Mutagenetix > Incidental Mutations

Incidental Mutation 'R4737:Chrna9'

359330

Institutional Source

Beutler Lab

Gene Symbol

Chrna9

Ensembl Gene

ENSMUSG00000029205

Gene Name

cholinergic receptor, nicotinic, alpha polypeptide 9

Synonyms

2410015I05Rik, Gm8311, Acra9

MMRRC Submission

042024-MU

Accession Numbers

Is this an essential gene?

Probably non essential (E-score: 0.109) question?

Stock #

R4737 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

65934921-65977326 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 65967871 bp

Zygosity

Heterozygous

Amino Acid Change

Threonine to Serine at position 52 (T52S)

Ref Sequence

ENSEMBL: ENSMUSP00000031108 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000031108] [ENSMUST00000201814] [ENSMUST00000202957]

Predicted Effect

probably damaging
Transcript: ENSMUST00000031108
AA Change: T52S

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000031108
Gene: ENSMUSG00000029205
AA Change: T52S

Domain	Start	End	E-Value	Type
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: ENSMUST00000153624
AA Change: T48S

PolyPhen 2 Score 0.059 (Sensitivity: 0.94; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000118246
Gene: ENSMUSG00000029205
AA Change: T48S

Domain	Start	End	E-Value	Type
Pfam:Neur_chan_LBD	27	233	1.3e-69	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000201814
AA Change: T48S

PolyPhen 2 Score 0.129 (Sensitivity: 0.93; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000144364
Gene: ENSMUSG00000029205
AA Change: T48S

Domain	Start	End	E-Value	Type
Pfam:Neur_chan_LBD	27	233	8.1e-71	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000202931

Predicted Effect

probably benign
Transcript: ENSMUST00000202957

Meta Mutation Damage Score

0.0975

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.2%
20x: 95.3%

Validation Efficiency

100% (94/94)

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: 88 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
A430110L20Rik	A	G	1: 181,227,819		noncoding transcript	Het
Acp2	A	T	2: 91,210,723	R419W	probably benign	Het
Actr5	A	G	2: 158,628,071	N207S	probably damaging	Het
Afap1	G	A	5: 35,961,782	V254M	probably benign	Het
Arfgef1	A	T	1: 10,189,611	M544K	possibly damaging	Het
Arhgap5	A	T	12: 52,519,077	M944L	probably benign	Het
Bnip3l-ps	G	A	12: 18,216,772		noncoding transcript	Het
Carf	A	G	1: 60,109,318	T58A	probably benign	Het
Carns1	A	G	19: 4,170,928		probably benign	Het
Ccp110	T	A	7: 118,724,548	I670K	possibly damaging	Het
Cftr	T	A	6: 18,299,883	D1218E	probably benign	Het
Chst9	T	C	18: 15,452,777	Y243C	probably damaging	Het
Clk2	A	T	3: 89,168,709	H62L	probably benign	Het
Cntnap2	A	T	6: 45,060,317	R10W	possibly damaging	Het
Cpt1b	C	T	15: 89,421,406	D369N	probably benign	Het
Crhr2	G	T	6: 55,091,305	H423Q	probably damaging	Het
D8Ertd738e	T	A	8: 84,249,521	I33F	probably damaging	Het
Dbt	T	C	3: 116,539,132	I200T	probably damaging	Het
Ddhd1	A	T	14: 45,628,821		probably benign	Het
Ddx27	A	G	2: 167,029,299	I480V	probably benign	Het
Dpp9	A	C	17: 56,198,970		probably null	Het
Dpy19l3	A	T	7: 35,703,501	M562K	probably damaging	Het
Dus3l	T	C	17: 56,767,868	L330P	probably damaging	Het
Efcab7	C	T	4: 99,831,568	Q96*	probably null	Het
Egfr	T	C	11: 16,869,231	F254L	probably damaging	Het
Eml5	C	T	12: 98,798,852	V1566M	probably damaging	Het
Entpd7	T	A	19: 43,691,195	Y62*	probably null	Het
Erbb4	T	C	1: 68,343,900	M313V	probably damaging	Het
Gm5528	A	G	1: 72,004,552		noncoding transcript	Het
H2-M9	G	T	17: 36,640,739	Y281*	probably null	Het
Hmcn1	T	G	1: 150,689,595	K2260N	possibly damaging	Het
Hnf4a	A	G	2: 163,564,219	I259V	probably benign	Het
Ick	A	G	9: 78,150,654	T162A	probably damaging	Het
Insm1	A	T	2: 146,222,902	T213S	probably benign	Het
Iqca	T	C	1: 90,077,822	D488G	probably damaging	Het
Kdm5a	T	A	6: 120,406,015		probably benign	Het
Kdm7a	G	C	6: 39,152,839	L468V	possibly damaging	Het
Lck	G	A	4: 129,555,984	T229I	possibly damaging	Het
Lig3	T	C	11: 82,787,727	L265P	probably damaging	Het
Lipa	T	A	19: 34,501,634	K229*	probably null	Het
Lrrk1	C	T	7: 66,306,873	S418N	probably benign	Het
Mark2	A	G	19: 7,281,232	V126A	probably damaging	Het
Met	T	C	6: 17,491,541	C101R	probably damaging	Het
Mkln1	A	T	6: 31,426,799	K85M	probably damaging	Het
Mst1	A	G	9: 108,080,521	R15G	probably benign	Het
Muc6	T	G	7: 141,640,159		probably benign	Het
Muc6	G	T	7: 141,638,772	T1996N	possibly damaging	Het
Myo7b	T	C	18: 31,998,602	S514G	probably damaging	Het
Narfl	A	T	17: 25,781,309	H322L	probably damaging	Het
Nars	T	C	18: 64,516,427	E11G	probably benign	Het
Ogdh	T	A	11: 6,297,044	F23I	probably benign	Het
Olfr1121	T	C	2: 87,372,321	I263T	probably damaging	Het
Olfr1186	C	T	2: 88,526,225	S214F	probably damaging	Het
Olfr1238	C	T	2: 89,406,486	V198I	probably benign	Het
Olfr1272	A	G	2: 90,282,381	S65P	probably damaging	Het
Olfr584	C	T	7: 103,085,914	A127V	probably damaging	Het
Olfr825	T	A	10: 130,162,838	T163S	probably benign	Het
Olfr979	A	T	9: 40,000,422	D268E	probably damaging	Het
Otub2	T	A	12: 103,392,844	L64Q	probably benign	Het
Pappa2	T	C	1: 158,957,012	R143G	probably benign	Het
Patl2	T	A	2: 122,125,306	T250S	probably damaging	Het
Pcdhac2	C	T	18: 37,145,899	T644I	possibly damaging	Het
Pi4kb	C	T	3: 95,004,338	T690I	probably damaging	Het
Pla2g4d	T	C	2: 120,266,790	Y776C	probably benign	Het
Plekhh2	C	T	17: 84,563,959	S215L	probably benign	Het
Psmd2	T	G	16: 20,659,815		probably benign	Het
Ptpn21	T	C	12: 98,708,844	E183G	probably benign	Het
Ptprg	T	A	14: 12,226,314	D527E	probably damaging	Het
Rhobtb1	T	A	10: 69,279,497		probably null	Het
Scel	T	A	14: 103,572,037	M271K	possibly damaging	Het
Senp3	A	T	11: 69,678,829	C310*	probably null	Het
Slc25a3	T	C	10: 91,122,188	T97A	possibly damaging	Het
Srsf11	A	T	3: 158,026,732	Y82*	probably null	Het
Tbc1d8	G	A	1: 39,402,878	T211I	possibly damaging	Het
Tbkbp1	T	C	11: 97,148,648	E145G	probably damaging	Het
Tln1	T	C	4: 43,540,588	N1471S	probably benign	Het
Tnn	T	G	1: 160,146,089	D236A	probably damaging	Het
Trmt2a	C	T	16: 18,251,286		probably benign	Het
Ttn	A	T	2: 76,811,243	L5176Q	possibly damaging	Het
Ubxn10	G	A	4: 138,735,948		probably benign	Het
Ulk4	G	A	9: 121,073,872	Q1180*	probably null	Het
Usp43	T	A	11: 67,855,505	K1120N	probably damaging	Het
Uspl1	T	A	5: 149,194,339	L244Q	possibly damaging	Het
Vmn1r32	T	C	6: 66,553,645	H49R	probably damaging	Het
Vmn2r4	T	C	3: 64,409,963	D118G	probably damaging	Het
Vwce	A	G	19: 10,650,579	I468V	probably benign	Het
Zbtb7c	G	T	18: 76,146,154	R561L	probably benign	Het
Zfp956	T	C	6: 47,962,542	S175P	probably damaging	Het

Other mutations in Chrna9

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00094:Chrna9	APN	5	65969257	missense	probably benign	0.25
IGL00742:Chrna9	APN	5	65971115	missense	probably benign	0.12
IGL01611:Chrna9	APN	5	65970944	missense	probably damaging	1.00
IGL02376:Chrna9	APN	5	65971159	missense	probably damaging	1.00
R0403:Chrna9	UTSW	5	65967892	missense	possibly damaging	0.89
R1506:Chrna9	UTSW	5	65969136	missense	probably benign	0.19
R2943:Chrna9	UTSW	5	65977095	missense	probably damaging	1.00
R4243:Chrna9	UTSW	5	65935036	critical splice donor site	probably null
R4290:Chrna9	UTSW	5	65977138	missense	probably benign	0.11
R4607:Chrna9	UTSW	5	65976735	missense	possibly damaging	0.77
R4814:Chrna9	UTSW	5	65977149	missense	probably damaging	1.00
R4932:Chrna9	UTSW	5	65969190	nonsense	probably null
R5044:Chrna9	UTSW	5	65971016	missense	probably damaging	0.99
R5128:Chrna9	UTSW	5	65971222	missense	probably benign	0.00
R5213:Chrna9	UTSW	5	65971084	nonsense	probably null
R5242:Chrna9	UTSW	5	65977080	missense	probably benign
R6760:Chrna9	UTSW	5	65971228	missense	probably damaging	1.00
R7131:Chrna9	UTSW	5	65977141	missense	possibly damaging	0.92
Z1177:Chrna9	UTSW	5	65971220	missense	probably damaging	1.00
Z1187:Chrna9	UTSW	5	65976780	missense	probably benign	0.03

Predicted Primers

PCR Primer
(F):5'- ATCATCAGGGTGGGTAAGACC -3'
(R):5'- CATTTCTGTCACACCCATTGAG -3'

Sequencing Primer
(F):5'- GAGCTCATCCACTCATTCCAAAG -3'
(R):5'- CCATTGAGAAGAAAACGCCTG -3'

Posted On

2015-11-11