Incidental Mutation 'R0497:Cnot2'
ID 40546
Institutional Source Beutler Lab
Gene Symbol Cnot2
Ensembl Gene ENSMUSG00000020166
Gene Name CCR4-NOT transcription complex, subunit 2
Synonyms 2810470K03Rik, 2600016M12Rik
MMRRC Submission 038693-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.865) question?
Stock # R0497 (G1)
Quality Score 225
Status Validated
Chromosome 10
Chromosomal Location 116485161-116581511 bp(-) (GRCm38)
Type of Mutation missense
DNA Base Change (assembly) A to T at 116498355 bp (GRCm38)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Asparagine at position 335 (I335N)
Ref Sequence ENSEMBL: ENSMUSP00000132152 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000105265] [ENSMUST00000105267] [ENSMUST00000164088] [ENSMUST00000167706] [ENSMUST00000168036] [ENSMUST00000169576] [ENSMUST00000169921]
AlphaFold Q8C5L3
Predicted Effect possibly damaging
Transcript: ENSMUST00000105265
AA Change: I250N

PolyPhen 2 Score 0.741 (Sensitivity: 0.85; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000100900
Gene: ENSMUSG00000020166
AA Change: I250N

DomainStartEndE-ValueType
low complexity region 68 87 N/A INTRINSIC
low complexity region 213 227 N/A INTRINSIC
Pfam:NOT2_3_5 310 437 1e-36 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000105267
AA Change: I335N

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000100902
Gene: ENSMUSG00000020166
AA Change: I335N

DomainStartEndE-ValueType
low complexity region 153 172 N/A INTRINSIC
low complexity region 298 312 N/A INTRINSIC
Pfam:NOT2_3_5 396 521 8.8e-33 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000164088
AA Change: I294N

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000127830
Gene: ENSMUSG00000020166
AA Change: I294N

DomainStartEndE-ValueType
low complexity region 112 131 N/A INTRINSIC
low complexity region 257 271 N/A INTRINSIC
Pfam:NOT2_3_5 354 481 2.6e-37 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000164383
Predicted Effect noncoding transcript
Transcript: ENSMUST00000166166
Predicted Effect probably damaging
Transcript: ENSMUST00000167706
AA Change: I285N

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000128837
Gene: ENSMUSG00000020166
AA Change: I285N

DomainStartEndE-ValueType
low complexity region 153 172 N/A INTRINSIC
low complexity region 248 262 N/A INTRINSIC
Pfam:NOT2_3_5 345 472 2.5e-37 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000168036
AA Change: I294N

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000132315
Gene: ENSMUSG00000020166
AA Change: I294N

DomainStartEndE-ValueType
low complexity region 112 131 N/A INTRINSIC
low complexity region 257 271 N/A INTRINSIC
Pfam:NOT2_3_5 354 481 2.6e-37 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000169576
Predicted Effect probably damaging
Transcript: ENSMUST00000169921
AA Change: I335N

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000132152
Gene: ENSMUSG00000020166
AA Change: I335N

DomainStartEndE-ValueType
low complexity region 153 172 N/A INTRINSIC
low complexity region 298 312 N/A INTRINSIC
Pfam:NOT2_3_5 395 522 1.2e-36 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000169937
Predicted Effect noncoding transcript
Transcript: ENSMUST00000171214
Predicted Effect noncoding transcript
Transcript: ENSMUST00000219544
Meta Mutation Damage Score 0.7571 question?
Coding Region Coverage
  • 1x: 99.6%
  • 3x: 98.7%
  • 10x: 96.6%
  • 20x: 93.1%
Validation Efficiency 100% (68/68)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a subunit of the multi-component CCR4-NOT complex. The CCR4-NOT complex regulates mRNA synthesis and degradation and is also thought to be involved in mRNA splicing, transport and localization. The encoded protein interacts with histone deacetylases and functions as a repressor of polymerase II transcription. Alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, Dec 2010]
Allele List at MGI
Other mutations in this stock
Total: 67 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
9530053A07Rik T A 7: 28,147,465 (GRCm38) C1158S probably damaging Het
Aatk A C 11: 120,018,780 (GRCm38) V110G probably damaging Het
Adcy6 A C 15: 98,597,725 (GRCm38) probably null Het
Adm A G 7: 110,629,121 (GRCm38) T170A probably benign Het
Afap1l2 G T 19: 56,930,209 (GRCm38) N171K probably benign Het
Aph1b G T 9: 66,790,618 (GRCm38) S112* probably null Het
Arhgap23 A G 11: 97,452,163 (GRCm38) S424G probably damaging Het
Asah2 T A 19: 32,054,631 (GRCm38) N46I probably benign Het
Braf G A 6: 39,640,549 (GRCm38) probably benign Het
Brd2 C T 17: 34,114,360 (GRCm38) R47Q probably damaging Het
C2cd5 A G 6: 143,012,093 (GRCm38) V972A probably benign Het
Car9 T A 4: 43,511,881 (GRCm38) L300H probably damaging Het
Chmp3 T C 6: 71,552,411 (GRCm38) S20P probably damaging Het
Chp1 A G 2: 119,571,782 (GRCm38) N79S possibly damaging Het
Cntnap4 T C 8: 112,570,151 (GRCm38) V6A probably benign Het
Ctcf T A 8: 105,675,040 (GRCm38) probably benign Het
Dennd1b A G 1: 139,039,986 (GRCm38) probably benign Het
Dirc2 A T 16: 35,735,604 (GRCm38) V162D probably benign Het
Dnmbp A G 19: 43,856,640 (GRCm38) probably benign Het
Eef2 T C 10: 81,181,586 (GRCm38) F782L probably benign Het
Eogt T A 6: 97,135,233 (GRCm38) Y153F probably benign Het
Fam81a G T 9: 70,096,119 (GRCm38) Q237K possibly damaging Het
Fat2 T A 11: 55,283,402 (GRCm38) T2162S probably benign Het
Gas6 T C 8: 13,470,387 (GRCm38) I434V possibly damaging Het
Gm42417 A T 1: 36,532,167 (GRCm38) L77Q probably damaging Het
Grik3 A T 4: 125,623,510 (GRCm38) N49Y possibly damaging Het
Gucy2e A T 11: 69,224,159 (GRCm38) V974E probably damaging Het
Helz2 A G 2: 181,229,656 (GRCm38) V2721A probably damaging Het
Klhl6 GT G 16: 19,956,966 (GRCm38) 279 probably null Het
Krt73 A G 15: 101,802,230 (GRCm38) L23P probably damaging Het
L3mbtl3 T C 10: 26,282,874 (GRCm38) probably benign Het
Lrrc15 A T 16: 30,272,892 (GRCm38) V543E probably damaging Het
Med13 G A 11: 86,276,983 (GRCm38) probably benign Het
Med25 T C 7: 44,892,100 (GRCm38) D60G probably damaging Het
Mgam T A 6: 40,664,892 (GRCm38) Y560N probably damaging Het
Mlkl A G 8: 111,327,873 (GRCm38) Y211H probably damaging Het
Msl2 A G 9: 101,101,294 (GRCm38) N289S probably benign Het
Nwd2 G T 5: 63,806,343 (GRCm38) W1090L probably damaging Het
Olfr1281 A G 2: 111,328,830 (GRCm38) D137G probably benign Het
Omt2b T C 9: 78,328,231 (GRCm38) probably benign Het
Pald1 A G 10: 61,341,315 (GRCm38) L652P probably damaging Het
Pard3b T A 1: 62,440,008 (GRCm38) probably null Het
Prdm15 G A 16: 97,794,334 (GRCm38) T1098I possibly damaging Het
Rock2 A G 12: 16,954,953 (GRCm38) T436A probably benign Het
Sema4c A T 1: 36,549,608 (GRCm38) D812E probably benign Het
Sla A T 15: 66,792,249 (GRCm38) I91K probably benign Het
Slc22a16 T G 10: 40,584,967 (GRCm38) M255R probably damaging Het
Smg8 C T 11: 87,086,084 (GRCm38) D224N possibly damaging Het
Spdef A T 17: 27,718,058 (GRCm38) D190E probably benign Het
Taok1 A G 11: 77,573,804 (GRCm38) I152T probably damaging Het
Tmem220 A G 11: 67,025,922 (GRCm38) D36G probably damaging Het
Tmem235 A C 11: 117,864,351 (GRCm38) I210L probably benign Het
Tmem266 C T 9: 55,380,884 (GRCm38) probably null Het
Tmprss12 A G 15: 100,281,039 (GRCm38) probably benign Het
Trim32 G A 4: 65,613,254 (GRCm38) R16Q probably damaging Het
Usp38 T A 8: 80,984,424 (GRCm38) probably benign Het
Usp44 C T 10: 93,846,806 (GRCm38) P373S possibly damaging Het
Vmn1r209 G T 13: 22,805,948 (GRCm38) Q191K probably damaging Het
Vmn1r70 T C 7: 10,634,026 (GRCm38) I147T probably benign Het
Vmn2r107 T A 17: 20,375,132 (GRCm38) I649N probably damaging Het
Vmn2r12 A T 5: 109,091,889 (GRCm38) Y269* probably null Het
Zan C T 5: 137,412,676 (GRCm38) probably benign Het
Zfp616 G T 11: 74,083,480 (GRCm38) V192L probably benign Het
Zfp644 A T 5: 106,638,333 (GRCm38) V116D probably damaging Het
Zgrf1 T C 3: 127,584,650 (GRCm38) probably benign Het
Zhx3 A T 2: 160,779,994 (GRCm38) L751* probably null Het
Znfx1 T A 2: 167,055,411 (GRCm38) Q531L probably benign Het
Other mutations in Cnot2
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00790:Cnot2 APN 10 116,507,071 (GRCm38) missense probably benign 0.02
IGL02433:Cnot2 APN 10 116,492,336 (GRCm38) missense possibly damaging 0.82
IGL03066:Cnot2 APN 10 116,499,357 (GRCm38) missense probably benign 0.15
IGL03383:Cnot2 APN 10 116,494,817 (GRCm38) splice site probably benign
R0145:Cnot2 UTSW 10 116,517,368 (GRCm38) missense possibly damaging 0.90
R0615:Cnot2 UTSW 10 116,498,236 (GRCm38) missense possibly damaging 0.89
R1935:Cnot2 UTSW 10 116,498,415 (GRCm38) missense possibly damaging 0.62
R1985:Cnot2 UTSW 10 116,527,876 (GRCm38) missense probably damaging 0.99
R2148:Cnot2 UTSW 10 116,506,280 (GRCm38) missense probably benign 0.01
R4063:Cnot2 UTSW 10 116,537,396 (GRCm38) missense possibly damaging 0.46
R4179:Cnot2 UTSW 10 116,498,143 (GRCm38) missense possibly damaging 0.81
R4196:Cnot2 UTSW 10 116,501,304 (GRCm38) missense possibly damaging 0.62
R4523:Cnot2 UTSW 10 116,581,474 (GRCm38) unclassified probably benign
R4572:Cnot2 UTSW 10 116,494,846 (GRCm38) missense probably benign 0.37
R4610:Cnot2 UTSW 10 116,499,418 (GRCm38) missense probably damaging 1.00
R5219:Cnot2 UTSW 10 116,506,310 (GRCm38) splice site probably null
R5847:Cnot2 UTSW 10 116,527,946 (GRCm38) missense probably damaging 0.98
R6444:Cnot2 UTSW 10 116,499,355 (GRCm38) missense probably benign 0.02
R6733:Cnot2 UTSW 10 116,498,153 (GRCm38) missense possibly damaging 0.81
R6734:Cnot2 UTSW 10 116,498,153 (GRCm38) missense possibly damaging 0.81
R6735:Cnot2 UTSW 10 116,498,153 (GRCm38) missense possibly damaging 0.81
R6944:Cnot2 UTSW 10 116,537,223 (GRCm38) intron probably benign
R7139:Cnot2 UTSW 10 116,495,019 (GRCm38) missense probably benign 0.00
R7248:Cnot2 UTSW 10 116,498,373 (GRCm38) missense probably benign 0.05
R7423:Cnot2 UTSW 10 116,492,398 (GRCm38) missense probably damaging 1.00
R7526:Cnot2 UTSW 10 116,507,080 (GRCm38) missense probably benign 0.12
R7851:Cnot2 UTSW 10 116,537,432 (GRCm38) missense possibly damaging 0.66
R8245:Cnot2 UTSW 10 116,510,389 (GRCm38) missense probably benign 0.07
R8350:Cnot2 UTSW 10 116,486,276 (GRCm38) missense probably damaging 1.00
R8463:Cnot2 UTSW 10 116,517,331 (GRCm38) missense probably benign 0.11
R9045:Cnot2 UTSW 10 116,486,255 (GRCm38) missense probably benign 0.05
R9175:Cnot2 UTSW 10 116,498,146 (GRCm38) missense possibly damaging 0.94
R9229:Cnot2 UTSW 10 116,549,055 (GRCm38) nonsense probably null
R9343:Cnot2 UTSW 10 116,510,421 (GRCm38) missense
R9508:Cnot2 UTSW 10 116,493,711 (GRCm38) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- GCCAATCATTCCAAATTGGTCCGTC -3'
(R):5'- CCTTCCAACATTCATGGCAGAGAGC -3'

Sequencing Primer
(F):5'- CAAATTGGTCCGTCACCATC -3'
(R):5'- ATGGACCCAAATTCCCTGGA -3'
Posted On 2013-05-23