Incidental Mutation 'R4052:Rif1'
ID 314184
Institutional Source Beutler Lab
Gene Symbol Rif1
Ensembl Gene ENSMUSG00000036202
Gene Name replication timing regulatory factor 1
Synonyms 6530403D07Rik, 5730435J01Rik, D2Ertd145e
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R4052 ()
Quality Score 225
Status Not validated
Chromosome 2
Chromosomal Location 52072832-52122383 bp(+) (GRCm38)
Type of Mutation nonsense
DNA Base Change (assembly) A to T at 52098471 bp (GRCm38)
Zygosity Heterozygous
Amino Acid Change Lysine to Stop codon at position 741 (K741*)
Ref Sequence ENSEMBL: ENSMUSP00000108313 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000069794] [ENSMUST00000112693]
AlphaFold no structure available at present
Predicted Effect probably null
Transcript: ENSMUST00000069794
AA Change: K741*
SMART Domains Protein: ENSMUSP00000064155
Gene: ENSMUSG00000036202
AA Change: K741*

DomainStartEndE-ValueType
Pfam:Rif1_N 22 368 3.3e-78 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 null
Transcript: ENSMUST00000112693
AA Change: K741*
SMART Domains Protein: ENSMUSP00000108313
Gene: ENSMUSG00000036202
AA Change: K741*

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 noncoding transcript
Transcript: ENSMUST00000125116
Predicted Effect noncoding transcript
Transcript: ENSMUST00000145130
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.4%
  • 10x: 96.8%
  • 20x: 93.5%
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a 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: 46 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
3110070M22Rik T G 13: 119,488,202 (GRCm38) probably benign Het
Abca8b G A 11: 109,981,725 (GRCm38) Q17* probably null Het
Abcc6 A C 7: 45,986,563 (GRCm38) L1020R probably damaging Het
Ace2 A G X: 164,169,585 (GRCm38) I110V probably benign Het
Adam29 T C 8: 55,872,282 (GRCm38) Y379C probably damaging Het
Apol10a A T 15: 77,488,985 (GRCm38) I274L probably benign Het
BC005537 T A 13: 24,809,898 (GRCm38) F119I possibly damaging Het
Crygs C T 16: 22,805,551 (GRCm38) G102D possibly damaging Het
Cts3 T A 13: 61,568,721 (GRCm38) I34L probably benign Het
Cyp4a30b A G 4: 115,454,342 (GRCm38) D69G probably benign Het
Dclk2 A G 3: 86,830,822 (GRCm38) probably null Het
Dhx30 A G 9: 110,100,821 (GRCm38) V69A possibly damaging Het
Dis3 T G 14: 99,095,316 (GRCm38) I227L probably benign Het
Dock3 A G 9: 106,973,796 (GRCm38) S836P probably damaging Het
Efhc2 T C X: 17,230,550 (GRCm38) N186S possibly damaging Het
Erap1 A G 13: 74,675,340 (GRCm38) N831S probably benign Het
Gimap3 T A 6: 48,766,513 (GRCm38) T3S possibly damaging Het
Gpr82 C T X: 13,665,659 (GRCm38) P149S probably damaging Het
H3f3a C T 1: 180,803,138 (GRCm38) R117H probably benign Het
Hcn2 A C 10: 79,733,687 (GRCm38) probably null Het
Helz2 A G 2: 181,240,475 (GRCm38) L175P probably damaging Het
Il1f8 T C 2: 24,159,832 (GRCm38) F152L probably damaging Het
Ino80b G C 6: 83,122,333 (GRCm38) P178R probably damaging Het
Ldlrad3 C T 2: 101,953,162 (GRCm38) D240N probably damaging Het
Lef1 A G 3: 131,194,689 (GRCm38) N236D probably damaging Het
Macf1 A G 4: 123,472,017 (GRCm38) S1419P probably benign Het
Me2 T C 18: 73,791,085 (GRCm38) K352R probably benign Het
Ncapd3 T A 9: 27,089,383 (GRCm38) probably null Het
Or52n3 A G 7: 104,881,603 (GRCm38) T299A probably damaging Het
P2rx7 T C 5: 122,666,277 (GRCm38) F293S probably damaging Het
Pabpc1l T C 2: 164,043,613 (GRCm38) W429R probably benign Het
Parp14 T C 16: 35,858,401 (GRCm38) E399G probably benign Het
Pde6h A G 6: 136,959,268 (GRCm38) D3G unknown Het
Pfkfb1 A T X: 150,622,188 (GRCm38) D208V possibly damaging Het
Rasgrp3 T C 17: 75,496,968 (GRCm38) F89L probably damaging Het
Rnase4 A G 14: 51,105,005 (GRCm38) K62R probably benign Het
Rnf207 C A 4: 152,311,437 (GRCm38) Q533H probably benign Het
Slc24a2 A G 4: 87,227,205 (GRCm38) V204A probably damaging Het
Spry2 A T 14: 105,893,201 (GRCm38) C184S probably damaging Het
Sulf2 T C 2: 166,094,590 (GRCm38) Y152C probably damaging Het
Thrap3 G A 4: 126,176,219 (GRCm38) A625V probably damaging Het
Tmem39a T A 16: 38,586,288 (GRCm38) V329D probably damaging Het
Trav7-3 A G 14: 53,443,746 (GRCm38) T82A probably benign Het
Trim30b T A 7: 104,357,478 (GRCm38) Q57L possibly damaging Het
Uggt1 A G 1: 36,164,489 (GRCm38) V1020A probably damaging Het
Zfp941 T G 7: 140,812,427 (GRCm38) K340Q possibly damaging 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
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
R7003:Rif1 UTSW 2 52,076,989 (GRCm38) missense probably benign 0.06
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'- GGTCCCTCTGACAAGTGAAGTG -3'
(R):5'- GCTCTATGTAGCACAAGGAAGG -3'

Sequencing Primer
(F):5'- CCTCTGACAAGTGAAGTGTGTCAC -3'
(R):5'- CAGAAGTGTCAATAAACCGTC -3'
Posted On 2015-04-30