Incidental Mutation 'R5249:Lig1'
ID 398790
Institutional Source Beutler Lab
Gene Symbol Lig1
Ensembl Gene ENSMUSG00000056394
Gene Name ligase I, DNA, ATP-dependent
Synonyms mLigI, LigI
MMRRC Submission 042820-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R5249 (G1)
Quality Score 223
Status Validated
Chromosome 7
Chromosomal Location 13011239-13045350 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to T at 13042432 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Histidine to Tyrosine at position 822 (H822Y)
Ref Sequence ENSEMBL: ENSMUSP00000136972 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000098814] [ENSMUST00000165964] [ENSMUST00000177588]
AlphaFold no structure available at present
Predicted Effect possibly damaging
Transcript: ENSMUST00000098814
AA Change: H822Y

PolyPhen 2 Score 0.598 (Sensitivity: 0.87; Specificity: 0.91)
SMART Domains Protein: ENSMUSP00000096411
Gene: ENSMUSG00000056394
AA Change: H822Y

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 possibly damaging
Transcript: ENSMUST00000165964
AA Change: H822Y

PolyPhen 2 Score 0.598 (Sensitivity: 0.87; Specificity: 0.91)
SMART Domains Protein: ENSMUSP00000126525
Gene: ENSMUSG00000056394
AA Change: H822Y

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 possibly damaging
Transcript: ENSMUST00000177588
AA Change: H822Y

PolyPhen 2 Score 0.598 (Sensitivity: 0.87; Specificity: 0.91)
SMART Domains Protein: ENSMUSP00000136972
Gene: ENSMUSG00000056394
AA Change: H822Y

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
Meta Mutation Damage Score 0.2044 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.6%
  • 10x: 97.1%
  • 20x: 94.8%
Validation Efficiency 98% (93/95)
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: 89 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
A4gnt A G 9: 99,502,284 (GRCm39) H148R probably damaging Het
Acrbp A G 6: 125,037,885 (GRCm39) D394G probably damaging Het
Adam18 T C 8: 25,115,868 (GRCm39) T609A probably benign Het
Adam25 T A 8: 41,208,991 (GRCm39) N752K probably benign Het
Ano6 A C 15: 95,811,469 (GRCm39) S176R probably benign Het
Ano7 T C 1: 93,302,918 (GRCm39) S19P probably benign Het
Ap1b1 A G 11: 4,976,364 (GRCm39) E437G probably damaging Het
Arfgap2 T A 2: 91,095,982 (GRCm39) C46* probably null Het
Arhgef26 T A 3: 62,247,981 (GRCm39) L355Q probably damaging Het
B4galnt4 C T 7: 140,644,983 (GRCm39) T219I probably damaging Het
Bap1 C T 14: 30,979,243 (GRCm39) probably benign Het
Catip T G 1: 74,401,954 (GRCm39) L43R probably damaging Het
Ccdc177 G A 12: 80,805,282 (GRCm39) R331C unknown Het
Cep85l T C 10: 53,195,690 (GRCm39) probably null Het
Cfap206 T A 4: 34,714,502 (GRCm39) Q398L probably benign Het
Clec18a A G 8: 111,800,368 (GRCm39) C352R probably damaging Het
Clic6 A T 16: 92,336,339 (GRCm39) Y549F probably damaging Het
Cpne9 C T 6: 113,270,034 (GRCm39) probably benign Het
Cyb5r3 A C 15: 83,042,836 (GRCm39) probably benign Het
Dnah6 C T 6: 73,090,471 (GRCm39) R2293K probably damaging Het
Dnmbp C A 19: 43,890,879 (GRCm39) R296L probably damaging Het
Dtwd1 C A 2: 125,996,694 (GRCm39) Q60K probably benign Het
Esyt1 C A 10: 128,352,443 (GRCm39) V723L probably benign Het
Fbxo42 T C 4: 140,926,335 (GRCm39) L339P probably damaging Het
Furin A T 7: 80,043,169 (GRCm39) N347K probably damaging Het
Fzd7 T C 1: 59,522,522 (GRCm39) M135T probably damaging Het
Garin1b A G 6: 29,323,896 (GRCm39) D207G probably damaging Het
Hlf A G 11: 90,278,632 (GRCm39) M144T probably benign Het
Hyal5 C T 6: 24,876,648 (GRCm39) Q174* probably null Het
Kcnb1 T A 2: 166,947,103 (GRCm39) M582L possibly damaging Het
Kdm5d T C Y: 916,692 (GRCm39) Y391H probably damaging Het
Khdc4 T A 3: 88,604,032 (GRCm39) I283N probably damaging Het
Kif21b C T 1: 136,096,966 (GRCm39) T1297M probably damaging Het
Krt8 T G 15: 101,906,875 (GRCm39) N317T possibly damaging Het
Lctl G T 9: 64,045,196 (GRCm39) V372L probably benign Het
Lrrc4b A G 7: 44,111,988 (GRCm39) D620G possibly damaging Het
Mboat4 C T 8: 34,582,275 (GRCm39) H10Y probably benign Het
Med1 A T 11: 98,048,066 (GRCm39) M910K probably benign Het
Mia2 A T 12: 59,154,911 (GRCm39) D209V probably damaging Het
Mpp4 C T 1: 59,184,017 (GRCm39) probably benign Het
Mrgprb1 A T 7: 48,097,225 (GRCm39) V229E possibly damaging Het
Mtor T A 4: 148,548,189 (GRCm39) C485S probably damaging Het
Mx1 T C 16: 97,258,628 (GRCm39) D23G probably damaging Het
Myrfl T C 10: 116,619,138 (GRCm39) D740G probably benign Het
Myt1l G A 12: 29,882,331 (GRCm39) G509R unknown Het
Nav2 G A 7: 49,185,661 (GRCm39) V874I probably damaging Het
Ntrk3 A T 7: 78,110,914 (GRCm39) N262K possibly damaging Het
Opa1 A T 16: 29,437,077 (GRCm39) D699V probably damaging Het
Or10u4 C T 10: 129,802,078 (GRCm39) A164T probably benign Het
Or8b51 A G 9: 38,569,374 (GRCm39) C105R possibly damaging Het
Otud7a A G 7: 63,407,181 (GRCm39) N495D possibly damaging Het
Pcsk9 T C 4: 106,320,950 (GRCm39) D53G probably benign Het
Pdcd5 A G 7: 35,346,421 (GRCm39) probably benign Het
Phf21a C T 2: 92,058,822 (GRCm39) P28L probably damaging Het
Pitpnm1 T A 19: 4,158,130 (GRCm39) D573E probably damaging Het
Ppp1r35 C T 5: 137,777,406 (GRCm39) probably benign Het
Ptprq T C 10: 107,535,496 (GRCm39) Q423R probably damaging Het
Pum1 A T 4: 130,490,125 (GRCm39) Y699F probably benign Het
Rabgef1 A G 5: 130,241,841 (GRCm39) D415G probably benign Het
Rapgef6 A G 11: 54,413,943 (GRCm39) E23G probably benign Het
Rpia G T 6: 70,760,563 (GRCm39) C121* probably null Het
Sanbr A G 11: 23,525,483 (GRCm39) *719Q probably null Het
Serpinb13 T A 1: 106,926,427 (GRCm39) W201R probably damaging Het
Sh3bp4 T C 1: 89,065,456 (GRCm39) C17R probably damaging Het
Sh3d21 A G 4: 126,055,858 (GRCm39) probably benign Het
Slamf6 A C 1: 171,764,249 (GRCm39) N214T probably damaging Het
Slc7a2 T C 8: 41,361,130 (GRCm39) Y365H possibly damaging Het
Sox18 T C 2: 181,312,971 (GRCm39) probably null Het
Spink7 A T 18: 62,725,507 (GRCm39) F79I possibly damaging Het
Srpk3 C T X: 72,818,555 (GRCm39) R82* probably null Het
Sspo A T 6: 48,470,244 (GRCm39) H4561L probably damaging Het
Tcaf1 T C 6: 42,653,793 (GRCm39) K700R probably benign Het
Tcf25 G T 8: 124,115,372 (GRCm39) R203L probably damaging Het
Tcp11 T C 17: 28,290,757 (GRCm39) I201V possibly damaging Het
Tex2 T C 11: 106,437,615 (GRCm39) D685G unknown Het
Themis G T 10: 28,637,195 (GRCm39) E100* probably null Het
Tmem52b G A 6: 129,491,221 (GRCm39) probably null Het
Tnr C T 1: 159,512,226 (GRCm39) probably benign Het
Tox3 T C 8: 90,975,444 (GRCm39) I396V probably benign Het
Tpm2 T A 4: 43,514,828 (GRCm39) E269V probably benign Het
Tulp1 C T 17: 28,581,651 (GRCm39) probably benign Het
Tymp GC GCC 15: 89,258,567 (GRCm39) probably null Het
Ube2j2 A C 4: 156,033,515 (GRCm39) K30Q possibly damaging Het
Usp19 T A 9: 108,369,807 (GRCm39) M1K probably null Het
Vmn2r52 C A 7: 9,910,197 (GRCm39) R6L probably benign Het
Zbed4 G A 15: 88,665,290 (GRCm39) V453M probably benign Het
Zfp319 T C 8: 96,055,099 (GRCm39) E368G probably benign Het
Zfp366 A C 13: 99,366,117 (GRCm39) E426A probably damaging Het
Zfp687 A T 3: 94,916,777 (GRCm39) I783N probably damaging 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
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'- CATGAAAACTACAGCCTTTCAGGG -3'
(R):5'- TTAGAGGCTCATGGCACTTC -3'

Sequencing Primer
(F):5'- CCTTTCAGGGCAGGGAATTG -3'
(R):5'- TGGCACTTCTCAGGGAAAAC -3'
Posted On 2016-07-06