Mutagenetix > Incidental Mutation

Incidental Mutation 'R6057:Lig1'

482964

Institutional Source

Beutler Lab

Gene Symbol

Lig1

Ensembl Gene

ENSMUSG00000056394

Gene Name

ligase I, DNA, ATP-dependent

Synonyms

mLigI, LigI

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R6057 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

13011239-13045350 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to A at 13022598 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glutamine to Lysine at position 143 (Q143K)

Ref Sequence

ENSEMBL: ENSMUSP00000136972 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000098814] [ENSMUST00000123025] [ENSMUST00000146998] [ENSMUST00000165964] [ENSMUST00000177588] [ENSMUST00000185145]

AlphaFold

no structure available at present

Predicted Effect

probably damaging
Transcript: ENSMUST00000098814
AA Change: Q143K

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000096411
Gene: ENSMUSG00000056394
AA Change: Q143K

Domain	Start	End	E-Value	Type
low complexity region	99	111	N/A	INTRINSIC
coiled coil region	149	173	N/A	INTRINSIC
Pfam:DNA_ligase_A_N	301	479	8.6e-50	PFAM
Pfam:DNA_ligase_A_M	556	760	3.4e-67	PFAM
Pfam:DNA_ligase_A_C	785	896	9.4e-28	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000123025
AA Change: Q142K

PolyPhen 2 Score 0.271 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000114872
Gene: ENSMUSG00000056394
AA Change: Q142K

Domain	Start	End	E-Value	Type
low complexity region	96	111	N/A	INTRINSIC
low complexity region	159	177	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000123846

SMART Domains

Protein: ENSMUSP00000119788
Gene: ENSMUSG00000056394

Domain	Start	End	E-Value	Type
low complexity region	99	111	N/A	INTRINSIC
coiled coil region	149	173	N/A	INTRINSIC
Pfam:DNA_ligase_A_N	301	479	4e-47	PFAM
Pfam:DNA_ligase_A_M	556	687	1e-38	PFAM

Predicted Effect

possibly damaging
Transcript: ENSMUST00000146998
AA Change: Q143K

PolyPhen 2 Score 0.904 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000121102
Gene: ENSMUSG00000056394
AA Change: Q143K

Domain	Start	End	E-Value	Type
low complexity region	99	111	N/A	INTRINSIC
low complexity region	160	178	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000147735

SMART Domains

Protein: ENSMUSP00000115286
Gene: ENSMUSG00000056394

Domain	Start	End	E-Value	Type
low complexity region	99	111	N/A	INTRINSIC
coiled coil region	149	173	N/A	INTRINSIC
Pfam:DNA_ligase_A_N	301	479	4e-47	PFAM
Pfam:DNA_ligase_A_M	556	687	1e-38	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000148471

SMART Domains

Protein: ENSMUSP00000114153
Gene: ENSMUSG00000056394

Domain	Start	End	E-Value	Type
low complexity region	99	111	N/A	INTRINSIC
coiled coil region	149	173	N/A	INTRINSIC
Pfam:DNA_ligase_A_N	301	479	4e-47	PFAM
Pfam:DNA_ligase_A_M	556	687	1e-38	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000156525

SMART Domains

Protein: ENSMUSP00000118055
Gene: ENSMUSG00000056394

Domain	Start	End	E-Value	Type
low complexity region	99	111	N/A	INTRINSIC
coiled coil region	149	173	N/A	INTRINSIC
Pfam:DNA_ligase_A_N	301	479	4e-47	PFAM
Pfam:DNA_ligase_A_M	556	687	1e-38	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000165964
AA Change: Q143K

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000126525
Gene: ENSMUSG00000056394
AA Change: Q143K

Domain	Start	End	E-Value	Type
low complexity region	99	111	N/A	INTRINSIC
coiled coil region	149	173	N/A	INTRINSIC
Pfam:DNA_ligase_A_N	302	478	1.7e-40	PFAM
Pfam:DNA_ligase_A_M	556	760	1.1e-69	PFAM
Pfam:DNA_ligase_A_C	785	896	1.6e-27	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000177588
AA Change: Q143K

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000136972
Gene: ENSMUSG00000056394
AA Change: Q143K

Domain	Start	End	E-Value	Type
low complexity region	99	111	N/A	INTRINSIC
coiled coil region	149	173	N/A	INTRINSIC
Pfam:DNA_ligase_A_N	301	479	8.6e-50	PFAM
Pfam:DNA_ligase_A_M	556	760	3.4e-67	PFAM
Pfam:DNA_ligase_A_C	785	896	9.4e-28	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000185145
AA Change: Q143K

PolyPhen 2 Score 0.271 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000138907
Gene: ENSMUSG00000056394
AA Change: Q143K

Domain	Start	End	E-Value	Type
low complexity region	99	111	N/A	INTRINSIC
coiled coil region	149	173	N/A	INTRINSIC
PDB:1X9N\|A	247	313	3e-24	PDB

Coding Region Coverage

1x: 99.9%
3x: 99.6%
10x: 97.9%
20x: 93.6%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the ATP-dependent DNA ligase protein family. The encoded protein functions in DNA replication, recombination, and the base excision repair process. Mutations in this gene that lead to DNA ligase I deficiency result in immunodeficiency and increased sensitivity to DNA-damaging agents. Disruption of this gene may also be associated with a variety of cancers. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2014]
PHENOTYPE: Mice homozygous for a null allele exhibit impaired fetal hematopoiesis, develop anemia, and die by E16.5. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 87 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
5730596B20Rik	A	G	6: 52,156,500 (GRCm39)		probably benign	Het
Acan	A	G	7: 78,749,530 (GRCm39)	S11G	probably null	Het
Ankrd13d	A	C	19: 4,332,256 (GRCm39)	V56G	probably damaging	Het
Arl15	A	G	13: 114,104,151 (GRCm39)	Y76C	probably damaging	Het
Aspg	G	A	12: 112,087,432 (GRCm39)	C296Y	probably damaging	Het
Astl	T	A	2: 127,187,889 (GRCm39)	D101E	probably benign	Het
Bmpr2	A	G	1: 59,881,977 (GRCm39)	N202S	probably benign	Het
Borcs7	T	C	19: 46,690,003 (GRCm39)	*106Q	probably null	Het
Brip1	A	G	11: 85,955,865 (GRCm39)	S883P	possibly damaging	Het
Cacng2	A	T	15: 78,002,991 (GRCm39)	L34Q	probably damaging	Het
Catip	A	C	1: 74,402,077 (GRCm39)	D84A	probably damaging	Het
Ccdc162	A	G	10: 41,510,037 (GRCm39)	L856S	possibly damaging	Het
Ccdc38	A	G	10: 93,417,608 (GRCm39)	K500E	probably damaging	Het
Ccser2	T	C	14: 36,663,122 (GRCm39)	K21E	probably damaging	Het
Cd93	A	T	2: 148,283,439 (GRCm39)	Y636N	probably damaging	Het
Cep128	A	T	12: 91,262,998 (GRCm39)	N300K	possibly damaging	Het
Cfap44	A	G	16: 44,269,460 (GRCm39)	T1155A	probably benign	Het
Clec16a	T	C	16: 10,447,951 (GRCm39)	L550P	probably damaging	Het
Csmd3	T	C	15: 47,618,787 (GRCm39)	Y1867C	probably damaging	Het
Cul3	A	T	1: 80,249,249 (GRCm39)	I674N	probably damaging	Het
Cybb	C	G	X: 9,316,989 (GRCm39)	D246H	probably benign	Het
Cyp2d34	T	C	15: 82,500,552 (GRCm39)	H429R	probably benign	Het
Dab2ip	T	A	2: 35,582,267 (GRCm39)	C4*	probably null	Het
Dcaf1	A	G	9: 106,731,446 (GRCm39)	E641G	probably damaging	Het
Dda1	T	A	8: 71,927,276 (GRCm39)		probably benign	Het
Dmgdh	C	T	13: 93,888,960 (GRCm39)	T866I	probably benign	Het
Ect2l	T	C	10: 18,037,250 (GRCm39)	T383A	probably benign	Het
Ets2	A	G	16: 95,515,416 (GRCm39)	N181D	probably benign	Het
Ezh2	A	G	6: 47,529,357 (GRCm39)	F222L	probably damaging	Het
Frem3	T	C	8: 81,342,216 (GRCm39)	L1503P	probably damaging	Het
Fsip2	C	A	2: 82,809,777 (GRCm39)	A2032E	probably damaging	Het
Gm1818	C	T	12: 48,602,346 (GRCm39)		noncoding transcript	Het
Gm9493	A	G	19: 23,597,106 (GRCm39)	S1G	probably damaging	Het
Grin2b	A	G	6: 135,710,942 (GRCm39)	I868T	possibly damaging	Het
Ift22	A	T	5: 136,939,987 (GRCm39)	T17S	possibly damaging	Het
Il4ra	T	C	7: 125,170,735 (GRCm39)	W216R	probably damaging	Het
Kcnj6	A	T	16: 94,633,236 (GRCm39)	W274R	probably damaging	Het
Kctd19	G	A	8: 106,123,082 (GRCm39)	H111Y	probably damaging	Het
Kremen2	A	G	17: 23,961,679 (GRCm39)	V276A	probably benign	Het
Lrp1	A	T	10: 127,403,359 (GRCm39)	D2071E	probably damaging	Het
Macf1	C	T	4: 123,404,536 (GRCm39)	M475I	probably damaging	Het
Mbtd1	G	A	11: 93,820,485 (GRCm39)	A427T	probably damaging	Het
Myof	A	G	19: 37,915,429 (GRCm39)		probably null	Het
Nbeal2	T	C	9: 110,470,945 (GRCm39)	D308G	possibly damaging	Het
Ncdn	T	C	4: 126,638,824 (GRCm39)	Q665R	probably benign	Het
Nkd1	T	C	8: 89,316,442 (GRCm39)		probably null	Het
Nktr	G	A	9: 121,577,455 (GRCm39)		probably benign	Het
Npc1l1	A	T	11: 6,167,806 (GRCm39)	M995K	possibly damaging	Het
Or10ag59	C	A	2: 87,406,363 (GRCm39)	R312S	probably benign	Het
Or11g7	A	T	14: 50,691,201 (GRCm39)	R231*	probably null	Het
Or14n1-ps1	T	A	7: 86,092,397 (GRCm39)	C69*	probably null	Het
Padi4	T	C	4: 140,487,351 (GRCm39)	T184A	probably damaging	Het
Pgm2l1	C	T	7: 99,915,881 (GRCm39)	P409S	probably benign	Het
Pgpep1	G	A	8: 71,105,101 (GRCm39)	T53M	probably damaging	Het
Pgr	T	C	9: 8,902,006 (GRCm39)	L513P	probably damaging	Het
Pikfyve	T	A	1: 65,311,730 (GRCm39)	I1989N	probably damaging	Het
Prrc2a	T	C	17: 35,371,716 (GRCm39)	T1806A	probably benign	Het
Psd	T	C	19: 46,311,753 (GRCm39)	E309G	possibly damaging	Het
Qtrt1	C	T	9: 21,323,299 (GRCm39)	T50I	probably damaging	Het
Rims2	A	C	15: 39,538,416 (GRCm39)	T1320P	probably damaging	Het
Scn11a	T	G	9: 119,594,514 (GRCm39)	N1293T	probably damaging	Het
Scn8a	T	C	15: 100,872,548 (GRCm39)	F529S	possibly damaging	Het
Sec14l4	A	T	11: 3,985,142 (GRCm39)	D25V	possibly damaging	Het
Sema3a	C	T	5: 13,615,832 (GRCm39)	R419C	probably damaging	Het
Slc12a1	T	C	2: 125,032,133 (GRCm39)	Y595H	probably damaging	Het
Slc25a28	A	T	19: 43,655,364 (GRCm39)	H170Q	possibly damaging	Het
Slc26a1	T	A	5: 108,821,631 (GRCm39)	Q86L	probably damaging	Het
Slc48a1	T	A	15: 97,687,798 (GRCm39)	W51R	probably damaging	Het
Sptlc3	T	A	2: 139,423,533 (GRCm39)	V309D	probably damaging	Het
Srcap	G	A	7: 127,140,528 (GRCm39)	S1375N	probably damaging	Het
Tanc1	C	A	2: 59,647,837 (GRCm39)	H986Q	possibly damaging	Het
Tbc1d4	A	G	14: 101,727,353 (GRCm39)	V486A	probably damaging	Het
Tceanc2	T	C	4: 107,004,776 (GRCm39)	D124G	probably damaging	Het
Tdrd9	A	G	12: 111,979,720 (GRCm39)	M402V	possibly damaging	Het
Tmem132d	T	C	5: 127,861,934 (GRCm39)	D729G	probably damaging	Het
Tmem62	T	A	2: 120,807,943 (GRCm39)	I55N	probably damaging	Het
Tnfrsf21	A	T	17: 43,350,606 (GRCm39)	N257Y	possibly damaging	Het
Trappc3	T	C	4: 126,167,834 (GRCm39)	L131P	probably damaging	Het
Vmn2r25	A	T	6: 123,799,900 (GRCm39)	M814K	possibly damaging	Het
Vmn2r87	T	C	10: 130,308,226 (GRCm39)	I671V	probably benign	Het
Vwa8	A	T	14: 79,320,313 (GRCm39)	D1108V	probably benign	Het
Xrcc4	C	G	13: 90,139,198 (GRCm39)	A241P	possibly damaging	Het
Xylt1	T	A	7: 117,191,135 (GRCm39)	D310E	probably benign	Het
Zfp27	T	G	7: 29,594,444 (GRCm39)	H507P	possibly damaging	Het
Zfp341	C	T	2: 154,466,954 (GRCm39)	P108S	probably benign	Het
Zfp641	T	C	15: 98,190,816 (GRCm39)	N76S	probably benign	Het
Zfp936	T	C	7: 42,839,787 (GRCm39)	V418A	probably benign	Het

Other mutations in Lig1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00093:Lig1	APN	7	13,035,378 (GRCm39)	nonsense	probably null
IGL00499:Lig1	APN	7	13,032,756 (GRCm39)	critical splice donor site	probably null
IGL01465:Lig1	APN	7	13,030,317 (GRCm39)	missense	probably benign	0.19
IGL01804:Lig1	APN	7	13,043,131 (GRCm39)	missense	probably benign	0.43
IGL02068:Lig1	APN	7	13,026,377 (GRCm39)	splice site	probably benign
IGL02955:Lig1	APN	7	13,030,273 (GRCm39)	missense	probably damaging	0.99
IGL03188:Lig1	APN	7	13,045,032 (GRCm39)	splice site	probably benign
IGL03327:Lig1	APN	7	13,037,781 (GRCm39)	missense	probably damaging	1.00
IGL03411:Lig1	APN	7	13,030,694 (GRCm39)	missense	probably damaging	1.00
PIT4142001:Lig1	UTSW	7	13,039,850 (GRCm39)	frame shift	probably null
R0085:Lig1	UTSW	7	13,041,495 (GRCm39)	missense	possibly damaging	0.66
R0348:Lig1	UTSW	7	13,043,122 (GRCm39)	missense	probably damaging	1.00
R0362:Lig1	UTSW	7	13,030,730 (GRCm39)	unclassified	probably benign
R0787:Lig1	UTSW	7	13,032,995 (GRCm39)	missense	probably benign	0.41
R1170:Lig1	UTSW	7	13,026,079 (GRCm39)	missense	probably benign	0.00
R1371:Lig1	UTSW	7	13,022,611 (GRCm39)	missense	probably damaging	1.00
R1610:Lig1	UTSW	7	13,019,266 (GRCm39)	missense	probably damaging	1.00
R1809:Lig1	UTSW	7	13,034,281 (GRCm39)	splice site	probably benign
R1986:Lig1	UTSW	7	13,043,067 (GRCm39)	nonsense	probably null
R2106:Lig1	UTSW	7	13,039,863 (GRCm39)	missense	probably damaging	1.00
R2343:Lig1	UTSW	7	13,026,121 (GRCm39)	splice site	probably null
R2380:Lig1	UTSW	7	13,037,722 (GRCm39)	splice site	probably benign
R3545:Lig1	UTSW	7	13,026,089 (GRCm39)	missense	possibly damaging	0.82
R4669:Lig1	UTSW	7	13,044,953 (GRCm39)	missense	probably damaging	1.00
R4928:Lig1	UTSW	7	13,032,664 (GRCm39)	missense	probably damaging	1.00
R5167:Lig1	UTSW	7	13,044,983 (GRCm39)	missense	probably damaging	0.97
R5249:Lig1	UTSW	7	13,042,432 (GRCm39)	missense	possibly damaging	0.60
R5351:Lig1	UTSW	7	13,034,875 (GRCm39)	missense	probably damaging	1.00
R5373:Lig1	UTSW	7	13,039,849 (GRCm39)	frame shift	probably null
R5607:Lig1	UTSW	7	13,039,933 (GRCm39)	missense	probably damaging	0.97
R5608:Lig1	UTSW	7	13,039,933 (GRCm39)	missense	probably damaging	0.97
R5620:Lig1	UTSW	7	13,020,532 (GRCm39)	missense	possibly damaging	0.66
R5799:Lig1	UTSW	7	13,030,184 (GRCm39)	missense	possibly damaging	0.67
R6897:Lig1	UTSW	7	13,039,840 (GRCm39)	missense	probably damaging	1.00
R7202:Lig1	UTSW	7	13,025,175 (GRCm39)	missense	probably benign	0.00
R7454:Lig1	UTSW	7	13,022,647 (GRCm39)	missense	probably damaging	0.99
R7548:Lig1	UTSW	7	13,035,344 (GRCm39)	missense	possibly damaging	0.79
R7596:Lig1	UTSW	7	13,039,923 (GRCm39)	missense	probably damaging	1.00
R7597:Lig1	UTSW	7	13,030,270 (GRCm39)	missense	probably benign
R7688:Lig1	UTSW	7	13,023,389 (GRCm39)	missense	probably benign
R7733:Lig1	UTSW	7	13,030,157 (GRCm39)	missense	possibly damaging	0.87
R8104:Lig1	UTSW	7	13,020,491 (GRCm39)	missense	possibly damaging	0.46
R8887:Lig1	UTSW	7	13,030,713 (GRCm39)	missense	probably damaging	1.00
R9025:Lig1	UTSW	7	13,037,746 (GRCm39)	missense	probably damaging	1.00
R9321:Lig1	UTSW	7	13,034,935 (GRCm39)	missense	probably damaging	1.00
R9555:Lig1	UTSW	7	13,025,400 (GRCm39)	missense	probably benign
X0020:Lig1	UTSW	7	13,030,700 (GRCm39)	missense	possibly damaging	0.48

Predicted Primers

PCR Primer
(F):5'- GGTCACAGATTCAGAGCTGG -3'
(R):5'- AATAGCTCCATCTCTGTGGCTG -3'

Posted On

2017-07-14