Incidental Mutation 'R3941:Xrcc4'
ID 307464
Institutional Source Beutler Lab
Gene Symbol Xrcc4
Ensembl Gene ENSMUSG00000021615
Gene Name X-ray repair complementing defective repair in Chinese hamster cells 4
Synonyms 2310057B22Rik
MMRRC Submission 040923-MU
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.392) question?
Stock # R3941 (G1)
Quality Score 225
Status Validated
Chromosome 13
Chromosomal Location 89997033-90237727 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 90219752 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Alanine at position 16 (V16A)
Ref Sequence ENSEMBL: ENSMUSP00000022115 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000022115] [ENSMUST00000159199] [ENSMUST00000160232] [ENSMUST00000161396]
AlphaFold no structure available at present
Predicted Effect probably benign
Transcript: ENSMUST00000022115
AA Change: V16A

PolyPhen 2 Score 0.011 (Sensitivity: 0.96; Specificity: 0.78)
SMART Domains Protein: ENSMUSP00000022115
Gene: ENSMUSG00000021615
AA Change: V16A

Pfam:XRCC4 1 326 1.5e-153 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000159199
AA Change: V16A

PolyPhen 2 Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)
SMART Domains Protein: ENSMUSP00000123934
Gene: ENSMUSG00000021615
AA Change: V16A

Pfam:XRCC4 1 310 2.7e-151 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000160232
AA Change: V16A

PolyPhen 2 Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)
SMART Domains Protein: ENSMUSP00000125486
Gene: ENSMUSG00000021615
AA Change: V16A

Pfam:XRCC4 1 94 4.8e-49 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000161396
AA Change: V16A

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)
SMART Domains Protein: ENSMUSP00000124573
Gene: ENSMUSG00000021615
AA Change: V16A

Pfam:XRCC4 1 83 5.4e-45 PFAM
Meta Mutation Damage Score 0.0898 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.4%
  • 20x: 95.3%
Validation Efficiency 98% (55/56)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene functions together with DNA ligase IV and the DNA-dependent protein kinase in the repair of DNA double-strand breaks. This protein plays a role in both non-homologous end joining and the completion of V(D)J recombination. Mutations in this gene can cause short stature, microcephaly, and endocrine dysfunction (SSMED). Alternative splicing generates several transcript variants. [provided by RefSeq, Dec 2015]
PHENOTYPE: Homozygous null mutants have massive neuronal apoptosis, growth retardation, hypoplastic thymus and die by embryonic day 17.5. Lethality is rescued by Trp53 deficiency, but double knockout mice die from pro-B-cell lymphomas with Myc-Igh translocations. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 52 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcc1 A T 16: 14,214,263 (GRCm39) T193S probably benign Het
Arhgap11a A T 2: 113,667,242 (GRCm39) L435Q probably damaging Het
Bin1 T C 18: 32,539,211 (GRCm39) V48A probably damaging Het
Brinp3 C A 1: 146,627,599 (GRCm39) D277E probably damaging Het
Btn1a1 T G 13: 23,643,434 (GRCm39) R338S probably benign Het
Cacnb4 C A 2: 52,359,501 (GRCm39) R169L probably damaging Het
Ccdc80 A G 16: 44,916,455 (GRCm39) T404A probably benign Het
Cd2ap G C 17: 43,119,690 (GRCm39) H488D probably damaging Het
Cdon A G 9: 35,375,467 (GRCm39) T498A probably benign Het
Cngb3 A G 4: 19,396,786 (GRCm39) N380D probably benign Het
Col6a5 G A 9: 105,817,033 (GRCm39) S426F unknown Het
Cr2 A T 1: 194,848,122 (GRCm39) H345Q probably damaging Het
Cttnbp2 T A 6: 18,427,452 (GRCm39) K743M probably benign Het
Depdc1b T C 13: 108,505,370 (GRCm39) S245P probably damaging Het
Dync2h1 G A 9: 7,124,825 (GRCm39) H2016Y probably benign Het
Eif2s3y G T Y: 1,012,079 (GRCm39) R98L probably benign Het
Eml6 C T 11: 29,753,167 (GRCm39) G915S probably damaging Het
Fcgr1 A G 3: 96,193,349 (GRCm39) L216P probably benign Het
Fpr-rs3 T C 17: 20,845,111 (GRCm39) N10S probably benign Het
Frem3 T C 8: 81,341,649 (GRCm39) I1314T possibly damaging Het
Gabrr3 A G 16: 59,253,864 (GRCm39) N194D probably damaging Het
Hey1 A G 3: 8,729,638 (GRCm39) L273P probably damaging Het
Irf6 A G 1: 192,850,857 (GRCm39) K365E probably benign Het
Kit A G 5: 75,769,978 (GRCm39) D130G probably benign Het
Lrp1 G A 10: 127,389,265 (GRCm39) A3217V probably damaging Het
Mei4 C T 9: 81,809,336 (GRCm39) R140C probably benign Het
Mir100hg T C 9: 41,501,570 (GRCm39) L143P probably damaging Het
Mpo A T 11: 87,688,175 (GRCm39) K278M probably benign Het
Mprip T C 11: 59,622,328 (GRCm39) probably benign Het
Mug2 G C 6: 122,040,522 (GRCm39) G691R probably benign Het
Neto2 G A 8: 86,400,747 (GRCm39) T16I probably damaging Het
Nipal4 C T 11: 46,041,473 (GRCm39) V241M probably damaging Het
Nlrp2 A T 7: 5,330,551 (GRCm39) L615* probably null Het
Pcdh1 A G 18: 38,332,511 (GRCm39) V164A probably benign Het
Phc2 T C 4: 128,641,037 (GRCm39) probably null Het
Plekhg3 A G 12: 76,620,133 (GRCm39) E623G probably damaging Het
Psors1c2 G T 17: 35,844,825 (GRCm39) G29* probably null Het
Slc25a54 A T 3: 109,019,479 (GRCm39) D361V probably damaging Het
Slc39a12 A T 2: 14,400,992 (GRCm39) H123L possibly damaging Het
Sorl1 T C 9: 41,900,764 (GRCm39) probably null Het
Strn A T 17: 78,965,369 (GRCm39) I641N probably damaging Het
Tapbp A G 17: 34,139,457 (GRCm39) E151G possibly damaging Het
Ticrr T C 7: 79,343,445 (GRCm39) probably benign Het
Tnfrsf21 G A 17: 43,348,901 (GRCm39) C171Y probably damaging Het
Ttyh1 T A 7: 4,132,317 (GRCm39) L155H probably damaging Het
Utrn T A 10: 12,587,329 (GRCm39) probably null Het
Vmn1r175 A G 7: 23,508,393 (GRCm39) V78A probably benign Het
Vmn1r73 T C 7: 11,490,682 (GRCm39) Y167H probably damaging Het
Washc1 T C 17: 66,425,123 (GRCm39) S376P probably damaging Het
Wnt10a T A 1: 74,842,656 (GRCm39) probably null Het
Zeb1 T C 18: 5,767,799 (GRCm39) V770A probably benign Het
Zfp410 A G 12: 84,385,527 (GRCm39) N90S probably damaging Het
Other mutations in Xrcc4
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01376:Xrcc4 APN 13 90,210,169 (GRCm39) missense probably benign 0.00
IGL01486:Xrcc4 APN 13 90,210,151 (GRCm39) nonsense probably null
R0624:Xrcc4 UTSW 13 90,140,594 (GRCm39) missense possibly damaging 0.81
R0629:Xrcc4 UTSW 13 90,149,024 (GRCm39) splice site probably benign
R1801:Xrcc4 UTSW 13 90,140,698 (GRCm39) missense probably damaging 1.00
R2567:Xrcc4 UTSW 13 90,210,261 (GRCm39) missense probably damaging 0.99
R3055:Xrcc4 UTSW 13 90,210,196 (GRCm39) missense probably benign 0.06
R3056:Xrcc4 UTSW 13 90,210,196 (GRCm39) missense probably benign 0.06
R4486:Xrcc4 UTSW 13 90,140,707 (GRCm39) missense possibly damaging 0.79
R4556:Xrcc4 UTSW 13 90,140,623 (GRCm39) missense probably benign 0.02
R4599:Xrcc4 UTSW 13 90,210,126 (GRCm39) critical splice donor site probably null
R6057:Xrcc4 UTSW 13 90,139,198 (GRCm39) missense possibly damaging 0.95
R6262:Xrcc4 UTSW 13 89,926,906 (GRCm39) missense probably benign 0.00
R6597:Xrcc4 UTSW 13 90,149,048 (GRCm39) missense probably benign 0.24
R9080:Xrcc4 UTSW 13 90,149,097 (GRCm39) missense probably damaging 0.99
R9535:Xrcc4 UTSW 13 90,089,118 (GRCm39) missense probably benign 0.00
Z1176:Xrcc4 UTSW 13 90,089,161 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer

Sequencing Primer
Posted On 2015-04-17