Incidental Mutation 'R5044:Chrna9'
ID 394247
Institutional Source Beutler Lab
Gene Symbol Chrna9
Ensembl Gene ENSMUSG00000029205
Gene Name cholinergic receptor, nicotinic, alpha polypeptide 9
Synonyms Acra9, 2410015I05Rik, Gm8311
MMRRC Submission 042634-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.081) question?
Stock # R5044 (G1)
Quality Score 225
Status Validated
Chromosome 5
Chromosomal Location 66092264-66134669 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 66128359 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Leucine to Proline at position 189 (L189P)
Ref Sequence ENSEMBL: ENSMUSP00000031108 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000031108] [ENSMUST00000201814] [ENSMUST00000202957]
AlphaFold G3X8Z7
Predicted Effect probably damaging
Transcript: ENSMUST00000031108
AA Change: L189P

PolyPhen 2 Score 0.992 (Sensitivity: 0.70; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000031108
Gene: ENSMUSG00000029205
AA Change: L189P

DomainStartEndE-ValueType
Pfam:Neur_chan_LBD 31 237 2.7e-69 PFAM
Pfam:Neur_chan_memb 244 475 8.6e-51 PFAM
Predicted Effect possibly damaging
Transcript: ENSMUST00000153624
AA Change: L185P

PolyPhen 2 Score 0.633 (Sensitivity: 0.87; Specificity: 0.91)
SMART Domains Protein: ENSMUSP00000118246
Gene: ENSMUSG00000029205
AA Change: L185P

DomainStartEndE-ValueType
Pfam:Neur_chan_LBD 27 233 1.3e-69 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000201664
Predicted Effect possibly damaging
Transcript: ENSMUST00000201814
AA Change: L185P

PolyPhen 2 Score 0.819 (Sensitivity: 0.84; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000144364
Gene: ENSMUSG00000029205
AA Change: L185P

DomainStartEndE-ValueType
Pfam:Neur_chan_LBD 27 233 8.1e-71 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000202957
Meta Mutation Damage Score 0.6467 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.4%
  • 10x: 96.6%
  • 20x: 93.3%
Validation Efficiency 96% (73/76)
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: 65 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca13 T A 11: 9,323,323 (GRCm39) F3387I possibly damaging Het
Acacb T A 5: 114,304,088 (GRCm39) S170R probably benign Het
Adamtsl4 A G 3: 95,588,960 (GRCm39) probably null Het
Adgrv1 A G 13: 81,637,050 (GRCm39) C3464R probably benign Het
Apbb1 A T 7: 105,214,889 (GRCm39) probably benign Het
Cad A G 5: 31,212,365 (GRCm39) T23A probably benign Het
Cdca7 A G 2: 72,313,759 (GRCm39) R183G probably benign Het
Cdpf1 T C 15: 85,693,513 (GRCm39) T5A probably benign Het
Cep85 T C 4: 133,883,490 (GRCm39) D133G probably damaging Het
Clca3a1 A C 3: 144,713,689 (GRCm39) probably null Het
Cntn1 G T 15: 92,140,876 (GRCm39) V201F probably damaging Het
Col4a3 A G 1: 82,644,267 (GRCm39) E352G unknown Het
Ddhd2 T C 8: 26,242,164 (GRCm39) Y237C probably damaging Het
Dnah6 A C 6: 73,014,605 (GRCm39) F3609V probably benign Het
Epha3 T C 16: 63,422,650 (GRCm39) K580R possibly damaging Het
Fam135b T C 15: 71,334,560 (GRCm39) N878S probably benign Het
Fbn1 T G 2: 125,171,022 (GRCm39) T1938P probably damaging Het
Foxg1 T C 12: 49,431,969 (GRCm39) V234A probably damaging Het
Garin5b T C 7: 4,761,660 (GRCm39) N351D probably benign Het
Glt1d1 A T 5: 127,721,478 (GRCm39) N55I probably benign Het
Gm17641 C A 3: 68,776,807 (GRCm39) probably benign Het
Gm7665 A G 18: 16,407,788 (GRCm39) noncoding transcript Het
Hgf A C 5: 16,819,892 (GRCm39) N541T probably benign Het
Hipk2 G A 6: 38,795,814 (GRCm39) P152S probably benign Het
Jarid2 C T 13: 45,060,041 (GRCm39) L720F probably damaging Het
Kifc5b A G 17: 27,143,761 (GRCm39) E511G probably damaging Het
Ldlr G A 9: 21,646,538 (GRCm39) A235T probably benign Het
Lmln A G 16: 32,894,550 (GRCm39) D231G possibly damaging Het
Lrp1 A G 10: 127,403,364 (GRCm39) C2070R probably damaging Het
Mbl1 A G 14: 40,880,681 (GRCm39) T190A possibly damaging Het
Mpdz A T 4: 81,299,934 (GRCm39) S355T probably benign Het
Muc19 C T 15: 91,772,332 (GRCm39) noncoding transcript Het
Mycbp2 A C 14: 103,376,671 (GRCm39) probably null Het
Naa20 T C 2: 145,757,762 (GRCm39) S164P probably damaging Het
Nme4 A T 17: 26,312,807 (GRCm39) probably benign Het
Npas2 A T 1: 39,386,587 (GRCm39) R619* probably null Het
Nudt19 G A 7: 35,255,171 (GRCm39) T20I possibly damaging Het
Or4c119 T A 2: 88,987,283 (GRCm39) K79* probably null Het
Or5b97 A G 19: 12,878,365 (GRCm39) Y260H probably damaging Het
Pitpnc1 A G 11: 107,187,054 (GRCm39) Y90H possibly damaging Het
Rcor2 A G 19: 7,247,150 (GRCm39) T6A probably benign Het
Rif1 T A 2: 51,999,940 (GRCm39) S1131R probably damaging Het
Rtkn T A 6: 83,127,972 (GRCm39) D377E probably benign Het
Rtn4rl2 T A 2: 84,702,846 (GRCm39) N242I probably damaging Het
Sbno2 G A 10: 79,898,022 (GRCm39) L719F probably benign Het
Scn11a G T 9: 119,648,897 (GRCm39) D55E probably damaging Het
Setd1b T A 5: 123,289,929 (GRCm39) I632N unknown Het
Spaca6 A G 17: 18,051,458 (GRCm39) T45A probably benign Het
Srpk2 A T 5: 23,729,390 (GRCm39) D416E possibly damaging Het
Sspo A T 6: 48,443,889 (GRCm39) probably null Het
Sycp1 A T 3: 102,752,370 (GRCm39) I804N probably benign Het
Tdp2 G A 13: 25,015,809 (GRCm39) R32Q probably benign Het
Tgfbr3 A G 5: 107,284,795 (GRCm39) V618A possibly damaging Het
Tmc3 C T 7: 83,258,326 (GRCm39) P439S probably benign Het
Tnxb A T 17: 34,936,457 (GRCm39) D2740V probably damaging Het
Tspyl4 A G 10: 34,173,933 (GRCm39) T142A probably benign Het
Ttn T C 2: 76,710,785 (GRCm39) probably benign Het
Tubgcp4 T C 2: 121,004,061 (GRCm39) L34P probably damaging Het
Tubgcp6 G T 15: 88,983,748 (GRCm39) probably benign Het
Unc79 T A 12: 103,078,962 (GRCm39) V1690E probably benign Het
Vps4b T C 1: 106,724,148 (GRCm39) probably null Het
Wtap A G 17: 13,186,525 (GRCm39) S341P possibly damaging Het
Wwc1 T C 11: 35,774,172 (GRCm39) T363A probably benign Het
Zbtb8a G A 4: 129,254,293 (GRCm39) T67M probably damaging Het
Zfp865 T C 7: 5,037,668 (GRCm39) probably benign 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
R1506:Chrna9 UTSW 5 66,126,479 (GRCm39) missense probably benign 0.19
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
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'- TCTTCAGAGCCGGTGAACAC -3'
(R):5'- CTGCTGGGAGGTAGAAACTC -3'

Sequencing Primer
(F):5'- CCAACGTGGTCCTGCGG -3'
(R):5'- CTGGGAGGTAGAAACTCAGCGG -3'
Posted On 2016-06-15