Mutagenetix > Incidental Mutation

Incidental Mutation 'R0115:Lig3'

20735

Institutional Source

Beutler Lab

Gene Symbol

Lig3

Ensembl Gene

ENSMUSG00000020697

Gene Name

ligase III, DNA, ATP-dependent

Synonyms

D11Wsu78e

MMRRC Submission

038401-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R0115 (G1)

Quality Score

225

Status

Validated (trace)

Chromosome

Chromosomal Location

82671977-82695100 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 82684761 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glycine at position 559 (D559G)

Ref Sequence

ENSEMBL: ENSMUSP00000133849 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000021039] [ENSMUST00000080461] [ENSMUST00000092849] [ENSMUST00000131537] [ENSMUST00000173722] [ENSMUST00000173347] [ENSMUST00000173727] [ENSMUST00000172837] [ENSMUST00000173009]

AlphaFold

no structure available at present

Predicted Effect

probably damaging
Transcript: ENSMUST00000021039
AA Change: D564G

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

SMART Domains

Protein: ENSMUSP00000021039
Gene: ENSMUSG00000020697
AA Change: D564G

Domain	Start	End	E-Value	Type
zf-PARP	97	183	8.89e-32	SMART
low complexity region	188	202	N/A	INTRINSIC
Pfam:DNA_ligase_A_N	265	440	3.5e-34	PFAM
Pfam:DNA_ligase_A_M	489	683	3.9e-65	PFAM
Pfam:DNA_ligase_A_C	710	820	3.8e-21	PFAM
low complexity region	855	885	N/A	INTRINSIC
BRCT	942	1010	9.77e-8	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000080461
AA Change: D560G

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

SMART Domains

Protein: ENSMUSP00000079317
Gene: ENSMUSG00000020697
AA Change: D560G

Domain	Start	End	E-Value	Type
zf-PARP	97	183	8.89e-32	SMART
low complexity region	188	202	N/A	INTRINSIC
Pfam:DNA_ligase_A_N	263	437	6.8e-53	PFAM
Pfam:DNA_ligase_A_M	485	679	1.3e-63	PFAM
Pfam:DNA_ligase_A_C	706	816	3.2e-21	PFAM
low complexity region	851	881	N/A	INTRINSIC
low complexity region	934	946	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000092849
AA Change: D560G

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

SMART Domains

Protein: ENSMUSP00000090525
Gene: ENSMUSG00000020697
AA Change: D560G

Domain	Start	End	E-Value	Type
zf-PARP	97	183	8.89e-32	SMART
low complexity region	188	202	N/A	INTRINSIC
Pfam:DNA_ligase_A_N	263	437	1.4e-52	PFAM
Pfam:DNA_ligase_A_M	485	679	7.2e-64	PFAM
Pfam:DNA_ligase_A_C	706	816	2.2e-21	PFAM
low complexity region	851	881	N/A	INTRINSIC
BRCT	938	1006	9.77e-8	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000131537

SMART Domains

Protein: ENSMUSP00000133672
Gene: ENSMUSG00000020697

Domain	Start	End	E-Value	Type
zf-PARP	97	183	8.89e-32	SMART
low complexity region	188	202	N/A	INTRINSIC
Pfam:DNA_ligase_A_N	263	431	3.1e-50	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000154887

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000155818

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000172609

Predicted Effect

probably damaging
Transcript: ENSMUST00000173722
AA Change: D560G

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

SMART Domains

Protein: ENSMUSP00000133805
Gene: ENSMUSG00000020697
AA Change: D560G

Domain	Start	End	E-Value	Type
zf-PARP	97	183	8.89e-32	SMART
low complexity region	188	202	N/A	INTRINSIC
Pfam:DNA_ligase_A_N	263	437	1.4e-52	PFAM
Pfam:DNA_ligase_A_M	485	679	7.2e-64	PFAM
Pfam:DNA_ligase_A_C	706	816	2.2e-21	PFAM
low complexity region	851	881	N/A	INTRINSIC
BRCT	938	1006	9.77e-8	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000173347
AA Change: D559G

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

SMART Domains

Protein: ENSMUSP00000134300
Gene: ENSMUSG00000020697
AA Change: D559G

Domain	Start	End	E-Value	Type
zf-PARP	97	183	8.89e-32	SMART
low complexity region	188	202	N/A	INTRINSIC
Pfam:DNA_ligase_A_N	262	436	1.4e-52	PFAM
Pfam:DNA_ligase_A_M	484	678	7.2e-64	PFAM
Pfam:DNA_ligase_A_C	705	815	2.2e-21	PFAM
low complexity region	850	880	N/A	INTRINSIC
BRCT	937	1005	9.77e-8	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000173727
AA Change: D559G

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

SMART Domains

Protein: ENSMUSP00000133849
Gene: ENSMUSG00000020697
AA Change: D559G

Domain	Start	End	E-Value	Type
zf-PARP	97	183	8.89e-32	SMART
low complexity region	188	202	N/A	INTRINSIC
Pfam:DNA_ligase_A_N	262	436	1.4e-52	PFAM
Pfam:DNA_ligase_A_M	484	678	7.2e-64	PFAM
Pfam:DNA_ligase_A_C	705	815	2.2e-21	PFAM
low complexity region	850	880	N/A	INTRINSIC
BRCT	937	1005	9.77e-8	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000172837

SMART Domains

Protein: ENSMUSP00000134101
Gene: ENSMUSG00000020697

Domain	Start	End	E-Value	Type
PDB:3L2P\|A	1	25	8e-9	PDB
low complexity region	41	71	N/A	INTRINSIC
PDB:3QVG\|C	115	173	2e-29	PDB
SCOP:d1in1a_	116	172	3e-34	SMART
Blast:BRCT	128	173	2e-25	BLAST

Predicted Effect

probably benign
Transcript: ENSMUST00000173009

SMART Domains

Protein: ENSMUSP00000133348
Gene: ENSMUSG00000020697

Domain	Start	End	E-Value	Type
zf-PARP	97	183	8.89e-32	SMART
low complexity region	188	202	N/A	INTRINSIC
Pfam:DNA_ligase_A_N	263	431	3.1e-50	PFAM

Meta Mutation Damage Score

0.9744

Coding Region Coverage

1x: 98.8%
3x: 97.7%
10x: 94.2%
20x: 86.0%

Validation Efficiency

98% (98/100)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene is a member of the DNA ligase family. Each member of this family encodes a protein that catalyzes the joining of DNA ends but they each have a distinct role in DNA metabolism. The protein encoded by this gene is involved in excision repair and is located in both the mitochondria and nucleus, with translation initiation from the upstream start codon allowing for transport to the mitochondria and translation initiation from a downstream start codon allowing for transport to the nucleus. Additionally, alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Jul 2008]
PHENOTYPE: Targeted inactivation of this gene causes embryonic growth arrest at 8.5 dpc, followed by excessive apoptosis at 9.5 dpc, and ultimately death, likely due to unrepaired DNA damage. Homozygous mutant cells display elevated sister chromatid exchange. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 85 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4921528I07Rik	A	G	9: 114,108,452 (GRCm39)		noncoding transcript	Het
Alas1	A	T	9: 106,115,451 (GRCm39)		probably null	Het
Arf5	A	G	6: 28,426,075 (GRCm39)	Y154C	probably damaging	Het
Arhgap20	T	A	9: 51,750,272 (GRCm39)	I344N	probably damaging	Het
Arhgap30	A	C	1: 171,235,516 (GRCm39)	E630A	possibly damaging	Het
B4galt5	A	G	2: 167,151,154 (GRCm39)	L118P	probably damaging	Het
Bdp1	A	G	13: 100,177,962 (GRCm39)	I1969T	probably benign	Het
Bysl	C	T	17: 47,921,867 (GRCm39)	R77Q	probably benign	Het
Cap1	A	T	4: 122,756,868 (GRCm39)	H272Q	possibly damaging	Het
Ccdc146	T	C	5: 21,527,754 (GRCm39)	I187M	possibly damaging	Het
Ccdc192	G	A	18: 57,727,214 (GRCm39)		probably benign	Het
Cdhr18	A	G	14: 13,899,571 (GRCm38)	V117A	probably damaging	Het
Cdk13	C	A	13: 17,894,079 (GRCm39)	A1123S	probably damaging	Het
Ces5a	A	T	8: 94,228,811 (GRCm39)	M473K	probably damaging	Het
Chd8	A	G	14: 52,474,663 (GRCm39)	S123P	probably benign	Het
Cwc22	G	A	2: 77,738,455 (GRCm39)	A497V	probably damaging	Het
Cwh43	T	C	5: 73,575,370 (GRCm39)	S296P	probably damaging	Het
Cyp2c50	T	A	19: 40,080,837 (GRCm39)		probably benign	Het
Dlg1	C	A	16: 31,624,508 (GRCm39)	Y399*	probably null	Het
Drosha	A	T	15: 12,846,216 (GRCm39)	E92D	probably benign	Het
Fanca	C	T	8: 123,995,278 (GRCm39)	G1408D	probably benign	Het
Frem1	T	A	4: 82,854,406 (GRCm39)	D1621V	possibly damaging	Het
Frem2	G	A	3: 53,563,629 (GRCm39)	R293C	probably damaging	Het
Fut8	T	A	12: 77,495,334 (GRCm39)	V308D	probably damaging	Het
Glipr1	A	G	10: 111,829,446 (GRCm39)	I105T	probably benign	Het
Glmn	A	T	5: 107,708,800 (GRCm39)	S385T	probably benign	Het
Gon4l	T	A	3: 88,802,989 (GRCm39)	V1200D	probably damaging	Het
Gpc1	G	A	1: 92,785,221 (GRCm39)	D387N	probably damaging	Het
Gsdmc	A	G	15: 63,675,486 (GRCm39)	Y110H	probably damaging	Het
Gucy1b1	T	A	3: 81,941,698 (GRCm39)	H586L	probably benign	Het
Gucy2e	A	G	11: 69,127,458 (GRCm39)	L5P	unknown	Het
Hectd4	A	G	5: 121,433,569 (GRCm39)		probably benign	Het
Hmcn1	T	A	1: 150,684,398 (GRCm39)	I391F	possibly damaging	Het
Hsf4	A	T	8: 105,999,336 (GRCm39)		probably null	Het
I830077J02Rik	G	A	3: 105,833,886 (GRCm39)	T90M	probably damaging	Het
Ino80	A	T	2: 119,261,497 (GRCm39)	H722Q	probably damaging	Het
Kcnma1	C	A	14: 23,364,243 (GRCm39)	R980L	probably damaging	Het
Kif1a	A	G	1: 92,974,500 (GRCm39)		probably benign	Het
Klhdc7b	A	G	15: 89,272,724 (GRCm39)	H1202R	probably benign	Het
Lyst	T	C	13: 13,852,537 (GRCm39)	V2179A	probably benign	Het
Mab21l4	A	T	1: 93,087,447 (GRCm39)	S135R	possibly damaging	Het
Mansc4	A	G	6: 146,976,725 (GRCm39)	I297T	possibly damaging	Het
Marchf6	A	T	15: 31,475,958 (GRCm39)	F633I	probably benign	Het
Marf1	C	T	16: 13,960,398 (GRCm39)	A549T	probably damaging	Het
Megf10	G	T	18: 57,392,874 (GRCm39)	V424L	possibly damaging	Het
Mfsd13a	C	T	19: 46,354,943 (GRCm39)	T40I	probably benign	Het
Mib2	A	G	4: 155,740,519 (GRCm39)		probably benign	Het
Mmut	C	T	17: 41,267,118 (GRCm39)	T564M	probably damaging	Het
Myh8	A	G	11: 67,197,090 (GRCm39)		probably benign	Het
Mypn	T	C	10: 63,028,159 (GRCm39)		probably benign	Het
Nf1	G	A	11: 79,359,702 (GRCm39)		probably null	Het
Notch3	T	A	17: 32,352,436 (GRCm39)	T1866S	possibly damaging	Het
Or1e30	A	G	11: 73,678,141 (GRCm39)	I126V	possibly damaging	Het
Or1o11	C	T	17: 37,756,670 (GRCm39)	A86V	probably benign	Het
Or4c102	A	T	2: 88,422,999 (GRCm39)	I284F	probably damaging	Het
Or4k51	T	A	2: 111,584,930 (GRCm39)	M112K	probably damaging	Het
Pkhd1	A	T	1: 20,420,714 (GRCm39)	I2464N	probably damaging	Het
Pkn1	A	G	8: 84,397,658 (GRCm39)	S817P	probably damaging	Het
Prkg2	A	T	5: 99,142,514 (GRCm39)		probably null	Het
Prl8a6	T	C	13: 27,617,084 (GRCm39)	D201G	probably benign	Het
Psmd1	C	T	1: 86,010,993 (GRCm39)	T356I	possibly damaging	Het
Ptk6	G	A	2: 180,844,320 (GRCm39)		probably benign	Het
Ptprn2	T	C	12: 117,175,466 (GRCm39)		probably benign	Het
Rbm42	G	A	7: 30,347,200 (GRCm39)	T106I	probably damaging	Het
Rims4	A	T	2: 163,706,040 (GRCm39)	V198E	probably damaging	Het
Ripk1	T	C	13: 34,193,733 (GRCm39)	S32P	probably damaging	Het
Rorc	T	C	3: 94,284,916 (GRCm39)		probably benign	Het
Rpl22l1	T	C	3: 28,860,685 (GRCm39)	F15L	probably damaging	Het
Slc6a20a	C	A	9: 123,507,823 (GRCm39)	A17S	possibly damaging	Het
Sorcs1	A	G	19: 50,624,891 (GRCm39)		probably benign	Het
Sp100	A	G	1: 85,577,852 (GRCm39)		probably benign	Het
Ssc5d	G	A	7: 4,930,880 (GRCm39)		probably benign	Het
Taf11	A	G	17: 28,126,635 (GRCm39)	L4P	probably benign	Het
Tm2d3	A	G	7: 65,345,082 (GRCm39)		probably benign	Het
Tmub2	T	C	11: 102,179,201 (GRCm39)		probably null	Het
Trim34a	T	A	7: 103,897,109 (GRCm39)	C58S	probably damaging	Het
Trpc3	T	C	3: 36,678,566 (GRCm39)	I840V	probably benign	Het
Trpm6	T	C	19: 18,807,316 (GRCm39)	V1020A	probably damaging	Het
Vmn1r214	T	A	13: 23,219,464 (GRCm39)	Y319*	probably null	Het
Vmn1r59	T	C	7: 5,457,115 (GRCm39)	N215S	probably benign	Het
Vmn2r74	T	C	7: 85,606,564 (GRCm39)	M261V	probably benign	Het
Vmn2r89	T	C	14: 51,693,577 (GRCm39)	F309S	probably damaging	Het
Wdr95	A	T	5: 149,487,855 (GRCm39)	D163V	probably damaging	Het
Xirp2	T	A	2: 67,340,253 (GRCm39)	F831L	possibly damaging	Het
Ythdc2	C	T	18: 44,974,490 (GRCm39)		probably benign	Het

Other mutations in Lig3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01066:Lig3	APN	11	82,688,141 (GRCm39)	missense	possibly damaging	0.90
IGL01577:Lig3	APN	11	82,674,303 (GRCm39)	missense	probably benign	0.00
IGL01643:Lig3	APN	11	82,689,118 (GRCm39)	missense	probably damaging	1.00
IGL01712:Lig3	APN	11	82,680,367 (GRCm39)	splice site	probably benign
IGL01724:Lig3	APN	11	82,681,448 (GRCm39)	missense	possibly damaging	0.95
IGL01749:Lig3	APN	11	82,680,693 (GRCm39)	missense	probably damaging	1.00
IGL01778:Lig3	APN	11	82,685,367 (GRCm39)	missense	probably damaging	1.00
IGL02798:Lig3	APN	11	82,686,531 (GRCm39)	splice site	probably benign
IGL03007:Lig3	APN	11	82,680,401 (GRCm39)	missense	probably damaging	1.00
IGL03178:Lig3	APN	11	82,680,548 (GRCm39)	splice site	probably benign
R0001:Lig3	UTSW	11	82,681,417 (GRCm39)	missense	probably damaging	1.00
R0834:Lig3	UTSW	11	82,689,113 (GRCm39)	missense	probably damaging	0.99
R1460:Lig3	UTSW	11	82,686,624 (GRCm39)	splice site	probably benign
R1602:Lig3	UTSW	11	82,683,020 (GRCm39)	critical splice donor site	probably null
R1969:Lig3	UTSW	11	82,686,544 (GRCm39)	missense	probably benign	0.14
R1971:Lig3	UTSW	11	82,686,544 (GRCm39)	missense	probably benign	0.14
R1997:Lig3	UTSW	11	82,678,492 (GRCm39)	missense	probably benign	0.00
R3817:Lig3	UTSW	11	82,686,941 (GRCm39)	missense	possibly damaging	0.75
R4083:Lig3	UTSW	11	82,681,320 (GRCm39)	missense	probably benign	0.31
R4084:Lig3	UTSW	11	82,686,250 (GRCm39)	missense	probably damaging	1.00
R4665:Lig3	UTSW	11	82,691,076 (GRCm39)	missense	probably damaging	0.99
R4737:Lig3	UTSW	11	82,678,553 (GRCm39)	missense	probably damaging	1.00
R5212:Lig3	UTSW	11	82,678,504 (GRCm39)	missense	probably benign
R5274:Lig3	UTSW	11	82,688,118 (GRCm39)	splice site	probably null
R6320:Lig3	UTSW	11	82,684,833 (GRCm39)	critical splice donor site	probably null
R6807:Lig3	UTSW	11	82,674,577 (GRCm39)	missense	probably benign	0.00
R7103:Lig3	UTSW	11	82,688,138 (GRCm39)	missense	probably benign	0.17
R7552:Lig3	UTSW	11	82,679,717 (GRCm39)	missense	probably benign	0.00
R7646:Lig3	UTSW	11	82,674,304 (GRCm39)	missense	probably benign	0.00
R7910:Lig3	UTSW	11	82,688,601 (GRCm39)	missense	probably damaging	0.99
R7966:Lig3	UTSW	11	82,681,342 (GRCm39)	missense	probably damaging	1.00
R8001:Lig3	UTSW	11	82,682,902 (GRCm39)	missense	probably benign	0.18
R8436:Lig3	UTSW	11	82,682,870 (GRCm39)	missense	possibly damaging	0.82
R8699:Lig3	UTSW	11	82,685,376 (GRCm39)	missense	probably damaging	1.00
R9352:Lig3	UTSW	11	82,686,971 (GRCm39)	missense	probably benign	0.01
R9392:Lig3	UTSW	11	82,680,666 (GRCm39)	missense	probably benign	0.06
R9452:Lig3	UTSW	11	82,681,448 (GRCm39)	missense	probably damaging	1.00
R9469:Lig3	UTSW	11	82,686,199 (GRCm39)	missense	probably benign	0.01
R9726:Lig3	UTSW	11	82,674,420 (GRCm39)	missense	possibly damaging	0.89

Predicted Primers

PCR Primer
(F):5'- GCTGTTTTGCCTGAGCCTTGATCAC -3'
(R):5'- AGTCCTGTCAGTGCCTCCATAGATG -3'

Sequencing Primer
(F):5'- GAGCCTTGATCACTCTGGCTTAG -3'
(R):5'- gcccaaatgctaaaggtttgttc -3'

Posted On

2013-04-11