het
Krt84 T C 15: 101,439,301 (GRCm39) N248D probably damaging Het
Lvrn G T 18: 47,011,356 (GRCm39) A438S probably damaging Het
Mast4 C T 13: 102,887,054 (GRCm39) V1204I probably damaging Het
Med21 G T 6: 146,550,710 (GRCm39) D74Y probably damaging Het
Nat8 T C 6: 85,807,506 (GRCm39) D209G probably benign Het
Nipal1 C A 5: 72,820,902 (GRCm39) F132L probably damaging Het
Npr2 A T 4: 43,644,329 (GRCm39) I613F probably damaging Het
Nrcam A G 12: 44,617,073 (GRCm39) T706A probably benign Het
Or5w1b A G 2: 87,475,895 (GRCm39) S191P probably damaging Het
Or8w1 T C 2: 87,465,503 (GRCm39) E196G probably benign Het
Pam A G 1: 97,759,215 (GRCm39) V823A probably damaging Het
Pdik1l A T 4: 134,011,565 (GRCm39) Y93N probably damaging Het
Perm1 T C 4: 156,303,336 (GRCm39) W627R probably damaging Het
Pofut1 G A 2: 153,101,713 (GRCm39) probably null Het
Prmt5 T C 14: 54,745,374 (GRCm39) I598V probably benign Het
Rab11fip5 T C 6: 85,351,369 (GRCm39) I48V probably damaging Het
Rad51d T A 11: 82,770,134 (GRCm39) K261N probably damaging Het
Rapgef6 T G 11: 54,559,512 (GRCm39) I1050S probably benign Het
Rif1 GCCACCA GCCA 2: 52,000,336 (GRCm39) probably benign Het
Ryr3 T C 2: 112,468,474 (GRCm39) E4688G probably damaging Het
Siva1 G T 12: 112,613,440 (GRCm39) R96L probably damaging Het
Slc13a4 T C 6: 35,264,799 (GRCm39) N140S probably damaging Het
Slc26a5 T A 5: 22,028,542 (GRCm39) D342V probably damaging Het
Slfn9 A G 11: 82,878,506 (GRCm39) S208P possibly damaging Het
Sspo C A 6: 48,443,250 (GRCm39) T1899N possibly damaging Het
Sytl1 T C 4: 132,984,774 (GRCm39) D200G probably benign Het
Tas2r118 T C 6: 23,969,569 (GRCm39) N164S probably benign Het
Tbc1d17 A G 7: 44,497,692 (GRCm39) probably null Het
Tex14 T C 11: 87,377,076 (GRCm39) M140T possibly damaging Het
Tm6sf2 T C 8: 70,532,396 (GRCm39) F352S probably benign Het
Tmem88 A G 11: 69,288,685 (GRCm39) L78P probably benign Het
Trafd1 A G 5: 121,511,274 (GRCm39) S515P probably benign Het
Trpm6 A T 19: 18,790,714 (GRCm39) E583V possibly damaging Het
Ttc23l A G 15: 10,547,342 (GRCm39) C91R probably damaging Het
Ubap1l T C 9: 65,281,089 (GRCm39) S256P probably benign Het
Vmn1r26 T G 6: 57,985,710 (GRCm39) S160R possibly damaging Het
Vmn2r97 A G 17: 19,168,100 (GRCm39) S785G probably damaging Het
Wdr27 T G 17: 15,141,116 (GRCm39) R278S probably benign Het
Wdr7 T C 18: 63,911,109 (GRCm39) S834P probably damaging Het
Zdhhc12 C T 2: 29,981,814 (GRCm39) C116Y probably damaging Het
Zfp946 T C 17: 22,672,466 (GRCm39) F22L probably benign Het
Zfp948 G T 17: 21,807,953 (GRCm39) E382* probably null Het
Zfp956 T A 6: 47,941,359 (GRCm39) *573K probably null Het
Zim1 T G 7: 6,681,073 (GRCm39) T197P 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
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
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'- TTCAGCATGCTAGTGGGATCTG -3'
(R):5'- GCACAGGTACAGCAAAGCTTC -3'

Sequencing Primer
(F):5'- GCAGTTAAAGCTCTAATACAGCAGTC -3'
(R):5'- GCAAAGCTTCAAACCTTGGG -3'
Posted On 2014-09-18