Mutagenetix > Incidental Mutation

Incidental Mutation 'R0834:Lig3'

77746

Institutional Source

Beutler Lab

Gene Symbol

Lig3

Ensembl Gene

ENSMUSG00000020697

Gene Name

ligase III, DNA, ATP-dependent

Synonyms

D11Wsu78e

MMRRC Submission

039013-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R0834 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

82671977-82695100 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 82689113 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glutamic Acid to Glycine at position 794 (E794G)

Ref Sequence

ENSEMBL: ENSMUSP00000021039 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000021039] [ENSMUST00000074515] [ENSMUST00000080461] [ENSMUST00000092849] [ENSMUST00000173722] [ENSMUST00000173727] [ENSMUST00000173347] [ENSMUST00000172837]

AlphaFold

no structure available at present

Predicted Effect

probably damaging
Transcript: ENSMUST00000021039
AA Change: E794G

PolyPhen 2 Score 0.989 (Sensitivity: 0.72; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000021039
Gene: ENSMUSG00000020697
AA Change: E794G

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 benign
Transcript: ENSMUST00000074515

SMART Domains

Protein: ENSMUSP00000074108
Gene: ENSMUSG00000020696

Domain	Start	End	E-Value	Type
PDB:1Y02\|A	27	145	4e-75	PDB
Blast:RING	47	88	2e-19	BLAST
low complexity region	163	175	N/A	INTRINSIC
RING	316	350	3.47e-4	SMART

Predicted Effect

possibly damaging
Transcript: ENSMUST00000080461
AA Change: E790G

PolyPhen 2 Score 0.946 (Sensitivity: 0.80; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000079317
Gene: ENSMUSG00000020697
AA Change: E790G

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

possibly damaging
Transcript: ENSMUST00000092849
AA Change: E790G

PolyPhen 2 Score 0.946 (Sensitivity: 0.80; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000090525
Gene: ENSMUSG00000020697
AA Change: E790G

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

noncoding transcript
Transcript: ENSMUST00000154887

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000155818

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000172609

Predicted Effect

possibly damaging
Transcript: ENSMUST00000173722
AA Change: E790G

PolyPhen 2 Score 0.946 (Sensitivity: 0.80; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000133805
Gene: ENSMUSG00000020697
AA Change: E790G

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

possibly damaging
Transcript: ENSMUST00000173727
AA Change: E789G

PolyPhen 2 Score 0.946 (Sensitivity: 0.80; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000133849
Gene: ENSMUSG00000020697
AA Change: E789G

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

possibly damaging
Transcript: ENSMUST00000173347
AA Change: E789G

PolyPhen 2 Score 0.946 (Sensitivity: 0.80; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000134300
Gene: ENSMUSG00000020697
AA Change: E789G

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

Meta Mutation Damage Score

0.2759

Coding Region Coverage

1x: 99.4%
3x: 98.9%
10x: 97.7%
20x: 95.7%

Validation Efficiency

100% (86/86)

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
Add2	A	T	6: 86,063,899 (GRCm39)	E66V	probably damaging	Het
Aldh1a3	T	C	7: 66,062,658 (GRCm39)	I156V	probably benign	Het
Ang4	T	A	14: 52,001,725 (GRCm39)	K74N	probably benign	Het
Arcn1	A	T	9: 44,670,172 (GRCm39)		probably benign	Het
Arhgef33	T	A	17: 80,655,026 (GRCm39)		probably benign	Het
Atn1	A	G	6: 124,720,188 (GRCm39)		probably benign	Het
Bmal2	A	G	6: 146,724,185 (GRCm39)	H359R	probably damaging	Het
Bmerb1	T	C	16: 13,911,795 (GRCm39)	L47P	probably damaging	Het
Brip1	T	C	11: 86,083,653 (GRCm39)	T123A	probably benign	Het
Camkv	A	G	9: 107,823,045 (GRCm39)	Y95C	probably damaging	Het
Cdk12	T	A	11: 98,095,211 (GRCm39)	S340T	probably benign	Het
Ckap2l	G	A	2: 129,138,224 (GRCm39)		probably benign	Het
Clmn	A	T	12: 104,738,085 (GRCm39)	L1042Q	probably damaging	Het
Clmn	G	T	12: 104,738,086 (GRCm39)	L1042M	probably damaging	Het
Cluh	T	C	11: 74,554,631 (GRCm39)	V737A	probably benign	Het
Cpne8	A	G	15: 90,424,462 (GRCm39)	V309A	probably benign	Het
Cpxm2	T	A	7: 131,756,342 (GRCm39)		probably benign	Het
Csmd3	A	T	15: 47,747,073 (GRCm39)		probably benign	Het
Ctr9	T	A	7: 110,650,159 (GRCm39)	S818T	probably benign	Het
Cyp26a1	C	T	19: 37,688,405 (GRCm39)	A309V	probably damaging	Het
Dbndd2	C	T	2: 164,332,122 (GRCm39)	T115I	possibly damaging	Het
Dhcr7	A	G	7: 143,394,964 (GRCm39)	N157S	probably benign	Het
Dlx2	C	A	2: 71,375,859 (GRCm39)	V155F	probably damaging	Het
Duox1	A	T	2: 122,176,982 (GRCm39)	I1470F	probably damaging	Het
Esrrb	A	T	12: 86,517,071 (GRCm39)	I68F	probably benign	Het
Fhod3	T	A	18: 25,248,862 (GRCm39)	L1347*	probably null	Het
Fip1l1	T	C	5: 74,755,721 (GRCm39)		probably benign	Het
Frem3	A	G	8: 81,413,637 (GRCm39)	Y1966C	probably damaging	Het
Gatd3a	T	C	10: 77,998,539 (GRCm39)	D229G	probably damaging	Het
Ggt5	C	T	10: 75,440,604 (GRCm39)	R242C	possibly damaging	Het
Gm14496	G	A	2: 181,637,480 (GRCm39)	V185I	probably benign	Het
Gnptab	T	C	10: 88,265,814 (GRCm39)	V409A	probably damaging	Het
Gramd1a	A	G	7: 30,837,589 (GRCm39)	F390S	possibly damaging	Het
Helz2	A	G	2: 180,872,570 (GRCm39)	S2477P	probably damaging	Het
Hsd17b3	T	C	13: 64,236,936 (GRCm39)	K3E	probably benign	Het
Ift172	T	C	5: 31,414,715 (GRCm39)	H1395R	probably benign	Het
Jam2	T	A	16: 84,609,855 (GRCm39)	C180S	probably damaging	Het
Kalrn	A	C	16: 33,870,289 (GRCm39)	S160A	possibly damaging	Het
Kcnk3	T	C	5: 30,779,979 (GRCm39)	I343T	probably damaging	Het
Kif13a	T	C	13: 46,967,712 (GRCm39)	E334G	probably damaging	Het
Klhl41	A	G	2: 69,508,491 (GRCm39)	K482E	possibly damaging	Het
Myh13	T	C	11: 67,240,436 (GRCm39)	M780T	possibly damaging	Het
Ndst2	A	G	14: 20,779,761 (GRCm39)	Y160H	probably damaging	Het
Ndufb10	T	C	17: 24,941,648 (GRCm39)	M90V	probably damaging	Het
Obscn	T	C	11: 59,024,104 (GRCm39)	K522R	probably benign	Het
Olfml2b	T	C	1: 170,475,413 (GRCm39)	S113P	probably benign	Het
Or14a257	T	A	7: 86,138,698 (GRCm39)	E20D	probably benign	Het
Or4a78	A	G	2: 89,497,423 (GRCm39)	I269T	probably benign	Het
Or4d10b	T	A	19: 12,036,979 (GRCm39)	M46L	probably benign	Het
Or51v14	T	C	7: 103,261,444 (GRCm39)	T39A	probably benign	Het
Or6k2	T	A	1: 173,986,930 (GRCm39)	M197K	possibly damaging	Het
Parg	T	C	14: 31,936,511 (GRCm39)		probably benign	Het
Pde7a	C	T	3: 19,284,482 (GRCm39)	C367Y	probably damaging	Het
Pigr	T	A	1: 130,772,281 (GRCm39)	C166*	probably null	Het
Pip4k2c	A	T	10: 127,036,704 (GRCm39)		probably benign	Het
Ppp1r16a	C	T	15: 76,577,869 (GRCm39)	Q328*	probably null	Het
Prkd2	A	T	7: 16,599,602 (GRCm39)		probably benign	Het
Ptprt	G	T	2: 161,654,059 (GRCm39)		probably null	Het
Rapgef5	C	T	12: 117,610,741 (GRCm39)		probably benign	Het
Retreg1	T	C	15: 25,971,756 (GRCm39)	L356P	probably benign	Het
Rigi	T	A	4: 40,239,596 (GRCm39)	E34V	possibly damaging	Het
Rnf43	A	G	11: 87,622,077 (GRCm39)	T393A	probably benign	Het
Samd3	T	C	10: 26,147,725 (GRCm39)	S467P	probably benign	Het
Scarf1	C	A	11: 75,405,229 (GRCm39)	C89*	probably null	Het
Sdk1	T	C	5: 141,227,779 (GRCm39)	L59S	probably benign	Het
Sgca	C	T	11: 94,861,512 (GRCm39)	W244*	probably null	Het
Sh3d21	T	C	4: 126,045,065 (GRCm39)	K538R	probably benign	Het
Smyd4	T	A	11: 75,281,958 (GRCm39)	L477Q	possibly damaging	Het
Sra1	A	G	18: 36,801,829 (GRCm39)	M87T	probably benign	Het
Ssh2	T	C	11: 77,328,459 (GRCm39)	Y336H	possibly damaging	Het
Steap1	T	C	5: 5,790,357 (GRCm39)	Y197C	probably damaging	Het
Strn3	A	G	12: 51,673,879 (GRCm39)		probably benign	Het
Tgm3	A	G	2: 129,868,677 (GRCm39)	T205A	probably benign	Het
Tll2	G	A	19: 41,101,512 (GRCm39)	T374I	probably damaging	Het
Tmem63b	C	A	17: 45,971,870 (GRCm39)	D782Y	possibly damaging	Het
Trim10	G	A	17: 37,183,283 (GRCm39)	S193N	probably benign	Het
Ttf1	A	T	2: 28,963,962 (GRCm39)	K613*	probably null	Het
Tube1	T	A	10: 39,010,168 (GRCm39)		probably null	Het
Uimc1	T	A	13: 55,224,222 (GRCm39)		probably null	Het
Wwp2	G	T	8: 108,283,428 (GRCm39)		probably benign	Het
Zfp101	C	T	17: 33,601,418 (GRCm39)	V113I	probably benign	Het
Zfp292	T	C	4: 34,809,114 (GRCm39)	D1310G	probably benign	Het
Zfp575	A	T	7: 24,285,245 (GRCm39)	L132H	probably damaging	Het
Zmym2	T	C	14: 57,194,420 (GRCm39)	F1226S	probably damaging	Het
Zswim6	A	C	13: 107,862,989 (GRCm39)		noncoding transcript	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
R0115:Lig3	UTSW	11	82,684,761 (GRCm39)	missense	probably damaging	1.00
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'- ATTCAAGAGGAGGCATAACTGGCAC -3'
(R):5'- TGGAAAGCTAGGCTCTTCAGGGAAC -3'

Sequencing Primer
(F):5'- GGCATAACTGGCACACAGG -3'
(R):5'- CATGTGAAGAGGCTAGATGCCC -3'

Posted On

2013-10-16