Mutagenetix > Incidental Mutations

Incidental Mutation 'R1496:Scn9a'

168836

Institutional Source

Beutler Lab

Gene Symbol

Scn9a

Ensembl Gene

ENSMUSG00000075316

Gene Name

sodium channel, voltage-gated, type IX, alpha

Synonyms

PN1

MMRRC Submission

039547-MU

Accession Numbers

Is this an essential gene?

Essential (E-score: 1.000) question?

Stock #

R1496 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

66480080-66634962 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 66526888 bp

Zygosity

Heterozygous

Amino Acid Change

Threonine to Isoleucine at position 1012 (T1012I)

Ref Sequence

ENSEMBL: ENSMUSP00000131711 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000100063] [ENSMUST00000100064] [ENSMUST00000112354] [ENSMUST00000164384] [ENSMUST00000169900]

Predicted Effect

probably benign
Transcript: ENSMUST00000100063
AA Change: T1014I

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000097641
Gene: ENSMUSG00000075316
AA Change: T1014I

Domain	Start	End	E-Value	Type
low complexity region	29	49	N/A	INTRINSIC
Pfam:Ion_trans	154	403	9.5e-78	PFAM
coiled coil region	404	442	N/A	INTRINSIC
Pfam:DUF3451	465	685	1.3e-62	PFAM
Pfam:Ion_trans	768	957	9.9e-48	PFAM
Pfam:Na_trans_assoc	972	1191	2.9e-72	PFAM
low complexity region	1203	1214	N/A	INTRINSIC
Pfam:Ion_trans	1217	1445	2.8e-55	PFAM
PDB:1BYY\|A	1447	1499	9e-27	PDB
Pfam:Ion_trans	1538	1748	3.4e-52	PFAM
Pfam:PKD_channel	1599	1755	1.1e-7	PFAM
IQ	1877	1899	1.03e-3	SMART
low complexity region	1956	1972	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000100064
AA Change: T1023I

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000097642
Gene: ENSMUSG00000075316
AA Change: T1023I

Domain	Start	End	E-Value	Type
low complexity region	29	49	N/A	INTRINSIC
Pfam:Ion_trans	125	412	2.2e-84	PFAM
low complexity region	433	446	N/A	INTRINSIC
Pfam:Na_trans_cytopl	483	693	7.5e-76	PFAM
Pfam:Ion_trans	742	977	4.1e-57	PFAM
Pfam:Na_trans_assoc	981	1185	1.4e-58	PFAM
Pfam:Ion_trans	1189	1466	7e-67	PFAM
Pfam:Ion_trans	1512	1769	1e-55	PFAM
Pfam:PKD_channel	1605	1763	2.6e-7	PFAM
IQ	1886	1908	1.03e-3	SMART
low complexity region	1965	1981	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000112354
AA Change: T1012I

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000107973
Gene: ENSMUSG00000075316
AA Change: T1012I

Domain	Start	End	E-Value	Type
low complexity region	29	49	N/A	INTRINSIC
Pfam:Ion_trans	154	401	1.2e-77	PFAM
coiled coil region	402	449	N/A	INTRINSIC
Pfam:DUF3451	463	683	1.3e-62	PFAM
Pfam:Ion_trans	766	955	9.9e-48	PFAM
Pfam:Na_trans_assoc	970	1189	2.9e-72	PFAM
low complexity region	1201	1212	N/A	INTRINSIC
Pfam:Ion_trans	1215	1443	2.8e-55	PFAM
PDB:1BYY\|A	1445	1497	7e-29	PDB
Pfam:Ion_trans	1536	1746	3.4e-52	PFAM
Pfam:PKD_channel	1597	1753	1.1e-7	PFAM
IQ	1875	1897	1.03e-3	SMART
low complexity region	1954	1970	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000119700

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000141149

Predicted Effect

probably benign
Transcript: ENSMUST00000164384
AA Change: T1023I

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000126528
Gene: ENSMUSG00000075316
AA Change: T1023I

Domain	Start	End	E-Value	Type
low complexity region	29	49	N/A	INTRINSIC
Pfam:Ion_trans	154	401	1.1e-77	PFAM
coiled coil region	402	449	N/A	INTRINSIC
Pfam:DUF3451	463	694	4.2e-66	PFAM
Pfam:Ion_trans	777	966	8.8e-48	PFAM
Pfam:Na_trans_assoc	981	1200	6e-72	PFAM
low complexity region	1212	1223	N/A	INTRINSIC
Pfam:Ion_trans	1226	1454	2.5e-55	PFAM
PDB:1BYY\|A	1456	1508	6e-29	PDB
Pfam:Ion_trans	1547	1757	3e-52	PFAM
Pfam:PKD_channel	1608	1764	8.1e-8	PFAM
IQ	1886	1908	1.03e-3	SMART
low complexity region	1965	1981	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000169900
AA Change: T1012I

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000131711
Gene: ENSMUSG00000075316
AA Change: T1012I

Domain	Start	End	E-Value	Type
low complexity region	29	49	N/A	INTRINSIC
Pfam:Ion_trans	154	401	3.7e-78	PFAM
coiled coil region	402	449	N/A	INTRINSIC
Pfam:DUF3451	463	683	1.3e-62	PFAM
Pfam:Ion_trans	766	955	9.9e-48	PFAM
Pfam:Na_trans_assoc	970	1189	2.9e-72	PFAM
low complexity region	1201	1212	N/A	INTRINSIC
Pfam:Ion_trans	1215	1443	2.8e-55	PFAM
PDB:1BYY\|A	1445	1497	7e-29	PDB
Pfam:Ion_trans	1536	1746	3.4e-52	PFAM
Pfam:PKD_channel	1597	1753	1.1e-7	PFAM
IQ	1875	1897	1.03e-3	SMART
low complexity region	1954	1970	N/A	INTRINSIC

Meta Mutation Damage Score

0.0898

Coding Region Coverage

1x: 99.1%
3x: 98.3%
10x: 96.3%
20x: 92.9%

Validation Efficiency

98% (94/96)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a voltage-gated sodium channel which plays a significant role in nociception signaling. Mutations in this gene have been associated with primary erythermalgia, channelopathy-associated insensitivity to pain, and paroxysmal extreme pain disorder. [provided by RefSeq, Aug 2009]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit prenatal/neonatal lethality. Mice homozygous for a knock-in allele exhibit increased susceptibility to electrically induced seizures. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 90 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4931429L15Rik	A	G	9: 46,310,254		probably benign	Het
4933411K16Rik	T	C	19: 42,053,050	Y207H	probably damaging	Het
Abcc1	T	A	16: 14,448,434	L832Q	probably damaging	Het
Acan	T	A	7: 79,100,804	H1774Q	probably benign	Het
Adss	T	C	1: 177,772,194	T275A	probably benign	Het
Ano5	G	A	7: 51,583,775	R595H	probably damaging	Het
Araf	G	T	X: 20,859,704	R522L	probably damaging	Het
Arhgef28	C	T	13: 97,965,546	V807I	possibly damaging	Het
Bin1	T	C	18: 32,412,704	I103T	probably damaging	Het
C4b	C	T	17: 34,740,021	R478Q	probably benign	Het
Cacna1b	G	A	2: 24,678,035	P1015S	probably benign	Het
Capn1	A	G	19: 6,007,498		probably null	Het
Cep290	A	G	10: 100,538,966	Q1358R	probably damaging	Het
Cfap126	T	C	1: 171,125,817		probably benign	Het
Chn1	T	C	2: 73,679,607		probably benign	Het
Cldn8	T	C	16: 88,562,401	E212G	probably benign	Het
Cpb1	T	C	3: 20,263,532	N249S	probably damaging	Het
Cxcr6	A	T	9: 123,810,347	I138F	probably benign	Het
Dab2ip	G	A	2: 35,718,791	R579H	probably damaging	Het
Dcaf8	T	C	1: 172,193,855	M538T	probably benign	Het
Dhrs4	T	G	14: 55,487,650	L201V	probably damaging	Het
Dnah12	C	T	14: 26,710,248	A407V	probably benign	Het
Elavl3	T	A	9: 22,026,165		probably benign	Het
Elp4	T	C	2: 105,832,161	H88R	probably benign	Het
Ercc3	T	C	18: 32,261,297		probably benign	Het
Eri1	A	G	8: 35,469,181	S329P	possibly damaging	Het
Erich2	A	T	2: 70,512,773		probably benign	Het
Esyt1	A	G	10: 128,512,428	S864P	possibly damaging	Het
Fam170b	A	G	14: 32,835,631	E141G	probably damaging	Het
Fat1	A	G	8: 45,033,390	Y3304C	probably damaging	Het
Fbn1	T	C	2: 125,309,495	T2531A	probably benign	Het
Fgfr3	T	C	5: 33,729,750	V166A	probably damaging	Het
Glt8d2	T	C	10: 82,659,538	D194G	probably damaging	Het
Gpr89	A	G	3: 96,905,210	I5T	probably benign	Het
Gpx6	A	T	13: 21,318,920	H168L	probably benign	Het
Gusb	T	C	5: 129,998,544	T307A	probably benign	Het
Hjurp	A	T	1: 88,275,050	Y71N	possibly damaging	Het
Ifngr1	A	G	10: 19,601,445	D118G	probably benign	Het
Ipcef1	A	T	10: 6,935,173		probably null	Het
Kbtbd3	A	T	9: 4,330,276	T217S	probably benign	Het
Kmt5a	GAA	GA	5: 124,459,885		probably null	Het
Lrp1	T	C	10: 127,539,011	D4526G	probably damaging	Het
Lrp1b	A	T	2: 42,323,662	V46D	probably damaging	Het
Lsm8	T	A	6: 18,849,659	M22K	probably benign	Het
Map1lc3b	C	T	8: 121,596,600	R70C	possibly damaging	Het
Meiob	T	A	17: 24,813,052	S14T	possibly damaging	Het
Mkx	G	T	18: 6,992,330	Y183*	probably null	Het
Mrs2	T	C	13: 25,005,034	Y99C	probably benign	Het
Mycbpap	T	C	11: 94,505,561	K151R	probably benign	Het
Neb	T	G	2: 52,328,734	Q88P	probably damaging	Het
Noc4l	T	A	5: 110,650,078	H319L	probably damaging	Het
Nt5c2	G	A	19: 46,904,978	T122I	probably damaging	Het
Nuggc	A	T	14: 65,624,133	N476I	probably damaging	Het
Obscn	T	A	11: 59,031,036	H5978L	probably benign	Het
Oc90	G	T	15: 65,876,521	A412D	probably damaging	Het
Olfr1080	A	T	2: 86,553,752	V124E	probably damaging	Het
Olfr1143	T	G	2: 87,802,868	S160A	probably benign	Het
Olfr1249	A	G	2: 89,630,014	S295P	possibly damaging	Het
Olfr168	T	A	16: 19,530,383	D179V	possibly damaging	Het
Olfr399	A	G	11: 74,053,824	*312Q	probably null	Het
Olfr8	T	A	10: 78,955,848	S214R	probably benign	Het
Pdzrn3	A	T	6: 101,150,969	V912E	probably benign	Het
Phactr1	T	A	13: 43,094,990	Y387N	probably damaging	Het
Picalm	T	A	7: 90,130,651	C27S	probably benign	Het
Pkd1l1	T	A	11: 8,941,077	I314F	possibly damaging	Het
Pold2	T	C	11: 5,874,175	E210G	possibly damaging	Het
Ptprz1	C	T	6: 23,049,524		probably benign	Het
Rac1	G	T	5: 143,507,338	A165E	probably damaging	Het
Rpap3	G	T	15: 97,686,483	T360K	possibly damaging	Het
Sdad1	A	G	5: 92,309,823	I20T	possibly damaging	Het
Setbp1	T	G	18: 78,859,912	K180T	probably damaging	Het
Sgpl1	T	C	10: 61,102,589	N475S	probably damaging	Het
Shroom3	T	C	5: 92,942,834	S1148P	possibly damaging	Het
Sin3a	T	A	9: 57,119,158	H1119Q	possibly damaging	Het
Slc26a7	T	A	4: 14,506,489	Y620F	probably benign	Het
Slc4a1	T	C	11: 102,361,171	I36V	probably benign	Het
Smarca2	C	G	19: 26,631,101	P263A	possibly damaging	Het
Sp100	T	C	1: 85,663,521		probably benign	Het
Spag6l	A	G	16: 16,780,614		probably benign	Het
Sptbn1	T	C	11: 30,121,498	N1491S	probably damaging	Het
Tbl1xr1	T	G	3: 22,190,951	V155G	possibly damaging	Het
Tmc1	A	G	19: 20,868,355	I168T	probably damaging	Het
Tmem87b	G	A	2: 128,826,393		probably null	Het
Tnfrsf9	T	A	4: 150,933,104		probably null	Het
Tnni3k	T	C	3: 154,939,658	D530G	probably damaging	Het
Vmn1r209	G	A	13: 22,805,764	S252F	probably damaging	Het
Zbtb3	A	T	19: 8,803,350	N109I	probably damaging	Het
Zdhhc17	T	G	10: 110,946,210	H541P	probably damaging	Het
Zfp84	A	G	7: 29,776,614	I244V	possibly damaging	Het
Zyx	A	G	6: 42,356,312	Y393C	probably damaging	Het

Other mutations in Scn9a

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00514:Scn9a	APN	2	66563601	missense	probably damaging	1.00
IGL00570:Scn9a	APN	2	66484142	missense	probably damaging	1.00
IGL00809:Scn9a	APN	2	66483935	missense	probably damaging	1.00
IGL00977:Scn9a	APN	2	66484301	missense	probably damaging	0.99
IGL01120:Scn9a	APN	2	66526972	missense	probably benign	0.00
IGL01134:Scn9a	APN	2	66504968	missense	probably damaging	1.00
IGL01300:Scn9a	APN	2	66488053	nonsense	probably null
IGL01452:Scn9a	APN	2	66527072	missense	probably damaging	1.00
IGL01531:Scn9a	APN	2	66537378	missense	probably benign	0.11
IGL01572:Scn9a	APN	2	66493886	missense	probably benign	0.00
IGL01645:Scn9a	APN	2	66487642	missense	possibly damaging	0.62
IGL01823:Scn9a	APN	2	66484042	missense	probably damaging	1.00
IGL01965:Scn9a	APN	2	66484433	missense	probably damaging	1.00
IGL02127:Scn9a	APN	2	66547135	missense	probably damaging	1.00
IGL02127:Scn9a	APN	2	66494826	missense	probably damaging	1.00
IGL02166:Scn9a	APN	2	66493103	missense	possibly damaging	0.95
IGL02183:Scn9a	APN	2	66484611	splice site	probably benign
IGL02640:Scn9a	APN	2	66536096	critical splice donor site	probably null
IGL02685:Scn9a	APN	2	66537293	missense	probably damaging	1.00
IGL02798:Scn9a	APN	2	66540559	missense	possibly damaging	0.52
IGL02832:Scn9a	APN	2	66568029	missense	probably damaging	1.00
IGL03008:Scn9a	APN	2	66562511	missense	probably damaging	1.00
IGL03270:Scn9a	APN	2	66484014	missense	probably damaging	1.00
IGL03408:Scn9a	APN	2	66526747	missense	probably benign	0.00
R0039:Scn9a	UTSW	2	66562444	missense	probably damaging	0.98
R0173:Scn9a	UTSW	2	66533093	missense	probably damaging	1.00
R0323:Scn9a	UTSW	2	66568131	missense	probably damaging	1.00
R0344:Scn9a	UTSW	2	66505010	missense	probably damaging	0.99
R0421:Scn9a	UTSW	2	66543277	missense	probably benign
R0465:Scn9a	UTSW	2	66526996	missense	probably damaging	1.00
R0514:Scn9a	UTSW	2	66483678	missense	probably damaging	1.00
R0599:Scn9a	UTSW	2	66526799	missense	probably damaging	0.96
R0627:Scn9a	UTSW	2	66537377	missense	probably benign	0.00
R0644:Scn9a	UTSW	2	66533061	critical splice donor site	probably null
R0653:Scn9a	UTSW	2	66533377	missense	probably damaging	1.00
R0685:Scn9a	UTSW	2	66483499	missense	probably benign	0.02
R0718:Scn9a	UTSW	2	66547112	missense	probably damaging	1.00
R0827:Scn9a	UTSW	2	66536124	nonsense	probably null
R0890:Scn9a	UTSW	2	66483735	missense	probably damaging	1.00
R1139:Scn9a	UTSW	2	66504997	missense	probably benign	0.02
R1385:Scn9a	UTSW	2	66563542	missense	probably damaging	1.00
R1398:Scn9a	UTSW	2	66484586	missense	probably benign	0.11
R1511:Scn9a	UTSW	2	66526813	missense	probably benign	0.01
R1517:Scn9a	UTSW	2	66505027	splice site	probably benign
R1564:Scn9a	UTSW	2	66484304	missense	probably damaging	1.00
R1634:Scn9a	UTSW	2	66488017	missense	probably damaging	1.00
R1662:Scn9a	UTSW	2	66483459	missense	probably benign	0.00
R1695:Scn9a	UTSW	2	66504876	nonsense	probably null
R1709:Scn9a	UTSW	2	66483506	missense	probably damaging	1.00
R1741:Scn9a	UTSW	2	66487594	missense	probably damaging	0.99
R1755:Scn9a	UTSW	2	66501716	missense	probably benign	0.38
R1914:Scn9a	UTSW	2	66566250	missense	probably damaging	1.00
R1962:Scn9a	UTSW	2	66484311	missense	probably damaging	1.00
R1970:Scn9a	UTSW	2	66515380	missense	probably damaging	0.97
R2017:Scn9a	UTSW	2	66515321	missense	probably damaging	0.99
R2092:Scn9a	UTSW	2	66533376	missense	probably damaging	0.99
R2105:Scn9a	UTSW	2	66568183	missense	probably benign	0.25
R2114:Scn9a	UTSW	2	66484052	missense	probably damaging	1.00
R2115:Scn9a	UTSW	2	66484052	missense	probably damaging	1.00
R2128:Scn9a	UTSW	2	66526654	missense	probably damaging	1.00
R2157:Scn9a	UTSW	2	66536325	missense	probably damaging	1.00
R2162:Scn9a	UTSW	2	66534229	missense	probably damaging	0.98
R2350:Scn9a	UTSW	2	66504968	missense	probably damaging	1.00
R3694:Scn9a	UTSW	2	66562405	missense	probably benign
R3771:Scn9a	UTSW	2	66483648	missense	probably benign	0.26
R3772:Scn9a	UTSW	2	66483648	missense	probably benign	0.26
R3773:Scn9a	UTSW	2	66483648	missense	probably benign	0.26
R3922:Scn9a	UTSW	2	66526873	missense	possibly damaging	0.88
R3926:Scn9a	UTSW	2	66526873	missense	possibly damaging	0.88
R4258:Scn9a	UTSW	2	66565054	intron	probably benign
R4385:Scn9a	UTSW	2	66484556	missense	probably damaging	1.00
R4415:Scn9a	UTSW	2	66526693	missense	probably damaging	1.00
R4570:Scn9a	UTSW	2	66483558	missense	possibly damaging	0.85
R4682:Scn9a	UTSW	2	66547018	missense	probably benign
R4783:Scn9a	UTSW	2	66540623	missense	probably benign	0.01
R4822:Scn9a	UTSW	2	66483749	missense	possibly damaging	0.55
R4829:Scn9a	UTSW	2	66551713	missense	probably benign
R4908:Scn9a	UTSW	2	66526743	missense	probably benign	0.03
R4983:Scn9a	UTSW	2	66566270	missense	probably benign	0.02
R5047:Scn9a	UTSW	2	66562480	missense	probably damaging	1.00
R5100:Scn9a	UTSW	2	66534119	missense	probably damaging	1.00
R5140:Scn9a	UTSW	2	66565167	missense	possibly damaging	0.81
R5398:Scn9a	UTSW	2	66488043	missense	probably damaging	1.00
R5557:Scn9a	UTSW	2	66547103	missense	probably damaging	0.99
R5582:Scn9a	UTSW	2	66565029	intron	probably benign
R6108:Scn9a	UTSW	2	66484049	missense	probably damaging	1.00
R6115:Scn9a	UTSW	2	66563629	missense	possibly damaging	0.70
R6143:Scn9a	UTSW	2	66487524	missense	probably benign	0.00
R6261:Scn9a	UTSW	2	66483896	missense	probably damaging	1.00
R6335:Scn9a	UTSW	2	66568264	start codon destroyed	possibly damaging	0.91
R6429:Scn9a	UTSW	2	66526963	missense	possibly damaging	0.95
R6632:Scn9a	UTSW	2	66483502	missense	probably benign	0.23
R6681:Scn9a	UTSW	2	66563342	missense	possibly damaging	0.90
R6830:Scn9a	UTSW	2	66568029	missense	probably damaging	1.00
R7102:Scn9a	UTSW	2	66549015	missense	probably damaging	1.00
R7186:Scn9a	UTSW	2	66534223	missense	probably damaging	1.00
R7243:Scn9a	UTSW	2	66540530	missense	probably damaging	1.00
R7311:Scn9a	UTSW	2	66484404	missense	possibly damaging	0.54
R7328:Scn9a	UTSW	2	66484587	missense	probably benign
R7386:Scn9a	UTSW	2	66540550	missense	probably damaging	1.00
R7438:Scn9a	UTSW	2	66547187	missense	possibly damaging	0.81
R7483:Scn9a	UTSW	2	66533348	missense	probably damaging	0.99
R7485:Scn9a	UTSW	2	66534217	missense	probably damaging	1.00
R7526:Scn9a	UTSW	2	66483646	missense	probably benign
R7617:Scn9a	UTSW	2	66540549	missense	possibly damaging	0.55
R7642:Scn9a	UTSW	2	66536236	missense	probably benign	0.02
R7653:Scn9a	UTSW	2	66527080	missense	probably damaging	1.00
R7747:Scn9a	UTSW	2	66484298	missense	probably damaging	1.00
R7823:Scn9a	UTSW	2	66483791	missense	probably damaging	1.00
X0003:Scn9a	UTSW	2	66508647	missense	probably benign	0.02
X0062:Scn9a	UTSW	2	66568077	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- AAATCAGACTCCCCAGGTGCAATG -3'
(R):5'- ATGATTCTCTGCTCTTCAGGGCAAC -3'

Sequencing Primer
(F):5'- CAATGGGCACTGTCACTGTG -3'
(R):5'- CATGTGCAGAGTATTGAACCCTC -3'

Posted On

2014-04-13