Mutagenetix > Incidental Mutation

Incidental Mutation 'R1969:Lig3'

219496

Institutional Source

Beutler Lab

Gene Symbol

Lig3

Ensembl Gene

ENSMUSG00000020697

Gene Name

ligase III, DNA, ATP-dependent

Synonyms

D11Wsu78e

MMRRC Submission

039982-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R1969 (G1)

Quality Score

225

Status

Not 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: 94.6%

Validation Efficiency

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: 105 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1110059E24Rik	T	C	19: 21,575,609 (GRCm39)		probably benign	Het
Apoh	G	A	11: 108,298,288 (GRCm39)	R196Q	probably benign	Het
Arnt	C	T	3: 95,355,704 (GRCm39)	S16L	possibly damaging	Het
B4galnt4	T	C	7: 140,644,761 (GRCm39)	F194L	probably benign	Het
BC034090	A	T	1: 155,100,972 (GRCm39)	L431M	possibly damaging	Het
Bdh2	G	T	3: 134,994,040 (GRCm39)	A31S	probably damaging	Het
Brd10	C	T	19: 29,694,075 (GRCm39)	S1873N	possibly damaging	Het
Cacna1s	T	C	1: 136,046,833 (GRCm39)	S1821P	probably benign	Het
Caskin1	A	T	17: 24,725,824 (GRCm39)	Q1370L	possibly damaging	Het
Ccdc83	T	A	7: 89,893,362 (GRCm39)	S132C	probably damaging	Het
Cdk15	A	T	1: 59,370,110 (GRCm39)	H384L	probably damaging	Het
Col24a1	T	C	3: 145,020,691 (GRCm39)	I354T	probably benign	Het
Coro7	T	C	16: 4,451,620 (GRCm39)	I451V	probably benign	Het
Ctnna2	T	C	6: 77,735,483 (GRCm39)	E65G	probably damaging	Het
Ctsll3	A	T	13: 60,948,162 (GRCm39)	W172R	probably benign	Het
D630045J12Rik	T	C	6: 38,145,078 (GRCm39)	D1316G	probably damaging	Het
Ddx19b	C	T	8: 111,734,890 (GRCm39)	A493T	probably benign	Het
Ddx4	C	T	13: 112,736,547 (GRCm39)	V608I	probably damaging	Het
Ddx4	T	A	13: 112,757,276 (GRCm39)	H348L	probably damaging	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
Dok7	A	G	5: 35,234,610 (GRCm39)		probably null	Het
Dpf3	T	A	12: 83,371,809 (GRCm39)		probably null	Het
Efcab3	A	G	11: 104,637,090 (GRCm39)	I988M	probably damaging	Het
Elfn1	G	C	5: 139,958,604 (GRCm39)	R536P	probably damaging	Het
Eml6	A	G	11: 29,783,075 (GRCm39)	V602A	probably benign	Het
Enpp2	T	C	15: 54,746,378 (GRCm39)	D296G	probably damaging	Het
Evi5	A	T	5: 107,896,230 (GRCm39)	F738I	probably benign	Het
Eya2	T	C	2: 165,558,039 (GRCm39)	S212P	probably benign	Het
Fam83a	T	C	15: 57,849,498 (GRCm39)	L14P	probably damaging	Het
Fanca	A	T	8: 124,014,803 (GRCm39)	M735K	probably benign	Het
Fancm	T	A	12: 65,148,466 (GRCm39)	S694T	probably benign	Het
Fibcd1	G	A	2: 31,706,673 (GRCm39)	T386I	probably damaging	Het
Foxd4	A	G	19: 24,877,178 (GRCm39)	S341P	probably benign	Het
Foxp4	C	T	17: 48,186,796 (GRCm39)	R378Q	unknown	Het
Fryl	A	T	5: 73,255,609 (GRCm39)	S807R	probably benign	Het
Fscb	T	C	12: 64,520,008 (GRCm39)	E486G	unknown	Het
Galnt17	A	G	5: 131,179,782 (GRCm39)	S122P	probably benign	Het
Ghitm	A	G	14: 36,853,586 (GRCm39)	F85L	probably benign	Het
Ghrh	C	A	2: 157,175,386 (GRCm39)	V32L	probably benign	Het
Gli2	C	T	1: 118,765,430 (GRCm39)	R907H	probably benign	Het
Gm28042	A	G	2: 119,872,096 (GRCm39)	*1015W	probably null	Het
Gpr179	T	C	11: 97,228,784 (GRCm39)	T1124A	probably benign	Het
Grid2	C	A	6: 63,885,902 (GRCm39)	C99*	probably null	Het
Grin1	A	T	2: 25,187,927 (GRCm39)	M523K	probably benign	Het
Gucy2g	T	C	19: 55,211,328 (GRCm39)	Y634C	possibly damaging	Het
Gucy2g	T	G	19: 55,221,485 (GRCm39)	T339P	probably benign	Het
Haus6	A	T	4: 86,522,483 (GRCm39)	L116H	probably damaging	Het
Hey1	T	C	3: 8,731,879 (GRCm39)	T18A	probably benign	Het
Hipk3	T	C	2: 104,264,186 (GRCm39)	N792D	probably damaging	Het
Il19	A	T	1: 130,866,893 (GRCm39)	L29Q	probably damaging	Het
Il21r	A	G	7: 125,228,144 (GRCm39)	Q205R	probably damaging	Het
Kcnip2	T	C	19: 45,782,122 (GRCm39)	D169G	probably null	Het
Kctd18	T	C	1: 58,006,779 (GRCm39)	I24V	probably benign	Het
Lcp1	T	C	14: 75,437,946 (GRCm39)	S119P	probably damaging	Het
Lrba	A	G	3: 86,515,696 (GRCm39)	K2166E	probably damaging	Het
Lrrn2	T	C	1: 132,866,972 (GRCm39)	V679A	probably benign	Het
Lyst	G	A	13: 13,904,929 (GRCm39)	R3202H	probably damaging	Het
Micall2	A	G	5: 139,721,885 (GRCm39)	C11R	probably damaging	Het
Morc2b	T	G	17: 33,356,065 (GRCm39)	Q569P	probably benign	Het
Mtrf1	A	G	14: 79,639,111 (GRCm39)	E81G	probably damaging	Het
Myh2	G	T	11: 67,080,004 (GRCm39)	S1099I	possibly damaging	Het
Nap1l1	T	A	10: 111,326,914 (GRCm39)	D158E	probably benign	Het
Nckap5l	T	A	15: 99,320,699 (GRCm39)	T1285S	probably damaging	Het
Nsrp1	A	T	11: 76,936,612 (GRCm39)	M528K	probably damaging	Het
Numa1	C	T	7: 101,658,529 (GRCm39)	A1605V	probably damaging	Het
Nutm2	T	C	13: 50,627,878 (GRCm39)	L453P	probably damaging	Het
Ofd1	T	C	X: 165,210,210 (GRCm39)	Y205C	probably benign	Het
Or2ag12	T	A	7: 106,276,877 (GRCm39)	N272I	probably damaging	Het
Or2n1c	A	G	17: 38,519,355 (GRCm39)	Y73C	probably damaging	Het
Or4c125	T	A	2: 89,170,640 (GRCm39)	N2I	probably damaging	Het
Or52k2	A	T	7: 102,253,777 (GRCm39)	D72V	probably damaging	Het
Or7a40	T	A	16: 16,491,447 (GRCm39)	M133L	probably benign	Het
Patl1	T	C	19: 11,898,782 (GRCm39)	L159P	probably benign	Het
Paxip1	G	A	5: 27,949,134 (GRCm39)	T1045I	probably damaging	Het
Phaf1	T	A	8: 105,973,132 (GRCm39)	D247E	possibly damaging	Het
Pik3ca	A	G	3: 32,505,903 (GRCm39)		probably null	Het
Pkhd1	T	A	1: 20,451,747 (GRCm39)	I2183F	probably damaging	Het
Plec	C	T	15: 76,073,372 (GRCm39)	R319H	probably damaging	Het
Pnkd	G	A	1: 74,391,008 (GRCm39)	G334D	probably damaging	Het
Prss50	A	G	9: 110,691,449 (GRCm39)	Y251C	probably damaging	Het
Rab11b	A	T	17: 33,979,209 (GRCm39)	Y10N	probably damaging	Het
Rfc1	G	A	5: 65,476,867 (GRCm39)	R4W	probably damaging	Het
Rgs19	A	T	2: 181,331,276 (GRCm39)	F119Y	probably damaging	Het
Safb	A	G	17: 56,912,821 (GRCm39)	H883R	probably benign	Het
Serpine1	G	A	5: 137,096,601 (GRCm39)	Q227*	probably null	Het
Slc25a13	A	G	6: 6,096,668 (GRCm39)		probably null	Het
Slc6a18	T	A	13: 73,812,308 (GRCm39)	T502S	possibly damaging	Het
Sox4	T	C	13: 29,136,631 (GRCm39)	D125G	probably damaging	Het
Spata31d1e	T	C	13: 59,890,599 (GRCm39)	D407G	probably damaging	Het
Stag3	C	T	5: 138,298,400 (GRCm39)	T731I	probably damaging	Het
Thada	G	T	17: 84,617,470 (GRCm39)	P1349T	probably damaging	Het
Tmem245	C	A	4: 56,937,964 (GRCm39)	V195F	probably benign	Het
Tnxb	A	G	17: 34,898,055 (GRCm39)	H901R	probably benign	Het
Trim39	A	T	17: 36,579,645 (GRCm39)	D103E	probably benign	Het
Ttn	A	T	2: 76,562,304 (GRCm39)	V28847E	probably damaging	Het
Tubb1	A	T	2: 174,297,484 (GRCm39)	D31V	possibly damaging	Het
Ush1g	A	G	11: 115,209,280 (GRCm39)	S305P	probably damaging	Het
Vmn1r191	A	T	13: 22,362,952 (GRCm39)	N267K	possibly damaging	Het
Vmn1r59	A	T	7: 5,457,038 (GRCm39)	Y241N	probably damaging	Het
Vmn2r49	T	C	7: 9,720,235 (GRCm39)	N419D	probably damaging	Het
Vps35	T	C	8: 86,005,623 (GRCm39)	D326G	possibly damaging	Het
Xdh	A	G	17: 74,199,746 (GRCm39)	S1187P	possibly damaging	Het
Xpc	A	C	6: 91,478,007 (GRCm39)		probably null	Het
Zfp273	T	C	13: 67,973,282 (GRCm39)	Y104H	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
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'- GCAGAGATCTGATGGTTGAAACC -3'
(R):5'- CCAGTTGAGTGGGAAAGACTC -3'

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

Posted On

2014-08-25