Incidental Mutation 'R1506:Chrna9'
ID 167927
Institutional Source Beutler Lab
Gene Symbol Chrna9
Ensembl Gene ENSMUSG00000029205
Gene Name cholinergic receptor, nicotinic, alpha polypeptide 9
Synonyms Acra9, 2410015I05Rik, Gm8311
MMRRC Submission 039554-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.081) question?
Stock # R1506 (G1)
Quality Score 225
Status Validated
Chromosome 5
Chromosomal Location 66092264-66134669 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 66126479 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Alanine at position 78 (T78A)
Ref Sequence ENSEMBL: ENSMUSP00000031108 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000031108] [ENSMUST00000201814] [ENSMUST00000202957]
AlphaFold G3X8Z7
Predicted Effect probably benign
Transcript: ENSMUST00000031108
AA Change: T78A

PolyPhen 2 Score 0.190 (Sensitivity: 0.92; Specificity: 0.87)
SMART Domains Protein: ENSMUSP00000031108
Gene: ENSMUSG00000029205
AA Change: T78A

DomainStartEndE-ValueType
Pfam:Neur_chan_LBD 31 237 2.7e-69 PFAM
Pfam:Neur_chan_memb 244 475 8.6e-51 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000201814
AA Change: T74A

PolyPhen 2 Score 0.140 (Sensitivity: 0.92; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000144364
Gene: ENSMUSG00000029205
AA Change: T74A

DomainStartEndE-ValueType
Pfam:Neur_chan_LBD 27 233 8.1e-71 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000202931
Predicted Effect unknown
Transcript: ENSMUST00000202957
AA Change: T9A
Meta Mutation Damage Score 0.3650 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.4%
  • 10x: 96.5%
  • 20x: 93.7%
Validation Efficiency 98% (61/62)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene is a member of the ligand-gated ionic channel family and nicotinic acetylcholine receptor gene superfamily. It encodes a plasma membrane protein that forms homo- or hetero-oligomeric divalent cation channels. This protein is involved in cochlea hair cell development and is also expressed in the outer hair cells (OHCs) of the adult cochlea. [provided by RefSeq, Feb 2012]
PHENOTYPE: Homozygous mutation of this gene results in abnormal innervation of the outer hair cells and depressed olivocochlear response. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 60 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcc3 G T 11: 94,248,144 (GRCm39) T1152K possibly damaging Het
Acp3 T A 9: 104,201,373 (GRCm39) T82S probably damaging Het
Adam23 C T 1: 63,586,973 (GRCm39) P445S probably benign Het
Ap3b1 T A 13: 94,582,651 (GRCm39) probably benign Het
Artn A G 4: 117,784,058 (GRCm39) V136A probably damaging Het
Ash1l A G 3: 88,965,806 (GRCm39) T2403A probably damaging Het
Bbof1 G T 12: 84,470,273 (GRCm39) V120L probably damaging Het
Boc A G 16: 44,323,928 (GRCm39) Y158H probably damaging Het
Casp8 A G 1: 58,863,355 (GRCm39) E105G probably damaging Het
Cers4 T C 8: 4,570,557 (GRCm39) F206L probably benign Het
Creb3 A T 4: 43,566,193 (GRCm39) T263S possibly damaging Het
Cyp2c40 A G 19: 39,766,443 (GRCm39) V384A probably damaging Het
Dip2b G A 15: 100,080,994 (GRCm39) V879M probably damaging Het
Dnah17 C A 11: 118,016,213 (GRCm39) V14F possibly damaging Het
Epb41l4b T A 4: 57,088,824 (GRCm39) K144N probably damaging Het
Ercc6 A T 14: 32,291,821 (GRCm39) I1062F probably benign Het
Fabp3 C T 4: 130,206,180 (GRCm39) T57I probably benign Het
Fat2 C A 11: 55,175,090 (GRCm39) E1874D probably benign Het
Fbxw21 T A 9: 108,977,257 (GRCm39) I151F probably damaging Het
Fhip2a A G 19: 57,357,007 (GRCm39) I33V probably benign Het
Foxn1 A G 11: 78,256,761 (GRCm39) probably benign Het
Gpr63 G A 4: 25,008,227 (GRCm39) R317H probably damaging Het
Grip1 C A 10: 119,814,356 (GRCm39) H296N probably damaging Het
Gtdc1 A T 2: 44,465,506 (GRCm39) M288K possibly damaging Het
Guf1 T A 5: 69,724,509 (GRCm39) D488E possibly damaging Het
Gvin3 C T 7: 106,200,788 (GRCm39) D819N probably benign Het
Heatr5b C A 17: 79,060,576 (GRCm39) R2033L probably damaging Het
Hsd17b2 T A 8: 118,429,004 (GRCm39) probably null Het
Ino80 A T 2: 119,255,746 (GRCm39) L913* probably null Het
Inppl1 A C 7: 101,473,174 (GRCm39) S1159A probably benign Het
Kcnk7 G A 19: 5,756,140 (GRCm39) C122Y probably damaging Het
Mtor A G 4: 148,620,962 (GRCm39) probably benign Het
Muc4 A T 16: 32,574,033 (GRCm39) S704C possibly damaging Het
Nckap5 A T 1: 125,953,650 (GRCm39) C967* probably null Het
Nek10 T C 14: 14,999,078 (GRCm38) probably benign Het
Oas1h A T 5: 121,009,951 (GRCm39) D342V possibly damaging Het
Or10j2 A G 1: 173,098,336 (GRCm39) N198S probably benign Het
Or2ak7 T A 11: 58,575,014 (GRCm39) L105Q probably benign Het
Or2n1 A T 17: 38,486,091 (GRCm39) M39L probably benign Het
Or4m1 A G 14: 50,557,941 (GRCm39) V117A probably benign Het
Or8b1b T C 9: 38,375,439 (GRCm39) M34T probably benign Het
Prex1 A T 2: 166,429,001 (GRCm39) V694E probably damaging Het
Rad50 G A 11: 53,570,312 (GRCm39) A810V probably damaging Het
Rcor1 T C 12: 111,076,271 (GRCm39) S410P probably damaging Het
Rps14 A T 18: 60,909,551 (GRCm39) N26I probably benign Het
Slc38a1 T C 15: 96,483,431 (GRCm39) D299G probably benign Het
Slc5a1 T A 5: 33,312,052 (GRCm39) N481K possibly damaging Het
Slco3a1 A T 7: 74,009,683 (GRCm39) probably null Het
Spart T C 3: 55,024,992 (GRCm39) S196P probably damaging Het
Speg A G 1: 75,394,307 (GRCm39) T1701A probably benign Het
Sugt1 A G 14: 79,862,365 (GRCm39) N271S probably benign Het
Tbx15 A T 3: 99,259,228 (GRCm39) L366F possibly damaging Het
Tnc G A 4: 63,925,921 (GRCm39) T953I possibly damaging Het
Uqcc1 A G 2: 155,753,738 (GRCm39) S46P probably damaging Het
Vmn2r18 T C 5: 151,499,099 (GRCm39) probably null Het
Vmn2r7 T A 3: 64,614,500 (GRCm39) Y438F probably benign Het
Vmn2r72 T A 7: 85,398,419 (GRCm39) K520N probably benign Het
Vps52 T C 17: 34,176,868 (GRCm39) L74P probably damaging Het
Xpo5 G T 17: 46,538,814 (GRCm39) M673I probably benign Het
Zscan18 A G 7: 12,508,129 (GRCm39) V457A probably damaging Het
Other mutations in Chrna9
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00094:Chrna9 APN 5 66,126,600 (GRCm39) missense probably benign 0.25
IGL00742:Chrna9 APN 5 66,128,458 (GRCm39) missense probably benign 0.12
IGL01611:Chrna9 APN 5 66,128,287 (GRCm39) missense probably damaging 1.00
IGL02376:Chrna9 APN 5 66,128,502 (GRCm39) missense probably damaging 1.00
R0403:Chrna9 UTSW 5 66,125,235 (GRCm39) missense possibly damaging 0.89
R2943:Chrna9 UTSW 5 66,134,438 (GRCm39) missense probably damaging 1.00
R4243:Chrna9 UTSW 5 66,092,379 (GRCm39) critical splice donor site probably null
R4290:Chrna9 UTSW 5 66,134,481 (GRCm39) missense probably benign 0.11
R4607:Chrna9 UTSW 5 66,134,078 (GRCm39) missense possibly damaging 0.77
R4737:Chrna9 UTSW 5 66,125,214 (GRCm39) missense probably damaging 1.00
R4814:Chrna9 UTSW 5 66,134,492 (GRCm39) missense probably damaging 1.00
R4932:Chrna9 UTSW 5 66,126,533 (GRCm39) nonsense probably null
R5044:Chrna9 UTSW 5 66,128,359 (GRCm39) missense probably damaging 0.99
R5128:Chrna9 UTSW 5 66,128,565 (GRCm39) missense probably benign 0.00
R5213:Chrna9 UTSW 5 66,128,427 (GRCm39) nonsense probably null
R5242:Chrna9 UTSW 5 66,134,423 (GRCm39) missense probably benign
R6760:Chrna9 UTSW 5 66,128,571 (GRCm39) missense probably damaging 1.00
R7131:Chrna9 UTSW 5 66,134,484 (GRCm39) missense possibly damaging 0.92
R9328:Chrna9 UTSW 5 66,128,569 (GRCm39) missense probably damaging 1.00
R9506:Chrna9 UTSW 5 66,128,213 (GRCm39) missense probably damaging 1.00
Z1177:Chrna9 UTSW 5 66,128,563 (GRCm39) missense probably damaging 1.00
Z1187:Chrna9 UTSW 5 66,134,123 (GRCm39) missense probably benign 0.03
Predicted Primers PCR Primer
(F):5'- GAAGGCATTGAATGCGGCCTTG -3'
(R):5'- AAGATGTAGCTCACGCTGGCAC -3'

Sequencing Primer
(F):5'- CATTGAATGCGGCCTTGATAATC -3'
(R):5'- GACGGCAAACACTAGGCTTTTATG -3'
Posted On 2014-04-13