Incidental Mutation 'R2409:Gen1'
ID 248141
Institutional Source Beutler Lab
Gene Symbol Gen1
Ensembl Gene ENSMUSG00000051235
Gene Name GEN1, Holliday junction 5' flap endonuclease
Synonyms 5830483C08Rik
MMRRC Submission 040375-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.152) question?
Stock # R2409 (G1)
Quality Score 225
Status Validated
Chromosome 12
Chromosomal Location 11288921-11315802 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 11299165 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Threonine at position 280 (I280T)
Ref Sequence ENSEMBL: ENSMUSP00000151310 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000166117] [ENSMUST00000218487] [ENSMUST00000218547]
AlphaFold Q8BMI4
Predicted Effect possibly damaging
Transcript: ENSMUST00000166117
AA Change: I345T

PolyPhen 2 Score 0.633 (Sensitivity: 0.87; Specificity: 0.91)
SMART Domains Protein: ENSMUSP00000132098
Gene: ENSMUSG00000051235
AA Change: I345T

DomainStartEndE-ValueType
XPGN 1 96 9.13e-22 SMART
XPGI 122 193 5.32e-23 SMART
HhH2 195 229 2.87e-5 SMART
low complexity region 704 713 N/A INTRINSIC
Predicted Effect possibly damaging
Transcript: ENSMUST00000218487
AA Change: I280T

PolyPhen 2 Score 0.748 (Sensitivity: 0.85; Specificity: 0.92)
Predicted Effect possibly damaging
Transcript: ENSMUST00000218547
AA Change: I280T

PolyPhen 2 Score 0.551 (Sensitivity: 0.88; Specificity: 0.91)
Predicted Effect noncoding transcript
Transcript: ENSMUST00000220261
Meta Mutation Damage Score 0.1529 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.4%
  • 10x: 96.9%
  • 20x: 94.0%
Validation Efficiency 100% (32/32)
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 Rad2/xeroderma pigmentosum group G nuclease family, whose members are characterized by N-terminal and internal xeroderma pigmentosum group G nuclease domains followed by helix-hairpin-helix domains and disordered C-terminal domains. The protein encoded by this gene is involved in resolution of Holliday junctions, which are intermediate four-way structures that covalently link DNA during homologous recombination and double-strand break repair. The protein resolves Holliday junctions by creating dual incisions across the junction to produce nicked duplex products that can be ligated. In addition, this protein has been found to localize to centrosomes where it has been implicated in regulation of centrosome integrity. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2016]
Allele List at MGI
Other mutations in this stock
Total: 29 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcb1a C T 5: 8,788,747 (GRCm39) T1042I probably benign Het
Adamts13 A G 2: 26,868,374 (GRCm39) T162A probably benign Het
Adamts7 T A 9: 90,062,740 (GRCm39) I398N probably damaging Het
Cib2 A G 9: 54,452,751 (GRCm39) probably null Het
Cyp3a16 T C 5: 145,377,177 (GRCm39) K470R probably benign Het
Dpy19l2 A G 9: 24,569,924 (GRCm39) M343T probably benign Het
Dyrk2 A G 10: 118,696,532 (GRCm39) V242A probably benign Het
Extl3 T C 14: 65,315,017 (GRCm39) D55G probably benign Het
Fabp7 A G 10: 57,661,772 (GRCm39) K82E possibly damaging Het
Fat1 G T 8: 45,493,567 (GRCm39) probably benign Het
Gm5117 T C 8: 32,227,306 (GRCm39) noncoding transcript Het
Gucy1b2 CCGTGTTT C 14: 62,643,628 (GRCm39) probably null Het
Il3ra G A 14: 14,349,377 (GRCm38) probably null Het
Myo1f A G 17: 33,795,641 (GRCm39) N66D probably damaging Het
Nfkb1 C T 3: 135,319,704 (GRCm39) E264K possibly damaging Het
Nsf C T 11: 103,821,578 (GRCm39) E26K possibly damaging Het
Or7d10 G T 9: 19,832,072 (GRCm39) R189L probably benign Het
Or7d10 G C 9: 19,832,077 (GRCm39) D191H probably damaging Het
Prdm10 A G 9: 31,260,418 (GRCm39) H624R possibly damaging Het
Rgs5 G T 1: 169,504,451 (GRCm39) V34F possibly damaging Het
Sec14l4 T C 11: 3,990,048 (GRCm39) S116P probably benign Het
Septin1 T C 7: 126,815,143 (GRCm39) probably null Het
Septin9 T A 11: 117,251,287 (GRCm39) I535N probably damaging Het
Sh2b1 C T 7: 126,070,651 (GRCm39) G350D probably damaging Het
Slc6a21 T C 7: 44,929,750 (GRCm39) V107A probably benign Het
Trim26 C A 17: 37,161,895 (GRCm39) H105N probably damaging Het
Trim71 A T 9: 114,342,781 (GRCm39) D500E possibly damaging Het
Vmn2r78 T A 7: 86,569,953 (GRCm39) probably benign Het
Vmn2r84 A G 10: 130,227,940 (GRCm39) S99P probably damaging Het
Other mutations in Gen1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00730:Gen1 APN 12 11,311,068 (GRCm39) missense probably damaging 1.00
IGL01308:Gen1 APN 12 11,306,871 (GRCm39) missense probably damaging 1.00
IGL01384:Gen1 APN 12 11,305,242 (GRCm39) missense probably benign 0.00
IGL01766:Gen1 APN 12 11,306,895 (GRCm39) missense probably damaging 1.00
IGL02132:Gen1 APN 12 11,291,867 (GRCm39) missense probably benign 0.37
IGL02191:Gen1 APN 12 11,292,297 (GRCm39) missense probably benign 0.18
IGL02452:Gen1 APN 12 11,292,576 (GRCm39) missense probably benign 0.02
IGL02479:Gen1 APN 12 11,291,936 (GRCm39) missense probably benign 0.01
IGL02690:Gen1 APN 12 11,291,576 (GRCm39) missense probably damaging 0.96
IGL03095:Gen1 APN 12 11,298,265 (GRCm39) missense probably benign 0.38
PIT4520001:Gen1 UTSW 12 11,291,509 (GRCm39) missense probably benign 0.12
R0014:Gen1 UTSW 12 11,291,642 (GRCm39) missense probably benign 0.44
R0014:Gen1 UTSW 12 11,291,642 (GRCm39) missense probably benign 0.44
R0355:Gen1 UTSW 12 11,298,355 (GRCm39) splice site probably benign
R0680:Gen1 UTSW 12 11,291,870 (GRCm39) missense probably benign 0.06
R0891:Gen1 UTSW 12 11,298,355 (GRCm39) splice site probably benign
R1192:Gen1 UTSW 12 11,305,219 (GRCm39) missense probably damaging 0.97
R1353:Gen1 UTSW 12 11,293,220 (GRCm39) missense probably benign 0.00
R1833:Gen1 UTSW 12 11,298,352 (GRCm39) splice site probably benign
R1898:Gen1 UTSW 12 11,291,609 (GRCm39) missense probably benign 0.10
R2138:Gen1 UTSW 12 11,291,622 (GRCm39) missense probably damaging 1.00
R2185:Gen1 UTSW 12 11,311,041 (GRCm39) missense probably null 0.95
R2876:Gen1 UTSW 12 11,292,069 (GRCm39) missense probably benign 0.13
R3815:Gen1 UTSW 12 11,302,034 (GRCm39) missense possibly damaging 0.84
R4402:Gen1 UTSW 12 11,292,363 (GRCm39) missense possibly damaging 0.71
R4572:Gen1 UTSW 12 11,292,419 (GRCm39) missense probably damaging 0.99
R4900:Gen1 UTSW 12 11,291,561 (GRCm39) missense probably benign 0.00
R5091:Gen1 UTSW 12 11,296,347 (GRCm39) missense probably damaging 0.97
R5952:Gen1 UTSW 12 11,310,897 (GRCm39) missense probably damaging 0.96
R6785:Gen1 UTSW 12 11,312,531 (GRCm39) missense possibly damaging 0.89
R6869:Gen1 UTSW 12 11,291,442 (GRCm39) missense probably benign 0.02
R7057:Gen1 UTSW 12 11,292,419 (GRCm39) missense probably benign 0.21
R7155:Gen1 UTSW 12 11,291,833 (GRCm39) missense probably benign 0.25
R7260:Gen1 UTSW 12 11,306,849 (GRCm39) missense probably damaging 0.99
R7316:Gen1 UTSW 12 11,291,470 (GRCm39) missense probably benign
R7512:Gen1 UTSW 12 11,310,977 (GRCm39) missense possibly damaging 0.79
R7692:Gen1 UTSW 12 11,292,167 (GRCm39) missense probably benign 0.22
R7800:Gen1 UTSW 12 11,291,863 (GRCm39) missense probably benign 0.00
R8061:Gen1 UTSW 12 11,311,077 (GRCm39) splice site probably benign
R8112:Gen1 UTSW 12 11,304,374 (GRCm39) nonsense probably null
R8147:Gen1 UTSW 12 11,305,051 (GRCm39) splice site probably null
R8152:Gen1 UTSW 12 11,293,266 (GRCm39) missense probably damaging 0.99
R8153:Gen1 UTSW 12 11,310,948 (GRCm39) missense probably damaging 1.00
R8161:Gen1 UTSW 12 11,291,465 (GRCm39) missense probably benign 0.21
R8942:Gen1 UTSW 12 11,292,287 (GRCm39) missense probably benign 0.01
R9004:Gen1 UTSW 12 11,305,022 (GRCm39) intron probably benign
R9183:Gen1 UTSW 12 11,299,186 (GRCm39) missense probably damaging 1.00
R9347:Gen1 UTSW 12 11,311,068 (GRCm39) missense probably damaging 1.00
R9367:Gen1 UTSW 12 11,291,309 (GRCm39) nonsense probably null
R9482:Gen1 UTSW 12 11,305,186 (GRCm39) missense possibly damaging 0.77
Predicted Primers PCR Primer
(F):5'- TTGCCTTATGGTCTGAAAAGTATGG -3'
(R):5'- TTGAAACTTCCAAGACTAGGCC -3'

Sequencing Primer
(F):5'- TATGGATCTTACACAGCCAAGG -3'
(R):5'- TTCCAAGACTAGGCCTAGCTTAG -3'
Posted On 2014-11-11