Mutagenetix > Incidental Mutation

Incidental Mutation 'R4665:Lig3'

351851

Institutional Source

Beutler Lab

Gene Symbol

Lig3

Ensembl Gene

ENSMUSG00000020697

Gene Name

ligase III, DNA, ATP-dependent

Synonyms

D11Wsu78e

MMRRC Submission

041923-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R4665 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

82671977-82695100 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 82691076 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Methionine at position 110 (V110M)

Ref Sequence

ENSEMBL: ENSMUSP00000134101 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000021039] [ENSMUST00000071152] [ENSMUST00000074515] [ENSMUST00000080461] [ENSMUST00000092849] [ENSMUST00000093975] [ENSMUST00000108173] [ENSMUST00000172837] [ENSMUST00000173347] [ENSMUST00000173722] [ENSMUST00000173727]

AlphaFold

no structure available at present

Predicted Effect

probably benign
Transcript: ENSMUST00000021039
AA Change: V924M

PolyPhen 2 Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)

SMART Domains

Protein: ENSMUSP00000021039
Gene: ENSMUSG00000020697
AA Change: V924M

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: ENSMUST00000071152

SMART Domains

Protein: ENSMUSP00000071150
Gene: ENSMUSG00000020696

Domain	Start	End	E-Value	Type
PDB:1Y02\|A	62	180	1e-74	PDB
Blast:RING	82	123	2e-19	BLAST
low complexity region	198	210	N/A	INTRINSIC
RING	351	385	3.47e-4	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: V920M

PolyPhen 2 Score 0.868 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000079317
Gene: ENSMUSG00000020697
AA Change: V920M

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: V920M

PolyPhen 2 Score 0.542 (Sensitivity: 0.88; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000090525
Gene: ENSMUSG00000020697
AA Change: V920M

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: ENSMUST00000093975

SMART Domains

Protein: ENSMUSP00000091510
Gene: ENSMUSG00000020696

Domain	Start	End	E-Value	Type
PDB:1Y02\|A	41	159	6e-75	PDB
Blast:RING	61	102	2e-19	BLAST
low complexity region	177	189	N/A	INTRINSIC
RING	330	364	3.47e-4	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000108173

SMART Domains

Protein: ENSMUSP00000103808
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

probably damaging
Transcript: ENSMUST00000172837
AA Change: V110M

PolyPhen 2 Score 0.988 (Sensitivity: 0.73; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000134101
Gene: ENSMUSG00000020697
AA Change: V110M

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: ENSMUST00000173347
AA Change: V919M

PolyPhen 2 Score 0.317 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000134300
Gene: ENSMUSG00000020697
AA Change: V919M

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: ENSMUST00000173722
AA Change: V920M

PolyPhen 2 Score 0.542 (Sensitivity: 0.88; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000133805
Gene: ENSMUSG00000020697
AA Change: V920M

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: ENSMUST00000173727
AA Change: V919M

PolyPhen 2 Score 0.317 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000133849
Gene: ENSMUSG00000020697
AA Change: V919M

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

noncoding transcript
Transcript: ENSMUST00000154887

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000155818

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000172609

Meta Mutation Damage Score

0.6467

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.3%
20x: 95.4%

Validation Efficiency

99% (89/90)

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: 86 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aak1	T	A	6: 86,902,059 (GRCm39)	M76K	probably null	Het
Abcc4	A	G	14: 118,766,414 (GRCm39)	I886T	probably benign	Het
Adam6a	T	C	12: 113,507,992 (GRCm39)	Y122H	possibly damaging	Het
Adgre1	A	G	17: 57,787,947 (GRCm39)	T905A	probably benign	Het
Arap2	A	G	5: 62,827,312 (GRCm39)	F969L	possibly damaging	Het
Arhgef4	G	T	1: 34,845,113 (GRCm39)	G1439V	possibly damaging	Het
Atm	A	G	9: 53,375,529 (GRCm39)	W2097R	probably benign	Het
Atmin	A	G	8: 117,684,698 (GRCm39)	D786G	probably damaging	Het
AU016765	T	A	17: 64,826,916 (GRCm39)		noncoding transcript	Het
Capn1	A	T	19: 6,061,045 (GRCm39)	N253K	probably benign	Het
Cdc42bpa	A	G	1: 179,972,130 (GRCm39)	T527A	probably damaging	Het
Chmp7	A	T	14: 69,958,404 (GRCm39)	V255D	probably damaging	Het
Cldn12	A	G	5: 5,558,385 (GRCm39)	F14S	probably damaging	Het
Cpsf2	T	C	12: 101,949,466 (GRCm39)	S61P	probably damaging	Het
Cpvl	C	T	6: 53,908,918 (GRCm39)	E282K	probably benign	Het
Crygn	T	A	5: 24,956,019 (GRCm39)		probably benign	Het
Csde1	C	T	3: 102,954,388 (GRCm39)	T386M	probably damaging	Het
Cux1	G	A	5: 136,315,653 (GRCm39)	T1129I	probably damaging	Het
Dcaf10	G	A	4: 45,372,769 (GRCm39)	R394Q	possibly damaging	Het
Dhx16	T	C	17: 36,190,835 (GRCm39)	V11A	probably damaging	Het
Dnah10	T	C	5: 124,905,536 (GRCm39)	M4060T	possibly damaging	Het
Duox1	C	T	2: 122,149,956 (GRCm39)	P116S	probably benign	Het
Eif5b	A	G	1: 38,084,793 (GRCm39)	E880G	probably damaging	Het
Eml6	A	T	11: 29,769,007 (GRCm39)	Y67*	probably null	Het
Faim2	C	A	15: 99,422,581 (GRCm39)		probably null	Het
Faim2	T	G	15: 99,422,582 (GRCm39)	S72R	probably benign	Het
Fanca	T	C	8: 123,995,711 (GRCm39)	T1364A	probably damaging	Het
Fhip1a	A	T	3: 85,637,988 (GRCm39)	W104R	probably damaging	Het
Gak	A	G	5: 108,730,826 (GRCm39)	I860T	probably benign	Het
Garem2	C	A	5: 30,319,665 (GRCm39)	R376S	probably damaging	Het
Gdf2	A	G	14: 33,667,408 (GRCm39)	T377A	probably damaging	Het
Gm2431	A	T	7: 141,811,440 (GRCm39)	C155S	unknown	Het
Gm5814	A	G	17: 47,721,288 (GRCm39)	M1V	probably null	Het
Gm5901	C	G	7: 105,026,438 (GRCm39)	Q69E	possibly damaging	Het
Gm9945	A	G	11: 53,371,202 (GRCm39)		probably benign	Het
Gmps	T	C	3: 63,908,956 (GRCm39)	V486A	probably benign	Het
Gtf2ird1	T	A	5: 134,412,756 (GRCm39)	E55V	probably damaging	Het
Hoxa11	T	A	6: 52,220,483 (GRCm39)	N267Y	probably damaging	Het
Ifngr2	C	A	16: 91,356,926 (GRCm39)	H153Q	possibly damaging	Het
Ift172	G	T	5: 31,442,598 (GRCm39)	Q190K	possibly damaging	Het
Iqch	A	G	9: 63,352,853 (GRCm39)	V899A	probably damaging	Het
Lactb2	T	C	1: 13,717,624 (GRCm39)	E133G	probably damaging	Het
Lin54	C	A	5: 100,600,943 (GRCm39)	Q262H	possibly damaging	Het
Lingo3	G	A	10: 80,671,372 (GRCm39)	T186I	probably damaging	Het
Lrrc7	GAAGTTGTTTGGAGATTCTTATCTTA	GA	3: 158,024,045 (GRCm39)		probably benign	Het
Ly86	T	A	13: 37,559,010 (GRCm39)	F70I	probably damaging	Het
Mospd2	A	T	X: 163,730,329 (GRCm39)	S301T	probably benign	Het
Mroh2a	A	C	1: 88,169,340 (GRCm39)	I672L	probably benign	Het
Myo15a	A	T	11: 60,395,705 (GRCm39)		probably null	Het
Nme8	C	G	13: 19,858,605 (GRCm39)	A78P	probably damaging	Het
Obscn	C	T	11: 59,015,578 (GRCm39)	V965M	probably damaging	Het
Or10ag57	T	A	2: 87,218,220 (GRCm39)	I57K	probably damaging	Het
Parn	T	C	16: 13,358,967 (GRCm39)	K592E	probably benign	Het
Pax6	C	A	2: 105,514,343 (GRCm39)		probably benign	Het
Pdcd6	A	T	13: 74,465,325 (GRCm39)	M1K	probably null	Het
Pex11b	T	C	3: 96,551,151 (GRCm39)	L198P	possibly damaging	Het
Phldb3	C	T	7: 24,310,852 (GRCm39)	A28V	probably benign	Het
Pkn3	C	A	2: 29,975,469 (GRCm39)		probably benign	Het
Pknox1	T	C	17: 31,814,300 (GRCm39)		probably null	Het
Ptprg	A	C	14: 12,215,288 (GRCm38)	I1092L	possibly damaging	Het
Pxylp1	A	C	9: 96,707,338 (GRCm39)	I281M	probably damaging	Het
Ramac	C	T	7: 81,418,178 (GRCm39)	R78W	probably damaging	Het
Retreg2	G	T	1: 75,121,310 (GRCm39)	L195F	probably damaging	Het
Rgs20	G	C	1: 5,091,231 (GRCm39)	F66L	probably benign	Het
Ripk4	C	T	16: 97,556,273 (GRCm39)	V157I	probably damaging	Het
Ryr2	T	C	13: 11,765,571 (GRCm39)		probably null	Het
Scaper	A	T	9: 55,819,339 (GRCm39)	S125R	probably damaging	Het
Sec16a	C	T	2: 26,302,970 (GRCm39)		probably benign	Het
Slc35f6	T	C	5: 30,812,957 (GRCm39)	L37P	probably damaging	Het
Slc6a12	T	A	6: 121,335,972 (GRCm39)		probably benign	Het
Slc9a5	A	G	8: 106,094,760 (GRCm39)	K784E	probably damaging	Het
Snd1	T	C	6: 28,707,053 (GRCm39)	V455A	probably damaging	Het
Ssbp2	A	T	13: 91,687,454 (GRCm39)	I46L	possibly damaging	Het
Stil	A	G	4: 114,898,841 (GRCm39)	D1157G	probably benign	Het
Tax1bp1	T	A	6: 52,714,116 (GRCm39)	C271S	probably benign	Het
Tdpoz6	G	A	3: 93,599,776 (GRCm39)	H198Y	probably damaging	Het
Tdrd6	T	A	17: 43,935,007 (GRCm39)	M2014L	probably benign	Het
Thsd7a	T	A	6: 12,504,012 (GRCm39)	I381F	possibly damaging	Het
Thsd7a	T	A	6: 12,337,313 (GRCm39)	T1235S	possibly damaging	Het
Tmprss11d	T	C	5: 86,457,260 (GRCm39)	D133G	probably damaging	Het
Tpr	C	T	1: 150,320,150 (GRCm39)	R2233W	probably damaging	Het
Ugt1a1	CAGAGAGAGAGAGA	CAGAGAGAGAGA	1: 88,139,706 (GRCm39)		probably benign	Het
Vgll1	A	G	X: 56,137,792 (GRCm39)	R54G	possibly damaging	Het
Wdr72	A	G	9: 74,117,306 (GRCm39)	T673A	probably benign	Het
Zfp169	C	T	13: 48,644,339 (GRCm39)		probably benign	Het
Zfp319	G	A	8: 96,052,201 (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
R0115:Lig3	UTSW	11	82,684,761 (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
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'- ATCCAGCTGATAGCCTTGCTC -3'
(R):5'- CTCTGCAAGGCAACAAGAGG -3'

Sequencing Primer
(F):5'- AGAATGGCTCTGAGCTTCTGAAC -3'
(R):5'- AGCAGCAGGACTGATCACCTG -3'

Posted On

2015-10-08