Incidental Mutation 'PIT4520001:Gen1'
ID 555193
Institutional Source Beutler Lab
Gene Symbol Gen1
Ensembl Gene ENSMUSG00000051235
Gene Name GEN1, Holliday junction 5' flap endonuclease
Synonyms 5830483C08Rik
Accession Numbers
Essential gene? Probably non essential (E-score: 0.152) question?
Stock # PIT4520001 (G1)
Quality Score 225.009
Status Not validated
Chromosome 12
Chromosomal Location 11288921-11315802 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 11291509 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Alanine at position 825 (V825A)
Ref Sequence ENSEMBL: ENSMUSP00000132098 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000166117] [ENSMUST00000218487] [ENSMUST00000218547]
AlphaFold Q8BMI4
Predicted Effect probably benign
Transcript: ENSMUST00000166117
AA Change: V825A

PolyPhen 2 Score 0.121 (Sensitivity: 0.93; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000132098
Gene: ENSMUSG00000051235
AA Change: V825A

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 probably benign
Transcript: ENSMUST00000218487
Predicted Effect probably benign
Transcript: ENSMUST00000218547
Coding Region Coverage
  • 1x: 93.5%
  • 3x: 91.1%
  • 10x: 86.1%
  • 20x: 75.5%
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 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: 59 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adcy1 A G 11: 7,117,133 (GRCm39) N1000S probably damaging Het
Adgrb1 A G 15: 74,413,508 (GRCm39) D564G probably damaging Het
Ankmy2 A G 12: 36,207,390 (GRCm39) E12G probably benign Het
Arid1a C T 4: 133,409,227 (GRCm39) S1375N unknown Het
Atp1a2 G A 1: 172,106,941 (GRCm39) A793V probably benign Het
Atp8b1 T C 18: 64,701,251 (GRCm39) Y369C probably benign Het
Catsperg2 A G 7: 29,409,586 (GRCm39) Y536H possibly damaging Het
Ccdc178 A G 18: 22,200,470 (GRCm39) Y445H probably damaging Het
Cep170 G T 1: 176,607,765 (GRCm39) N230K unknown Het
Cftr A G 6: 18,277,842 (GRCm39) I977V probably benign Het
Chek2 A G 5: 111,011,195 (GRCm39) Y331C probably damaging Het
Chst13 A T 6: 90,286,167 (GRCm39) I265K probably benign Het
Coil T C 11: 88,872,437 (GRCm39) M266T probably benign Het
Col16a1 T A 4: 129,945,456 (GRCm39) C28S unknown Het
Col3a1 T C 1: 45,374,943 (GRCm39) probably null Het
Csmd1 C T 8: 15,956,023 (GRCm39) V3395M probably benign Het
Cyp51 A G 5: 4,151,200 (GRCm39) V143A probably damaging Het
Eif2ak1 C T 5: 143,836,027 (GRCm39) Q573* probably null Het
Eif2ak4 T A 2: 118,292,808 (GRCm39) I1344N probably damaging Het
Fhip1a G A 3: 85,579,779 (GRCm39) Q809* probably null Het
Gm28042 A T 2: 119,870,148 (GRCm39) K696* probably null Het
Gm4952 A G 19: 12,602,048 (GRCm39) Y152C probably benign Het
Hdac3 G A 18: 38,074,817 (GRCm39) T308I probably damaging Het
Hpx T C 7: 105,241,341 (GRCm39) T357A probably benign Het
Hscb A T 5: 110,983,851 (GRCm39) Y139N probably damaging Het
Kcnk9 T A 15: 72,384,332 (GRCm39) H282L probably benign Het
Kdm2b G A 5: 123,079,110 (GRCm39) T287M probably damaging Het
Kif19a C T 11: 114,672,034 (GRCm39) T207M probably damaging Het
Kmt2c A C 5: 25,520,664 (GRCm39) N1815K probably benign Het
Ktn1 C T 14: 47,923,774 (GRCm39) T511M probably damaging Het
Lrp1 C G 10: 127,443,843 (GRCm39) Q141H possibly damaging Het
Lrrc43 T C 5: 123,630,530 (GRCm39) V131A possibly damaging Het
Man1b1 T A 2: 25,233,282 (GRCm39) H218Q probably damaging Het
Mapk8ip2 T A 15: 89,344,900 (GRCm39) C766S probably damaging Het
Mfn1 A G 3: 32,615,695 (GRCm39) N353D probably benign Het
Mtcl1 A T 17: 66,692,907 (GRCm39) L474Q possibly damaging Het
Mtr T A 13: 12,212,871 (GRCm39) R915* probably null Het
Myh6 C A 14: 55,187,581 (GRCm39) V1263L probably benign Het
Nt5m C A 11: 59,765,415 (GRCm39) L148M probably benign Het
Or4a67 A G 2: 88,597,921 (GRCm39) V246A possibly damaging Het
Or51t4 A T 7: 102,597,921 (GRCm39) D83V probably damaging Het
Or8k21 T C 2: 86,145,142 (GRCm39) I163V possibly damaging Het
Pbrm1 T A 14: 30,789,818 (GRCm39) F811I probably damaging Het
Pcnt A G 10: 76,256,069 (GRCm39) S724P probably damaging Het
Pfdn5 C A 15: 102,237,158 (GRCm39) D98E probably benign Het
Ptprs G A 17: 56,721,980 (GRCm39) P1715S probably damaging Het
Rtkn2 T A 10: 67,823,291 (GRCm39) L65Q probably damaging Het
Scn2a G A 2: 65,518,763 (GRCm39) R379H probably damaging Het
Scn5a G T 9: 119,363,636 (GRCm39) D501E possibly damaging Het
Spn C A 7: 126,735,611 (GRCm39) G299W probably damaging Het
St6galnac1 T C 11: 116,660,175 (GRCm39) N46S probably benign Het
Stx19 A G 16: 62,642,871 (GRCm39) D229G probably benign Het
Tmc6 A T 11: 117,663,556 (GRCm39) M552K possibly damaging Het
Tnpo3 G C 6: 29,555,221 (GRCm39) D787E possibly damaging Het
Tyw5 T C 1: 57,427,674 (GRCm39) Y310C probably damaging Het
Vmn2r15 A G 5: 109,434,871 (GRCm39) F611S probably damaging Het
Vmn2r49 C T 7: 9,722,988 (GRCm39) M95I probably benign Het
Wfdc8 A G 2: 164,445,223 (GRCm39) S131P probably benign Het
Zfp407 A T 18: 84,450,545 (GRCm39) M1597K 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
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
R2409:Gen1 UTSW 12 11,299,165 (GRCm39) missense possibly damaging 0.75
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'- AAAGGTAGAGGATTTTCCCAGG -3'
(R):5'- CCAGTCTTCAAGTTGGGCTG -3'

Sequencing Primer
(F):5'- CCAGGAGGCAGTAGAGTTCTCATC -3'
(R):5'- TTGGGCTGCCAACTGCTG -3'
Posted On 2019-06-07