Incidental Mutation 'R7583:Cdt1'
ID 586891
Institutional Source Beutler Lab
Gene Symbol Cdt1
Ensembl Gene ENSMUSG00000006585
Gene Name chromatin licensing and DNA replication factor 1
Synonyms 2610318F11Rik, Ris2
MMRRC Submission 045666-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.966) question?
Stock # R7583 (G1)
Quality Score 225.009
Status Validated
Chromosome 8
Chromosomal Location 123294754-123299869 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to A at 123296995 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Arginine to Histidine at position 263 (R263H)
Ref Sequence ENSEMBL: ENSMUSP00000006760 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000006760] [ENSMUST00000006764] [ENSMUST00000127664] [ENSMUST00000211823] [ENSMUST00000212093] [ENSMUST00000213029] [ENSMUST00000213062]
AlphaFold Q8R4E9
PDB Structure Structure of the Cdt1 C-terminal domain [SOLUTION NMR]
Structure of C-terminal region of Cdt1 [SOLUTION NMR]
Crystal structure of Cdt1/geminin complex [X-RAY DIFFRACTION]
Crystal structure of cdt1 C terminal domain [X-RAY DIFFRACTION]
Predicted Effect probably damaging
Transcript: ENSMUST00000006760
AA Change: R263H

PolyPhen 2 Score 0.986 (Sensitivity: 0.74; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000006760
Gene: ENSMUSG00000006585
AA Change: R263H

DomainStartEndE-ValueType
low complexity region 41 52 N/A INTRINSIC
low complexity region 59 70 N/A INTRINSIC
low complexity region 72 108 N/A INTRINSIC
CDT1 199 362 3.68e-91 SMART
low complexity region 401 427 N/A INTRINSIC
Pfam:CDT1_C 431 525 1.4e-30 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000006764
SMART Domains Protein: ENSMUSP00000006764
Gene: ENSMUSG00000006589

DomainStartEndE-ValueType
Pfam:Pribosyltran 28 178 2.3e-25 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000127664
SMART Domains Protein: ENSMUSP00000118564
Gene: ENSMUSG00000092329

DomainStartEndE-ValueType
Pfam:Glycos_transf_2 104 287 7.4e-31 PFAM
Pfam:Glyco_transf_7C 261 331 4.9e-8 PFAM
RICIN 406 531 9.28e-27 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000211823
Predicted Effect probably benign
Transcript: ENSMUST00000212093
Predicted Effect probably benign
Transcript: ENSMUST00000213029
Predicted Effect probably benign
Transcript: ENSMUST00000213062
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.7%
  • 20x: 98.9%
Validation Efficiency 99% (95/96)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is involved in the formation of the pre-replication complex that is necessary for DNA replication. The encoded protein can bind geminin, which prevents replication and may function to prevent this protein from initiating replication at inappropriate origins. Phosphorylation of this protein by cyclin A-dependent kinases results in degradation of the protein. [provided by RefSeq, Mar 2011]
PHENOTYPE: Mice homozygous for a small in-frame deletion in exon 2 are viable and fertile. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 98 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4932414N04Rik A T 2: 68,569,670 (GRCm39) D462V probably damaging Het
Abcc1 T C 16: 14,221,902 (GRCm39) W222R probably damaging Het
Adamts13 A G 2: 26,863,965 (GRCm39) K48E probably benign Het
Adgrd1 A C 5: 129,256,652 (GRCm39) T674P probably benign Het
Agbl4 A T 4: 110,976,150 (GRCm39) Y169F possibly damaging Het
Ahnak T A 19: 8,983,457 (GRCm39) N1580K possibly damaging Het
Angptl8 A C 9: 21,747,210 (GRCm39) probably null Het
Ap3d1 G A 10: 80,545,292 (GRCm39) T1053I probably benign Het
Atad2 T C 15: 57,990,060 (GRCm39) T139A probably benign Het
Bdp1 T A 13: 100,186,320 (GRCm39) T1711S probably damaging Het
Bod1l T C 5: 41,991,133 (GRCm39) I141V probably damaging Het
Cavin2 A T 1: 51,328,777 (GRCm39) N78I possibly damaging Het
Ccnb1 T C 13: 100,916,262 (GRCm39) H406R probably benign Het
Cd200r4 A G 16: 44,653,784 (GRCm39) T194A probably damaging Het
Cep85l A T 10: 53,157,450 (GRCm39) I751N probably damaging Het
Clasp2 A G 9: 113,737,755 (GRCm39) D1043G probably benign Het
Cmip A T 8: 118,181,691 (GRCm39) N578I probably damaging Het
Col2a1 T G 15: 97,874,065 (GRCm39) K1440N unknown Het
Cpne2 A T 8: 95,282,209 (GRCm39) M252L probably benign Het
Crb2 A G 2: 37,680,607 (GRCm39) T512A probably benign Het
Csmd1 A G 8: 16,048,833 (GRCm39) Y2290H probably damaging Het
Ctnnd1 A T 2: 84,442,405 (GRCm39) D642E probably damaging Het
Ctns A G 11: 73,079,296 (GRCm39) S141P probably benign Het
Cwh43 A G 5: 73,591,632 (GRCm39) Q575R probably benign Het
Cyp2b19 C A 7: 26,458,489 (GRCm39) T68K probably damaging Het
Dcaf6 A G 1: 165,160,879 (GRCm39) S849P probably damaging Het
Dnm3 T A 1: 162,305,343 (GRCm39) Q17L possibly damaging Het
Enpp3 A T 10: 24,711,990 (GRCm39) M1K probably null Het
Fam124a T A 14: 62,844,008 (GRCm39) C505* probably null Het
Fhip2a T A 19: 57,367,034 (GRCm39) D192E probably benign Het
Fsip2 A G 2: 82,805,585 (GRCm39) I635V probably benign Het
Gm5878 A T 6: 85,095,682 (GRCm39) probably null Het
Gpld1 C A 13: 25,159,743 (GRCm39) A437D probably damaging Het
Grk5 G T 19: 61,071,642 (GRCm39) V401L possibly damaging Het
Gucy2g A T 19: 55,224,047 (GRCm39) L259Q probably damaging Het
Habp2 T A 19: 56,300,236 (GRCm39) D191E probably benign Het
Helz2 T A 2: 180,879,365 (GRCm39) H751L probably benign Het
Hgsnat A G 8: 26,461,592 (GRCm39) probably null Het
Hivep1 T A 13: 42,317,716 (GRCm39) V2064E probably damaging Het
Ikbke C T 1: 131,204,216 (GRCm39) A26T probably damaging Het
Ivd C A 2: 118,692,612 (GRCm39) D37E probably damaging Het
Kif26b G A 1: 178,358,010 (GRCm39) W40* probably null Het
Klrc2 A G 6: 129,636,274 (GRCm39) S114P probably damaging Het
Lama1 A T 17: 68,068,616 (GRCm39) T772S Het
Lamc1 T A 1: 153,118,978 (GRCm39) K880N possibly damaging Het
Lmf1 G A 17: 25,874,423 (GRCm39) D12N Het
Lpin2 G T 17: 71,538,391 (GRCm39) E384* probably null Het
Lrrc23 T C 6: 124,756,541 (GRCm39) probably benign Het
Lrrc31 T C 3: 30,745,248 (GRCm39) probably null Het
Luc7l2 A G 6: 38,528,820 (GRCm39) Q13R probably damaging Het
Ly6c1 G T 15: 74,920,346 (GRCm39) H5Q probably damaging Het
Lyst A T 13: 13,810,472 (GRCm39) H714L probably damaging Het
Man2a2 C T 7: 80,016,692 (GRCm39) R374H probably damaging Het
Mchr1 A T 15: 81,121,642 (GRCm39) T131S probably benign Het
Msto1 T C 3: 88,820,236 (GRCm39) probably null Het
Myh1 C T 11: 67,111,739 (GRCm39) T1698I probably benign Het
Ncapd3 G T 9: 26,983,144 (GRCm39) C964F probably damaging Het
Nefh T C 11: 4,891,089 (GRCm39) E510G probably damaging Het
Or10g3b T C 14: 52,587,360 (GRCm39) T48A possibly damaging Het
Or13a24 A G 7: 140,154,123 (GRCm39) E19G probably benign Het
Or1b1 A T 2: 36,995,539 (GRCm39) L41* probably null Het
Or1q1 A C 2: 36,887,092 (GRCm39) K90T probably damaging Het
Or4a73 A T 2: 89,421,095 (GRCm39) Y121* probably null Het
P4ha1 T A 10: 59,205,462 (GRCm39) S497R probably benign Het
Palb2 T C 7: 121,726,565 (GRCm39) D435G probably benign Het
Papola C T 12: 105,777,304 (GRCm39) P282L probably damaging Het
Pcdhgb1 A G 18: 37,815,377 (GRCm39) R623G probably damaging Het
Pcolce T G 5: 137,605,707 (GRCm39) K229Q probably benign Het
Pkhd1l1 T C 15: 44,431,760 (GRCm39) probably null Het
Ppp6r3 T A 19: 3,540,790 (GRCm39) T443S probably benign Het
Pramel58 A T 5: 94,830,753 (GRCm39) T84S possibly damaging Het
Psg20 T A 7: 18,416,408 (GRCm39) D236V probably damaging Het
Ptgr2 T G 12: 84,355,179 (GRCm39) S304R probably damaging Het
Ptpn22 A T 3: 103,809,430 (GRCm39) D681V probably benign Het
Rab3gap1 T C 1: 127,858,612 (GRCm39) S574P probably benign Het
Slc36a1 A G 11: 55,104,754 (GRCm39) probably null Het
Slc9a5 A G 8: 106,089,904 (GRCm39) S621G possibly damaging Het
Sntg1 A G 1: 8,515,249 (GRCm39) probably null Het
Snx17 A G 5: 31,353,877 (GRCm39) N222D possibly damaging Het
Spata19 G T 9: 27,311,729 (GRCm39) S116I possibly damaging Het
Spn G A 7: 126,736,234 (GRCm39) A91V probably damaging Het
Srrm3 T C 5: 135,881,135 (GRCm39) V145A probably benign Het
St7 A T 6: 17,942,753 (GRCm39) T575S possibly damaging Het
Taf2 A T 15: 54,928,072 (GRCm39) Y110* probably null Het
Tcf20 T C 15: 82,739,477 (GRCm39) E658G possibly damaging Het
Tdrd6 G T 17: 43,935,129 (GRCm39) A1973E probably benign Het
Tg T G 15: 66,636,267 (GRCm39) L2237W probably damaging Het
Ticrr C A 7: 79,346,487 (GRCm39) Y1882* probably null Het
Trim45 T A 3: 100,832,339 (GRCm39) C191S probably damaging Het
Upf3a G A 8: 13,835,889 (GRCm39) probably null Het
Vmn2r42 A T 7: 8,197,740 (GRCm39) L293* probably null Het
Vmn2r62 T A 7: 42,437,466 (GRCm39) Q339H possibly damaging Het
Wdr24 A T 17: 26,044,804 (GRCm39) R220W probably null Het
Wdr5 T A 2: 27,408,787 (GRCm39) S22T probably benign Het
Zfp37 G A 4: 62,110,253 (GRCm39) probably benign Het
Zfp735 A T 11: 73,601,933 (GRCm39) L292F possibly damaging Het
Zfp985 T A 4: 147,667,946 (GRCm39) C271* probably null Het
Zranb1 G A 7: 132,585,625 (GRCm39) R691Q probably benign Het
Other mutations in Cdt1
AlleleSourceChrCoordTypePredicted EffectPPH Score
BB001:Cdt1 UTSW 8 123,296,091 (GRCm39) missense probably damaging 1.00
BB011:Cdt1 UTSW 8 123,296,091 (GRCm39) missense probably damaging 1.00
R0014:Cdt1 UTSW 8 123,299,305 (GRCm39) missense probably benign 0.00
R0494:Cdt1 UTSW 8 123,298,799 (GRCm39) missense possibly damaging 0.64
R0614:Cdt1 UTSW 8 123,294,876 (GRCm39) missense probably benign 0.04
R0645:Cdt1 UTSW 8 123,298,884 (GRCm39) unclassified probably benign
R1699:Cdt1 UTSW 8 123,296,722 (GRCm39) missense probably damaging 0.99
R1889:Cdt1 UTSW 8 123,298,791 (GRCm39) missense possibly damaging 0.85
R3114:Cdt1 UTSW 8 123,297,221 (GRCm39) nonsense probably null
R4243:Cdt1 UTSW 8 123,298,157 (GRCm39) missense probably benign 0.04
R4532:Cdt1 UTSW 8 123,298,495 (GRCm39) missense probably benign 0.00
R5496:Cdt1 UTSW 8 123,297,239 (GRCm39) missense probably damaging 0.99
R5498:Cdt1 UTSW 8 123,297,239 (GRCm39) missense probably damaging 0.99
R5501:Cdt1 UTSW 8 123,297,239 (GRCm39) missense probably damaging 0.99
R5523:Cdt1 UTSW 8 123,294,832 (GRCm39) missense possibly damaging 0.95
R5647:Cdt1 UTSW 8 123,296,947 (GRCm39) missense possibly damaging 0.79
R6160:Cdt1 UTSW 8 123,298,107 (GRCm39) missense probably benign 0.36
R6892:Cdt1 UTSW 8 123,296,951 (GRCm39) missense probably damaging 1.00
R7001:Cdt1 UTSW 8 123,299,249 (GRCm39) missense probably damaging 1.00
R7089:Cdt1 UTSW 8 123,298,719 (GRCm39) missense probably damaging 1.00
R7214:Cdt1 UTSW 8 123,295,012 (GRCm39) critical splice donor site probably null
R7924:Cdt1 UTSW 8 123,296,091 (GRCm39) missense probably damaging 1.00
R7976:Cdt1 UTSW 8 123,298,585 (GRCm39) missense probably damaging 1.00
R8116:Cdt1 UTSW 8 123,298,728 (GRCm39) missense probably benign 0.05
R8236:Cdt1 UTSW 8 123,298,767 (GRCm39) missense probably damaging 1.00
R8436:Cdt1 UTSW 8 123,296,070 (GRCm39) missense probably benign 0.03
Predicted Primers PCR Primer
(F):5'- TCTGAGACTGTGACCTTTGCC -3'
(R):5'- AGCCTCTGTAAGCCAAAGAC -3'

Sequencing Primer
(F):5'- GAGACTGTGACCTTTGCCAAAGTC -3'
(R):5'- TCTGTAAGCCAAAGACCACCTGTG -3'
Posted On 2019-10-24