Incidental Mutation 'R7003:Rif1'
ID 544645
Institutional Source Beutler Lab
Gene Symbol Rif1
Ensembl Gene ENSMUSG00000036202
Gene Name replication timing regulatory factor 1
Synonyms 6530403D07Rik, 5730435J01Rik, D2Ertd145e
MMRRC Submission 045108-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R7003 (G1)
Quality Score 225.009
Status Not validated
Chromosome 2
Chromosomal Location 52072832-52122383 bp(+) (GRCm38)
Type of Mutation missense
DNA Base Change (assembly) A to G at 52076989 bp (GRCm38)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Valine at position 97 (I97V)
Ref Sequence ENSEMBL: ENSMUSP00000108313 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000112693] [ENSMUST00000126218]
AlphaFold no structure available at present
Predicted Effect probably benign
Transcript: ENSMUST00000112693
AA Change: I97V

PolyPhen 2 Score 0.063 (Sensitivity: 0.94; Specificity: 0.84)
SMART Domains Protein: ENSMUSP00000108313
Gene: ENSMUSG00000036202
AA Change: I97V

DomainStartEndE-ValueType
Pfam:Rif1_N 18 381 1.4e-85 PFAM
low complexity region 432 444 N/A INTRINSIC
low complexity region 586 598 N/A INTRINSIC
low complexity region 1018 1038 N/A INTRINSIC
low complexity region 1180 1205 N/A INTRINSIC
low complexity region 1310 1321 N/A INTRINSIC
low complexity region 1423 1446 N/A INTRINSIC
low complexity region 1576 1586 N/A INTRINSIC
low complexity region 1677 1690 N/A INTRINSIC
low complexity region 1702 1712 N/A INTRINSIC
low complexity region 2176 2195 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000126218
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 100.0%
  • 10x: 99.7%
  • 20x: 99.1%
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein that shares homology with the yeast teleomere binding protein, Rap1 interacting factor 1. This protein localizes to aberrant telomeres may be involved in DNA repair. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Apr 2010]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit embryonic lethality. Mice homozygous for a gene trap allele exhibit embryonic and postnatal lethality, reduced fertility, and decreased cell proliferation. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 57 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Actbl2 T A 13: 111,255,956 (GRCm38) I275N probably damaging Het
Actr3b A C 5: 25,798,463 (GRCm38) Y21S probably damaging Het
Adam6b C T 12: 113,490,042 (GRCm38) Q160* probably null Het
Adgrv1 C T 13: 81,522,104 (GRCm38) probably null Het
Akr1c6 A G 13: 4,454,515 (GRCm38) N300D probably benign Het
Alox8 T C 11: 69,191,590 (GRCm38) D170G possibly damaging Het
Amhr2 A G 15: 102,446,333 (GRCm38) N40S probably benign Het
Ap2a2 A G 7: 141,629,196 (GRCm38) N767S probably benign Het
Armc3 T C 2: 19,270,028 (GRCm38) I358T probably damaging Het
Atg2b A G 12: 105,654,249 (GRCm38) S732P probably benign Het
Atp12a A G 14: 56,373,380 (GRCm38) Y327C possibly damaging Het
Bcr T C 10: 75,061,561 (GRCm38) V179A probably benign Het
Cep104 T C 4: 153,993,561 (GRCm38) L642P probably benign Het
Clspn T A 4: 126,592,720 (GRCm38) S1302R possibly damaging Het
Cmip T C 8: 117,384,988 (GRCm38) F153L probably benign Het
Cplane1 T G 15: 8,228,762 (GRCm38) L2164R probably damaging Het
D630039A03Rik T C 4: 57,910,521 (GRCm38) D97G probably damaging Het
Dok7 A T 5: 35,079,555 (GRCm38) T396S probably benign Het
Dsel C T 1: 111,860,295 (GRCm38) V837I probably benign Het
Etl4 C T 2: 20,805,884 (GRCm38) T926I probably benign Het
Gpatch2l G A 12: 86,244,184 (GRCm38) R47H probably damaging Het
Gpr155 A G 2: 73,343,617 (GRCm38) I816T probably damaging Het
Hpn C T 7: 31,110,942 (GRCm38) probably benign Het
Inpp5e A G 2: 26,397,865 (GRCm38) S640P probably benign Het
Irs3 C T 5: 137,645,277 (GRCm38) V82I probably benign Het
Kif16b A C 2: 142,758,829 (GRCm38) D461E possibly damaging Het
Krba1 A G 6: 48,413,080 (GRCm38) T592A possibly damaging Het
Lgsn T A 1: 31,203,943 (GRCm38) S369T possibly damaging Het
Lrrc4b C T 7: 44,445,156 (GRCm38) P83S probably damaging Het
Mplkipl1 A G 19: 61,175,881 (GRCm38) S39P possibly damaging Het
Neil3 T C 8: 53,600,966 (GRCm38) T343A possibly damaging Het
Nt5e A G 9: 88,364,752 (GRCm38) Y347C probably damaging Het
Olfr1532-ps1 A T 7: 106,915,112 (GRCm38) T305S probably benign Het
Or1j1 A G 2: 36,813,035 (GRCm38) I19T possibly damaging Het
Or2f2 C T 6: 42,790,465 (GRCm38) T142I probably benign Het
Or8g26 A T 9: 39,184,943 (GRCm38) Y255F probably benign Het
P2rx5 T C 11: 73,167,974 (GRCm38) probably null Het
Phtf2 A G 5: 20,794,401 (GRCm38) V248A probably benign Het
Plekhd1 T C 12: 80,721,960 (GRCm38) C406R possibly damaging Het
Plod3 T A 5: 136,989,644 (GRCm38) N245K probably damaging Het
Polr3c G T 3: 96,723,638 (GRCm38) H155Q possibly damaging Het
Psap T A 10: 60,299,497 (GRCm38) C317S probably damaging Het
Rnf123 T A 9: 108,063,683 (GRCm38) probably null Het
Rnf19a G A 15: 36,254,504 (GRCm38) R303* probably null Het
Sdk1 G A 5: 142,096,734 (GRCm38) V1036I probably benign Het
Shc3 T A 13: 51,466,552 (GRCm38) Y146F probably benign Het
Skint6 A G 4: 113,105,912 (GRCm38) Y441H probably benign Het
Slc7a12 T C 3: 14,505,520 (GRCm38) I173T probably damaging Het
Spesp1 A T 9: 62,282,020 (GRCm38) S15T possibly damaging Het
Tarm1 A T 7: 3,497,423 (GRCm38) probably null Het
Tenm3 T C 8: 48,240,444 (GRCm38) Y1817C probably damaging Het
Ttc9c A T 19: 8,818,540 (GRCm38) L45Q probably damaging Het
Ube3a C T 7: 59,276,440 (GRCm38) T322I probably damaging Het
Vac14 T A 8: 110,712,798 (GRCm38) V669E probably damaging Het
Vmn1r225 A G 17: 20,503,154 (GRCm38) M286V probably null Het
Zfp658 A G 7: 43,574,748 (GRCm38) K816E possibly damaging Het
Zfp846 T C 9: 20,587,892 (GRCm38) M1T probably null Het
Other mutations in Rif1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00465:Rif1 APN 2 52,121,007 (GRCm38) missense probably damaging 0.96
IGL00711:Rif1 APN 2 52,111,070 (GRCm38) missense probably benign 0.00
IGL00721:Rif1 APN 2 52,119,117 (GRCm38) missense probably damaging 1.00
IGL01085:Rif1 APN 2 52,085,140 (GRCm38) missense possibly damaging 0.71
IGL01093:Rif1 APN 2 52,095,948 (GRCm38) missense probably damaging 1.00
IGL01107:Rif1 APN 2 52,111,303 (GRCm38) missense probably benign 0.00
IGL01138:Rif1 APN 2 52,111,522 (GRCm38) missense probably damaging 1.00
IGL01844:Rif1 APN 2 52,112,543 (GRCm38) missense probably benign 0.07
IGL02441:Rif1 APN 2 52,105,515 (GRCm38) missense probably benign 0.00
IGL02448:Rif1 APN 2 52,116,696 (GRCm38) missense probably damaging 0.99
IGL02563:Rif1 APN 2 52,077,065 (GRCm38) missense probably damaging 1.00
IGL02704:Rif1 APN 2 52,093,576 (GRCm38) missense probably damaging 1.00
IGL02946:Rif1 APN 2 52,110,125 (GRCm38) nonsense probably null
IGL03060:Rif1 APN 2 52,112,137 (GRCm38) missense probably damaging 0.97
IGL03206:Rif1 APN 2 52,103,622 (GRCm38) missense probably damaging 1.00
IGL03263:Rif1 APN 2 52,090,261 (GRCm38) missense probably damaging 0.99
IGL03267:Rif1 APN 2 52,076,988 (GRCm38) missense possibly damaging 0.94
IGL03280:Rif1 APN 2 52,112,599 (GRCm38) missense probably benign 0.32
hifi UTSW 2 52,110,324 (GRCm38) unclassified probably benign
nietzsche UTSW 2 52,077,020 (GRCm38) missense probably benign 0.08
PIT4305001:Rif1 UTSW 2 52,111,958 (GRCm38) missense
R0017:Rif1 UTSW 2 52,116,674 (GRCm38) missense probably benign 0.18
R0017:Rif1 UTSW 2 52,116,674 (GRCm38) missense probably benign 0.18
R0060:Rif1 UTSW 2 52,111,117 (GRCm38) missense probably damaging 1.00
R0060:Rif1 UTSW 2 52,111,117 (GRCm38) missense probably damaging 1.00
R0104:Rif1 UTSW 2 52,110,092 (GRCm38) missense possibly damaging 0.77
R0268:Rif1 UTSW 2 52,090,286 (GRCm38) critical splice donor site probably null
R0276:Rif1 UTSW 2 52,110,324 (GRCm38) unclassified probably benign
R0278:Rif1 UTSW 2 52,110,324 (GRCm38) unclassified probably benign
R0288:Rif1 UTSW 2 52,110,013 (GRCm38) missense probably damaging 1.00
R0314:Rif1 UTSW 2 52,110,324 (GRCm38) unclassified probably benign
R0345:Rif1 UTSW 2 52,110,324 (GRCm38) unclassified probably benign
R0346:Rif1 UTSW 2 52,110,324 (GRCm38) unclassified probably benign
R0383:Rif1 UTSW 2 52,085,141 (GRCm38) missense probably damaging 0.96
R0384:Rif1 UTSW 2 52,110,324 (GRCm38) unclassified probably benign
R0387:Rif1 UTSW 2 52,110,324 (GRCm38) unclassified probably benign
R0388:Rif1 UTSW 2 52,110,324 (GRCm38) unclassified probably benign
R0456:Rif1 UTSW 2 52,110,324 (GRCm38) unclassified probably benign
R0477:Rif1 UTSW 2 52,110,324 (GRCm38) unclassified probably benign
R0505:Rif1 UTSW 2 52,110,737 (GRCm38) missense probably damaging 0.99
R0510:Rif1 UTSW 2 52,110,324 (GRCm38) unclassified probably benign
R0511:Rif1 UTSW 2 52,110,324 (GRCm38) unclassified probably benign
R0512:Rif1 UTSW 2 52,110,324 (GRCm38) unclassified probably benign
R0633:Rif1 UTSW 2 52,112,563 (GRCm38) missense probably benign 0.00
R0637:Rif1 UTSW 2 52,110,324 (GRCm38) unclassified probably benign
R0638:Rif1 UTSW 2 52,111,588 (GRCm38) missense probably benign 0.12
R0666:Rif1 UTSW 2 52,110,324 (GRCm38) unclassified probably benign
R0675:Rif1 UTSW 2 52,110,324 (GRCm38) unclassified probably benign
R0707:Rif1 UTSW 2 52,110,324 (GRCm38) unclassified probably benign
R0726:Rif1 UTSW 2 52,110,353 (GRCm38) missense possibly damaging 0.52
R0743:Rif1 UTSW 2 52,110,324 (GRCm38) unclassified probably benign
R0744:Rif1 UTSW 2 52,110,324 (GRCm38) unclassified probably benign
R0938:Rif1 UTSW 2 52,110,324 (GRCm38) unclassified probably benign
R0939:Rif1 UTSW 2 52,110,324 (GRCm38) unclassified probably benign
R0940:Rif1 UTSW 2 52,110,324 (GRCm38) unclassified probably benign
R0941:Rif1 UTSW 2 52,110,324 (GRCm38) unclassified probably benign
R0942:Rif1 UTSW 2 52,110,324 (GRCm38) unclassified probably benign
R0943:Rif1 UTSW 2 52,110,324 (GRCm38) unclassified probably benign
R1006:Rif1 UTSW 2 52,085,029 (GRCm38) missense probably damaging 0.99
R1052:Rif1 UTSW 2 52,111,562 (GRCm38) missense probably benign 0.01
R1061:Rif1 UTSW 2 52,110,324 (GRCm38) unclassified probably benign
R1175:Rif1 UTSW 2 52,107,628 (GRCm38) unclassified probably benign
R1183:Rif1 UTSW 2 52,110,324 (GRCm38) unclassified probably benign
R1184:Rif1 UTSW 2 52,110,324 (GRCm38) unclassified probably benign
R1271:Rif1 UTSW 2 52,110,324 (GRCm38) unclassified probably benign
R1332:Rif1 UTSW 2 52,078,314 (GRCm38) missense probably benign 0.06
R1336:Rif1 UTSW 2 52,078,314 (GRCm38) missense probably benign 0.06
R1351:Rif1 UTSW 2 52,111,555 (GRCm38) missense possibly damaging 0.74
R1517:Rif1 UTSW 2 52,110,324 (GRCm38) unclassified probably benign
R1527:Rif1 UTSW 2 52,110,324 (GRCm38) unclassified probably benign
R1560:Rif1 UTSW 2 52,111,131 (GRCm38) missense probably damaging 1.00
R1563:Rif1 UTSW 2 52,073,223 (GRCm38) missense probably damaging 0.99
R1571:Rif1 UTSW 2 52,110,324 (GRCm38) unclassified probably benign
R1625:Rif1 UTSW 2 52,103,640 (GRCm38) missense probably benign 0.25
R1679:Rif1 UTSW 2 52,110,324 (GRCm38) unclassified probably benign
R1689:Rif1 UTSW 2 52,110,324 (GRCm38) unclassified probably benign
R1731:Rif1 UTSW 2 52,110,324 (GRCm38) unclassified probably benign
R1744:Rif1 UTSW 2 52,112,392 (GRCm38) missense possibly damaging 0.56
R1746:Rif1 UTSW 2 52,110,324 (GRCm38) unclassified probably benign
R1748:Rif1 UTSW 2 52,110,324 (GRCm38) unclassified probably benign
R1831:Rif1 UTSW 2 52,078,495 (GRCm38) nonsense probably null
R1902:Rif1 UTSW 2 52,116,673 (GRCm38) missense possibly damaging 0.93
R1964:Rif1 UTSW 2 52,098,409 (GRCm38) missense probably benign 0.01
R1978:Rif1 UTSW 2 52,110,324 (GRCm38) unclassified probably benign
R2000:Rif1 UTSW 2 52,081,298 (GRCm38) missense probably damaging 0.99
R2030:Rif1 UTSW 2 52,092,346 (GRCm38) missense probably damaging 1.00
R2056:Rif1 UTSW 2 52,093,576 (GRCm38) missense probably damaging 1.00
R2106:Rif1 UTSW 2 52,110,324 (GRCm38) unclassified probably benign
R2109:Rif1 UTSW 2 52,110,324 (GRCm38) unclassified probably benign
R2125:Rif1 UTSW 2 52,110,324 (GRCm38) unclassified probably benign
R2126:Rif1 UTSW 2 52,110,324 (GRCm38) unclassified probably benign
R2145:Rif1 UTSW 2 52,111,400 (GRCm38) missense possibly damaging 0.63
R2152:Rif1 UTSW 2 52,110,324 (GRCm38) unclassified probably benign
R2153:Rif1 UTSW 2 52,110,324 (GRCm38) unclassified probably benign
R2213:Rif1 UTSW 2 52,110,324 (GRCm38) unclassified probably benign
R2327:Rif1 UTSW 2 52,110,324 (GRCm38) unclassified probably benign
R2512:Rif1 UTSW 2 52,110,324 (GRCm38) unclassified probably benign
R2513:Rif1 UTSW 2 52,110,324 (GRCm38) unclassified probably benign
R2516:Rif1 UTSW 2 52,110,324 (GRCm38) unclassified probably benign
R2520:Rif1 UTSW 2 52,110,324 (GRCm38) unclassified probably benign
R2905:Rif1 UTSW 2 52,098,504 (GRCm38) missense probably damaging 0.99
R3005:Rif1 UTSW 2 52,082,764 (GRCm38) missense probably damaging 1.00
R3155:Rif1 UTSW 2 52,110,324 (GRCm38) unclassified probably benign
R3156:Rif1 UTSW 2 52,110,324 (GRCm38) unclassified probably benign
R3429:Rif1 UTSW 2 52,110,324 (GRCm38) unclassified probably benign
R3707:Rif1 UTSW 2 52,093,580 (GRCm38) missense probably damaging 1.00
R3907:Rif1 UTSW 2 52,112,545 (GRCm38) missense probably benign 0.03
R3978:Rif1 UTSW 2 52,116,747 (GRCm38) critical splice donor site probably null
R4023:Rif1 UTSW 2 52,121,087 (GRCm38) missense probably benign 0.01
R4052:Rif1 UTSW 2 52,098,471 (GRCm38) nonsense probably null
R4668:Rif1 UTSW 2 52,111,952 (GRCm38) missense probably benign 0.01
R4674:Rif1 UTSW 2 52,106,942 (GRCm38) missense probably null 1.00
R4715:Rif1 UTSW 2 52,073,139 (GRCm38) utr 5 prime probably benign
R4766:Rif1 UTSW 2 52,098,934 (GRCm38) missense probably damaging 1.00
R4783:Rif1 UTSW 2 52,112,747 (GRCm38) missense probably damaging 0.96
R4785:Rif1 UTSW 2 52,112,747 (GRCm38) missense probably damaging 0.96
R4869:Rif1 UTSW 2 52,093,611 (GRCm38) intron probably benign
R4911:Rif1 UTSW 2 52,110,518 (GRCm38) missense probably damaging 0.98
R4951:Rif1 UTSW 2 52,084,986 (GRCm38) splice site probably null
R5044:Rif1 UTSW 2 52,109,928 (GRCm38) missense probably damaging 0.99
R5088:Rif1 UTSW 2 52,092,295 (GRCm38) missense possibly damaging 0.91
R5151:Rif1 UTSW 2 52,120,309 (GRCm38) missense probably damaging 1.00
R5187:Rif1 UTSW 2 52,081,289 (GRCm38) missense probably damaging 1.00
R5222:Rif1 UTSW 2 52,077,020 (GRCm38) missense probably benign 0.08
R5243:Rif1 UTSW 2 52,111,824 (GRCm38) missense possibly damaging 0.86
R5436:Rif1 UTSW 2 52,120,971 (GRCm38) intron probably benign
R5476:Rif1 UTSW 2 52,089,595 (GRCm38) missense probably damaging 1.00
R5496:Rif1 UTSW 2 52,098,916 (GRCm38) missense probably damaging 1.00
R5641:Rif1 UTSW 2 52,121,158 (GRCm38) missense possibly damaging 0.80
R5883:Rif1 UTSW 2 52,105,639 (GRCm38) critical splice donor site probably null
R5987:Rif1 UTSW 2 52,095,844 (GRCm38) missense probably damaging 1.00
R5990:Rif1 UTSW 2 52,095,844 (GRCm38) missense probably damaging 1.00
R5992:Rif1 UTSW 2 52,095,844 (GRCm38) missense probably damaging 1.00
R6019:Rif1 UTSW 2 52,095,844 (GRCm38) missense probably damaging 1.00
R6020:Rif1 UTSW 2 52,095,844 (GRCm38) missense probably damaging 1.00
R6255:Rif1 UTSW 2 52,085,053 (GRCm38) missense probably damaging 1.00
R6342:Rif1 UTSW 2 52,119,156 (GRCm38) missense probably damaging 0.97
R6364:Rif1 UTSW 2 52,107,669 (GRCm38) missense probably damaging 0.97
R6747:Rif1 UTSW 2 52,078,263 (GRCm38) splice site probably null
R6928:Rif1 UTSW 2 52,095,961 (GRCm38) missense probably damaging 1.00
R6954:Rif1 UTSW 2 52,112,691 (GRCm38) missense probably benign 0.00
R7310:Rif1 UTSW 2 52,105,619 (GRCm38) missense probably benign 0.12
R7549:Rif1 UTSW 2 52,078,507 (GRCm38) missense possibly damaging 0.52
R7603:Rif1 UTSW 2 52,076,175 (GRCm38) missense probably damaging 1.00
R7673:Rif1 UTSW 2 52,088,654 (GRCm38) missense probably damaging 1.00
R7741:Rif1 UTSW 2 52,085,141 (GRCm38) missense probably damaging 0.96
R7777:Rif1 UTSW 2 52,116,356 (GRCm38) missense probably benign 0.00
R7910:Rif1 UTSW 2 52,078,387 (GRCm38) nonsense probably null
R7962:Rif1 UTSW 2 52,074,276 (GRCm38) missense probably damaging 1.00
R8264:Rif1 UTSW 2 52,090,278 (GRCm38) missense noncoding transcript
R8390:Rif1 UTSW 2 52,110,923 (GRCm38) missense probably damaging 1.00
R8479:Rif1 UTSW 2 52,112,551 (GRCm38) missense possibly damaging 0.52
R8490:Rif1 UTSW 2 52,110,999 (GRCm38) missense probably damaging 0.96
R8762:Rif1 UTSW 2 52,111,730 (GRCm38) missense
R8785:Rif1 UTSW 2 52,110,481 (GRCm38) missense probably benign 0.06
R8890:Rif1 UTSW 2 52,098,863 (GRCm38) missense probably damaging 0.99
R9081:Rif1 UTSW 2 52,110,977 (GRCm38) missense probably damaging 0.99
R9225:Rif1 UTSW 2 52,111,850 (GRCm38) missense probably benign 0.22
R9284:Rif1 UTSW 2 52,108,552 (GRCm38) missense probably benign 0.00
R9300:Rif1 UTSW 2 52,111,139 (GRCm38) missense probably damaging 1.00
R9366:Rif1 UTSW 2 52,120,344 (GRCm38) missense
R9477:Rif1 UTSW 2 52,111,330 (GRCm38) missense probably benign 0.02
R9522:Rif1 UTSW 2 52,081,299 (GRCm38) missense probably damaging 1.00
R9573:Rif1 UTSW 2 52,110,454 (GRCm38) missense probably benign 0.29
R9630:Rif1 UTSW 2 52,089,595 (GRCm38) missense probably damaging 1.00
X0064:Rif1 UTSW 2 52,094,633 (GRCm38) missense probably damaging 0.96
X0064:Rif1 UTSW 2 52,074,315 (GRCm38) missense probably benign 0.00
Z1177:Rif1 UTSW 2 52,088,648 (GRCm38) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- CCCTTCGGTCAGGATTGTTTAC -3'
(R):5'- TCAACAACAGCAGAATGTATCTCTC -3'

Sequencing Primer
(F):5'- CAGGATTGTTTACTTTTTGCAAGAAG -3'
(R):5'- ACAGCAGAATGTATCTCTCCTTTAC -3'
Posted On 2019-05-13