Incidental Mutation 'R6942:Cnot9'
ID 540581
Institutional Source Beutler Lab
Gene Symbol Cnot9
Ensembl Gene ENSMUSG00000026174
Gene Name CCR4-NOT transcription complex, subunit 9
Synonyms 2610007F23Rik, Rqcd1, FL10
MMRRC Submission 045056-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R6942 (G1)
Quality Score 225.009
Status Validated
Chromosome 1
Chromosomal Location 74545217-74570001 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 74558154 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Glutamic Acid at position 100 (V100E)
Ref Sequence ENSEMBL: ENSMUSP00000084466 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000087215] [ENSMUST00000189257]
AlphaFold Q9JKY0
Predicted Effect probably damaging
Transcript: ENSMUST00000087215
AA Change: V100E

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000084466
Gene: ENSMUSG00000026174
AA Change: V100E

DomainStartEndE-ValueType
low complexity region 4 17 N/A INTRINSIC
Pfam:Rcd1 25 283 2e-138 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000189257
SMART Domains Protein: ENSMUSP00000140670
Gene: ENSMUSG00000033364

DomainStartEndE-ValueType
PDB:3U12|B 4 125 2e-71 PDB
low complexity region 182 200 N/A INTRINSIC
Pfam:UCH_1 341 608 4.3e-19 PFAM
low complexity region 628 646 N/A INTRINSIC
UIM 704 723 1.33e1 SMART
UIM 806 825 1.04e-1 SMART
UIM 828 847 2.11e-2 SMART
low complexity region 893 909 N/A INTRINSIC
Meta Mutation Damage Score 0.6329 question?
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.8%
  • 10x: 98.9%
  • 20x: 96.2%
Validation Efficiency 100% (49/49)
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 RCD1 protein family. The encoded protein is a transcriptional cofactor and a core protein of the CCR4-NOT complex. It may be involved in signal transduction as well as retinoic acid-regulated cell differentiation and development. Alternatively spliced transcript variants have been described for this gene. [provided by RefSeq, Oct 2012]
PHENOTYPE: Embryos homozygous for an ENU-induced allele exhibit abnormal nervous system and brain morphology, cranioedema, and caudal body truncation. Mice carrying a targeted allele exhibit embryonic lethality. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 49 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Acacb T C 5: 114,330,024 (GRCm39) probably null Het
Adap2 A G 11: 80,045,891 (GRCm39) D57G probably benign Het
Atmin G T 8: 117,683,452 (GRCm39) V371F probably benign Het
Cacna1h G T 17: 25,604,013 (GRCm39) A1273E probably benign Het
Cdh23 G A 10: 60,274,635 (GRCm39) T483I possibly damaging Het
Cog2 T A 8: 125,271,875 (GRCm39) V463D probably benign Het
Crybg3 C T 16: 59,360,183 (GRCm39) R2500H possibly damaging Het
Cyp11b2 G A 15: 74,728,094 (GRCm39) probably benign Het
Cyp2j12 A T 4: 96,001,101 (GRCm39) probably null Het
Dipk1c A C 18: 84,748,549 (GRCm39) Y49S possibly damaging Het
Dlc1 T C 8: 37,405,364 (GRCm39) K142E probably benign Het
Dpp6 G A 5: 27,674,457 (GRCm39) V140M possibly damaging Het
Fktn G A 4: 53,735,128 (GRCm39) probably null Het
Gas7 A T 11: 67,550,977 (GRCm39) probably null Het
Grin3b T A 10: 79,811,953 (GRCm39) probably null Het
Hhatl G A 9: 121,617,246 (GRCm39) A329V probably benign Het
Homer3 C T 8: 70,744,201 (GRCm39) T276I probably benign Het
Igdcc4 G A 9: 65,027,550 (GRCm39) S204N probably benign Het
Ino80 A G 2: 119,213,983 (GRCm39) F1196L probably damaging Het
Iqsec3 C T 6: 121,450,062 (GRCm39) C154Y probably damaging Het
Kank1 A T 19: 25,401,537 (GRCm39) D1048V possibly damaging Het
Kif2c A G 4: 117,023,575 (GRCm39) L379P probably damaging Het
Kpna6 A T 4: 129,545,514 (GRCm39) probably null Het
Large2 C T 2: 92,201,167 (GRCm39) R28H probably damaging Het
Map4k2 T A 19: 6,396,739 (GRCm39) W552R possibly damaging Het
Mark3 A G 12: 111,559,088 (GRCm39) I43M probably null Het
Med13l C A 5: 118,883,071 (GRCm39) probably null Het
Mtbp T A 15: 55,430,596 (GRCm39) Y218N probably damaging Het
Or52n5 C T 7: 104,588,104 (GRCm39) R124C possibly damaging Het
Pcdhgb5 T C 18: 37,865,696 (GRCm39) L497P probably damaging Het
Pkhd1l1 A G 15: 44,386,025 (GRCm39) T1221A probably damaging Het
Pth1r C T 9: 110,557,084 (GRCm39) probably null Het
Samd8 T C 14: 21,825,221 (GRCm39) I59T possibly damaging Het
Scgb2b18 A G 7: 32,871,564 (GRCm39) V85A possibly damaging Het
Sema6c G T 3: 95,080,519 (GRCm39) V906L probably benign Het
Semp2l2b A T 10: 21,943,160 (GRCm39) D273E probably benign Het
Serpinb9g A T 13: 33,678,888 (GRCm39) T253S probably benign Het
Sipa1l3 T C 7: 29,085,516 (GRCm39) T694A probably damaging Het
Slc8a1 A G 17: 81,715,549 (GRCm39) L828P probably damaging Het
Spry1 T A 3: 37,697,193 (GRCm39) D145E probably benign Het
Stat6 A T 10: 127,487,131 (GRCm39) N213Y probably damaging Het
Tep1 A G 14: 51,074,194 (GRCm39) V1897A possibly damaging Het
Tmem45a T C 16: 56,646,145 (GRCm39) N25S probably benign Het
Tmem70 T A 1: 16,747,380 (GRCm39) Y166N probably damaging Het
Trrap T A 5: 144,720,853 (GRCm39) I230N possibly damaging Het
Ttn A G 2: 76,732,190 (GRCm39) probably benign Het
Unc79 T A 12: 103,088,704 (GRCm39) probably null Het
Vmn1r43 T A 6: 89,847,319 (GRCm39) I56F probably benign Het
Zfyve16 A T 13: 92,653,139 (GRCm39) N815K probably benign Het
Other mutations in Cnot9
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00791:Cnot9 APN 1 74,561,533 (GRCm39) missense probably benign 0.00
IGL02066:Cnot9 APN 1 74,566,212 (GRCm39) missense possibly damaging 0.88
Icebreaker UTSW 1 74,556,285 (GRCm39) missense probably benign 0.00
R1495:Cnot9 UTSW 1 74,562,759 (GRCm39) missense probably damaging 1.00
R4163:Cnot9 UTSW 1 74,568,006 (GRCm39) missense probably damaging 0.97
R6060:Cnot9 UTSW 1 74,556,285 (GRCm39) missense probably benign 0.00
R6165:Cnot9 UTSW 1 74,567,952 (GRCm39) missense probably benign 0.03
R6914:Cnot9 UTSW 1 74,558,154 (GRCm39) missense probably damaging 1.00
R7082:Cnot9 UTSW 1 74,566,165 (GRCm39) missense probably damaging 1.00
R7224:Cnot9 UTSW 1 74,556,388 (GRCm39) missense probably benign 0.16
R7514:Cnot9 UTSW 1 74,567,921 (GRCm39) missense probably benign
R7772:Cnot9 UTSW 1 74,566,151 (GRCm39) missense probably damaging 0.96
R9000:Cnot9 UTSW 1 74,561,544 (GRCm39) missense probably benign 0.21
R9065:Cnot9 UTSW 1 74,558,142 (GRCm39) nonsense probably null
Z1187:Cnot9 UTSW 1 74,556,285 (GRCm39) missense probably benign 0.00
Z1189:Cnot9 UTSW 1 74,556,285 (GRCm39) missense probably benign 0.00
Z1190:Cnot9 UTSW 1 74,556,285 (GRCm39) missense probably benign 0.00
Z1192:Cnot9 UTSW 1 74,556,285 (GRCm39) missense probably benign 0.00
Predicted Primers PCR Primer
(F):5'- GTCTTGCCTACTTAGTTTAGTACGC -3'
(R):5'- GTCACTGCCATGACTGAGC -3'

Sequencing Primer
(F):5'- CGCTTGTAATGAAAGGGTTATTCAG -3'
(R):5'- CTGATCACACAGCAAAGG -3'
Posted On 2018-11-06