Incidental Mutation 'R5501:Cdt1'
ID 430617
Institutional Source Beutler Lab
Gene Symbol Cdt1
Ensembl Gene ENSMUSG00000006585
Gene Name chromatin licensing and DNA replication factor 1
Synonyms 2610318F11Rik, Ris2
MMRRC Submission 043062-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.966) question?
Stock # R5501 (G1)
Quality Score 197
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: 97.3%
  • 10x: 95.1%
  • 20x: 90.3%
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
Adam26a A C 8: 44,022,941 (GRCm39) L183* probably null Het
Alox12e G T 11: 70,207,055 (GRCm39) Q584K probably benign Het
Atp1a4 A G 1: 172,074,399 (GRCm39) S285P probably damaging Het
Col25a1 A G 3: 130,389,312 (GRCm39) T632A probably benign Het
Coro6 T C 11: 77,358,622 (GRCm39) F227S probably damaging Het
Diras2 C T 13: 52,661,786 (GRCm39) V174M probably benign Het
Dop1a A G 9: 86,389,783 (GRCm39) D569G probably benign Het
Dync1li2 A G 8: 105,167,104 (GRCm39) probably null Het
Dysf T C 6: 84,064,800 (GRCm39) V508A probably damaging Het
Edem1 T C 6: 108,820,061 (GRCm39) probably null Het
Eef2k A G 7: 120,488,471 (GRCm39) D452G probably benign Het
Espl1 A G 15: 102,225,565 (GRCm39) R1539G possibly damaging Het
Fat4 A G 3: 38,941,364 (GRCm39) S86G probably benign Het
Hpgd A T 8: 56,751,391 (GRCm39) D73V probably benign Het
Ltb4r1 A G 14: 56,005,539 (GRCm39) N281D probably damaging Het
Map7 T C 10: 20,151,948 (GRCm39) S638P unknown Het
Mical1 G A 10: 41,362,075 (GRCm39) A934T probably benign Het
Micu3 C A 8: 40,807,341 (GRCm39) probably null Het
Mmp24 T A 2: 155,640,056 (GRCm39) Y129N probably damaging Het
Mras A T 9: 99,293,599 (GRCm39) Y14N probably damaging Het
Msmo1 A T 8: 65,175,523 (GRCm39) I169N probably damaging Het
Mtrr G T 13: 68,727,766 (GRCm39) T60K probably damaging Het
Or4c113 A T 2: 88,885,230 (GRCm39) L180* probably null Het
Or5p6 G T 7: 107,631,360 (GRCm39) Y63* probably null Het
Or7g30 T A 9: 19,352,290 (GRCm39) I27N possibly damaging Het
Pam A T 1: 97,768,090 (GRCm39) C8* probably null Het
Phrf1 T G 7: 140,839,834 (GRCm39) S1169A possibly damaging Het
Pkd1l2 T C 8: 117,792,569 (GRCm39) T408A probably damaging Het
Plch1 G T 3: 63,615,162 (GRCm39) Q778K probably damaging Het
Ppp1r3a A G 6: 14,719,417 (GRCm39) V499A probably benign Het
Rnd2 C T 11: 101,359,825 (GRCm39) L57F probably damaging Het
Ryr3 C A 2: 112,492,849 (GRCm39) S3736I possibly damaging Het
Serpinb13 T C 1: 106,909,915 (GRCm39) F11L possibly damaging Het
Slc45a2 C T 15: 11,027,871 (GRCm39) T480I probably damaging Het
Smcp A G 3: 92,491,731 (GRCm39) C39R unknown Het
Sox9 T A 11: 112,674,685 (GRCm39) L161Q probably damaging Het
Tanc2 T C 11: 105,805,811 (GRCm39) probably null Het
Tlr3 C T 8: 45,851,851 (GRCm39) D349N possibly damaging Het
Tmem131l G T 3: 83,833,435 (GRCm39) N809K probably damaging Het
Tyk2 T C 9: 21,032,908 (GRCm39) Y285C probably damaging Het
Usp15 T A 10: 123,011,804 (GRCm39) N98Y 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
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'- GTGTATCCCACGTCGTATCG -3'
(R):5'- GGGACTCAGAGGAACCTTTCTTC -3'

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