Mutagenetix > Incidental Mutation

Incidental Mutation 'R7733:Lig1'

595986

Institutional Source

Beutler Lab

Gene Symbol

Lig1

Ensembl Gene

ENSMUSG00000056394

Gene Name

ligase I, DNA, ATP-dependent

Synonyms

mLigI, LigI

MMRRC Submission

045789-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R7733 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

13011239-13045350 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to T at 13030157 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Arginine to Leucine at position 378 (R378L)

Ref Sequence

ENSEMBL: ENSMUSP00000096411 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000098814] [ENSMUST00000123025] [ENSMUST00000146998] [ENSMUST00000165964] [ENSMUST00000177588] [ENSMUST00000185145]

AlphaFold

no structure available at present

Predicted Effect

possibly damaging
Transcript: ENSMUST00000098814
AA Change: R378L

PolyPhen 2 Score 0.873 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000096411
Gene: ENSMUSG00000056394
AA Change: R378L

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

probably benign
Transcript: ENSMUST00000123025

SMART Domains

Protein: ENSMUSP00000114872
Gene: ENSMUSG00000056394

Domain	Start	End	E-Value	Type
low complexity region	96	111	N/A	INTRINSIC
low complexity region	159	177	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000146998

SMART Domains

Protein: ENSMUSP00000121102
Gene: ENSMUSG00000056394

Domain	Start	End	E-Value	Type
low complexity region	99	111	N/A	INTRINSIC
low complexity region	160	178	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000165964
AA Change: R378L

PolyPhen 2 Score 0.873 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000126525
Gene: ENSMUSG00000056394
AA Change: R378L

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

possibly damaging
Transcript: ENSMUST00000177588
AA Change: R378L

PolyPhen 2 Score 0.873 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000136972
Gene: ENSMUSG00000056394
AA Change: R378L

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

probably benign
Transcript: ENSMUST00000185145

SMART Domains

Protein: ENSMUSP00000138907
Gene: ENSMUSG00000056394

Domain	Start	End	E-Value	Type
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

0.6316

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 99.3%

Validation Efficiency

100% (83/83)

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: 82 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
5530400C23Rik	T	A	6: 133,271,240 (GRCm39)	S95T	probably benign	Het
Abca8a	A	G	11: 109,945,413 (GRCm39)	F1070L	probably benign	Het
Acsl3	G	C	1: 78,665,953 (GRCm39)		probably null	Het
Adarb2	T	A	13: 8,802,644 (GRCm39)	S640T	possibly damaging	Het
Adgre5	T	C	8: 84,456,025 (GRCm39)	D257G	probably benign	Het
Adora2b	A	T	11: 62,156,165 (GRCm39)	I205F	possibly damaging	Het
Asb14	A	G	14: 26,634,309 (GRCm39)	M505V	probably benign	Het
Atrnl1	T	C	19: 57,690,420 (GRCm39)	V876A	probably benign	Het
AU040320	A	G	4: 126,729,322 (GRCm39)	N495D	possibly damaging	Het
Bcam	A	T	7: 19,494,313 (GRCm39)	V361E	probably benign	Het
Ccdc7a	T	A	8: 129,719,533 (GRCm39)	E247V	probably damaging	Het
Cd84	T	A	1: 171,668,226 (GRCm39)	M1K	probably null	Het
Cfap43	C	T	19: 47,886,432 (GRCm39)	R61H	possibly damaging	Het
Clec4a1	A	G	6: 122,909,109 (GRCm39)	D159G	possibly damaging	Het
Ctcfl	C	T	2: 172,958,985 (GRCm39)	R247Q	probably benign	Het
Ctdnep1	G	A	11: 69,880,835 (GRCm39)	R236Q	probably damaging	Het
Cwf19l2	A	T	9: 3,450,066 (GRCm39)	H589L	probably benign	Het
Cyp2u1	G	T	3: 131,096,676 (GRCm39)	A34E	probably benign	Het
Cyp4x1	A	G	4: 114,977,391 (GRCm39)	S281P	possibly damaging	Het
Dag1	T	C	9: 108,086,047 (GRCm39)	T365A	probably benign	Het
Dhx57	A	T	17: 80,572,503 (GRCm39)		probably null	Het
Dnajb1	T	G	8: 84,335,006 (GRCm39)	S16A	probably benign	Het
Dsc2	A	T	18: 20,181,372 (GRCm39)	L145Q	probably benign	Het
Dsc2	G	C	18: 20,181,373 (GRCm39)	L145V	probably benign	Het
Eefsec	T	C	6: 88,353,202 (GRCm39)	T156A	possibly damaging	Het
Eif6	T	A	2: 155,665,152 (GRCm39)	D169V	probably benign	Het
Ell3	C	A	2: 121,273,001 (GRCm39)	G3V	possibly damaging	Het
Eprs1	A	T	1: 185,129,358 (GRCm39)	H615L	probably benign	Het
Fbxw10	A	G	11: 62,764,223 (GRCm39)	Y630C	unknown	Het
Fcgbpl1	A	T	7: 27,839,390 (GRCm39)	D401V	probably damaging	Het
G6pc2	C	T	2: 69,050,527 (GRCm39)	Q51*	probably null	Het
Glt8d1	C	T	14: 30,723,935 (GRCm39)		probably benign	Het
Gpr4	T	C	7: 18,956,635 (GRCm39)	Y186H	probably damaging	Het
Grhpr	T	C	4: 44,981,494 (GRCm39)		probably benign	Het
Gsdma3	A	G	11: 98,526,041 (GRCm39)	H264R	probably damaging	Het
Hcfc2	A	G	10: 82,575,013 (GRCm39)	Y224C	probably benign	Het
Helz2	A	G	2: 180,872,148 (GRCm39)	F2608S	possibly damaging	Het
Herc2	C	T	7: 55,838,412 (GRCm39)	T3313M	probably damaging	Het
Hmgcl	A	T	4: 135,687,394 (GRCm39)	H223L	probably benign	Het
Igf2r	A	G	17: 12,958,256 (GRCm39)	V139A	possibly damaging	Het
Iqcn	A	G	8: 71,170,100 (GRCm39)	T1397A	possibly damaging	Het
Kif5a	T	A	10: 127,072,609 (GRCm39)	T727S	probably benign	Het
Kifc1	G	A	17: 34,102,543 (GRCm39)	R357W	probably damaging	Het
Krt81	T	A	15: 101,361,395 (GRCm39)	S62C	probably damaging	Het
Lgi2	T	C	5: 52,695,873 (GRCm39)	N362S	probably benign	Het
Map3k13	C	T	16: 21,740,436 (GRCm39)	R588C	probably damaging	Het
Mov10l1	T	A	15: 88,909,004 (GRCm39)	F1008L	probably damaging	Het
Nr4a2	A	G	2: 57,002,333 (GRCm39)	V40A	probably benign	Het
Nrde2	A	T	12: 100,110,399 (GRCm39)	C206S	possibly damaging	Het
Or4f14d	C	T	2: 111,960,386 (GRCm39)	V257I	probably benign	Het
Parp1	T	C	1: 180,427,777 (GRCm39)		probably null	Het
Pcdhb12	A	G	18: 37,570,089 (GRCm39)	T412A	probably damaging	Het
Plekhh2	T	A	17: 84,890,952 (GRCm39)	Y839*	probably null	Het
Pnpla6	T	A	8: 3,572,660 (GRCm39)	F316I	probably benign	Het
Prcp	C	T	7: 92,550,506 (GRCm39)	T101M	probably damaging	Het
Prex2	G	T	1: 11,252,183 (GRCm39)	R1076L	probably benign	Het
Prpf40b	T	C	15: 99,206,224 (GRCm39)		probably null	Het
Psd3	T	G	8: 68,573,568 (GRCm39)	K204N	possibly damaging	Het
Ptpro	C	A	6: 137,391,284 (GRCm39)	C801*	probably null	Het
Ptprt	A	G	2: 161,417,707 (GRCm39)	V923A	probably damaging	Het
Ptprz1	T	A	6: 23,000,383 (GRCm39)	D824E	probably benign	Het
Rasgrf1	A	G	9: 89,863,780 (GRCm39)	D582G	probably benign	Het
Rfc2	T	C	5: 134,622,070 (GRCm39)	L183P	probably damaging	Het
Rnf114	T	C	2: 167,354,438 (GRCm39)	V173A	probably damaging	Het
Scn3a	T	A	2: 65,338,994 (GRCm39)	I562F	probably benign	Het
Setmar	T	C	6: 108,053,088 (GRCm39)	I194T	probably damaging	Het
Sptb	A	T	12: 76,644,695 (GRCm39)		probably null	Het
Sptbn2	C	G	19: 4,799,040 (GRCm39)	R2037G	probably benign	Het
Sptlc3	G	T	2: 139,473,288 (GRCm39)	M512I	possibly damaging	Het
Svep1	C	A	4: 58,049,239 (GRCm39)	A3423S	probably benign	Het
Sycp1	T	C	3: 102,803,278 (GRCm39)	T511A	probably benign	Het
Synm	T	A	7: 67,385,693 (GRCm39)		probably null	Het
Tada1	C	T	1: 166,217,511 (GRCm39)	P216L	probably damaging	Het
Tas2r117	T	A	6: 132,780,138 (GRCm39)	M92K	probably benign	Het
Thoc2l	T	C	5: 104,667,826 (GRCm39)	F783L	possibly damaging	Het
Thsd1	T	C	8: 22,748,737 (GRCm39)	L536P	probably damaging	Het
Timp2	T	G	11: 118,208,355 (GRCm39)		probably null	Het
Trak1	T	A	9: 121,196,291 (GRCm39)	V41D	possibly damaging	Het
Ubqln3	T	A	7: 103,790,283 (GRCm39)	L602F	probably damaging	Het
Vmn2r59	A	G	7: 41,661,443 (GRCm39)	F791L	probably benign	Het
Wbp4	A	G	14: 79,714,480 (GRCm39)		probably null	Het
Zng1	T	C	19: 24,918,158 (GRCm39)	D204G	probably damaging	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
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
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'- TTTACACTGACCTAATGGGAGC -3'
(R):5'- ACCACAGGCTTTGTTCTGGG -3'

Sequencing Primer
(F):5'- CCTAATGGGAGCAGGCATTTAC -3'
(R):5'- AGGTTGGGATAAGCCACCCTG -3'

Posted On

2019-11-12