Incidental Mutation 'R2367:Scn1a'
ID 246363
Institutional Source Beutler Lab
Gene Symbol Scn1a
Ensembl Gene ENSMUSG00000064329
Gene Name sodium channel, voltage-gated, type I, alpha
Synonyms Nav1.1
MMRRC Submission 040348-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R2367 (G1)
Quality Score 225
Status Not validated
Chromosome 2
Chromosomal Location 66270778-66440840 bp(-) (GRCm38)
Type of Mutation missense
DNA Base Change (assembly) T to C at 66327679 bp (GRCm38)
Zygosity Heterozygous
Amino Acid Change Glutamine to Arginine at position 450 (Q450R)
Ref Sequence ENSEMBL: ENSMUSP00000116881 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000077489] [ENSMUST00000094951] [ENSMUST00000112366] [ENSMUST00000112371] [ENSMUST00000138910]
AlphaFold A2APX8
Predicted Effect probably damaging
Transcript: ENSMUST00000077489
AA Change: Q450R

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000076697
Gene: ENSMUSG00000064329
AA Change: Q450R

DomainStartEndE-ValueType
low complexity region 23 52 N/A INTRINSIC
Pfam:Ion_trans 156 422 5.4e-77 PFAM
low complexity region 431 466 N/A INTRINSIC
Pfam:DUF3451 484 708 5.5e-73 PFAM
Pfam:Ion_trans 791 980 6.8e-47 PFAM
Pfam:Na_trans_assoc 995 1217 1.2e-74 PFAM
Pfam:Ion_trans 1243 1471 1.1e-56 PFAM
PDB:1BYY|A 1473 1525 4e-31 PDB
Pfam:Ion_trans 1564 1774 1.1e-51 PFAM
Pfam:PKD_channel 1623 1781 3.9e-7 PFAM
low complexity region 1826 1838 N/A INTRINSIC
IQ 1903 1925 1.65e-2 SMART
Predicted Effect probably damaging
Transcript: ENSMUST00000094951
AA Change: Q450R

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000092558
Gene: ENSMUSG00000064329
AA Change: Q450R

DomainStartEndE-ValueType
low complexity region 23 52 N/A INTRINSIC
Pfam:Ion_trans 156 422 5.3e-77 PFAM
low complexity region 431 466 N/A INTRINSIC
Pfam:DUF3451 484 691 2e-62 PFAM
Pfam:Ion_trans 774 963 6.7e-47 PFAM
Pfam:Na_trans_assoc 978 1200 1.2e-74 PFAM
Pfam:Ion_trans 1226 1454 1e-56 PFAM
PDB:1BYY|A 1456 1508 4e-31 PDB
Pfam:Ion_trans 1547 1757 1.1e-51 PFAM
Pfam:PKD_channel 1606 1764 3.8e-7 PFAM
low complexity region 1809 1821 N/A INTRINSIC
IQ 1886 1908 1.65e-2 SMART
Predicted Effect probably damaging
Transcript: ENSMUST00000112366
AA Change: Q450R

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000107985
Gene: ENSMUSG00000064329
AA Change: Q450R

DomainStartEndE-ValueType
low complexity region 23 52 N/A INTRINSIC
Pfam:Ion_trans 127 434 2.8e-82 PFAM
Pfam:Na_trans_cytopl 502 718 2e-91 PFAM
Pfam:Ion_trans 767 1002 6.5e-57 PFAM
Pfam:Na_trans_assoc 1006 1213 1.2e-60 PFAM
Pfam:Ion_trans 1217 1493 3.3e-67 PFAM
Pfam:Ion_trans 1540 1797 6.3e-56 PFAM
Pfam:PKD_channel 1637 1791 1.1e-6 PFAM
low complexity region 1837 1849 N/A INTRINSIC
IQ 1914 1936 1.65e-2 SMART
Predicted Effect probably damaging
Transcript: ENSMUST00000112371
AA Change: Q450R

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000107990
Gene: ENSMUSG00000064329
AA Change: Q450R

DomainStartEndE-ValueType
low complexity region 23 52 N/A INTRINSIC
Pfam:Ion_trans 156 422 5.4e-77 PFAM
low complexity region 431 466 N/A INTRINSIC
Pfam:DUF3451 484 708 5.5e-73 PFAM
Pfam:Ion_trans 791 980 6.8e-47 PFAM
Pfam:Na_trans_assoc 995 1217 1.2e-74 PFAM
Pfam:Ion_trans 1243 1471 1.1e-56 PFAM
PDB:1BYY|A 1473 1525 4e-31 PDB
Pfam:Ion_trans 1564 1774 1.1e-51 PFAM
Pfam:PKD_channel 1623 1781 3.9e-7 PFAM
low complexity region 1826 1838 N/A INTRINSIC
IQ 1903 1925 1.65e-2 SMART
Predicted Effect probably damaging
Transcript: ENSMUST00000138910
AA Change: Q450R

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000116881
Gene: ENSMUSG00000064329
AA Change: Q450R

DomainStartEndE-ValueType
low complexity region 23 52 N/A INTRINSIC
transmembrane domain 125 147 N/A INTRINSIC
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.7%
  • 10x: 97.3%
  • 20x: 95.2%
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] Voltage-dependent sodium channels are heteromeric complexes that regulate sodium exchange between intracellular and extracellular spaces and are essential for the generation and propagation of action potentials in muscle cells and neurons. Each sodium channel is composed of a large pore-forming, glycosylated alpha subunit and two smaller beta subunits. This gene encodes a sodium channel alpha subunit, which has four homologous domains, each of which contains six transmembrane regions. Allelic variants of this gene are associated with generalized epilepsy with febrile seizures and epileptic encephalopathy. Alternative splicing results in multiple transcript variants. The RefSeq Project has decided to create four representative RefSeq records. Three of the transcript variants are supported by experimental evidence and the fourth contains alternate 5' untranslated exons, the exact combination of which have not been experimentally confirmed for the full-length transcript. [provided by RefSeq, Oct 2015]
PHENOTYPE: Homozygous null mice show postnatal lethality, seizures and behavioral deficits whereas heterozygotes die prematurely with seizures and abnormal electrophysiology. In addition, knock-in mice exhibit increased susceptibility to febrile and flurothyl-induced seizures, and reduced inhibitory signaling. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 33 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adipoq T C 16: 23,155,319 (GRCm38) V32A probably benign Het
Ceacam3 T C 7: 17,151,888 (GRCm38) probably null Het
Cep250 G A 2: 155,992,632 (GRCm38) R2159K probably damaging Het
Cfap46 C A 7: 139,653,498 (GRCm38) V296F probably damaging Het
Ctdspl2 T C 2: 121,987,018 (GRCm38) V182A probably benign Het
Cyp2c69 T C 19: 39,877,594 (GRCm38) N185S probably benign Het
Daxx C T 17: 33,911,847 (GRCm38) R279W probably benign Het
Dnajc28 G A 16: 91,616,867 (GRCm38) T187M probably damaging Het
Fat3 G A 9: 15,998,271 (GRCm38) S2145F probably damaging Het
Galnt13 A T 2: 55,112,944 (GRCm38) M552L probably benign Het
Gstt2 C T 10: 75,832,690 (GRCm38) G108S probably benign Het
Heatr1 T A 13: 12,433,724 (GRCm38) L422Q probably damaging Het
Kntc1 C T 5: 123,781,192 (GRCm38) L845F probably damaging Het
Krtap26-1 C A 16: 88,647,325 (GRCm38) R136L probably benign Het
Mrgprb5 C T 7: 48,168,599 (GRCm38) W129* probably null Het
Ms4a3 G A 19: 11,629,744 (GRCm38) P186S probably benign Het
Myo15a T A 11: 60,517,238 (GRCm38) M3184K probably damaging Het
Olig2 G A 16: 91,226,566 (GRCm38) R56Q possibly damaging Het
Or8u9 T C 2: 86,171,637 (GRCm38) Y60C probably damaging Het
Pgap3 C T 11: 98,391,159 (GRCm38) probably null Het
Phgdh C G 3: 98,314,296 (GRCm38) G440A probably benign Het
Sema4d CGGGG CGGGGGGG 13: 51,703,140 (GRCm38) probably benign Het
Sik1 C T 17: 31,846,297 (GRCm38) V776I possibly damaging Het
Slc25a39 T A 11: 102,403,651 (GRCm38) T316S possibly damaging Het
Slc38a10 C T 11: 120,110,261 (GRCm38) E578K probably benign Het
Slc44a5 T A 3: 154,247,809 (GRCm38) I276K possibly damaging Het
Smarcc2 A G 10: 128,482,167 (GRCm38) T610A possibly damaging Het
Spag9 G A 11: 94,116,757 (GRCm38) S1090N probably damaging Het
Tpr T C 1: 150,433,728 (GRCm38) V277A probably damaging Het
Traf3ip1 T G 1: 91,507,520 (GRCm38) S314A possibly damaging Het
Tril T A 6: 53,819,166 (GRCm38) D357V probably damaging Het
Tube1 T C 10: 39,144,919 (GRCm38) L267P probably damaging Het
Vmn1r11 A G 6: 57,137,431 (GRCm38) I27V probably benign Het
Other mutations in Scn1a
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00513:Scn1a APN 2 66,335,531 (GRCm38) critical splice acceptor site probably null
IGL00650:Scn1a APN 2 66,280,793 (GRCm38) missense probably damaging 1.00
IGL00658:Scn1a APN 2 66,286,038 (GRCm38) missense probably damaging 1.00
IGL00823:Scn1a APN 2 66,324,935 (GRCm38) missense probably benign 0.04
IGL00907:Scn1a APN 2 66,327,797 (GRCm38) missense probably damaging 1.00
IGL01339:Scn1a APN 2 66,325,960 (GRCm38) missense probably benign 0.09
IGL01401:Scn1a APN 2 66,289,111 (GRCm38) missense probably damaging 1.00
IGL01503:Scn1a APN 2 66,322,343 (GRCm38) missense probably damaging 1.00
IGL01575:Scn1a APN 2 66,273,236 (GRCm38) missense probably damaging 1.00
IGL01598:Scn1a APN 2 66,302,485 (GRCm38) missense possibly damaging 0.63
IGL01613:Scn1a APN 2 66,285,937 (GRCm38) missense probably damaging 1.00
IGL01796:Scn1a APN 2 66,332,301 (GRCm38) splice site probably benign
IGL02079:Scn1a APN 2 66,323,360 (GRCm38) missense probably benign 0.14
IGL02171:Scn1a APN 2 66,273,199 (GRCm38) missense probably damaging 1.00
IGL02335:Scn1a APN 2 66,277,661 (GRCm38) missense possibly damaging 0.93
IGL02406:Scn1a APN 2 66,326,036 (GRCm38) missense possibly damaging 0.88
IGL02436:Scn1a APN 2 66,351,153 (GRCm38) missense probably benign 0.01
IGL02507:Scn1a APN 2 66,277,813 (GRCm38) missense probably damaging 1.00
IGL02646:Scn1a APN 2 66,299,618 (GRCm38) splice site probably null
IGL02729:Scn1a APN 2 66,299,650 (GRCm38) missense probably damaging 1.00
IGL02740:Scn1a APN 2 66,318,077 (GRCm38) missense probably benign 0.00
IGL02740:Scn1a APN 2 66,324,762 (GRCm38) missense probably damaging 1.00
IGL02752:Scn1a APN 2 66,331,412 (GRCm38) missense probably damaging 1.00
IGL02815:Scn1a APN 2 66,324,858 (GRCm38) missense probably damaging 1.00
IGL03163:Scn1a APN 2 66,318,074 (GRCm38) missense probably benign 0.00
IGL03229:Scn1a APN 2 66,299,713 (GRCm38) missense probably damaging 1.00
IGL03286:Scn1a APN 2 66,277,576 (GRCm38) missense probably damaging 0.99
IGL03393:Scn1a APN 2 66,318,018 (GRCm38) missense probably benign 0.19
BB008:Scn1a UTSW 2 66,317,812 (GRCm38) missense probably damaging 0.99
BB018:Scn1a UTSW 2 66,317,812 (GRCm38) missense probably damaging 0.99
PIT4791001:Scn1a UTSW 2 66,273,282 (GRCm38) missense probably benign 0.18
R0053:Scn1a UTSW 2 66,299,775 (GRCm38) missense probably benign 0.05
R0053:Scn1a UTSW 2 66,299,775 (GRCm38) missense probably benign 0.05
R0107:Scn1a UTSW 2 66,324,633 (GRCm38) missense probably benign 0.07
R0141:Scn1a UTSW 2 66,289,062 (GRCm38) missense probably damaging 1.00
R0485:Scn1a UTSW 2 66,273,925 (GRCm38) missense probably damaging 0.98
R0517:Scn1a UTSW 2 66,302,407 (GRCm38) missense possibly damaging 0.88
R0532:Scn1a UTSW 2 66,317,823 (GRCm38) missense probably damaging 1.00
R0746:Scn1a UTSW 2 66,351,126 (GRCm38) missense probably benign 0.25
R0755:Scn1a UTSW 2 66,321,035 (GRCm38) missense probably damaging 1.00
R0830:Scn1a UTSW 2 66,299,784 (GRCm38) missense probably damaging 1.00
R0846:Scn1a UTSW 2 66,324,755 (GRCm38) missense probably benign 0.43
R0918:Scn1a UTSW 2 66,323,307 (GRCm38) splice site probably null
R1055:Scn1a UTSW 2 66,337,996 (GRCm38) missense probably benign 0.08
R1432:Scn1a UTSW 2 66,322,429 (GRCm38) missense probably damaging 1.00
R1497:Scn1a UTSW 2 66,332,287 (GRCm38) missense probably damaging 1.00
R1512:Scn1a UTSW 2 66,331,285 (GRCm38) missense possibly damaging 0.82
R1525:Scn1a UTSW 2 66,319,462 (GRCm38) nonsense probably null
R1567:Scn1a UTSW 2 66,273,331 (GRCm38) missense probably damaging 1.00
R1702:Scn1a UTSW 2 66,318,223 (GRCm38) missense probably damaging 1.00
R1744:Scn1a UTSW 2 66,322,276 (GRCm38) missense probably benign 0.06
R1834:Scn1a UTSW 2 66,324,617 (GRCm38) missense probably benign 0.00
R1834:Scn1a UTSW 2 66,324,616 (GRCm38) missense probably benign 0.04
R1860:Scn1a UTSW 2 66,317,982 (GRCm38) missense probably damaging 0.99
R1871:Scn1a UTSW 2 66,318,025 (GRCm38) missense probably damaging 0.98
R1909:Scn1a UTSW 2 66,331,352 (GRCm38) missense possibly damaging 0.58
R1967:Scn1a UTSW 2 66,328,425 (GRCm38) missense probably damaging 1.00
R1976:Scn1a UTSW 2 66,331,271 (GRCm38) missense probably benign 0.02
R2291:Scn1a UTSW 2 66,288,968 (GRCm38) missense probably benign 0.44
R2302:Scn1a UTSW 2 66,277,745 (GRCm38) missense probably damaging 1.00
R2418:Scn1a UTSW 2 66,273,843 (GRCm38) missense probably damaging 0.98
R2517:Scn1a UTSW 2 66,273,832 (GRCm38) missense probably damaging 1.00
R2568:Scn1a UTSW 2 66,273,469 (GRCm38) missense probably damaging 1.00
R3083:Scn1a UTSW 2 66,299,637 (GRCm38) missense probably damaging 1.00
R3903:Scn1a UTSW 2 66,318,132 (GRCm38) missense probably benign 0.08
R3909:Scn1a UTSW 2 66,273,988 (GRCm38) missense probably damaging 1.00
R3916:Scn1a UTSW 2 66,277,613 (GRCm38) missense probably damaging 1.00
R3935:Scn1a UTSW 2 66,327,776 (GRCm38) missense probably damaging 0.99
R3936:Scn1a UTSW 2 66,327,776 (GRCm38) missense probably damaging 0.99
R4043:Scn1a UTSW 2 66,326,036 (GRCm38) missense possibly damaging 0.60
R4429:Scn1a UTSW 2 66,350,985 (GRCm38) missense possibly damaging 0.77
R4495:Scn1a UTSW 2 66,280,802 (GRCm38) critical splice acceptor site probably null
R4662:Scn1a UTSW 2 66,350,988 (GRCm38) missense probably benign 0.23
R4834:Scn1a UTSW 2 66,328,522 (GRCm38) nonsense probably null
R4873:Scn1a UTSW 2 66,328,476 (GRCm38) missense possibly damaging 0.92
R4875:Scn1a UTSW 2 66,328,476 (GRCm38) missense possibly damaging 0.92
R5099:Scn1a UTSW 2 66,277,801 (GRCm38) missense probably damaging 1.00
R5255:Scn1a UTSW 2 66,277,669 (GRCm38) missense probably damaging 0.99
R5435:Scn1a UTSW 2 66,273,534 (GRCm38) missense probably damaging 1.00
R5449:Scn1a UTSW 2 66,321,002 (GRCm38) missense probably damaging 0.96
R5519:Scn1a UTSW 2 66,332,213 (GRCm38) missense probably damaging 1.00
R5541:Scn1a UTSW 2 66,324,633 (GRCm38) missense probably benign 0.07
R5556:Scn1a UTSW 2 66,324,797 (GRCm38) missense probably benign 0.00
R5587:Scn1a UTSW 2 66,273,081 (GRCm38) missense probably benign 0.01
R5972:Scn1a UTSW 2 66,351,110 (GRCm38) missense possibly damaging 0.65
R5992:Scn1a UTSW 2 66,335,456 (GRCm38) missense probably damaging 1.00
R6195:Scn1a UTSW 2 66,277,618 (GRCm38) missense possibly damaging 0.59
R6233:Scn1a UTSW 2 66,277,618 (GRCm38) missense possibly damaging 0.59
R6328:Scn1a UTSW 2 66,273,316 (GRCm38) missense probably damaging 1.00
R6417:Scn1a UTSW 2 66,273,198 (GRCm38) missense probably damaging 1.00
R6420:Scn1a UTSW 2 66,273,198 (GRCm38) missense probably damaging 1.00
R6421:Scn1a UTSW 2 66,272,927 (GRCm38) missense probably damaging 1.00
R6461:Scn1a UTSW 2 66,326,122 (GRCm38) missense probably null 0.01
R6701:Scn1a UTSW 2 66,337,960 (GRCm38) missense probably damaging 0.99
R6717:Scn1a UTSW 2 66,332,287 (GRCm38) missense probably damaging 1.00
R6834:Scn1a UTSW 2 66,327,742 (GRCm38) missense probably damaging 1.00
R6918:Scn1a UTSW 2 66,332,213 (GRCm38) missense probably damaging 1.00
R6953:Scn1a UTSW 2 66,319,469 (GRCm38) missense probably damaging 1.00
R6996:Scn1a UTSW 2 66,287,731 (GRCm38) missense probably damaging 1.00
R7022:Scn1a UTSW 2 66,317,899 (GRCm38) missense probably damaging 1.00
R7109:Scn1a UTSW 2 66,350,942 (GRCm38) missense possibly damaging 0.62
R7115:Scn1a UTSW 2 66,324,618 (GRCm38) nonsense probably null
R7239:Scn1a UTSW 2 66,277,656 (GRCm38) splice site probably null
R7434:Scn1a UTSW 2 66,273,045 (GRCm38) missense probably benign
R7646:Scn1a UTSW 2 66,287,758 (GRCm38) missense possibly damaging 0.93
R7711:Scn1a UTSW 2 66,303,660 (GRCm38) missense probably benign
R7879:Scn1a UTSW 2 66,286,005 (GRCm38) nonsense probably null
R7931:Scn1a UTSW 2 66,317,812 (GRCm38) missense probably damaging 0.99
R7962:Scn1a UTSW 2 66,328,442 (GRCm38) missense probably damaging 1.00
R8025:Scn1a UTSW 2 66,318,213 (GRCm38) missense probably benign 0.02
R8055:Scn1a UTSW 2 66,319,501 (GRCm38) missense probably damaging 1.00
R8095:Scn1a UTSW 2 66,302,465 (GRCm38) missense possibly damaging 0.93
R8167:Scn1a UTSW 2 66,324,838 (GRCm38) missense probably damaging 0.98
R8339:Scn1a UTSW 2 66,286,029 (GRCm38) missense probably damaging 1.00
R8363:Scn1a UTSW 2 66,322,257 (GRCm38) missense probably damaging 1.00
R8516:Scn1a UTSW 2 66,326,134 (GRCm38) missense possibly damaging 0.79
R8559:Scn1a UTSW 2 66,287,733 (GRCm38) missense probably damaging 1.00
R8726:Scn1a UTSW 2 66,303,639 (GRCm38) missense probably benign
R8733:Scn1a UTSW 2 66,324,600 (GRCm38) missense probably benign
R8779:Scn1a UTSW 2 66,350,913 (GRCm38) critical splice donor site probably benign
R8841:Scn1a UTSW 2 66,326,122 (GRCm38) missense probably benign 0.09
R8916:Scn1a UTSW 2 66,277,783 (GRCm38) missense probably damaging 1.00
R8919:Scn1a UTSW 2 66,337,986 (GRCm38) missense probably benign 0.16
R9040:Scn1a UTSW 2 66,317,901 (GRCm38) missense probably damaging 0.99
R9086:Scn1a UTSW 2 66,351,014 (GRCm38) missense probably benign 0.01
R9176:Scn1a UTSW 2 66,273,345 (GRCm38) missense probably damaging 1.00
R9228:Scn1a UTSW 2 66,299,755 (GRCm38) missense probably benign 0.10
R9275:Scn1a UTSW 2 66,299,682 (GRCm38) missense probably damaging 1.00
R9365:Scn1a UTSW 2 66,318,121 (GRCm38) missense probably benign 0.10
R9478:Scn1a UTSW 2 66,326,149 (GRCm38) missense probably benign 0.01
R9560:Scn1a UTSW 2 66,327,787 (GRCm38) missense probably damaging 1.00
R9608:Scn1a UTSW 2 66,322,343 (GRCm38) missense probably benign 0.02
R9624:Scn1a UTSW 2 66,323,422 (GRCm38) missense probably benign
Z1176:Scn1a UTSW 2 66,326,128 (GRCm38) missense possibly damaging 0.92
Z1177:Scn1a UTSW 2 66,324,952 (GRCm38) critical splice acceptor site probably null
Predicted Primers PCR Primer
(F):5'- TACAACTTAGTGATGTGACTAGGCC -3'
(R):5'- GCTGCTGGCAAAACCTACATG -3'

Sequencing Primer
(F):5'- GATGACCCATACATAGAAGTCCTTGG -3'
(R):5'- GGGCTCATTCTACCTGAT -3'
Posted On 2014-10-30