Mutagenetix > Incidental Mutation

Incidental Mutation 'R1971:Lig3'

220928

Institutional Source

Beutler Lab

Gene Symbol

Lig3

Ensembl Gene

ENSMUSG00000020697

Gene Name

ligase III, DNA, ATP-dependent

Synonyms

D11Wsu78e

MMRRC Submission

039984-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R1971 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

82671977-82695100 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to C at 82686544 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Histidine at position 642 (D642H)

Ref Sequence

ENSEMBL: ENSMUSP00000133849 (fasta)

Gene Model

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

AlphaFold

no structure available at present

Predicted Effect

probably benign
Transcript: ENSMUST00000021039
AA Change: D647H

PolyPhen 2 Score 0.141 (Sensitivity: 0.92; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000021039
Gene: ENSMUSG00000020697
AA Change: D647H

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: ENSMUST00000080461
AA Change: D643H

PolyPhen 2 Score 0.068 (Sensitivity: 0.94; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000079317
Gene: ENSMUSG00000020697
AA Change: D643H

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 benign
Transcript: ENSMUST00000092849
AA Change: D643H

PolyPhen 2 Score 0.141 (Sensitivity: 0.92; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000090525
Gene: ENSMUSG00000020697
AA Change: D643H

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

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: ENSMUST00000173347
AA Change: D642H

PolyPhen 2 Score 0.141 (Sensitivity: 0.92; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000134300
Gene: ENSMUSG00000020697
AA Change: D642H

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: ENSMUST00000173722
AA Change: D643H

PolyPhen 2 Score 0.141 (Sensitivity: 0.92; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000133805
Gene: ENSMUSG00000020697
AA Change: D643H

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: D642H

PolyPhen 2 Score 0.141 (Sensitivity: 0.92; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000133849
Gene: ENSMUSG00000020697
AA Change: D642H

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

Meta Mutation Damage Score

0.1340

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 96.9%
20x: 94.3%

Validation Efficiency

99% (115/116)

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: 113 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700001O22Rik	A	T	2: 30,686,566 (GRCm39)	I242N	probably benign	Het
2510009E07Rik	G	T	16: 21,472,048 (GRCm39)	Y217*	probably null	Het
4931429L15Rik	C	T	9: 46,220,086 (GRCm39)	V149M	probably benign	Het
Abcg8	G	T	17: 85,002,587 (GRCm39)		probably benign	Het
Acox1	A	G	11: 116,089,087 (GRCm39)	F77S	probably benign	Het
Adgrb3	G	T	1: 25,586,525 (GRCm39)	H389Q	probably benign	Het
Ak7	A	G	12: 105,692,504 (GRCm39)	N186S	probably damaging	Het
Apobr	A	G	7: 126,185,397 (GRCm39)	T303A	probably benign	Het
Arnt	C	T	3: 95,355,704 (GRCm39)	S16L	possibly damaging	Het
Bcl9l	T	C	9: 44,419,996 (GRCm39)		probably null	Het
Bco2	T	C	9: 50,457,284 (GRCm39)	D86G	probably damaging	Het
Bmpr1b	T	A	3: 141,563,333 (GRCm39)	I204F	probably damaging	Het
Bpifb5	C	A	2: 154,072,264 (GRCm39)	Q324K	probably benign	Het
Cacna2d2	G	A	9: 107,389,205 (GRCm39)	V223I	probably damaging	Het
Capn3	A	G	2: 120,311,228 (GRCm39)	D105G	possibly damaging	Het
Ccdc40	G	T	11: 119,153,901 (GRCm39)		probably null	Het
Ccdc83	T	A	7: 89,893,362 (GRCm39)	S132C	probably damaging	Het
Ckap2l	A	G	2: 129,127,342 (GRCm39)	S279P	possibly damaging	Het
Cldn12	C	A	5: 5,558,137 (GRCm39)	A97S	probably benign	Het
Clec2l	T	G	6: 38,640,309 (GRCm39)	S47A	probably benign	Het
Csnk1d	C	A	11: 120,863,274 (GRCm39)	R222M	possibly damaging	Het
Ctnna1	T	A	18: 35,287,580 (GRCm39)	D96E	probably benign	Het
D630045J12Rik	T	C	6: 38,145,078 (GRCm39)	D1316G	probably damaging	Het
Ddx4	C	T	13: 112,736,547 (GRCm39)	V608I	probably damaging	Het
Dmtf1	T	C	5: 9,198,989 (GRCm39)	E48G	probably benign	Het
Dnah17	G	C	11: 117,995,361 (GRCm39)	Q996E	probably benign	Het
Dnah9	G	C	11: 65,739,197 (GRCm39)	N4180K	probably damaging	Het
Dpf3	T	A	12: 83,371,809 (GRCm39)		probably null	Het
Drd2	T	C	9: 49,318,359 (GRCm39)	F434L	probably damaging	Het
En1	A	G	1: 120,534,742 (GRCm39)	T344A	unknown	Het
Eri3	A	G	4: 117,421,964 (GRCm39)	T81A	probably benign	Het
Fam20a	T	C	11: 109,576,237 (GRCm39)	Y174C	probably damaging	Het
Fam234a	G	C	17: 26,435,629 (GRCm39)		probably null	Het
Fam76a	A	T	4: 132,631,294 (GRCm39)	I217N	probably damaging	Het
Fancm	T	A	12: 65,148,466 (GRCm39)	S694T	probably benign	Het
Fcgbpl1	C	A	7: 27,830,937 (GRCm39)	A50E	possibly damaging	Het
Foxo3	A	G	10: 42,073,258 (GRCm39)	S420P	probably benign	Het
Foxp4	C	T	17: 48,186,796 (GRCm39)	R378Q	unknown	Het
Gm136	T	G	4: 34,755,986 (GRCm39)	D9A	probably benign	Het
Gstt2	G	T	10: 75,668,499 (GRCm39)	T116N	probably benign	Het
Hs3st6	A	G	17: 24,972,267 (GRCm39)	T70A	probably benign	Het
Hspa14	A	G	2: 3,490,804 (GRCm39)	V461A	possibly damaging	Het
Itih5	A	T	2: 10,243,379 (GRCm39)	D372V	probably damaging	Het
Kcna2	A	T	3: 107,012,140 (GRCm39)	R240S	probably damaging	Het
Kctd18	T	C	1: 58,006,779 (GRCm39)	I24V	probably benign	Het
Lap3	T	C	5: 45,663,508 (GRCm39)		probably benign	Het
Lcp1	T	C	14: 75,437,946 (GRCm39)	S119P	probably damaging	Het
Lpin1	A	T	12: 16,630,724 (GRCm39)	L58H	probably damaging	Het
Map4k5	G	T	12: 69,873,102 (GRCm39)	P468Q	possibly damaging	Het
Med31	G	A	11: 72,106,244 (GRCm39)		probably benign	Het
Mki67	A	T	7: 135,315,688 (GRCm39)		probably null	Het
Mrc1	G	A	2: 14,249,103 (GRCm39)		probably null	Het
Msh3	A	G	13: 92,359,784 (GRCm39)	I16T	probably damaging	Het
Msh3	T	A	13: 92,386,328 (GRCm39)		probably benign	Het
Mst1r	A	T	9: 107,790,411 (GRCm39)	I675F	probably benign	Het
Myb	A	C	10: 21,016,555 (GRCm39)	S652A	probably benign	Het
Myh2	G	T	11: 67,080,004 (GRCm39)	S1099I	possibly damaging	Het
Myl6b	A	G	10: 128,330,512 (GRCm39)	V181A	probably damaging	Het
Myt1l	A	T	12: 29,877,091 (GRCm39)	K247N	unknown	Het
Nanos2	G	T	7: 18,721,629 (GRCm39)	V34L	probably benign	Het
Nav1	T	C	1: 135,460,091 (GRCm39)	T411A	probably benign	Het
Nedd9	T	A	13: 41,492,424 (GRCm39)	I23F	probably damaging	Het
Nes	G	A	3: 87,885,634 (GRCm39)	V1254I	possibly damaging	Het
Nol6	A	G	4: 41,119,542 (GRCm39)	F588S	probably damaging	Het
Numa1	C	T	7: 101,658,529 (GRCm39)	A1605V	probably damaging	Het
Ofd1	T	C	X: 165,210,210 (GRCm39)	Y205C	probably benign	Het
Olr1	T	C	6: 129,470,498 (GRCm39)	E223G	probably benign	Het
Or1e30	T	A	11: 73,678,616 (GRCm39)	M284K	probably damaging	Het
Or2ag12	T	A	7: 106,276,877 (GRCm39)	N272I	probably damaging	Het
Or4c118	A	T	2: 88,975,078 (GRCm39)	C96*	probably null	Het
Or51k2	A	T	7: 103,596,150 (GRCm39)	I126F	probably damaging	Het
Or51l4	C	T	7: 103,404,527 (GRCm39)	W88*	probably null	Het
Pate6	T	A	9: 35,700,309 (GRCm39)	H92L	probably benign	Het
Pclo	A	G	5: 14,763,487 (GRCm39)	T3987A	unknown	Het
Pik3cg	A	T	12: 32,242,152 (GRCm39)	V986D	probably damaging	Het
Pitpnm1	T	A	19: 4,162,450 (GRCm39)	D1093E	probably damaging	Het
Ppp1r12b	T	C	1: 134,793,651 (GRCm39)	D571G	probably benign	Het
Rfx1	A	G	8: 84,822,126 (GRCm39)	E875G	probably damaging	Het
Rnf145	T	A	11: 44,439,642 (GRCm39)	I146N	probably damaging	Het
Rttn	G	A	18: 89,108,557 (GRCm39)	R1587H	probably benign	Het
Safb	A	G	17: 56,912,821 (GRCm39)	H883R	probably benign	Het
Sdhb	A	G	4: 140,700,260 (GRCm39)	D120G	possibly damaging	Het
Serpine3	A	G	14: 62,902,533 (GRCm39)	N48S	probably damaging	Het
Sgms1	T	A	19: 32,137,357 (GRCm39)	I70L	probably benign	Het
Slc1a7	G	T	4: 107,825,782 (GRCm39)	D14Y	probably benign	Het
Smtnl2	C	T	11: 72,302,183 (GRCm39)	A93T	probably benign	Het
Srpra	T	C	9: 35,124,834 (GRCm39)		probably null	Het
Taf6l	A	G	19: 8,752,866 (GRCm39)		probably null	Het
Tbc1d10b	A	T	7: 126,807,036 (GRCm39)	V167E	probably benign	Het
Tbc1d9	G	A	8: 83,976,139 (GRCm39)	R566H	probably damaging	Het
Tenm3	A	G	8: 48,689,348 (GRCm39)	Y2080H	probably damaging	Het
Tex14	A	G	11: 87,402,431 (GRCm39)	N506S	probably damaging	Het
Thada	G	T	17: 84,617,470 (GRCm39)	P1349T	probably damaging	Het
Tjp1	G	T	7: 64,973,826 (GRCm39)	T476K	probably damaging	Het
Tlr11	A	T	14: 50,598,691 (GRCm39)	T226S	probably benign	Het
Tmem131	G	A	1: 36,843,680 (GRCm39)	Q1394*	probably null	Het
Tmem161a	C	T	8: 70,629,559 (GRCm39)	R58W	probably damaging	Het
Tmem219	T	C	7: 126,496,422 (GRCm39)	S13G	probably benign	Het
Trp53bp1	T	C	2: 121,035,517 (GRCm39)	Y47C	probably damaging	Het
Ttn	T	A	2: 76,731,922 (GRCm39)		probably benign	Het
Ush1g	A	G	11: 115,209,280 (GRCm39)	S305P	probably damaging	Het
Usp37	A	T	1: 74,479,127 (GRCm39)	Y948*	probably null	Het
Vav1	A	T	17: 57,634,697 (GRCm39)	Y805F	probably damaging	Het
Vmn1r59	A	T	7: 5,457,038 (GRCm39)	Y241N	probably damaging	Het
Vmn2r2	T	A	3: 64,034,121 (GRCm39)	Y467F	probably damaging	Het
Vps35l	A	C	7: 118,374,557 (GRCm39)	R352S	probably damaging	Het
Vps54	C	A	11: 21,242,051 (GRCm39)	L389I	probably damaging	Het
Vwa8	G	T	14: 79,162,694 (GRCm39)		probably benign	Het
Wdr19	G	T	5: 65,398,503 (GRCm39)		probably benign	Het
Wnt2b	A	T	3: 104,861,933 (GRCm39)		probably benign	Het
Xirp2	A	G	2: 67,342,039 (GRCm39)	R1427G	possibly damaging	Het
Ylpm1	T	C	12: 85,087,560 (GRCm39)	S1115P	probably damaging	Het
Zfp946	T	A	17: 22,674,406 (GRCm39)	C387S	probably damaging	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
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'- GCAGAGATCTGATGGTTGAAACC -3'
(R):5'- CCAGTTGAGTGGGAAAGACTC -3'

Sequencing Primer
(F):5'- CAGAGCAGAGAACCCCATGG -3'
(R):5'- TGGGAAAGACTCCTACATTGCTC -3'

Posted On

2014-08-25