Mutagenetix > Incidental Mutation

Incidental Mutation 'R1809:Lig1'

203695

Institutional Source

Beutler Lab

Gene Symbol

Lig1

Ensembl Gene

ENSMUSG00000056394

Gene Name

ligase I, DNA, ATP-dependent

Synonyms

mLigI, LigI

MMRRC Submission

039838-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R1809 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

13011239-13045350 bp(+) (GRCm39)

Type of Mutation

splice site

DNA Base Change (assembly)

T to C at 13034281 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

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 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: ENSMUST00000138453

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

Coding Region Coverage

1x: 97.5%
3x: 96.8%
10x: 94.9%
20x: 91.2%

Validation Efficiency

96% (107/111)

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: 104 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Ablim2	A	G	5: 36,000,614 (GRCm39)		probably benign	Het
Adamts20	C	T	15: 94,238,968 (GRCm39)	S750N	probably damaging	Het
Adh6a	G	A	3: 138,036,722 (GRCm39)	R370H	possibly damaging	Het
Akr1b7	A	G	6: 34,396,046 (GRCm39)	N183D	probably damaging	Het
Aktip	A	T	8: 91,856,348 (GRCm39)	I43N	probably damaging	Het
Ankrd26	A	T	6: 118,502,883 (GRCm39)		probably benign	Het
Ano9	G	A	7: 140,688,717 (GRCm39)	T144I	possibly damaging	Het
Anpep	G	T	7: 79,491,571 (GRCm39)	D143E	probably benign	Het
Aox1	C	A	1: 58,333,484 (GRCm39)	Q234K	probably benign	Het
Ap1g1	C	G	8: 110,559,814 (GRCm39)		probably benign	Het
Arhgef4	G	A	1: 34,849,636 (GRCm39)		probably null	Het
Arsj	A	G	3: 126,231,944 (GRCm39)	Y230C	possibly damaging	Het
Asmt	C	T	X: 169,109,480 (GRCm39)		probably benign	Het
Astl	A	T	2: 127,187,405 (GRCm39)	K72N	probably damaging	Het
Atp2b2	G	A	6: 113,780,704 (GRCm39)		probably benign	Het
Baiap2l1	A	C	5: 144,261,365 (GRCm39)		probably null	Het
C7	A	T	15: 5,063,821 (GRCm39)	N193K	probably damaging	Het
Cacna2d4	G	T	6: 119,247,785 (GRCm39)	R362L	probably damaging	Het
Cct4	T	A	11: 22,947,615 (GRCm39)	D189E	probably benign	Het
Cd300lg	G	A	11: 101,933,938 (GRCm39)	G62S	probably benign	Het
Cdk14	T	A	5: 5,060,901 (GRCm39)	M307L	probably damaging	Het
Cfi	G	A	3: 129,666,768 (GRCm39)		probably null	Het
Clec2g	G	T	6: 128,957,273 (GRCm39)		probably null	Het
Cntnap2	T	C	6: 46,965,609 (GRCm39)	S807P	probably damaging	Het
Col6a3	T	A	1: 90,755,671 (GRCm39)	H206L	probably damaging	Het
Ct55	A	G	X: 52,735,716 (GRCm39)	E99G	probably benign	Het
Cyp2c23	A	T	19: 44,009,997 (GRCm39)		probably benign	Het
Degs1l	T	C	1: 180,887,252 (GRCm39)	I279T	probably damaging	Het
Dlec1	T	C	9: 118,965,767 (GRCm39)	V1058A	probably benign	Het
Dpp9	A	G	17: 56,506,038 (GRCm39)	Y454H	probably damaging	Het
Drosha	G	A	15: 12,890,198 (GRCm39)	G920R	probably null	Het
Duox2	A	G	2: 122,114,378 (GRCm39)	S1142P	possibly damaging	Het
Fam13a	C	T	6: 58,942,045 (GRCm39)		probably null	Het
Filip1l	A	G	16: 57,327,023 (GRCm39)	R18G	probably benign	Het
Foxa1	A	G	12: 57,589,527 (GRCm39)	V231A	probably damaging	Het
Gm4787	A	T	12: 81,425,303 (GRCm39)	M285K	possibly damaging	Het
Gm5084	T	A	13: 60,360,320 (GRCm39)		noncoding transcript	Het
Gm6788	G	A	19: 28,740,586 (GRCm39)		noncoding transcript	Het
Gm9922	G	T	14: 101,966,841 (GRCm39)		probably benign	Het
Gtf3c4	A	T	2: 28,723,988 (GRCm39)	Y440*	probably null	Het
Helq	A	G	5: 100,921,820 (GRCm39)	S795P	probably damaging	Het
Helz	T	A	11: 107,489,997 (GRCm39)	S151T	possibly damaging	Het
Irgm1	T	C	11: 48,757,440 (GRCm39)	T124A	probably benign	Het
Itgam	C	T	7: 127,670,109 (GRCm39)	P134S	possibly damaging	Het
Kdm6a	T	C	X: 18,102,923 (GRCm39)	Y217H	probably benign	Het
Kif6	T	C	17: 50,208,812 (GRCm39)	L744P	probably benign	Het
Kmt2c	C	T	5: 25,489,190 (GRCm39)	R1203H	probably damaging	Het
Ksr2	A	G	5: 117,693,535 (GRCm39)	T328A	probably damaging	Het
Lpar3	G	A	3: 145,946,303 (GRCm39)		probably benign	Het
Lrrk2	T	C	15: 91,584,095 (GRCm39)	F285S	possibly damaging	Het
Marchf7	A	G	2: 60,062,637 (GRCm39)	D148G	probably benign	Het
Mcee	T	C	7: 64,050,049 (GRCm39)	L60S	probably damaging	Het
Mob2	A	G	7: 141,570,111 (GRCm39)	I81T	probably damaging	Het
Mphosph8	T	A	14: 56,909,909 (GRCm39)	D87E	probably damaging	Het
Msantd5f9	A	G	4: 73,835,754 (GRCm39)	F237L	probably benign	Het
Myo1g	T	C	11: 6,462,283 (GRCm39)	T560A	probably benign	Het
Nagk	C	T	6: 83,774,169 (GRCm39)	T42I	probably benign	Het
Naip1	G	T	13: 100,562,747 (GRCm39)	T806K	probably benign	Het
Ncor2	A	G	5: 125,195,857 (GRCm39)		probably benign	Het
Ocln	G	T	13: 100,647,967 (GRCm39)	Y401*	probably null	Het
Odad2	T	A	18: 7,211,630 (GRCm39)	Y748F	probably benign	Het
Oma1	T	A	4: 103,182,374 (GRCm39)	N292K	probably damaging	Het
Or8b55	G	A	9: 38,727,443 (GRCm39)	V215I	probably benign	Het
Ovch2	T	A	7: 107,389,412 (GRCm39)		probably null	Het
Pcdhb16	T	C	18: 37,611,441 (GRCm39)	F134L	probably damaging	Het
Pipox	A	T	11: 77,772,360 (GRCm39)	Y337N	probably benign	Het
Polr3b	A	G	10: 84,528,865 (GRCm39)	D763G	probably damaging	Het
Pygo1	T	A	9: 72,852,078 (GRCm39)	N88K	probably damaging	Het
Rab3gap1	T	C	1: 127,862,251 (GRCm39)	M674T	probably damaging	Het
Rbm25	T	C	12: 83,719,501 (GRCm39)		probably benign	Het
Rbm26	C	T	14: 105,354,542 (GRCm39)		probably benign	Het
Rbms2	G	A	10: 127,974,055 (GRCm39)	T187I	possibly damaging	Het
Rnase11	T	A	14: 51,287,184 (GRCm39)	R123S	probably benign	Het
Rngtt	A	G	4: 33,443,614 (GRCm39)	N485D	probably benign	Het
Rp1l1	A	T	14: 64,265,415 (GRCm39)	M334L	probably benign	Het
Rps9	T	A	7: 3,707,726 (GRCm39)	L56Q	probably damaging	Het
Saysd1	C	A	14: 20,133,170 (GRCm39)		probably benign	Het
Sema4d	C	T	13: 51,867,727 (GRCm39)		probably null	Het
Shisa5	A	T	9: 108,869,998 (GRCm39)	D34V	probably damaging	Het
Skil	A	G	3: 31,171,655 (GRCm39)	D547G	probably damaging	Het
Slc2a5	T	A	4: 150,227,514 (GRCm39)	F444L	probably damaging	Het
Slc9b2	T	G	3: 135,022,892 (GRCm39)	C10G	possibly damaging	Het
Sorcs2	G	T	5: 36,386,564 (GRCm39)		probably benign	Het
Stk17b	T	G	1: 53,805,140 (GRCm39)	K140N	possibly damaging	Het
Stradb	T	A	1: 59,033,549 (GRCm39)	L404Q	possibly damaging	Het
Synj2	T	C	17: 6,076,826 (GRCm39)	M432T	possibly damaging	Het
Tanc1	G	T	2: 59,630,441 (GRCm39)	R800L	probably damaging	Het
Tenm4	A	G	7: 96,522,987 (GRCm39)	M1473V	probably benign	Het
Tesc	A	G	5: 118,199,667 (GRCm39)	I190V	probably benign	Het
Tex15	T	C	8: 34,064,262 (GRCm39)	F1231L	probably benign	Het
Thrsp	T	C	7: 97,066,332 (GRCm39)	I127V	probably benign	Het
Tlr6	A	T	5: 65,111,055 (GRCm39)	C617*	probably null	Het
Trank1	A	T	9: 111,221,893 (GRCm39)	I2877F	probably benign	Het
Tut4	T	A	4: 108,406,552 (GRCm39)	H1373Q	probably damaging	Het
Ucp1	T	C	8: 84,024,496 (GRCm39)	S274P	probably damaging	Het
Ucp2	T	A	7: 100,147,606 (GRCm39)	V195E	probably damaging	Het
Vars2	T	C	17: 35,973,108 (GRCm39)	T394A	probably damaging	Het
Vmn1r1	A	G	1: 181,985,371 (GRCm39)	V98A	possibly damaging	Het
Vmn1r225	A	G	17: 20,722,918 (GRCm39)	I120V	probably benign	Het
Vmn2r102	A	T	17: 19,897,881 (GRCm39)	M299L	probably benign	Het
Vmn2r25	A	G	6: 123,802,337 (GRCm39)	V522A	probably benign	Het
Vmn2r70	T	C	7: 85,215,130 (GRCm39)	I135V	probably benign	Het
Vwf	T	C	6: 125,567,138 (GRCm39)		probably benign	Het
Zfp446	T	C	7: 12,713,048 (GRCm39)	F29L	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
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'- GGTATGGTATAGTCCAGCAGC -3'
(R):5'- AGCAAATTCTGTGGCCAAGC -3'

Sequencing Primer
(F):5'- GTCCAGCAGCAGAATATTTTCTTC -3'
(R):5'- AAGCCACTGCCTTCTGGAC -3'

Posted On

2014-06-23