Incidental Mutation 'IGL03056:Lig4'
ID409232
Institutional Source Australian Phenomics Network (link to record)
Gene Symbol Lig4
Ensembl Gene ENSMUSG00000049717
Gene Nameligase IV, DNA, ATP-dependent
SynonymsDNA ligase IV, 5830471N16Rik, tiny
Accession Numbers
Is this an essential gene? Essential (E-score: 1.000) question?
Stock #IGL03056
Quality Score
Status
Chromosome8
Chromosomal Location9969049-9977686 bp(-) (GRCm38)
Type of Mutationmissense
DNA Base Change (assembly) A to G at 9972580 bp
ZygosityHeterozygous
Amino Acid Change Isoleucine to Threonine at position 400 (I400T)
Ref Sequence ENSEMBL: ENSMUSP00000130807 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000095476] [ENSMUST00000170033]
Predicted Effect possibly damaging
Transcript: ENSMUST00000095476
AA Change: I400T

PolyPhen 2 Score 0.900 (Sensitivity: 0.82; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000093130
Gene: ENSMUSG00000049717
AA Change: I400T

DomainStartEndE-ValueType
Pfam:DNA_ligase_A_N 14 209 1.3e-43 PFAM
Pfam:DNA_ligase_A_M 248 451 2e-50 PFAM
Pfam:DNA_ligase_A_C 476 588 3.3e-16 PFAM
BRCT 656 733 2.8e-14 SMART
Pfam:DNA_ligase_IV 749 784 7.3e-21 PFAM
BRCT 816 901 1.6e-5 SMART
Predicted Effect possibly damaging
Transcript: ENSMUST00000170033
AA Change: I400T

PolyPhen 2 Score 0.900 (Sensitivity: 0.82; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000130807
Gene: ENSMUSG00000049717
AA Change: I400T

DomainStartEndE-ValueType
Pfam:DNA_ligase_A_N 15 208 8.8e-39 PFAM
Pfam:DNA_ligase_A_M 248 451 2.3e-52 PFAM
Pfam:DNA_ligase_A_C 476 588 4.8e-18 PFAM
BRCT 656 733 2.9e-14 SMART
Pfam:DNA_ligase_IV 750 783 5.5e-17 PFAM
BRCT 816 901 1.6e-5 SMART
Coding Region Coverage
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is a DNA ligase that joins single-strand breaks in a double-stranded polydeoxynucleotide in an ATP-dependent reaction. This protein is essential for V(D)J recombination and DNA double-strand break (DSB) repair through nonhomologous end joining (NHEJ). This protein forms a complex with the X-ray repair cross complementing protein 4 (XRCC4), and further interacts with the DNA-dependent protein kinase (DNA-PK). Both XRCC4 and DNA-PK are known to be required for NHEJ. The crystal structure of the complex formed by this protein and XRCC4 has been resolved. Defects in this gene are the cause of LIG4 syndrome. Alternatively spliced transcript variants encoding the same protein have been observed. [provided by RefSeq, Jul 2008]
PHENOTYPE: Null homozygotes die late in gestation with extensive CNS apoptosis, blocked lymphopoeiesis and failure of V(D)J joining. Carrier fibroblasts show elevated chromosome breaks. ~40% of homozygous hypomorphs survive, with retarded growth, reduced PBL and progressive loss of hematopoietic stem cells. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 33 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
A2m A G 6: 121,670,903 H1118R probably damaging Het
Aff1 G A 5: 103,811,081 V339I probably damaging Het
Ank1 G T 8: 23,141,179 V107F probably damaging Het
Aox3 T C 1: 58,159,021 probably null Het
Cd160 T C 3: 96,805,811 T46A probably benign Het
Col20a1 A T 2: 180,994,889 Y221F probably damaging Het
Ddx18 C T 1: 121,564,535 A148T probably benign Het
Dennd5b A G 6: 149,055,072 M307T probably damaging Het
Fam166a T A 2: 25,221,355 M232K possibly damaging Het
Fam216b G A 14: 78,082,783 H86Y probably benign Het
Fh1 A T 1: 175,606,162 C374S probably damaging Het
Fkbp14 A G 6: 54,579,544 V207A probably benign Het
Gucy1a1 T C 3: 82,113,287 K101R probably benign Het
Kcnk2 G T 1: 189,295,711 Q116K possibly damaging Het
Kdm5b C A 1: 134,587,979 Q114K probably damaging Het
Kif12 C T 4: 63,166,956 R516Q probably null Het
Lca5l C T 16: 96,161,351 C463Y probably benign Het
Lgsn T A 1: 31,203,624 Y262* probably null Het
Mink1 T A 11: 70,612,583 probably null Het
Mprip T A 11: 59,771,692 I2243N probably damaging Het
Myo1f A T 17: 33,585,600 Y426F probably damaging Het
Naip2 T A 13: 100,162,287 S414C possibly damaging Het
Nrg1 T C 8: 31,821,423 I363V possibly damaging Het
Olfr1278 A T 2: 111,293,172 R301S possibly damaging Het
Olfr582 A T 7: 103,041,751 I86L possibly damaging Het
Serpinb9d T C 13: 33,202,753 V268A probably damaging Het
Slc15a1 A G 14: 121,491,283 F17L possibly damaging Het
Slc9a3 T A 13: 74,150,819 V119E probably damaging Het
Sspo T A 6: 48,470,538 M2346K probably benign Het
Tcf4 G T 18: 69,651,212 probably benign Het
Trabd2b T C 4: 114,409,338 V183A probably damaging Het
Ust T C 10: 8,207,562 H350R probably benign Het
Zfp952 T A 17: 33,002,766 V35E probably damaging Het
Other mutations in Lig4
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00229:Lig4 APN 8 9972775 missense probably damaging 1.00
IGL00655:Lig4 APN 8 9973305 missense probably benign 0.09
IGL01388:Lig4 APN 8 9973586 missense probably damaging 1.00
IGL01669:Lig4 APN 8 9973673 missense probably benign 0.01
IGL01757:Lig4 APN 8 9971185 missense probably benign 0.10
IGL02115:Lig4 APN 8 9973247 missense possibly damaging 0.58
IGL02167:Lig4 APN 8 9971821 missense probably benign 0.06
IGL02239:Lig4 APN 8 9972473 missense probably damaging 1.00
IGL02576:Lig4 APN 8 9971116 missense probably damaging 1.00
IGL02955:Lig4 APN 8 9972103 missense possibly damaging 0.95
posey UTSW 8 9972955 missense probably damaging 1.00
posey2 UTSW 8 9971585 missense probably benign
R0791:Lig4 UTSW 8 9973012 missense possibly damaging 0.70
R1208:Lig4 UTSW 8 9971062 missense probably damaging 1.00
R1208:Lig4 UTSW 8 9971062 missense probably damaging 1.00
R1368:Lig4 UTSW 8 9971176 missense possibly damaging 0.89
R1522:Lig4 UTSW 8 9973012 missense possibly damaging 0.70
R1566:Lig4 UTSW 8 9973650 missense probably benign 0.41
R1674:Lig4 UTSW 8 9971692 missense probably benign 0.01
R2024:Lig4 UTSW 8 9972436 missense probably damaging 1.00
R2025:Lig4 UTSW 8 9972436 missense probably damaging 1.00
R2026:Lig4 UTSW 8 9972436 missense probably damaging 1.00
R2155:Lig4 UTSW 8 9972766 missense probably benign 0.00
R2243:Lig4 UTSW 8 9972161 missense possibly damaging 0.81
R2917:Lig4 UTSW 8 9971596 missense possibly damaging 0.56
R4763:Lig4 UTSW 8 9972955 missense probably damaging 1.00
R4819:Lig4 UTSW 8 9971885 missense probably benign
R5153:Lig4 UTSW 8 9973003 missense possibly damaging 0.95
R5397:Lig4 UTSW 8 9972644 missense probably benign 0.01
R5618:Lig4 UTSW 8 9972021 missense probably benign
R6102:Lig4 UTSW 8 9972872 missense probably damaging 1.00
R6210:Lig4 UTSW 8 9971585 missense probably benign
R6312:Lig4 UTSW 8 9971739 missense probably benign
R6955:Lig4 UTSW 8 9973384 missense probably damaging 1.00
R6991:Lig4 UTSW 8 9971098 missense probably damaging 0.99
R7207:Lig4 UTSW 8 9972101 nonsense probably null
Posted On2016-08-02