Mutagenetix > Incidental Mutation

Incidental Mutation 'R4669:Lig1'

352254

Institutional Source

Beutler Lab

Gene Symbol

Lig1

Ensembl Gene

ENSMUSG00000056394

Gene Name

ligase I, DNA, ATP-dependent

Synonyms

mLigI, LigI

MMRRC Submission

041925-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R4669 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

13011239-13045350 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to G at 13044953 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Serine at position 882 (I882S)

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: I882S

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000096411
Gene: ENSMUSG00000056394
AA Change: I882S

Domain	Start	End	E-Value	Type
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

Domain	Start	End	E-Value	Type
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: ENSMUST00000147735

SMART Domains

Protein: ENSMUSP00000115286
Gene: ENSMUSG00000056394

Domain	Start	End	E-Value	Type
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

Domain	Start	End	E-Value	Type
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

Domain	Start	End	E-Value	Type
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: I882S

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000126525
Gene: ENSMUSG00000056394
AA Change: I882S

Domain	Start	End	E-Value	Type
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: I882S

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000136972
Gene: ENSMUSG00000056394
AA Change: I882S

Domain	Start	End	E-Value	Type
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: 99.2%
3x: 98.6%
10x: 97.3%
20x: 95.4%

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: 98 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acad8	A	G	9: 26,901,923 (GRCm39)	L147P	probably damaging	Het
Acan	A	G	7: 78,750,890 (GRCm39)	E464G	probably benign	Het
Agap1	A	G	1: 89,765,528 (GRCm39)		probably null	Het
Akap13	A	G	7: 75,378,842 (GRCm39)	T2128A	probably damaging	Het
Ap2a1	A	T	7: 44,552,343 (GRCm39)		probably benign	Het
Arap3	T	C	18: 38,129,307 (GRCm39)	D217G	probably benign	Het
Arl2	C	A	19: 6,184,716 (GRCm39)	R179L	probably damaging	Het
Atg2a	T	A	19: 6,309,017 (GRCm39)		probably null	Het
B3gat1	T	A	9: 26,663,052 (GRCm39)	L6Q	probably benign	Het
Bcl10	A	G	3: 145,636,327 (GRCm39)	N75S	probably damaging	Het
Bmpr2	T	C	1: 59,906,875 (GRCm39)	L656S	probably damaging	Het
Brms1l	A	G	12: 55,888,356 (GRCm39)	E48G	possibly damaging	Het
C2cd2l	A	T	9: 44,226,322 (GRCm39)	N414K	possibly damaging	Het
Capn2	C	T	1: 182,298,345 (GRCm39)	C640Y	probably benign	Het
Ccdc153	G	T	9: 44,157,021 (GRCm39)	R99M	probably damaging	Het
Ccdc51	A	G	9: 108,920,030 (GRCm39)	N142S	probably benign	Het
Cdipt	A	G	7: 126,577,578 (GRCm39)	H108R	possibly damaging	Het
Ceacam20	T	C	7: 19,719,952 (GRCm39)	Y495H	probably damaging	Het
Celf2	T	C	2: 6,726,339 (GRCm39)	I47V	probably benign	Het
Cts3	C	T	13: 61,714,637 (GRCm39)	E223K	probably benign	Het
Cyp2a22	T	C	7: 26,637,280 (GRCm39)	D168G	possibly damaging	Het
Cyp2c67	T	A	19: 39,632,098 (GRCm39)	H90L	probably benign	Het
Ddx4	T	C	13: 112,758,778 (GRCm39)	Y261C	probably damaging	Het
Dnah17	T	C	11: 117,965,119 (GRCm39)	T2308A	probably benign	Het
Dnah6	T	C	6: 73,014,671 (GRCm39)	T3587A	probably damaging	Het
Dpy19l1	C	T	9: 24,343,664 (GRCm39)	V494I	possibly damaging	Het
Dse	T	G	10: 34,029,008 (GRCm39)	Y694S	probably damaging	Het
Emilin3	T	C	2: 160,752,717 (GRCm39)	I78V	probably benign	Het
Esam	T	A	9: 37,447,952 (GRCm39)	Y195*	probably null	Het
Extl3	T	A	14: 65,313,745 (GRCm39)	N479I	possibly damaging	Het
Fat2	A	G	11: 55,202,441 (GRCm39)	V211A	probably benign	Het
Ganc	G	T	2: 120,261,548 (GRCm39)	V343F	probably benign	Het
Ggt5	T	C	10: 75,438,865 (GRCm39)	L121P	probably damaging	Het
Gnmt	A	T	17: 47,037,225 (GRCm39)	C186*	probably null	Het
Gpr75	A	T	11: 30,842,072 (GRCm39)	I326F	probably damaging	Het
Gsdme	C	T	6: 50,185,102 (GRCm39)	V451M	probably damaging	Het
H2-T23	G	T	17: 36,342,690 (GRCm39)	D149E	probably damaging	Het
Hmcn2	G	T	2: 31,325,804 (GRCm39)	R4277L	probably benign	Het
Irf9	C	A	14: 55,843,223 (GRCm39)	H94N	probably benign	Het
Jhy	T	C	9: 40,872,449 (GRCm39)	N20S	probably benign	Het
Klf17	C	A	4: 117,617,568 (GRCm39)	C263F	probably damaging	Het
Lama5	T	C	2: 179,822,430 (GRCm39)	Y2881C	probably damaging	Het
Ltn1	A	T	16: 87,215,375 (GRCm39)	M420K	possibly damaging	Het
Mael	T	C	1: 166,063,077 (GRCm39)	E125G	probably damaging	Het
Mib2	C	T	4: 155,741,872 (GRCm39)	D275N	possibly damaging	Het
Mical3	C	T	6: 120,934,664 (GRCm39)	R1805Q	probably damaging	Het
Mix23	A	G	16: 35,903,089 (GRCm39)	D27G	probably damaging	Het
Mllt10	A	G	2: 18,208,444 (GRCm39)	D158G	probably damaging	Het
Mocs1	A	G	17: 49,761,613 (GRCm39)	D569G	possibly damaging	Het
Msh6	T	C	17: 88,292,234 (GRCm39)	S330P	possibly damaging	Het
Mtmr2	T	C	9: 13,707,260 (GRCm39)	S199P	probably damaging	Het
Ndufaf5	T	C	2: 140,029,675 (GRCm39)	V164A	probably benign	Het
Nek9	T	C	12: 85,360,978 (GRCm39)	E518G	probably benign	Het
Nfatc2	T	C	2: 168,413,410 (GRCm39)	I72V	probably benign	Het
Nlrp9c	C	T	7: 26,074,793 (GRCm39)	A746T	possibly damaging	Het
Nup42	A	G	5: 24,387,415 (GRCm39)	R402G	probably benign	Het
Ogdh	G	T	11: 6,290,600 (GRCm39)	C406F	probably benign	Het
Or3a1d	A	G	11: 74,237,789 (GRCm39)	V207A	probably benign	Het
Or4c120	G	A	2: 89,001,245 (GRCm39)	H104Y	probably damaging	Het
Or8b35	A	T	9: 37,904,381 (GRCm39)	I198F	possibly damaging	Het
Or8g17	T	A	9: 38,930,675 (GRCm39)	Y54F	probably benign	Het
Or8j3	A	T	2: 86,028,277 (GRCm39)	M273K	possibly damaging	Het
Otof	A	G	5: 30,578,318 (GRCm39)		probably null	Het
Pcdhb17	T	C	18: 37,619,259 (GRCm39)	S350P	probably damaging	Het
Phf3	T	C	1: 30,869,027 (GRCm39)	T674A	probably damaging	Het
Pikfyve	T	A	1: 65,289,432 (GRCm39)	C1235S	probably damaging	Het
Ppfia3	T	C	7: 45,001,517 (GRCm39)	E465G	probably damaging	Het
Prkg1	T	A	19: 31,641,639 (GRCm39)	I15F	probably damaging	Het
Rab5c	A	G	11: 100,610,843 (GRCm39)	F22L	probably damaging	Het
Raf1	A	G	6: 115,609,880 (GRCm39)	S220P	probably damaging	Het
Rgl1	T	G	1: 152,397,122 (GRCm39)	R716S	probably damaging	Het
Rhbg	C	A	3: 88,153,273 (GRCm39)	W205L	probably damaging	Het
Rimbp3	A	G	16: 17,027,053 (GRCm39)	E159G	possibly damaging	Het
Ryr1	T	C	7: 28,759,256 (GRCm39)	D3338G	probably null	Het
Sash1	T	C	10: 8,606,149 (GRCm39)	N747S	probably benign	Het
Serpina3g	A	T	12: 104,205,479 (GRCm39)	I73F	probably damaging	Het
Sfxn2	C	A	19: 46,574,213 (GRCm39)	N134K	probably damaging	Het
Slc12a6	A	G	2: 112,184,640 (GRCm39)	H853R	probably damaging	Het
Slc16a12	C	T	19: 34,649,965 (GRCm39)	D357N	probably damaging	Het
Slc39a8	T	C	3: 135,561,772 (GRCm39)	Y164H	probably benign	Het
Snx9	A	G	17: 5,977,499 (GRCm39)	K518E	probably damaging	Het
Spdye4c	G	A	2: 128,434,273 (GRCm39)	V5I	possibly damaging	Het
Spef2	A	G	15: 9,676,459 (GRCm39)	V704A	probably benign	Het
Stard3nl	T	A	13: 19,560,689 (GRCm39)	N29Y	probably damaging	Het
Strap	C	A	6: 137,712,384 (GRCm39)	S11*	probably null	Het
Synpo2	A	G	3: 122,906,712 (GRCm39)	L868P	probably damaging	Het
Tenm2	A	G	11: 35,901,314 (GRCm39)	V2474A	probably damaging	Het
Tm9sf4	T	A	2: 153,029,228 (GRCm39)	V92D	probably damaging	Het
Tmf1	A	T	6: 97,147,388 (GRCm39)	M526K	probably benign	Het
Top2b	T	G	14: 16,409,189 (GRCm38)	I777M	probably damaging	Het
Ttc39d	A	G	17: 80,525,068 (GRCm39)	I576V	probably benign	Het
Upk1a	T	G	7: 30,304,554 (GRCm39)	T193P	probably benign	Het
Vmn2r67	A	T	7: 84,799,732 (GRCm39)	V502E	probably benign	Het
Wdr17	A	G	8: 55,143,083 (GRCm39)	V189A	possibly damaging	Het
Wrap73	A	T	4: 154,236,153 (GRCm39)	S161C	probably benign	Het
Zfp568	A	G	7: 29,722,702 (GRCm39)	H549R	probably damaging	Het
Zfp605	T	A	5: 110,275,227 (GRCm39)	M115K	possibly damaging	Het
Zp1	T	A	19: 10,896,269 (GRCm39)	H152L	probably benign	Het

Other mutations in Lig1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH 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
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'- GCACTCATGGTTATCAGGATGC -3'
(R):5'- TCCGGTACAAAGAGGCAAC -3'

Sequencing Primer
(F):5'- CTCATGGTTATCAGGATGCTAATAAC -3'
(R):5'- CGGTACAAAGAGGCAACCTGAG -3'

Posted On

2015-10-08