Incidental Mutation 'R6160:Cdt1'
ID 489810
Institutional Source Beutler Lab
Gene Symbol Cdt1
Ensembl Gene ENSMUSG00000006585
Gene Name chromatin licensing and DNA replication factor 1
Synonyms 2610318F11Rik, Ris2
MMRRC Submission 044307-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.966) question?
Stock # R6160 (G1)
Quality Score 225.009
Status Validated
Chromosome 8
Chromosomal Location 123294754-123299869 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to T at 123298107 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Isoleucine at position 366 (T366I)
Ref Sequence ENSEMBL: ENSMUSP00000006760 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000006760] [ENSMUST00000006764] [ENSMUST00000127664] [ENSMUST00000211823] [ENSMUST00000213062] [ENSMUST00000212093] [ENSMUST00000213029]
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 benign
Transcript: ENSMUST00000006760
AA Change: T366I

PolyPhen 2 Score 0.357 (Sensitivity: 0.90; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000006760
Gene: ENSMUSG00000006585
AA Change: T366I

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 noncoding transcript
Transcript: ENSMUST00000211810
Predicted Effect probably benign
Transcript: ENSMUST00000211823
Predicted Effect noncoding transcript
Transcript: ENSMUST00000212053
Predicted Effect noncoding transcript
Transcript: ENSMUST00000212967
Predicted Effect noncoding transcript
Transcript: ENSMUST00000213030
Predicted Effect probably benign
Transcript: ENSMUST00000213062
Predicted Effect noncoding transcript
Transcript: ENSMUST00000212201
Predicted Effect probably benign
Transcript: ENSMUST00000212093
Predicted Effect noncoding transcript
Transcript: ENSMUST00000212834
Predicted Effect noncoding transcript
Transcript: ENSMUST00000213017
Predicted Effect probably benign
Transcript: ENSMUST00000213029
Predicted Effect noncoding transcript
Transcript: ENSMUST00000212821
Meta Mutation Damage Score 0.0898 question?
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.6%
  • 10x: 98.2%
  • 20x: 94.8%
Validation Efficiency 94% (62/66)
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: 66 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4930433I11Rik T A 7: 40,642,950 (GRCm39) S297R possibly damaging Het
5530400C23Rik A G 6: 133,271,289 (GRCm39) E111G possibly damaging Het
8030423J24Rik T A 13: 71,032,029 (GRCm39) S34T unknown Het
Ace3 T A 11: 105,885,558 (GRCm39) W20R possibly damaging Het
Adgrf1 A G 17: 43,621,578 (GRCm39) E605G probably damaging Het
Arhgap44 G A 11: 65,053,375 (GRCm39) probably benign Het
Atm A C 9: 53,402,259 (GRCm39) H1404Q probably benign Het
AW209491 A G 13: 14,811,306 (GRCm39) E53G probably damaging Het
Bhmt1b G A 18: 87,775,245 (GRCm39) C256Y probably damaging Het
Cerk A T 15: 86,026,974 (GRCm39) C179S probably benign Het
Cldn10 T C 14: 119,099,255 (GRCm39) V123A possibly damaging Het
Clip1 T C 5: 123,751,604 (GRCm39) K726E possibly damaging Het
Dcaf12 A T 4: 41,294,043 (GRCm39) Y365N probably damaging Het
Dennd6b A G 15: 89,073,024 (GRCm39) L171P probably damaging Het
Dip2c G A 13: 9,583,290 (GRCm39) V91I probably benign Het
Dlec1 A G 9: 118,972,387 (GRCm39) I1431V probably benign Het
Egln1 T C 8: 125,675,231 (GRCm39) D188G probably damaging Het
Enpp5 T A 17: 44,392,259 (GRCm39) N229K possibly damaging Het
Fmo1 T G 1: 162,663,867 (GRCm39) I221L probably benign Het
Fsip2 G A 2: 82,818,289 (GRCm39) W4674* probably null Het
Gm12185 G A 11: 48,799,255 (GRCm39) Q413* probably null Het
Gm7298 A T 6: 121,741,886 (GRCm39) H436L probably benign Het
Gucy2c G A 6: 136,717,684 (GRCm39) Q430* probably null Het
Hgd A G 16: 37,433,660 (GRCm39) H134R probably damaging Het
Hoxd8 A G 2: 74,536,343 (GRCm39) E151G probably damaging Het
Il15ra A G 2: 11,724,827 (GRCm39) D99G probably damaging Het
Ints4 T A 7: 97,158,790 (GRCm39) probably null Het
Itgb1 T A 8: 129,446,764 (GRCm39) F426L possibly damaging Het
Itpr1 A C 6: 108,495,716 (GRCm39) I2534L probably benign Het
Kcnq4 T A 4: 120,573,756 (GRCm39) H235L probably damaging Het
Kcnt1 T A 2: 25,782,395 (GRCm39) I178N probably damaging Het
Kidins220 A G 12: 25,047,310 (GRCm39) D252G probably damaging Het
Krt23 A G 11: 99,376,544 (GRCm39) I204T probably damaging Het
Lipo4 A G 19: 33,480,693 (GRCm39) L225P probably damaging Het
Lrp3 T C 7: 34,903,548 (GRCm39) D245G possibly damaging Het
Mmp16 A G 4: 18,051,857 (GRCm39) D282G probably damaging Het
Myo1c A T 11: 75,541,568 (GRCm39) H18L probably benign Het
Myo1f C A 17: 33,823,318 (GRCm39) P981Q probably benign Het
Nle1 A T 11: 82,798,983 (GRCm39) F33I probably benign Het
Nlrp4e T G 7: 23,020,731 (GRCm39) M406R probably damaging Het
Obscn A T 11: 58,942,611 (GRCm39) V4857E probably damaging Het
Palb2 A T 7: 121,727,643 (GRCm39) probably null Het
Phospho1 A T 11: 95,721,450 (GRCm39) E22V probably damaging Het
Pom121l2 C T 13: 22,167,838 (GRCm39) S703L possibly damaging Het
Prex2 T C 1: 11,064,075 (GRCm39) L20P probably damaging Het
Psmb7 T C 2: 38,533,393 (GRCm39) T45A probably damaging Het
R3hdm2 T C 10: 127,320,376 (GRCm39) I532T probably damaging Het
Rcn1 T C 2: 105,222,362 (GRCm39) D208G probably damaging Het
Recql5 A G 11: 115,823,613 (GRCm39) probably null Het
Resf1 G A 6: 149,233,005 (GRCm39) probably null Het
Rfc4 A T 16: 22,933,433 (GRCm39) I242N probably damaging Het
Rims1 T C 1: 22,503,235 (GRCm39) Y650C probably damaging Het
Shc2 C T 10: 79,462,853 (GRCm39) probably null Het
Slc14a2 A T 18: 78,202,190 (GRCm39) probably null Het
Slc6a6 A T 6: 91,716,995 (GRCm39) probably null Het
Synj2 C A 17: 6,058,336 (GRCm39) H275N possibly damaging Het
T A T 17: 8,660,618 (GRCm39) T410S probably benign Het
Tars3 A G 7: 65,332,527 (GRCm39) I543V probably benign Het
Tbc1d8 T A 1: 39,411,484 (GRCm39) K1117N probably damaging Het
Tm7sf3 A T 6: 146,507,787 (GRCm39) L425* probably null Het
Trav14-3 A G 14: 54,000,978 (GRCm39) Y63C probably damaging Het
Tyro3 A C 2: 119,633,751 (GRCm39) D133A probably damaging Het
Vmn1r119 T G 7: 20,745,740 (GRCm39) H214P possibly damaging Het
Vmn2r120 G A 17: 57,816,418 (GRCm39) P646S probably benign Het
Zbtb7c A T 18: 76,278,904 (GRCm39) Y454F probably benign Het
Zmym2 T C 14: 57,187,766 (GRCm39) L1144P probably damaging 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
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
R7583:Cdt1 UTSW 8 123,296,995 (GRCm39) missense probably damaging 0.99
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'- GCACAGAACAGCTAAGTTGG -3'
(R):5'- TGCGTACAAAGCACACCTTC -3'

Sequencing Primer
(F):5'- GTGTTCTGGTTGGAAATACTGAAATG -3'
(R):5'- GTACAAAGCACACCTTCTTTGTG -3'
Posted On 2017-10-10