Incidental Mutation 'R4572:Cnot2'
ID 342208
Institutional Source Beutler Lab
Gene Symbol Cnot2
Ensembl Gene ENSMUSG00000020166
Gene Name CCR4-NOT transcription complex, subunit 2
Synonyms 2600016M12Rik, 2810470K03Rik
MMRRC Submission 041796-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.894) question?
Stock # R4572 (G1)
Quality Score 225
Status Validated
Chromosome 10
Chromosomal Location 116321066-116417416 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 116330751 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Alanine at position 423 (T423A)
Ref Sequence ENSEMBL: ENSMUSP00000132152 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000105265] [ENSMUST00000105267] [ENSMUST00000164088] [ENSMUST00000167706] [ENSMUST00000168036] [ENSMUST00000169921] [ENSMUST00000169576]
AlphaFold Q8C5L3
Predicted Effect probably benign
Transcript: ENSMUST00000105265
AA Change: T338A

PolyPhen 2 Score 0.374 (Sensitivity: 0.90; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000100900
Gene: ENSMUSG00000020166
AA Change: T338A

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 benign
Transcript: ENSMUST00000105267
AA Change: T423A

PolyPhen 2 Score 0.374 (Sensitivity: 0.90; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000100902
Gene: ENSMUSG00000020166
AA Change: T423A

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 benign
Transcript: ENSMUST00000164088
AA Change: T382A

PolyPhen 2 Score 0.219 (Sensitivity: 0.91; Specificity: 0.88)
SMART Domains Protein: ENSMUSP00000127830
Gene: ENSMUSG00000020166
AA Change: T382A

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 benign
Transcript: ENSMUST00000167706
AA Change: T373A

PolyPhen 2 Score 0.219 (Sensitivity: 0.91; Specificity: 0.88)
SMART Domains Protein: ENSMUSP00000128837
Gene: ENSMUSG00000020166
AA Change: T373A

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 benign
Transcript: ENSMUST00000168036
AA Change: T382A

PolyPhen 2 Score 0.219 (Sensitivity: 0.91; Specificity: 0.88)
SMART Domains Protein: ENSMUSP00000132315
Gene: ENSMUSG00000020166
AA Change: T382A

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: ENSMUST00000169921
AA Change: T423A

PolyPhen 2 Score 0.374 (Sensitivity: 0.90; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000132152
Gene: ENSMUSG00000020166
AA Change: T423A

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
Predicted Effect probably benign
Transcript: ENSMUST00000169576
Meta Mutation Damage Score 0.1600 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.6%
  • 10x: 97.2%
  • 20x: 95.0%
Validation Efficiency 100% (71/71)
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: 65 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca6 A T 11: 110,107,374 (GRCm39) I747N probably benign Het
Adamtsl2 A G 2: 26,973,268 (GRCm39) Y97C probably damaging Het
Alox12e A G 11: 70,212,007 (GRCm39) probably benign Het
Alpk2 A T 18: 65,414,075 (GRCm39) S2014T probably damaging Het
Ankrd36 A T 11: 5,639,340 (GRCm39) probably null Het
Apobec1 T C 6: 122,558,356 (GRCm39) D133G probably damaging Het
Arfgef1 A T 1: 10,283,366 (GRCm39) I181N probably damaging Het
Cilp2 A G 8: 70,335,060 (GRCm39) V646A probably damaging Het
Clasrp A G 7: 19,318,389 (GRCm39) probably null Het
Crtap T C 9: 114,213,874 (GRCm39) D227G probably benign Het
Cyp17a1 A G 19: 46,658,990 (GRCm39) F217S probably damaging Het
Ddx60 A G 8: 62,440,455 (GRCm39) M1036V probably damaging Het
Dnah11 A T 12: 117,973,860 (GRCm39) I2818N probably benign Het
Dok6 T A 18: 89,492,071 (GRCm39) I169F possibly damaging Het
Duox2 T A 2: 122,112,207 (GRCm39) R1326S probably benign Het
Epha10 A G 4: 124,796,361 (GRCm39) T357A unknown Het
Ephb2 A C 4: 136,383,251 (GRCm39) F942C probably damaging Het
Fscn3 T A 6: 28,430,634 (GRCm39) probably null Het
Gabrb2 A G 11: 42,484,744 (GRCm39) N267S possibly damaging Het
Gabrr3 A T 16: 59,282,001 (GRCm39) Y452F probably benign Het
Gen1 A G 12: 11,292,419 (GRCm39) S457P probably damaging Het
Gm1993 C T X: 25,515,656 (GRCm39) R77H probably damaging Het
Gm5592 G A 7: 40,865,583 (GRCm39) probably benign Het
Hmbox1 A G 14: 65,140,682 (GRCm39) probably null Het
Hus1 A T 11: 8,957,617 (GRCm39) probably null Het
Ino80 G A 2: 119,232,839 (GRCm39) R1160W probably damaging Het
Kalrn A T 16: 34,212,412 (GRCm39) F27L probably damaging Het
Kri1 A T 9: 21,191,680 (GRCm39) F187L probably damaging Het
Lekr1 A T 3: 65,691,336 (GRCm39) noncoding transcript Het
Mapk15 T C 15: 75,870,599 (GRCm39) probably benign Het
Mrgpre G A 7: 143,334,841 (GRCm39) L221F probably damaging Het
Mrpl50 A T 4: 49,514,399 (GRCm39) S91T possibly damaging Het
Muc4 T C 16: 32,753,802 (GRCm38) I1226T probably benign Het
Mup15 A G 4: 61,356,454 (GRCm39) probably null Het
Ncapd3 A G 9: 27,005,911 (GRCm39) D1469G probably damaging Het
Nlrp9b G A 7: 19,760,606 (GRCm39) probably null Het
Npy6r A T 18: 44,408,984 (GRCm39) Y135F probably benign Het
Or7e170 A C 9: 19,795,275 (GRCm39) C109G probably benign Het
Phf14 G A 6: 12,006,823 (GRCm39) R825Q probably damaging Het
Pigg A G 5: 108,480,751 (GRCm39) M379V probably benign Het
Plppr3 T A 10: 79,701,897 (GRCm39) Q315L probably benign Het
Plxnd1 C A 6: 115,932,717 (GRCm39) C1921F probably damaging Het
Ptger4 A C 15: 5,272,614 (GRCm39) S2A probably benign Het
Qrfprl A T 6: 65,431,975 (GRCm39) M293L probably benign Het
Rab4a A T 8: 124,560,799 (GRCm39) D196V probably benign Het
Rbck1 G A 2: 152,160,653 (GRCm39) Q428* probably null Het
Rgs14 A T 13: 55,527,875 (GRCm39) N266I probably damaging Het
Serpina1c A T 12: 103,864,967 (GRCm39) probably benign Het
Sesn3 G A 9: 14,232,516 (GRCm39) R263H probably benign Het
Slfn1 A T 11: 83,012,289 (GRCm39) D135V probably benign Het
Spata17 T C 1: 186,926,193 (GRCm39) K46E possibly damaging Het
Srcin1 A C 11: 97,425,760 (GRCm39) D432E probably damaging Het
Stxbp5 T C 10: 9,713,888 (GRCm39) E217G probably damaging Het
Terf2ip A G 8: 112,738,649 (GRCm39) D179G probably damaging Het
Tll1 A G 8: 64,509,343 (GRCm39) F556L possibly damaging Het
Tmed4 CTCTTTCT CTCT 11: 6,224,461 (GRCm39) probably null Het
Trappc9 G T 15: 72,808,916 (GRCm39) Q537K possibly damaging Het
Trim30a G T 7: 104,060,395 (GRCm39) C460* probably null Het
Trim35 T C 14: 66,545,322 (GRCm39) Y298H probably damaging Het
Ugt3a1 T A 15: 9,306,479 (GRCm39) H209Q probably benign Het
Ulk4 T C 9: 121,021,830 (GRCm39) K627R probably damaging Het
Wnk1 T C 6: 119,928,872 (GRCm39) T1319A possibly damaging Het
Wnt9b G A 11: 103,622,981 (GRCm39) R141C probably damaging Het
Zfp735 A G 11: 73,580,611 (GRCm39) M37V probably benign Het
Zmym1 A T 4: 126,944,628 (GRCm39) N186K probably benign Het
Other mutations in Cnot2
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00790:Cnot2 APN 10 116,342,976 (GRCm39) missense probably benign 0.02
IGL02433:Cnot2 APN 10 116,328,241 (GRCm39) missense possibly damaging 0.82
IGL03066:Cnot2 APN 10 116,335,262 (GRCm39) missense probably benign 0.15
IGL03383:Cnot2 APN 10 116,330,722 (GRCm39) splice site probably benign
R0145:Cnot2 UTSW 10 116,353,273 (GRCm39) missense possibly damaging 0.90
R0497:Cnot2 UTSW 10 116,334,260 (GRCm39) missense probably damaging 1.00
R0615:Cnot2 UTSW 10 116,334,141 (GRCm39) missense possibly damaging 0.89
R1935:Cnot2 UTSW 10 116,334,320 (GRCm39) missense possibly damaging 0.62
R1985:Cnot2 UTSW 10 116,363,781 (GRCm39) missense probably damaging 0.99
R2148:Cnot2 UTSW 10 116,342,185 (GRCm39) missense probably benign 0.01
R4063:Cnot2 UTSW 10 116,373,301 (GRCm39) missense possibly damaging 0.46
R4179:Cnot2 UTSW 10 116,334,048 (GRCm39) missense possibly damaging 0.81
R4196:Cnot2 UTSW 10 116,337,209 (GRCm39) missense possibly damaging 0.62
R4523:Cnot2 UTSW 10 116,417,379 (GRCm39) unclassified probably benign
R4610:Cnot2 UTSW 10 116,335,323 (GRCm39) missense probably damaging 1.00
R5219:Cnot2 UTSW 10 116,342,215 (GRCm39) splice site probably null
R5847:Cnot2 UTSW 10 116,363,851 (GRCm39) missense probably damaging 0.98
R6444:Cnot2 UTSW 10 116,335,260 (GRCm39) missense probably benign 0.02
R6733:Cnot2 UTSW 10 116,334,058 (GRCm39) missense possibly damaging 0.81
R6734:Cnot2 UTSW 10 116,334,058 (GRCm39) missense possibly damaging 0.81
R6735:Cnot2 UTSW 10 116,334,058 (GRCm39) missense possibly damaging 0.81
R6944:Cnot2 UTSW 10 116,373,128 (GRCm39) intron probably benign
R7139:Cnot2 UTSW 10 116,330,924 (GRCm39) missense probably benign 0.00
R7248:Cnot2 UTSW 10 116,334,278 (GRCm39) missense probably benign 0.05
R7423:Cnot2 UTSW 10 116,328,303 (GRCm39) missense probably damaging 1.00
R7526:Cnot2 UTSW 10 116,342,985 (GRCm39) missense probably benign 0.12
R7851:Cnot2 UTSW 10 116,373,337 (GRCm39) missense possibly damaging 0.66
R8245:Cnot2 UTSW 10 116,346,294 (GRCm39) missense probably benign 0.07
R8350:Cnot2 UTSW 10 116,322,181 (GRCm39) missense probably damaging 1.00
R8463:Cnot2 UTSW 10 116,353,236 (GRCm39) missense probably benign 0.11
R9045:Cnot2 UTSW 10 116,322,160 (GRCm39) missense probably benign 0.05
R9175:Cnot2 UTSW 10 116,334,051 (GRCm39) missense possibly damaging 0.94
R9229:Cnot2 UTSW 10 116,384,960 (GRCm39) nonsense probably null
R9343:Cnot2 UTSW 10 116,346,326 (GRCm39) missense
R9508:Cnot2 UTSW 10 116,329,616 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- CAGGAAGAGAATCACCAAATTTTCC -3'
(R):5'- AAGCGCTCTTGGGTTACTTTTC -3'

Sequencing Primer
(F):5'- GTATTTCCATTCACTATGGTTAC -3'
(R):5'- GGGTTACTTTTCTGCTATAAAGTTGC -3'
Posted On 2015-09-24