Incidental Mutation 'R5498:Cdt1'
ID 432477
Institutional Source Beutler Lab
Gene Symbol Cdt1
Ensembl Gene ENSMUSG00000006585
Gene Name chromatin licensing and DNA replication factor 1
Synonyms 2610318F11Rik, Ris2
MMRRC Submission 043059-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.966) question?
Stock # R5498 (G1)
Quality Score 122
Status Not validated
Chromosome 8
Chromosomal Location 123294754-123299869 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to T at 123297239 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Arginine to Tryptophan at position 311 (R311W)
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: R311W

PolyPhen 2 Score 0.987 (Sensitivity: 0.73; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000006760
Gene: ENSMUSG00000006585
AA Change: R311W

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 noncoding transcript
Transcript: ENSMUST00000212053
Predicted Effect probably benign
Transcript: ENSMUST00000212093
Predicted Effect probably benign
Transcript: ENSMUST00000213029
Predicted Effect noncoding transcript
Transcript: ENSMUST00000213017
Predicted Effect noncoding transcript
Transcript: ENSMUST00000212967
Predicted Effect probably benign
Transcript: ENSMUST00000213062
Predicted Effect noncoding transcript
Transcript: ENSMUST00000212201
Predicted Effect noncoding transcript
Transcript: ENSMUST00000212834
Predicted Effect noncoding transcript
Transcript: ENSMUST00000213030
Predicted Effect noncoding transcript
Transcript: ENSMUST00000212821
Coding Region Coverage
  • 1x: 98.2%
  • 3x: 97.2%
  • 10x: 94.8%
  • 20x: 89.2%
Validation Efficiency
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: 41 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4930522L14Rik T A 5: 109,885,413 (GRCm39) K148N probably benign Het
Abca6 T A 11: 110,099,670 (GRCm39) D959V possibly damaging Het
Acot12 T C 13: 91,929,352 (GRCm39) V393A probably damaging Het
Ano3 C A 2: 110,527,448 (GRCm39) V587F possibly damaging Het
Bub1 T C 2: 127,656,629 (GRCm39) D471G possibly damaging Het
Cdh15 G T 8: 123,591,917 (GRCm39) V601F possibly damaging Het
Cnot1 A T 8: 96,483,983 (GRCm39) I706N possibly damaging Het
Fbn1 A G 2: 125,202,096 (GRCm39) I1259T probably damaging Het
Furin A T 7: 80,041,542 (GRCm39) W539R probably damaging Het
Hivep1 A T 13: 42,276,634 (GRCm39) probably null Het
Igkv3-9 A G 6: 70,565,727 (GRCm39) M109V probably benign Het
Klf10 G A 15: 38,296,283 (GRCm39) R421W probably damaging Het
Mtor A T 4: 148,624,821 (GRCm39) Y2144F possibly damaging Het
Mybpc2 T C 7: 44,165,689 (GRCm39) Y297C probably damaging Het
Myom2 G A 8: 15,179,142 (GRCm39) E1325K probably benign Het
Nsd1 A T 13: 55,361,115 (GRCm39) K28* probably null Het
Or2r11 C T 6: 42,437,228 (GRCm39) A242T probably benign Het
Or51b4 T G 7: 103,530,839 (GRCm39) T204P probably damaging Het
Phc2 C A 4: 128,602,787 (GRCm39) N120K probably benign Het
Pias3 A G 3: 96,609,504 (GRCm39) T274A possibly damaging Het
Plcb4 T A 2: 135,818,092 (GRCm39) I786N probably damaging Het
Plec G A 15: 76,061,654 (GRCm39) S2626L probably damaging Het
Polg A G 7: 79,104,418 (GRCm39) L819P probably damaging Het
Ppp2r3d T C 9: 124,439,123 (GRCm38) probably benign Het
Resf1 A G 6: 149,229,738 (GRCm39) D928G probably damaging Het
Rnd2 C T 11: 101,359,825 (GRCm39) L57F probably damaging Het
Rnpc3 A G 3: 113,404,856 (GRCm39) probably null Het
Sarnp T A 10: 128,689,063 (GRCm39) D65E probably benign Het
Sh3bp5 C A 14: 31,099,452 (GRCm39) R265L probably benign Het
Slc16a10 C T 10: 39,913,323 (GRCm39) V462M probably damaging Het
Slc45a2 C T 15: 11,027,871 (GRCm39) T480I probably damaging Het
Slfn5 A T 11: 82,847,973 (GRCm39) H286L possibly damaging Het
Spag17 G A 3: 100,010,661 (GRCm39) A2052T possibly damaging Het
Sptbn5 A T 2: 119,907,119 (GRCm39) probably benign Het
Tlr3 C T 8: 45,851,851 (GRCm39) D349N possibly damaging Het
Trim45 T C 3: 100,832,457 (GRCm39) V230A possibly damaging Het
Ube3b T C 5: 114,556,635 (GRCm39) F989L probably damaging Het
Vps51 T G 19: 6,121,063 (GRCm39) E283D probably benign Het
Wdr24 A G 17: 26,043,535 (GRCm39) H119R probably damaging Het
Yars2 T A 16: 16,124,387 (GRCm39) H331Q possibly damaging Het
Zscan21 T C 5: 138,131,522 (GRCm39) S349P 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
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'- GCAATGTCCCCACCTTCAAG -3'
(R):5'- GGACTCAGAGGAACCTTTCTTC -3'

Sequencing Primer
(F):5'- TCAAGAGATCTGATTACCAGCTC -3'
(R):5'- GAGGAACCTTTCTTCACATTTGAGGC -3'
Posted On 2016-10-05