Incidental Mutation 'R8699:Ccnt1'
ID 668955
Institutional Source Beutler Lab
Gene Symbol Ccnt1
Ensembl Gene ENSMUSG00000011960
Gene Name cyclin T1
Synonyms 2810478G24Rik, CycT1
MMRRC Submission 068553-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.911) question?
Stock # R8699 (G1)
Quality Score 225.009
Status Not validated
Chromosome 15
Chromosomal Location 98436570-98468340 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 98462995 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Threonine at position 59 (I59T)
Ref Sequence ENSEMBL: ENSMUSP00000012104 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000012104] [ENSMUST00000168928] [ENSMUST00000169707]
AlphaFold Q9QWV9
Predicted Effect probably damaging
Transcript: ENSMUST00000012104
AA Change: I59T

PolyPhen 2 Score 0.975 (Sensitivity: 0.76; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000012104
Gene: ENSMUSG00000011960
AA Change: I59T

DomainStartEndE-ValueType
CYCLIN 43 142 5.89e-17 SMART
SCOP:d1jkw_2 152 257 1e-24 SMART
Blast:CYCLIN 155 243 2e-54 BLAST
low complexity region 308 326 N/A INTRINSIC
coiled coil region 388 419 N/A INTRINSIC
low complexity region 512 529 N/A INTRINSIC
low complexity region 559 570 N/A INTRINSIC
low complexity region 706 723 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000168928
AA Change: I59T

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000130286
Gene: ENSMUSG00000011960
AA Change: I59T

DomainStartEndE-ValueType
CYCLIN 43 142 5.89e-17 SMART
Blast:CYCLIN 155 182 3e-9 BLAST
Predicted Effect probably damaging
Transcript: ENSMUST00000169707
AA Change: I59T

PolyPhen 2 Score 0.975 (Sensitivity: 0.76; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000126874
Gene: ENSMUSG00000011960
AA Change: I59T

DomainStartEndE-ValueType
CYCLIN 43 142 5.89e-17 SMART
SCOP:d1jkw_2 152 257 1e-24 SMART
Blast:CYCLIN 155 243 2e-54 BLAST
low complexity region 308 326 N/A INTRINSIC
coiled coil region 388 419 N/A INTRINSIC
low complexity region 512 529 N/A INTRINSIC
low complexity region 559 570 N/A INTRINSIC
low complexity region 706 723 N/A INTRINSIC
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 100.0%
  • 10x: 99.7%
  • 20x: 99.1%
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the highly conserved cyclin C subfamily. The encoded protein tightly associates with cyclin-dependent kinase 9, and is a major subunit of positive transcription elongation factor b (p-TEFb). In humans, there are multiple forms of positive transcription elongation factor b, which may include one of several different cyclins along with cyclin-dependent kinase 9. The complex containing the encoded cyclin and cyclin-dependent kinase 9 acts as a cofactor of human immunodeficiency virus type 1 (HIV-1) Tat protein, and is both necessary and sufficient for full activation of viral transcription. This cyclin and its kinase partner are also involved in triggering transcript elongation through phosphorylation of the carboxy-terminal domain of the largest RNA polymerase II subunit. Overexpression of this gene is implicated in tumor growth. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2013]
Allele List at MGI
Other mutations in this stock
Total: 79 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4933430I17Rik T C 4: 62,450,515 (GRCm39) W30R probably damaging Het
Abca3 A G 17: 24,627,199 (GRCm39) D1555G probably benign Het
Anapc1 T C 2: 128,483,373 (GRCm39) T1241A probably damaging Het
Ano5 G A 7: 51,243,519 (GRCm39) V881I probably benign Het
Appl1 G A 14: 26,662,212 (GRCm39) S490L probably benign Het
Asxl3 A G 18: 22,567,664 (GRCm39) T81A probably benign Het
Bclaf1 T C 10: 20,209,184 (GRCm39) S754P possibly damaging Het
Bicra G T 7: 15,723,113 (GRCm39) Q135K probably benign Het
Cad T C 5: 31,233,605 (GRCm39) V1951A possibly damaging Het
Cadm3 T A 1: 173,168,683 (GRCm39) Y295F probably damaging Het
Ccr6 C T 17: 8,475,398 (GRCm39) T201M probably benign Het
Cd5 A G 19: 10,702,556 (GRCm39) F209S possibly damaging Het
Cep126 A C 9: 8,087,362 (GRCm39) D1017E probably damaging Het
Cfap298 T C 16: 90,727,945 (GRCm39) K82E probably benign Het
Cntnap4 A T 8: 113,484,228 (GRCm39) D427V probably damaging Het
Col4a4 T A 1: 82,433,455 (GRCm39) N1496I unknown Het
Crybg3 A G 16: 59,375,291 (GRCm39) Y274H probably damaging Het
Cubn C A 2: 13,388,770 (GRCm39) S1479I probably damaging Het
Diras2 A T 13: 52,662,143 (GRCm39) C55S probably damaging Het
Dleu7 G A 14: 62,530,279 (GRCm39) R41C probably benign Het
Dync2i1 T C 12: 116,171,321 (GRCm39) T972A probably benign Het
Efcab3 A G 11: 104,672,072 (GRCm39) T1464A probably benign Het
Exo5 A G 4: 120,779,193 (GRCm39) I224T probably damaging Het
Fcho1 T C 8: 72,162,277 (GRCm39) I774V possibly damaging Het
Gclm T G 3: 122,059,972 (GRCm39) S251A possibly damaging Het
Gm13889 T C 2: 93,787,327 (GRCm39) Q49R unknown Het
Gm35315 T A 5: 110,228,392 (GRCm39) H18L probably benign Het
Gm9949 G A 18: 62,317,043 (GRCm39) G65R unknown Het
Gpr153 C T 4: 152,363,558 (GRCm39) probably benign Het
Gria4 C A 9: 4,424,347 (GRCm39) K839N probably damaging Het
Gria4 T G 9: 4,424,351 (GRCm39) Y838S probably damaging Het
Hrh3 A G 2: 179,743,149 (GRCm39) W160R probably damaging Het
Htr4 G A 18: 62,570,763 (GRCm39) A273T probably damaging Het
Lig3 G T 11: 82,685,376 (GRCm39) C599F probably damaging Het
Lrp1b A T 2: 41,172,207 (GRCm39) V1594E Het
Map3k10 A T 7: 27,367,780 (GRCm39) V286D probably damaging Het
Map4k4 T A 1: 40,015,910 (GRCm39) V117E unknown Het
Mdga1 C T 17: 30,061,348 (GRCm39) V548M possibly damaging Het
Mms22l A T 4: 24,507,363 (GRCm39) L248F possibly damaging Het
Ncaph T C 2: 126,963,096 (GRCm39) D379G possibly damaging Het
Neb A G 2: 52,037,246 (GRCm39) V7064A probably benign Het
Neb G A 2: 52,102,563 (GRCm39) T4570M probably benign Het
Npy5r G T 8: 67,134,274 (GRCm39) T173K probably damaging Het
Or52a33 A T 7: 103,288,822 (GRCm39) I175N probably damaging Het
Or5b94 A G 19: 12,652,246 (GRCm39) M226V probably benign Het
Or5b97 A T 19: 12,878,828 (GRCm39) F105L possibly damaging Het
Or5g25 A T 2: 85,478,330 (GRCm39) C112S possibly damaging Het
Or8u10 A T 2: 85,915,518 (GRCm39) I201N probably damaging Het
Oxsm A G 14: 16,242,631 (GRCm38) I46T possibly damaging Het
Pcdha1 A T 18: 37,064,076 (GRCm39) I247F probably benign Het
Pcdhgb6 A T 18: 37,875,975 (GRCm39) I228L probably benign Het
Peg10 T TCCA 6: 4,756,451 (GRCm39) probably benign Het
Ppp1r9a A G 6: 5,115,474 (GRCm39) S866G probably benign Het
Ppp6r3 T A 19: 3,546,587 (GRCm39) S304C probably damaging Het
Pramel11 A T 4: 143,623,762 (GRCm39) N137K probably benign Het
Ptprd A T 4: 75,959,629 (GRCm39) F279I probably benign Het
Repin1 G T 6: 48,574,279 (GRCm39) E403* probably null Het
Rest G A 5: 77,429,389 (GRCm39) G603R probably benign Het
Rgs17 A T 10: 5,868,194 (GRCm39) L9M probably benign Het
Rtp1 A G 16: 23,250,133 (GRCm39) Y166C probably damaging Het
Sec24b C A 3: 129,798,653 (GRCm39) R572I probably damaging Het
Setd1a G T 7: 127,385,774 (GRCm39) R827L possibly damaging Het
Sh3tc1 T C 5: 35,859,235 (GRCm39) Y1091C probably damaging Het
Sorbs1 G C 19: 40,365,244 (GRCm39) R180G probably benign Het
Stat4 T A 1: 52,111,096 (GRCm39) M181K probably benign Het
Stk16 A G 1: 75,188,682 (GRCm39) E67G probably benign Het
Supv3l1 A G 10: 62,268,234 (GRCm39) V537A possibly damaging Het
Tmc8 A G 11: 117,674,361 (GRCm39) E101G possibly damaging Het
Tmem106a A T 11: 101,473,120 (GRCm39) probably benign Het
Tpr T A 1: 150,293,772 (GRCm39) I922N probably damaging Het
Uaca G T 9: 60,778,347 (GRCm39) L911F probably damaging Het
Ubn1 A T 16: 4,881,567 (GRCm39) I200L possibly damaging Het
Ush2a A G 1: 188,643,574 (GRCm39) D4312G probably damaging Het
Virma A T 4: 11,528,678 (GRCm39) Y1255F probably benign Het
Vmn1r170 C T 7: 23,306,080 (GRCm39) Q161* probably null Het
Vmn1r175 G T 7: 23,508,234 (GRCm39) A131D probably benign Het
Vmn1r52 T A 6: 90,155,742 (GRCm39) N15K probably benign Het
Wdr46 T A 17: 34,167,826 (GRCm39) I513N probably damaging Het
Zfp788 A G 7: 41,297,840 (GRCm39) N159D probably benign Het
Other mutations in Ccnt1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00336:Ccnt1 APN 15 98,462,990 (GRCm39) missense possibly damaging 0.75
IGL00900:Ccnt1 APN 15 98,452,514 (GRCm39) missense probably damaging 1.00
IGL01798:Ccnt1 APN 15 98,442,122 (GRCm39) missense probably benign 0.00
IGL02126:Ccnt1 APN 15 98,465,484 (GRCm39) missense probably damaging 1.00
IGL02341:Ccnt1 APN 15 98,444,664 (GRCm39) missense possibly damaging 0.92
Lifecycle UTSW 15 98,463,005 (GRCm39) nonsense probably null
R0049:Ccnt1 UTSW 15 98,462,960 (GRCm39) missense probably benign 0.05
R0049:Ccnt1 UTSW 15 98,462,960 (GRCm39) missense probably benign 0.05
R1116:Ccnt1 UTSW 15 98,442,219 (GRCm39) missense probably damaging 1.00
R2063:Ccnt1 UTSW 15 98,449,823 (GRCm39) missense probably benign 0.25
R2065:Ccnt1 UTSW 15 98,449,823 (GRCm39) missense probably benign 0.25
R2066:Ccnt1 UTSW 15 98,449,823 (GRCm39) missense probably benign 0.25
R2068:Ccnt1 UTSW 15 98,449,823 (GRCm39) missense probably benign 0.25
R2180:Ccnt1 UTSW 15 98,441,481 (GRCm39) missense possibly damaging 0.74
R3917:Ccnt1 UTSW 15 98,441,940 (GRCm39) missense probably benign 0.00
R4805:Ccnt1 UTSW 15 98,442,189 (GRCm39) missense probably benign 0.00
R4830:Ccnt1 UTSW 15 98,441,332 (GRCm39) missense probably damaging 1.00
R4836:Ccnt1 UTSW 15 98,465,444 (GRCm39) missense probably damaging 0.96
R5320:Ccnt1 UTSW 15 98,442,124 (GRCm39) missense probably benign 0.35
R5740:Ccnt1 UTSW 15 98,442,381 (GRCm39) missense probably benign 0.01
R5870:Ccnt1 UTSW 15 98,441,394 (GRCm39) nonsense probably null
R6074:Ccnt1 UTSW 15 98,441,205 (GRCm39) missense probably damaging 1.00
R6413:Ccnt1 UTSW 15 98,441,850 (GRCm39) missense probably benign 0.01
R6610:Ccnt1 UTSW 15 98,462,982 (GRCm39) missense probably damaging 1.00
R7260:Ccnt1 UTSW 15 98,463,005 (GRCm39) nonsense probably null
R7752:Ccnt1 UTSW 15 98,441,797 (GRCm39) missense probably benign 0.00
R7901:Ccnt1 UTSW 15 98,441,797 (GRCm39) missense probably benign 0.00
R7988:Ccnt1 UTSW 15 98,463,024 (GRCm39) splice site probably null
R8959:Ccnt1 UTSW 15 98,441,096 (GRCm39) utr 3 prime probably benign
R9143:Ccnt1 UTSW 15 98,441,688 (GRCm39) missense probably damaging 1.00
R9153:Ccnt1 UTSW 15 98,441,159 (GRCm39) missense probably benign 0.28
R9331:Ccnt1 UTSW 15 98,441,097 (GRCm39) nonsense probably null
R9549:Ccnt1 UTSW 15 98,441,574 (GRCm39) missense probably damaging 0.99
R9684:Ccnt1 UTSW 15 98,446,566 (GRCm39) missense probably damaging 0.98
Predicted Primers PCR Primer
(F):5'- ACATTTGTCTTCTTACTCGGAAAGC -3'
(R):5'- AGCACATGTTGTCAATTGGC -3'

Sequencing Primer
(F):5'- TAGGCAGCTACACTCAAAC -3'
(R):5'- TGGCAGTTAATTTCATTAGAGAAGG -3'
Posted On 2021-04-30