Incidental Mutation 'R9225:Rif1'
ID 699749
Institutional Source Beutler Lab
Gene Symbol Rif1
Ensembl Gene ENSMUSG00000036202
Gene Name replication timing regulatory factor 1
Synonyms 6530403D07Rik, 5730435J01Rik, D2Ertd145e
MMRRC Submission
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R9225 (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 52111850 bp (GRCm38)
Zygosity Heterozygous
Amino Acid Change Glutamic Acid to Glycine at position 130 (E130G)
Gene Model predicted gene model for transcript(s): [ENSMUST00000112693]
AlphaFold no structure available at present
Predicted Effect probably benign
Transcript: ENSMUST00000112693
AA Change: E1772G

PolyPhen 2 Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)
SMART Domains Protein: ENSMUSP00000108313
Gene: ENSMUSG00000036202
AA Change: E1772G

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: ENSMUST00000125322
AA Change: E289G

PolyPhen 2 Score 0.189 (Sensitivity: 0.92; Specificity: 0.87)
Predicted Effect probably benign
Transcript: ENSMUST00000125376
AA Change: E130G

PolyPhen 2 Score 0.215 (Sensitivity: 0.92; Specificity: 0.88)
Predicted Effect probably benign
Transcript: ENSMUST00000152178
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 100.0%
  • 10x: 99.8%
  • 20x: 99.3%
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: 90 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2310003L06Rik G T 5: 87,972,574 V397L probably benign Het
Adam26b G T 8: 43,520,416 Y516* probably null Het
Afap1 A G 5: 35,976,624 K468E possibly damaging Het
Ank2 A G 3: 126,942,462 S3258P unknown Het
Ap1g1 A G 8: 109,858,877 K783E probably benign Het
Apbb1 A G 7: 105,568,856 S20P Het
Atg13 T C 2: 91,688,783 probably null Het
Atg16l2 A G 7: 101,301,981 V16A probably benign Het
Atp11a G A 8: 12,817,005 R144Q probably benign Het
Avpr1a A T 10: 122,449,561 T253S probably benign Het
B4galnt3 T C 6: 120,218,967 T300A probably damaging Het
Bag4 A G 8: 25,771,242 V157A probably benign Het
Brsk2 A G 7: 141,993,302 H494R probably damaging Het
Cacna2d2 G A 9: 107,526,204 G955S probably benign Het
Ccdc42 A T 11: 68,588,235 E83V probably damaging Het
Cep120 T C 18: 53,706,824 Q788R probably benign Het
Cnbd1 A G 4: 18,907,010 I188T probably benign Het
Col6a6 C T 9: 105,782,238 E503K possibly damaging Het
Cpt1c A T 7: 44,960,789 L661H probably damaging Het
Cyp2a22 T C 7: 26,937,777 D194G possibly damaging Het
Cyp2c70 C A 19: 40,180,468 R125L probably damaging Het
Cyp3a41a A T 5: 145,713,604 D76E probably benign Het
Cyp4f13 A T 17: 32,925,345 I458N probably damaging Het
Cyp4f13 T C 17: 32,929,201 Q350R probably damaging Het
Ddx60 G A 8: 62,017,841 V1456I probably benign Het
Dgkh T C 14: 78,725,067 H8R probably damaging Het
Diaph3 A G 14: 87,007,324 probably null Het
Dnah8 A C 17: 30,635,673 D103A probably benign Het
Dock4 G A 12: 40,829,670 R1551Q probably benign Het
Eps8 A T 6: 137,530,563 S56T probably benign Het
Fam171b T A 2: 83,880,042 L686Q probably damaging Het
Fndc3b A C 3: 27,456,531 L814* probably null Het
Gcnt2 T A 13: 40,860,860 L169Q probably damaging Het
Gm21103 T A 14: 6,303,883 I56F possibly damaging Het
Gpc1 A T 1: 92,856,020 K276N probably damaging Het
Hivep1 T A 13: 42,183,708 V2421D probably damaging Het
Hoxb1 T C 11: 96,366,293 L156P probably benign Het
Ifi208 A G 1: 173,690,728 D467G possibly damaging Het
Klhl22 A G 16: 17,776,753 M249V probably damaging Het
Kmt2b A G 7: 30,586,747 V240A unknown Het
Lacc1 A T 14: 77,034,974 Y127* probably null Het
Lgr4 C A 2: 110,012,140 H823Q probably benign Het
Llgl1 T C 11: 60,710,063 S662P probably damaging Het
Lrrc1 G A 9: 77,452,673 T279I probably benign Het
Lrrc8e T A 8: 4,234,561 V262E probably damaging Het
Magi1 G T 6: 93,785,530 P292T possibly damaging Het
Mccc1 T A 3: 35,964,362 I608F probably benign Het
Mroh8 T A 2: 157,265,090 I220L probably damaging Het
Mycn C A 12: 12,937,608 D263Y probably damaging Het
Myrip A G 9: 120,464,784 K782E probably damaging Het
Ncoa6 T A 2: 155,407,521 I1288F possibly damaging Het
Nebl A G 2: 17,400,511 I399T possibly damaging Het
Neurod1 A T 2: 79,454,387 H217Q probably benign Het
Nlrp5 T C 7: 23,417,946 V365A probably benign Het
Olfr1452-ps1 A G 19: 13,017,006 *261W probably null Het
Olfr1452-ps1 G C 19: 13,017,007 *261Y probably null Het
Olfr20 C A 11: 73,353,769 N5K probably damaging Het
Olfr693 A G 7: 106,677,769 V239A probably benign Het
Otud7a A G 7: 63,757,721 T591A possibly damaging Het
Pbx3 T C 2: 34,370,926 probably benign Het
Pcdhb4 A T 18: 37,308,642 Q335L possibly damaging Het
Plxnc1 C A 10: 94,793,199 C1571F probably damaging Het
Pola2 G A 19: 5,950,464 P330S probably benign Het
Ppm1l A T 3: 69,552,911 N274Y probably benign Het
Ppp4r3b A G 11: 29,205,648 D538G possibly damaging Het
Ptx4 C T 17: 25,122,722 T57I probably benign Het
Rchy1 A T 5: 91,957,537 C108* probably null Het
Rmdn1 A T 4: 19,601,385 Y219F probably damaging Het
Rnf144a A G 12: 26,327,607 C46R probably damaging Het
Rpl13a C A 7: 45,126,203 G146V probably damaging Het
Rpl13a C A 7: 45,126,204 G146W probably damaging Het
Rtn3 A T 19: 7,457,489 N379K probably damaging Het
Sdc1 G T 12: 8,771,817 R19L unknown Het
Shank1 A G 7: 44,334,046 I651V unknown Het
Slamf6 T C 1: 171,936,703 V221A probably benign Het
Soga3 A T 10: 29,196,331 K540* probably null Het
Sp9 C A 2: 73,273,495 S131* probably null Het
Spen T C 4: 141,475,632 T1895A possibly damaging Het
Taf6l CGCAGCCGCACCTG CG 19: 8,774,324 probably benign Het
Thada G T 17: 84,441,744 H600N possibly damaging Het
Trmt11 G T 10: 30,547,757 P384Q probably damaging Het
Tsnaxip1 T C 8: 105,840,027 L165P probably damaging Het
Ttc7 A G 17: 87,330,074 Y419C probably damaging Het
Ugt1a6a T C 1: 88,138,838 F122S probably benign Het
Vmn1r218 G A 13: 23,136,654 C57Y probably benign Het
Vmn2r14 T C 5: 109,221,422 N95S probably damaging Het
Vmn2r2 G T 3: 64,126,600 H500Q probably benign Het
Vmn2r70 T A 7: 85,559,034 Y745F probably damaging Het
Zfp189 C T 4: 49,530,193 S432F probably benign Het
Zscan2 C T 7: 80,863,273 A2V probably damaging Het
Other mutations in Rif1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00465:Rif1 APN 2 52121007 missense probably damaging 0.96
IGL00711:Rif1 APN 2 52111070 missense probably benign 0.00
IGL00721:Rif1 APN 2 52119117 missense probably damaging 1.00
IGL01085:Rif1 APN 2 52085140 missense possibly damaging 0.71
IGL01093:Rif1 APN 2 52095948 missense probably damaging 1.00
IGL01107:Rif1 APN 2 52111303 missense probably benign 0.00
IGL01138:Rif1 APN 2 52111522 missense probably damaging 1.00
IGL01844:Rif1 APN 2 52112543 missense probably benign 0.07
IGL02441:Rif1 APN 2 52105515 missense probably benign 0.00
IGL02448:Rif1 APN 2 52116696 missense probably damaging 0.99
IGL02563:Rif1 APN 2 52077065 missense probably damaging 1.00
IGL02704:Rif1 APN 2 52093576 missense probably damaging 1.00
IGL02946:Rif1 APN 2 52110125 nonsense probably null
IGL03060:Rif1 APN 2 52112137 missense probably damaging 0.97
IGL03206:Rif1 APN 2 52103622 missense probably damaging 1.00
IGL03263:Rif1 APN 2 52090261 missense probably damaging 0.99
IGL03267:Rif1 APN 2 52076988 missense possibly damaging 0.94
IGL03280:Rif1 APN 2 52112599 missense probably benign 0.32
hifi UTSW 2 52110324 unclassified probably benign
nietzsche UTSW 2 52077020 missense probably benign 0.08
PIT4305001:Rif1 UTSW 2 52111958 missense
R0017:Rif1 UTSW 2 52116674 missense probably benign 0.18
R0017:Rif1 UTSW 2 52116674 missense probably benign 0.18
R0060:Rif1 UTSW 2 52111117 missense probably damaging 1.00
R0060:Rif1 UTSW 2 52111117 missense probably damaging 1.00
R0104:Rif1 UTSW 2 52110092 missense possibly damaging 0.77
R0268:Rif1 UTSW 2 52090286 critical splice donor site probably null
R0276:Rif1 UTSW 2 52110324 unclassified probably benign
R0278:Rif1 UTSW 2 52110324 unclassified probably benign
R0288:Rif1 UTSW 2 52110013 missense probably damaging 1.00
R0314:Rif1 UTSW 2 52110324 unclassified probably benign
R0345:Rif1 UTSW 2 52110324 unclassified probably benign
R0346:Rif1 UTSW 2 52110324 unclassified probably benign
R0383:Rif1 UTSW 2 52085141 missense probably damaging 0.96
R0384:Rif1 UTSW 2 52110324 unclassified probably benign
R0387:Rif1 UTSW 2 52110324 unclassified probably benign
R0388:Rif1 UTSW 2 52110324 unclassified probably benign
R0456:Rif1 UTSW 2 52110324 unclassified probably benign
R0477:Rif1 UTSW 2 52110324 unclassified probably benign
R0505:Rif1 UTSW 2 52110737 missense probably damaging 0.99
R0510:Rif1 UTSW 2 52110324 unclassified probably benign
R0511:Rif1 UTSW 2 52110324 unclassified probably benign
R0512:Rif1 UTSW 2 52110324 unclassified probably benign
R0633:Rif1 UTSW 2 52112563 missense probably benign 0.00
R0637:Rif1 UTSW 2 52110324 unclassified probably benign
R0638:Rif1 UTSW 2 52111588 missense probably benign 0.12
R0666:Rif1 UTSW 2 52110324 unclassified probably benign
R0675:Rif1 UTSW 2 52110324 unclassified probably benign
R0707:Rif1 UTSW 2 52110324 unclassified probably benign
R0726:Rif1 UTSW 2 52110353 missense possibly damaging 0.52
R0743:Rif1 UTSW 2 52110324 unclassified probably benign
R0744:Rif1 UTSW 2 52110324 unclassified probably benign
R0938:Rif1 UTSW 2 52110324 unclassified probably benign
R0939:Rif1 UTSW 2 52110324 unclassified probably benign
R0940:Rif1 UTSW 2 52110324 unclassified probably benign
R0941:Rif1 UTSW 2 52110324 unclassified probably benign
R0942:Rif1 UTSW 2 52110324 unclassified probably benign
R0943:Rif1 UTSW 2 52110324 unclassified probably benign
R1006:Rif1 UTSW 2 52085029 missense probably damaging 0.99
R1052:Rif1 UTSW 2 52111562 missense probably benign 0.01
R1061:Rif1 UTSW 2 52110324 unclassified probably benign
R1175:Rif1 UTSW 2 52107628 unclassified probably benign
R1183:Rif1 UTSW 2 52110324 unclassified probably benign
R1184:Rif1 UTSW 2 52110324 unclassified probably benign
R1271:Rif1 UTSW 2 52110324 unclassified probably benign
R1332:Rif1 UTSW 2 52078314 missense probably benign 0.06
R1336:Rif1 UTSW 2 52078314 missense probably benign 0.06
R1351:Rif1 UTSW 2 52111555 missense possibly damaging 0.74
R1517:Rif1 UTSW 2 52110324 unclassified probably benign
R1527:Rif1 UTSW 2 52110324 unclassified probably benign
R1560:Rif1 UTSW 2 52111131 missense probably damaging 1.00
R1563:Rif1 UTSW 2 52073223 missense probably damaging 0.99
R1571:Rif1 UTSW 2 52110324 unclassified probably benign
R1625:Rif1 UTSW 2 52103640 missense probably benign 0.25
R1679:Rif1 UTSW 2 52110324 unclassified probably benign
R1689:Rif1 UTSW 2 52110324 unclassified probably benign
R1731:Rif1 UTSW 2 52110324 unclassified probably benign
R1744:Rif1 UTSW 2 52112392 missense possibly damaging 0.56
R1746:Rif1 UTSW 2 52110324 unclassified probably benign
R1748:Rif1 UTSW 2 52110324 unclassified probably benign
R1831:Rif1 UTSW 2 52078495 nonsense probably null
R1902:Rif1 UTSW 2 52116673 missense possibly damaging 0.93
R1964:Rif1 UTSW 2 52098409 missense probably benign 0.01
R1978:Rif1 UTSW 2 52110324 unclassified probably benign
R2000:Rif1 UTSW 2 52081298 missense probably damaging 0.99
R2030:Rif1 UTSW 2 52092346 missense probably damaging 1.00
R2056:Rif1 UTSW 2 52093576 missense probably damaging 1.00
R2106:Rif1 UTSW 2 52110324 unclassified probably benign
R2109:Rif1 UTSW 2 52110324 unclassified probably benign
R2125:Rif1 UTSW 2 52110324 unclassified probably benign
R2126:Rif1 UTSW 2 52110324 unclassified probably benign
R2145:Rif1 UTSW 2 52111400 missense possibly damaging 0.63
R2152:Rif1 UTSW 2 52110324 unclassified probably benign
R2153:Rif1 UTSW 2 52110324 unclassified probably benign
R2213:Rif1 UTSW 2 52110324 unclassified probably benign
R2327:Rif1 UTSW 2 52110324 unclassified probably benign
R2512:Rif1 UTSW 2 52110324 unclassified probably benign
R2513:Rif1 UTSW 2 52110324 unclassified probably benign
R2516:Rif1 UTSW 2 52110324 unclassified probably benign
R2520:Rif1 UTSW 2 52110324 unclassified probably benign
R2905:Rif1 UTSW 2 52098504 missense probably damaging 0.99
R3005:Rif1 UTSW 2 52082764 missense probably damaging 1.00
R3155:Rif1 UTSW 2 52110324 unclassified probably benign
R3156:Rif1 UTSW 2 52110324 unclassified probably benign
R3429:Rif1 UTSW 2 52110324 unclassified probably benign
R3707:Rif1 UTSW 2 52093580 missense probably damaging 1.00
R3907:Rif1 UTSW 2 52112545 missense probably benign 0.03
R3978:Rif1 UTSW 2 52116747 critical splice donor site probably null
R4023:Rif1 UTSW 2 52121087 missense probably benign 0.01
R4052:Rif1 UTSW 2 52098471 nonsense probably null
R4668:Rif1 UTSW 2 52111952 missense probably benign 0.01
R4674:Rif1 UTSW 2 52106942 missense probably null 1.00
R4715:Rif1 UTSW 2 52073139 utr 5 prime probably benign
R4766:Rif1 UTSW 2 52098934 missense probably damaging 1.00
R4783:Rif1 UTSW 2 52112747 missense probably damaging 0.96
R4785:Rif1 UTSW 2 52112747 missense probably damaging 0.96
R4869:Rif1 UTSW 2 52093611 intron probably benign
R4911:Rif1 UTSW 2 52110518 missense probably damaging 0.98
R4951:Rif1 UTSW 2 52084986 splice site probably null
R5044:Rif1 UTSW 2 52109928 missense probably damaging 0.99
R5088:Rif1 UTSW 2 52092295 missense possibly damaging 0.91
R5151:Rif1 UTSW 2 52120309 missense probably damaging 1.00
R5187:Rif1 UTSW 2 52081289 missense probably damaging 1.00
R5222:Rif1 UTSW 2 52077020 missense probably benign 0.08
R5243:Rif1 UTSW 2 52111824 missense possibly damaging 0.86
R5436:Rif1 UTSW 2 52120971 intron probably benign
R5476:Rif1 UTSW 2 52089595 missense probably damaging 1.00
R5496:Rif1 UTSW 2 52098916 missense probably damaging 1.00
R5641:Rif1 UTSW 2 52121158 missense possibly damaging 0.80
R5883:Rif1 UTSW 2 52105639 critical splice donor site probably null
R5987:Rif1 UTSW 2 52095844 missense probably damaging 1.00
R5990:Rif1 UTSW 2 52095844 missense probably damaging 1.00
R5992:Rif1 UTSW 2 52095844 missense probably damaging 1.00
R6019:Rif1 UTSW 2 52095844 missense probably damaging 1.00
R6020:Rif1 UTSW 2 52095844 missense probably damaging 1.00
R6255:Rif1 UTSW 2 52085053 missense probably damaging 1.00
R6342:Rif1 UTSW 2 52119156 missense probably damaging 0.97
R6364:Rif1 UTSW 2 52107669 missense probably damaging 0.97
R6747:Rif1 UTSW 2 52078263 splice site probably null
R6928:Rif1 UTSW 2 52095961 missense probably damaging 1.00
R6954:Rif1 UTSW 2 52112691 missense probably benign 0.00
R7003:Rif1 UTSW 2 52076989 missense probably benign 0.06
R7310:Rif1 UTSW 2 52105619 missense probably benign 0.12
R7549:Rif1 UTSW 2 52078507 missense possibly damaging 0.52
R7603:Rif1 UTSW 2 52076175 missense probably damaging 1.00
R7673:Rif1 UTSW 2 52088654 missense probably damaging 1.00
R7741:Rif1 UTSW 2 52085141 missense probably damaging 0.96
R7777:Rif1 UTSW 2 52116356 missense probably benign 0.00
R7910:Rif1 UTSW 2 52078387 nonsense probably null
R7962:Rif1 UTSW 2 52074276 missense probably damaging 1.00
R8264:Rif1 UTSW 2 52090278 missense noncoding transcript
R8390:Rif1 UTSW 2 52110923 missense probably damaging 1.00
R8479:Rif1 UTSW 2 52112551 missense possibly damaging 0.52
R8490:Rif1 UTSW 2 52110999 missense probably damaging 0.96
R8762:Rif1 UTSW 2 52111730 missense
R8785:Rif1 UTSW 2 52110481 missense probably benign 0.06
R8890:Rif1 UTSW 2 52098863 missense probably damaging 0.99
R9081:Rif1 UTSW 2 52110977 missense probably damaging 0.99
R9284:Rif1 UTSW 2 52108552 missense probably benign 0.00
R9300:Rif1 UTSW 2 52111139 missense probably damaging 1.00
R9366:Rif1 UTSW 2 52120344 missense
R9477:Rif1 UTSW 2 52111330 missense probably benign 0.02
R9522:Rif1 UTSW 2 52081299 missense probably damaging 1.00
R9573:Rif1 UTSW 2 52110454 missense probably benign 0.29
R9630:Rif1 UTSW 2 52089595 missense probably damaging 1.00
X0064:Rif1 UTSW 2 52074315 missense probably benign 0.00
X0064:Rif1 UTSW 2 52094633 missense probably damaging 0.96
Z1177:Rif1 UTSW 2 52088648 missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- CTAAAAGTTGTGACTGCTGTGG -3'
(R):5'- ACTTAAGCCTGGGTCCTCAG -3'

Sequencing Primer
(F):5'- CTGCTGTGGCGAAAAATCAC -3'
(R):5'- CAGGGCTGTGGTTCTCACTAC -3'
Posted On 2022-02-07