Mutagenetix > Incidental Mutation

Incidental Mutation 'R2216:Scn5a'

241166

Institutional Source

Beutler Lab

Gene Symbol

Scn5a

Ensembl Gene

ENSMUSG00000032511

Gene Name

sodium channel, voltage-gated, type V, alpha

Synonyms

Nav1.5c, Nav1.5, mH1, SkM2

MMRRC Submission

040218-MU

Accession Numbers

Ncbi RefSeq: NM_021544.4, NM_001253860.1; MGI:98251

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R2216 (G1)

Quality Score

196

Status

Not validated

Chromosome

Chromosomal Location

119483408-119579016 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 119513085 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Cysteine at position 1138 (Y1138C)

Ref Sequence

ENSEMBL: ENSMUSP00000113272 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000065196] [ENSMUST00000117911] [ENSMUST00000120420]

AlphaFold

Q9JJV9

Predicted Effect

probably benign
Transcript: ENSMUST00000065196
AA Change: Y1139C

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

SMART Domains

Protein: ENSMUSP00000066228
Gene: ENSMUSG00000032511
AA Change: Y1139C

Domain	Start	End	E-Value	Type
Pfam:Ion_trans	130	423	2.4e-82	PFAM
Pfam:Na_trans_cytopl	478	667	5.2e-49	PFAM
Pfam:Ion_trans	716	950	1.1e-54	PFAM
Pfam:Na_trans_assoc	955	1203	2.9e-57	PFAM
Pfam:Ion_trans	1207	1484	2e-66	PFAM
Pfam:Ion_trans	1530	1786	7.2e-55	PFAM
Pfam:PKD_channel	1627	1780	3.5e-7	PFAM
IQ	1903	1925	5e-2	SMART
low complexity region	1961	1983	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000117911
AA Change: Y1139C

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

SMART Domains

Protein: ENSMUSP00000112838
Gene: ENSMUSG00000032511
AA Change: Y1139C

Domain	Start	End	E-Value	Type
Pfam:Ion_trans	159	412	9.6e-76	PFAM
coiled coil region	413	451	N/A	INTRINSIC
Pfam:DUF3451	461	668	4.9e-44	PFAM
Pfam:Ion_trans	751	940	2.3e-46	PFAM
Pfam:Na_trans_assoc	955	1218	1.2e-73	PFAM
Pfam:Ion_trans	1244	1472	2e-56	PFAM
PDB:1BYY\|A	1474	1526	5e-29	PDB
Pfam:Ion_trans	1565	1774	1.5e-49	PFAM
Pfam:PKD_channel	1627	1781	2.6e-10	PFAM
IQ	1903	1925	5e-2	SMART
low complexity region	1961	1983	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000120420
AA Change: Y1138C

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

SMART Domains

Protein: ENSMUSP00000113272
Gene: ENSMUSG00000032511
AA Change: Y1138C

Domain	Start	End	E-Value	Type
Pfam:Ion_trans	159	412	4.5e-75	PFAM
coiled coil region	413	451	N/A	INTRINSIC
Pfam:DUF3451	461	668	7.4e-43	PFAM
Pfam:Ion_trans	751	940	1.2e-45	PFAM
Pfam:Na_trans_assoc	955	1217	1.6e-72	PFAM
Pfam:Ion_trans	1243	1471	1.1e-55	PFAM
PDB:1BYY\|A	1473	1525	5e-29	PDB
Pfam:Ion_trans	1564	1773	8.2e-49	PFAM
Pfam:PKD_channel	1626	1780	2.6e-9	PFAM
IQ	1902	1924	5e-2	SMART
low complexity region	1960	1982	N/A	INTRINSIC

Coding Region Coverage

1x: 99.1%
3x: 98.5%
10x: 97.0%
20x: 94.2%

Validation Efficiency

MGI Phenotype

Strain: 2179753; 3765977
Lethality: E10-E12
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is an integral membrane protein and tetrodotoxin-resistant voltage-gated sodium channel subunit. This protein is found primarily in cardiac muscle and is responsible for the initial upstroke of the action potential in an electrocardiogram. Defects in this gene are a cause of long QT syndrome type 3 (LQT3), an autosomal dominant cardiac disease. Alternative splicing results in several transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for mutations in this gene die prenatally usually during organogenesis and may display decreased embryo size and abnormal cardiovascular system physiology. Heterozygous mice typically display abnormal heartbeats and defects in the function of the impulse conduction system. [provided by MGI curators]

Allele List at MGI

All alleles(11) : Targeted(9) Gene trapped(2)

Other mutations in this stock

Total: 53 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aipl1	G	T	11: 72,031,446	P146T	probably damaging	Het
Arnt2	T	A	7: 84,275,351	T423S	probably damaging	Het
Bend5	A	G	4: 111,448,590	N277S	probably null	Het
Cd22	G	T	7: 30,867,046	T816N	probably damaging	Het
Cep126	G	A	9: 8,120,678	R115C	probably damaging	Het
Cep85	T	C	4: 134,131,430	H710R	possibly damaging	Het
Cmya5	A	T	13: 93,093,495	L1695H	probably damaging	Het
Col24a1	T	C	3: 145,314,981	V371A	probably benign	Het
Csmd1	T	A	8: 17,027,339		probably null	Het
Cyp1a1	T	A	9: 57,702,069		probably null	Het
Dennd1c	C	T	17: 57,074,492		probably null	Het
Dmxl1	G	A	18: 49,893,923	V2033I	probably benign	Het
Dtna	A	G	18: 23,569,565	H51R	probably damaging	Het
Dysf	G	A	6: 84,207,245		probably null	Het
Gcn1l1	T	A	5: 115,593,661	V945E	probably benign	Het
Gm12800	T	A	4: 101,910,060	W169R	probably damaging	Het
Gpbar1	C	G	1: 74,278,894	L99V	probably damaging	Het
Hdac9	A	T	12: 34,429,517	D212E	probably damaging	Het
Itga1	A	T	13: 114,997,029	D448E	probably benign	Het
Itga2b	T	A	11: 102,467,866	N75I	probably benign	Het
Klra7	T	C	6: 130,228,586	E117G	probably benign	Het
Kmt2b	G	A	7: 30,574,065	R2349C	probably benign	Het
Masp1	T	C	16: 23,492,055	N209S	probably benign	Het
Mybpc2	C	T	7: 44,512,500		probably null	Het
Myh15	C	G	16: 49,165,838	S1557*	probably null	Het
Myo3a	A	C	2: 22,577,771	T346P	probably benign	Het
Nim1k	A	G	13: 119,714,215	Y152H	probably damaging	Het
Nrp2	C	T	1: 62,762,918	R507*	probably null	Het
Olfr513	C	T	7: 108,755,612	T252M	probably damaging	Het
Olfr702	T	A	7: 106,823,998	H176L	probably damaging	Het
Parp14	T	C	16: 35,857,205	I798V	probably benign	Het
Pcnx2	C	T	8: 125,888,077	A212T	probably benign	Het
Pkhd1l1	A	T	15: 44,573,895	H3522L	probably damaging	Het
Pram1	C	T	17: 33,641,284	A275V	probably benign	Het
Prkag1	A	T	15: 98,815,946	M1K	probably null	Het
Prss52	T	C	14: 64,113,593	S276P	probably damaging	Het
Ranbp17	A	T	11: 33,481,125	V284D	probably damaging	Het
Reln	T	C	5: 22,048,005	D648G	probably benign	Het
Rnf112	A	G	11: 61,452,279	L190P	probably damaging	Het
Slc4a9	A	G	18: 36,530,745	H274R	probably benign	Het
Slc5a6	T	G	5: 31,039,335	E391D	possibly damaging	Het
Speer2	T	C	16: 69,858,842	Q32R	possibly damaging	Het
Tars	A	G	15: 11,389,708	V372A	probably benign	Het
Thsd7a	A	T	6: 12,337,268	L1250Q	possibly damaging	Het
Tnnt3	A	G	7: 142,512,564	Y222C	probably benign	Het
Trim40	T	C	17: 36,888,983	I68V	probably benign	Het
Trp53tg5	T	C	2: 164,471,306	I150V	probably benign	Het
Ube2u	T	C	4: 100,532,168	V109A	probably benign	Het
Usp54	A	T	14: 20,561,840	D969E	probably benign	Het
Vil1	G	T	1: 74,425,679	R495L	probably benign	Het
Wfs1	T	A	5: 36,967,220	K700*	probably null	Het
Zcchc8	A	G	5: 123,707,403	L298P	probably damaging	Het
Zfp946	A	T	17: 22,454,716	Q150H	possibly damaging	Het

Other mutations in Scn5a

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00336:Scn5a	APN	9	119486224	missense	probably damaging	1.00
IGL00480:Scn5a	APN	9	119517538	missense	possibly damaging	0.73
IGL00542:Scn5a	APN	9	119492126	missense	probably damaging	1.00
IGL00852:Scn5a	APN	9	119537682	missense	probably benign	0.26
IGL00895:Scn5a	APN	9	119513104	splice site	probably null
IGL00905:Scn5a	APN	9	119536501	missense	probably damaging	1.00
IGL01347:Scn5a	APN	9	119562441	nonsense	probably null
IGL01396:Scn5a	APN	9	119534704	missense	probably damaging	0.98
IGL01402:Scn5a	APN	9	119486470	missense	probably damaging	1.00
IGL01404:Scn5a	APN	9	119486470	missense	probably damaging	1.00
IGL01487:Scn5a	APN	9	119562623	start codon destroyed	probably null	0.90
IGL01612:Scn5a	APN	9	119486025	missense	possibly damaging	0.86
IGL02134:Scn5a	APN	9	119485892	missense	probably damaging	0.98
IGL02434:Scn5a	APN	9	119533793	missense	possibly damaging	0.83
IGL02698:Scn5a	APN	9	119521097	missense	probably damaging	1.00
IGL02717:Scn5a	APN	9	119529010	missense	probably benign	0.12
IGL02746:Scn5a	APN	9	119550637	missense	probably damaging	1.00
IGL02951:Scn5a	APN	9	119495685	missense	probably damaging	1.00
IGL03155:Scn5a	APN	9	119512182	missense	possibly damaging	0.74
IGL03188:Scn5a	APN	9	119522566	missense	probably damaging	1.00
IGL03268:Scn5a	APN	9	119521231	missense	probably damaging	1.00
IGL03287:Scn5a	APN	9	119489778	missense	probably damaging	1.00
IGL03328:Scn5a	APN	9	119537636	missense	probably benign	0.12
PIT4142001:Scn5a	UTSW	9	119486258	missense	probably damaging	1.00
PIT4520001:Scn5a	UTSW	9	119534570	missense	possibly damaging	0.56
R0026:Scn5a	UTSW	9	119522566	missense	probably damaging	1.00
R0044:Scn5a	UTSW	9	119492047	critical splice donor site	probably null
R0044:Scn5a	UTSW	9	119492047	critical splice donor site	probably null
R0267:Scn5a	UTSW	9	119543135	missense	probably damaging	0.98
R0313:Scn5a	UTSW	9	119534571	missense	probably damaging	1.00
R0360:Scn5a	UTSW	9	119522599	missense	probably damaging	0.99
R0364:Scn5a	UTSW	9	119522599	missense	probably damaging	0.99
R0369:Scn5a	UTSW	9	119533772	missense	probably damaging	0.99
R0512:Scn5a	UTSW	9	119550658	missense	probably damaging	1.00
R0681:Scn5a	UTSW	9	119539640	missense	probably damaging	0.96
R1163:Scn5a	UTSW	9	119533927	missense	probably damaging	1.00
R1469:Scn5a	UTSW	9	119533661	critical splice donor site	probably null
R1469:Scn5a	UTSW	9	119533661	critical splice donor site	probably null
R1470:Scn5a	UTSW	9	119536475	missense	possibly damaging	0.82
R1470:Scn5a	UTSW	9	119536475	missense	possibly damaging	0.82
R1530:Scn5a	UTSW	9	119495562	missense	probably damaging	1.00
R1532:Scn5a	UTSW	9	119533847	missense	probably damaging	1.00
R1544:Scn5a	UTSW	9	119486633	missense	probably damaging	1.00
R1588:Scn5a	UTSW	9	119521301	missense	probably damaging	1.00
R1597:Scn5a	UTSW	9	119562497	missense	probably damaging	0.99
R1607:Scn5a	UTSW	9	119486092	missense	probably damaging	1.00
R1657:Scn5a	UTSW	9	119562380	missense	probably damaging	1.00
R1664:Scn5a	UTSW	9	119521177	missense	possibly damaging	0.84
R1785:Scn5a	UTSW	9	119521129	missense	probably damaging	1.00
R1925:Scn5a	UTSW	9	119529019	missense	probably benign
R1956:Scn5a	UTSW	9	119517413	missense	possibly damaging	0.82
R2006:Scn5a	UTSW	9	119536480	missense	probably damaging	1.00
R2061:Scn5a	UTSW	9	119485651	missense	probably damaging	0.98
R2083:Scn5a	UTSW	9	119492123	missense	probably benign	0.45
R2180:Scn5a	UTSW	9	119516051	missense	probably benign
R2216:Scn5a	UTSW	9	119485612	missense	probably benign	0.37
R2320:Scn5a	UTSW	9	119529956	critical splice donor site	probably null
R2377:Scn5a	UTSW	9	119539727	missense	probably damaging	1.00
R2510:Scn5a	UTSW	9	119533685	missense	probably benign	0.05
R3113:Scn5a	UTSW	9	119485672	missense	probably damaging	1.00
R3769:Scn5a	UTSW	9	119552076	critical splice acceptor site	probably benign
R4133:Scn5a	UTSW	9	119486372	missense	probably damaging	1.00
R4164:Scn5a	UTSW	9	119495778	missense	probably damaging	1.00
R4447:Scn5a	UTSW	9	119550627	missense	probably damaging	1.00
R4635:Scn5a	UTSW	9	119528985	missense	possibly damaging	0.47
R4734:Scn5a	UTSW	9	119539538	missense	probably damaging	0.98
R4829:Scn5a	UTSW	9	119534707	missense	probably benign	0.00
R4867:Scn5a	UTSW	9	119550671	nonsense	probably null
R5055:Scn5a	UTSW	9	119522566	missense	probably damaging	1.00
R5229:Scn5a	UTSW	9	119535976	missense	probably damaging	1.00
R5344:Scn5a	UTSW	9	119534007	missense	probably benign	0.25
R5424:Scn5a	UTSW	9	119501734	missense	probably damaging	1.00
R5517:Scn5a	UTSW	9	119495713	missense	probably damaging	1.00
R5526:Scn5a	UTSW	9	119521171	missense	probably damaging	1.00
R5560:Scn5a	UTSW	9	119560286	missense	probably damaging	1.00
R5719:Scn5a	UTSW	9	119530052	missense	possibly damaging	0.91
R5726:Scn5a	UTSW	9	119533847	missense	probably damaging	1.00
R5800:Scn5a	UTSW	9	119501666	missense	probably damaging	1.00
R5826:Scn5a	UTSW	9	119521333	missense	probably damaging	1.00
R6046:Scn5a	UTSW	9	119562374	missense	probably damaging	1.00
R6101:Scn5a	UTSW	9	119522650	missense	probably damaging	0.98
R6162:Scn5a	UTSW	9	119522555	missense	probably damaging	0.98
R6375:Scn5a	UTSW	9	119543356	missense	probably damaging	1.00
R6378:Scn5a	UTSW	9	119486036	missense	probably damaging	1.00
R6464:Scn5a	UTSW	9	119534580	missense	probably damaging	1.00
R6794:Scn5a	UTSW	9	119535889	missense	probably damaging	0.98
R6799:Scn5a	UTSW	9	119495622	missense	possibly damaging	0.62
R6850:Scn5a	UTSW	9	119501749	missense	possibly damaging	0.92
R6858:Scn5a	UTSW	9	119492090	missense	probably benign	0.11
R6861:Scn5a	UTSW	9	119530023	missense	probably damaging	1.00
R6875:Scn5a	UTSW	9	119486644	missense	probably damaging	1.00
R6989:Scn5a	UTSW	9	119486329	missense	probably damaging	1.00
R7009:Scn5a	UTSW	9	119485930	missense	probably damaging	1.00
R7064:Scn5a	UTSW	9	119489911	missense	probably damaging	0.99
R7145:Scn5a	UTSW	9	119486371	missense	probably damaging	1.00
R7212:Scn5a	UTSW	9	119543385	missense	possibly damaging	0.94
R7238:Scn5a	UTSW	9	119491544	missense	possibly damaging	0.73
R7266:Scn5a	UTSW	9	119562560	missense	probably benign	0.37
R7348:Scn5a	UTSW	9	119535833	missense	probably benign	0.00
R7399:Scn5a	UTSW	9	119486530	missense	probably damaging	1.00
R7453:Scn5a	UTSW	9	119522590	missense	possibly damaging	0.82
R7495:Scn5a	UTSW	9	119543134	missense	probably damaging	0.99
R7681:Scn5a	UTSW	9	119529977	missense	probably benign	0.01
R7729:Scn5a	UTSW	9	119495540	missense	probably damaging	1.00
R7791:Scn5a	UTSW	9	119543336	missense	possibly damaging	0.47
R7794:Scn5a	UTSW	9	119529087	missense	probably damaging	0.99
R7873:Scn5a	UTSW	9	119498127	missense	probably damaging	1.00
R7951:Scn5a	UTSW	9	119529079	missense	probably damaging	1.00
R8154:Scn5a	UTSW	9	119562545	missense	possibly damaging	0.48
R8306:Scn5a	UTSW	9	119521291	missense	probably damaging	1.00
R8329:Scn5a	UTSW	9	119535964	missense	probably damaging	0.96
R8390:Scn5a	UTSW	9	119539538	missense	possibly damaging	0.59
R8536:Scn5a	UTSW	9	119539745	missense	probably damaging	1.00
R8922:Scn5a	UTSW	9	119534700	missense	probably benign
R9000:Scn5a	UTSW	9	119492105	missense	possibly damaging	0.95
R9015:Scn5a	UTSW	9	119552076	critical splice acceptor site	probably benign
R9272:Scn5a	UTSW	9	119486651	missense	probably damaging	1.00
R9394:Scn5a	UTSW	9	119495616	missense	probably damaging	1.00
R9448:Scn5a	UTSW	9	119552061	missense	probably damaging	0.99
R9511:Scn5a	UTSW	9	119522545	missense	probably benign	0.00
R9563:Scn5a	UTSW	9	119486737	missense	probably damaging	1.00
R9593:Scn5a	UTSW	9	119486773	missense	probably damaging	1.00
X0023:Scn5a	UTSW	9	119517769	missense	probably damaging	1.00
X0065:Scn5a	UTSW	9	119485669	missense	probably damaging	1.00
Z1177:Scn5a	UTSW	9	119522518	missense	probably damaging	1.00
Z1177:Scn5a	UTSW	9	119533931	missense	probably benign	0.04

Predicted Primers

PCR Primer
(F):5'- AACTAGCTCACACGTGCCTG -3'
(R):5'- TGTGGCAGACATTGAGACAC -3'

Sequencing Primer
(F):5'- GAAGCAGACTCCAGCTCAGG -3'
(R):5'- TTGAGACACCTCCACCTCAGAG -3'

Posted On

2014-10-15