Mutagenetix > Incidental Mutation

Incidental Mutation 'R0362:Lig1'

36237

Institutional Source

Beutler Lab

Gene Symbol

Lig1

Ensembl Gene

ENSMUSG00000056394

Gene Name

ligase I, DNA, ATP-dependent

Synonyms

mLigI, LigI

MMRRC Submission

038568-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R0362 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

13011239-13045350 bp(+) (GRCm39)

Type of Mutation

unclassified

DNA Base Change (assembly)

T to A at 13030730 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000138907 (fasta)

Gene Model

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

AlphaFold

no structure available at present

Predicted Effect

probably benign
Transcript: ENSMUST00000098814

SMART Domains

Protein: ENSMUSP00000096411
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	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: 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 benign
Transcript: ENSMUST00000165964

SMART Domains

Protein: ENSMUSP00000126525
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	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

SMART Domains

Protein: ENSMUSP00000136972
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	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

Coding Region Coverage

1x: 99.4%
3x: 98.6%
10x: 96.8%
20x: 94.0%

Validation Efficiency

99% (104/105)

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: 103 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4932414N04Rik	A	G	2: 68,563,261 (GRCm39)	Q401R	probably benign	Het
Acp3	A	G	9: 104,191,626 (GRCm39)	F220S	probably damaging	Het
Adam7	A	G	14: 68,747,105 (GRCm39)		probably benign	Het
Adamts6	A	G	13: 104,526,584 (GRCm39)		probably null	Het
Ascc3	T	C	10: 50,625,051 (GRCm39)		probably benign	Het
Atg10	T	C	13: 91,189,109 (GRCm39)		probably null	Het
Atm	T	C	9: 53,370,138 (GRCm39)	I2325V	possibly damaging	Het
Btnl9	C	T	11: 49,060,443 (GRCm39)	R435H	possibly damaging	Het
Ccdc180	A	G	4: 45,923,551 (GRCm39)	K1111E	probably damaging	Het
Ciao2b	T	C	8: 105,368,222 (GRCm39)	D34G	probably null	Het
Col11a2	T	A	17: 34,281,420 (GRCm39)		probably null	Het
Ctcfl	A	G	2: 172,960,236 (GRCm39)	W116R	probably damaging	Het
Ctsk	A	T	3: 95,408,255 (GRCm39)	Y37F	probably damaging	Het
Daam2	G	C	17: 49,787,813 (GRCm39)		probably null	Het
Dcdc2b	T	C	4: 129,504,031 (GRCm39)		probably null	Het
Ddx28	C	T	8: 106,737,926 (GRCm39)	R44Q	probably damaging	Het
Dhx29	T	A	13: 113,099,393 (GRCm39)	N1139K	probably benign	Het
Dnah17	A	T	11: 117,989,365 (GRCm39)	M1281K	probably benign	Het
Dnah6	T	C	6: 73,185,592 (GRCm39)	S110G	probably benign	Het
Drc7	T	C	8: 95,799,483 (GRCm39)	Y553H	probably benign	Het
Dync2h1	T	C	9: 7,005,487 (GRCm39)		probably null	Het
Ecm1	A	G	3: 95,644,369 (GRCm39)	I152T	possibly damaging	Het
Edc4	C	G	8: 106,613,407 (GRCm39)	P307R	probably damaging	Het
Eeig2	C	T	3: 108,887,497 (GRCm39)	E256K	probably benign	Het
Egr1	A	G	18: 34,996,366 (GRCm39)	T383A	possibly damaging	Het
Eml2	A	G	7: 18,924,731 (GRCm39)		probably null	Het
Eno4	A	G	19: 58,932,056 (GRCm39)		probably benign	Het
Erbb4	A	T	1: 68,369,429 (GRCm39)	I404K	probably damaging	Het
Exoc7	G	T	11: 116,186,488 (GRCm39)	T310K	probably benign	Het
Fam83e	G	T	7: 45,376,393 (GRCm39)	V369L	probably benign	Het
Fancc	A	T	13: 63,545,970 (GRCm39)	I91K	possibly damaging	Het
Fbn1	T	C	2: 125,151,697 (GRCm39)	Q2519R	probably damaging	Het
Fhod3	T	A	18: 25,223,133 (GRCm39)	C826*	probably null	Het
Foxi3	A	G	6: 70,933,612 (GRCm39)	D33G	probably benign	Het
Gcn1	T	C	5: 115,714,167 (GRCm39)		probably benign	Het
Gm14221	T	C	2: 160,410,310 (GRCm39)		noncoding transcript	Het
Golga4	T	A	9: 118,384,853 (GRCm39)	H630Q	probably benign	Het
Gpat4	T	C	8: 23,670,949 (GRCm39)	S88G	probably benign	Het
Gucy2d	A	T	7: 98,092,892 (GRCm39)	S90C	probably damaging	Het
Has2	A	C	15: 56,545,057 (GRCm39)	C182G	probably damaging	Het
Heatr5a	A	T	12: 51,935,644 (GRCm39)	S1647R	probably damaging	Het
Ifi35	T	C	11: 101,348,038 (GRCm39)	V48A	probably benign	Het
Magi2	A	G	5: 19,432,573 (GRCm39)	K96R	probably damaging	Het
Map7d1	G	T	4: 126,128,787 (GRCm39)	P462Q	probably damaging	Het
Mdn1	A	T	4: 32,746,439 (GRCm39)		probably null	Het
Mfsd4a	A	T	1: 131,987,013 (GRCm39)	V105E	probably damaging	Het
Mrpl53	C	T	6: 83,086,526 (GRCm39)	R77C	probably damaging	Het
Mtnr1b	C	T	9: 15,785,600 (GRCm39)	V53M	probably damaging	Het
Myo9b	T	C	8: 71,800,414 (GRCm39)	W990R	probably damaging	Het
Myt1	A	T	2: 181,405,186 (GRCm39)		probably benign	Het
Nf1	C	T	11: 79,427,704 (GRCm39)	A1766V	probably damaging	Het
Nlrp3	T	C	11: 59,439,623 (GRCm39)	V400A	possibly damaging	Het
Nup205	T	A	6: 35,173,649 (GRCm39)		probably null	Het
Nxf1	T	C	19: 8,741,515 (GRCm39)		probably null	Het
Or7a36	A	T	10: 78,820,220 (GRCm39)	M199L	probably benign	Het
P4hb	T	C	11: 120,454,162 (GRCm39)	K311E	probably benign	Het
Pafah1b1	T	C	11: 74,574,457 (GRCm39)	N243S	probably benign	Het
Parp8	G	A	13: 117,061,504 (GRCm39)	Q141*	probably null	Het
Pkd2l2	A	C	18: 34,568,380 (GRCm39)	D543A	probably benign	Het
Pld5	A	T	1: 175,803,146 (GRCm39)	L311*	probably null	Het
Plekha5	G	A	6: 140,537,473 (GRCm39)	R646K	possibly damaging	Het
Plpp5	A	T	8: 26,214,219 (GRCm39)	T144S	probably benign	Het
Ppp6r3	A	G	19: 3,528,285 (GRCm39)	L542S	probably damaging	Het
Prkar2b	A	T	12: 32,037,973 (GRCm39)		probably null	Het
Psmg1	A	T	16: 95,789,171 (GRCm39)	S129T	possibly damaging	Het
Radil	T	C	5: 142,529,582 (GRCm39)	D38G	probably benign	Het
Ric1	T	C	19: 29,578,411 (GRCm39)		probably null	Het
Rp1l1	T	A	14: 64,268,515 (GRCm39)	L1367*	probably null	Het
Rxfp1	A	T	3: 79,645,100 (GRCm39)	M1K	probably null	Het
Serpina6	G	T	12: 103,618,208 (GRCm39)	L202I	probably damaging	Het
Simc1	T	C	13: 54,676,280 (GRCm39)	I98T	probably damaging	Het
Slc17a6	A	G	7: 51,308,519 (GRCm39)	Y281C	probably damaging	Het
Slc26a11	T	A	11: 119,270,767 (GRCm39)		probably benign	Het
Slc34a1	T	A	13: 55,550,711 (GRCm39)		probably null	Het
Slfn10-ps	T	A	11: 82,926,600 (GRCm39)		noncoding transcript	Het
Sohlh2	A	G	3: 55,115,163 (GRCm39)	N383D	probably damaging	Het
Spag6	T	A	2: 18,715,302 (GRCm39)	L27H	probably damaging	Het
Sptlc3	A	G	2: 139,388,475 (GRCm39)		probably benign	Het
St3gal4	T	A	9: 34,964,469 (GRCm39)	K199*	probably null	Het
Stat5a	T	A	11: 100,772,909 (GRCm39)	D712E	probably benign	Het
Stmn2	A	T	3: 8,610,750 (GRCm39)	D78V	probably damaging	Het
Stpg1	C	T	4: 135,233,777 (GRCm39)	P20S	possibly damaging	Het
Taf2	A	T	15: 54,909,325 (GRCm39)	V640E	probably damaging	Het
Tbce	T	C	13: 14,172,747 (GRCm39)	E501G	probably benign	Het
Tecpr2	A	G	12: 110,935,374 (GRCm39)	S1398G	probably damaging	Het
Tenm4	T	A	7: 96,421,242 (GRCm39)	Y598*	probably null	Het
Ticrr	A	G	7: 79,327,088 (GRCm39)	S599G	probably damaging	Het
Tnc	A	C	4: 63,935,679 (GRCm39)	V419G	probably damaging	Het
Trappc1	C	A	11: 69,216,402 (GRCm39)	P110T	probably benign	Het
Trbv12-2	C	T	6: 41,095,993 (GRCm39)		probably benign	Het
Ttbk2	A	T	2: 120,576,264 (GRCm39)	N835K	possibly damaging	Het
Tubgcp5	A	G	7: 55,450,432 (GRCm39)	D181G	probably damaging	Het
Tut1	T	C	19: 8,932,891 (GRCm39)	Y75H	possibly damaging	Het
Ulk2	C	A	11: 61,678,412 (GRCm39)	C769F	probably benign	Het
Vdac1	T	C	11: 52,265,800 (GRCm39)		probably benign	Het
Vmn2r124	T	C	17: 18,284,486 (GRCm39)		probably null	Het
Vps8	T	C	16: 21,426,977 (GRCm39)		probably benign	Het
Wdr35	T	C	12: 9,045,625 (GRCm39)		probably benign	Het
Zdhhc7	T	A	8: 120,813,386 (GRCm39)	E141V	probably null	Het
Zfp12	C	A	5: 143,230,978 (GRCm39)	S435Y	probably damaging	Het
Zfp974	A	T	7: 27,626,819 (GRCm39)		probably benign	Het
Zfyve9	T	A	4: 108,538,166 (GRCm39)	K1033N	probably damaging	Het
Zswim8	T	A	14: 20,772,013 (GRCm39)	S1572T	possibly 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
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
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'- GGCAGTGGCAGATTTTCCAAAGC -3'
(R):5'- CCTTCTCTAGGCAGCATCACCAATG -3'

Sequencing Primer
(F):5'- CTGAAAAATGTTCTCTGATGGTTCC -3'
(R):5'- cctcccccacacactcc -3'

Posted On

2013-05-09