Incidental Mutation 'R4532:Cdt1'
ID 333153
Institutional Source Beutler Lab
Gene Symbol Cdt1
Ensembl Gene ENSMUSG00000006585
Gene Name chromatin licensing and DNA replication factor 1
Synonyms 2610318F11Rik, Ris2
MMRRC Submission 041772-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.966) question?
Stock # R4532 (G1)
Quality Score 225
Status Validated
Chromosome 8
Chromosomal Location 123294754-123299869 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 123298495 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Proline at position 407 (S407P)
Ref Sequence ENSEMBL: ENSMUSP00000006760 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000006760] [ENSMUST00000006764] [ENSMUST00000127664] [ENSMUST00000211823] [ENSMUST00000213029] [ENSMUST00000212093] [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 benign
Transcript: ENSMUST00000006760
AA Change: S407P

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000006760
Gene: ENSMUSG00000006585
AA Change: S407P

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: ENSMUST00000212834
Predicted Effect noncoding transcript
Transcript: ENSMUST00000213017
Predicted Effect probably benign
Transcript: ENSMUST00000213029
Predicted Effect noncoding transcript
Transcript: ENSMUST00000212201
Predicted Effect probably benign
Transcript: ENSMUST00000212093
Predicted Effect noncoding transcript
Transcript: ENSMUST00000212821
Predicted Effect noncoding transcript
Transcript: ENSMUST00000212967
Predicted Effect noncoding transcript
Transcript: ENSMUST00000213030
Predicted Effect probably benign
Transcript: ENSMUST00000213062
Meta Mutation Damage Score 0.0898 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.5%
  • 10x: 97.0%
  • 20x: 94.3%
Validation Efficiency 100% (54/54)
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: 44 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Akap9 T A 5: 4,093,948 (GRCm39) F2157I probably damaging Het
Aoc1l1 A G 6: 48,955,101 (GRCm39) E647G possibly damaging Het
Ap3b1 A G 13: 94,702,243 (GRCm39) K1099E unknown Het
Arhgap42 T C 9: 9,011,433 (GRCm39) D451G probably damaging Het
Cd19 C T 7: 126,011,281 (GRCm39) C301Y probably damaging Het
Cdh23 T C 10: 60,370,202 (GRCm39) T198A probably benign Het
Cyp26c1 A G 19: 37,674,227 (GRCm39) T34A probably damaging Het
Dbh C A 2: 27,067,343 (GRCm39) H409Q possibly damaging Het
Eif5 T A 12: 111,506,318 (GRCm39) C52* probably null Het
Fhod3 A G 18: 25,243,278 (GRCm39) Y1212C probably damaging Het
Ggh T A 4: 20,046,225 (GRCm39) F44L probably benign Het
Gm12185 T C 11: 48,798,747 (GRCm39) Y582C probably damaging Het
Gm12185 T C 11: 48,798,921 (GRCm39) N524S possibly damaging Het
Gm21095 A G Y: 84,131,953 (GRCm39) N149S probably damaging Het
Gys2 T A 6: 142,400,867 (GRCm39) H311L probably damaging Het
Hcn4 C T 9: 58,765,081 (GRCm39) R558C unknown Het
Heatr6 T C 11: 83,660,498 (GRCm39) L546P probably damaging Het
Lin54 G A 5: 100,594,419 (GRCm39) T582I possibly damaging Het
Lpin1 C T 12: 16,603,963 (GRCm39) G623S probably benign Het
Lrfn2 A G 17: 49,377,564 (GRCm39) D215G probably damaging Het
Lrrc3c C A 11: 98,489,859 (GRCm39) S72* probably null Het
Me3 G A 7: 89,282,108 (GRCm39) probably benign Het
Msln A G 17: 25,969,698 (GRCm39) I344T probably damaging Het
Oma1 G A 4: 103,176,571 (GRCm39) V112I probably benign Het
Or5al6 A T 2: 85,976,274 (GRCm39) L268Q possibly damaging Het
Or5p4 T C 7: 107,680,756 (GRCm39) Y252H probably benign Het
Orc4 G A 2: 48,827,501 (GRCm39) P31S probably benign Het
Pabir3 G A X: 52,382,376 (GRCm39) R94H possibly damaging Het
Pdgfra A G 5: 75,341,744 (GRCm39) N659S probably damaging Het
Rmnd5a A T 6: 71,376,109 (GRCm39) probably null Het
Slc12a8 C A 16: 33,371,403 (GRCm39) R180S probably damaging Het
Slc6a15 G A 10: 103,245,648 (GRCm39) V544M possibly damaging Het
Slco5a1 T A 1: 12,949,447 (GRCm39) T648S probably damaging Het
Snx13 T C 12: 35,194,219 (GRCm39) F921L probably damaging Het
Stard6 A C 18: 70,616,605 (GRCm39) D88A probably damaging Het
Svep1 G T 4: 58,068,886 (GRCm39) H2967N possibly damaging Het
Tcaf2 A C 6: 42,603,371 (GRCm39) Y730D probably damaging Het
Tes G A 6: 17,097,407 (GRCm39) V172M possibly damaging Het
Ttc3 T A 16: 94,267,736 (GRCm39) probably benign Het
Vmn1r23 A G 6: 57,902,914 (GRCm39) I288T probably benign Het
Vmn1r38 G T 6: 66,754,016 (GRCm39) H33Q probably benign Het
Vmn2r75 G T 7: 85,797,349 (GRCm39) C821* probably null Het
Zfp282 C T 6: 47,867,567 (GRCm39) P248S probably benign Het
Zfp655 T A 5: 145,181,507 (GRCm39) I455N 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
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
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'- AGGTTACCAGATACTTCCTCAGC -3'
(R):5'- GTCAGCAGCCAATGGTCAAC -3'

Sequencing Primer
(F):5'- AAGGTGTGCTTTGTACGCACAC -3'
(R):5'- TGGTCAACAAGGAAAGCCC -3'
Posted On 2015-08-18