Incidental Mutation 'R3936:Scn1a'
ID 307162
Institutional Source Beutler Lab
Gene Symbol Scn1a
Ensembl Gene ENSMUSG00000064329
Gene Name sodium channel, voltage-gated, type I, alpha
Synonyms Nav1.1
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R3936 (G1)
Quality Score 225
Status Not validated
Chromosome 2
Chromosomal Location 66101125-66271181 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 66158120 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Valine at position 418 (I418V)
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: I418V

PolyPhen 2 Score 0.988 (Sensitivity: 0.73; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000076697
Gene: ENSMUSG00000064329
AA Change: I418V

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: I418V

PolyPhen 2 Score 0.988 (Sensitivity: 0.73; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000092558
Gene: ENSMUSG00000064329
AA Change: I418V

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: I418V

PolyPhen 2 Score 0.988 (Sensitivity: 0.73; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000107985
Gene: ENSMUSG00000064329
AA Change: I418V

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: I418V

PolyPhen 2 Score 0.988 (Sensitivity: 0.73; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000107990
Gene: ENSMUSG00000064329
AA Change: I418V

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: I418V

PolyPhen 2 Score 0.988 (Sensitivity: 0.73; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000116881
Gene: ENSMUSG00000064329
AA Change: I418V

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: 97.4%
  • 20x: 95.3%
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: 30 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Akap6 C T 12: 53,187,227 (GRCm39) T1547M possibly damaging Het
Alk T A 17: 72,512,949 (GRCm39) I337F probably damaging Het
Ank3 A T 10: 69,715,819 (GRCm39) K491* probably null Het
Arx T A X: 92,340,975 (GRCm39) L554Q probably damaging Het
Axdnd1 T C 1: 156,159,209 (GRCm39) N203S probably benign Het
Baz2b A G 2: 59,743,105 (GRCm39) V1622A possibly damaging Het
Btnl6 T A 17: 34,736,316 (GRCm39) H4L probably benign Het
Dync2h1 C A 9: 7,001,482 (GRCm39) L3835F probably damaging Het
Fcgbp T C 7: 27,774,824 (GRCm39) F133L probably benign Het
Fnip1 A G 11: 54,371,065 (GRCm39) probably null Het
G6pc1 A G 11: 101,265,429 (GRCm39) I154V probably benign Het
Golgb1 G T 16: 36,734,418 (GRCm39) E1222* probably null Het
Gpr85 A G 6: 13,836,044 (GRCm39) F287L probably benign Het
Gzmk A T 13: 113,309,559 (GRCm39) S164T probably damaging Het
Il22ra2 T A 10: 19,507,456 (GRCm39) S156R probably benign Het
Kansl1 A T 11: 104,234,369 (GRCm39) D712E possibly damaging Het
Mc3r T A 2: 172,091,216 (GRCm39) I146N probably damaging Het
Mcm2 G A 6: 88,869,990 (GRCm39) R60C probably damaging Het
Mitf C T 6: 97,970,214 (GRCm39) P54S probably damaging Het
Or13c7b T A 4: 43,821,359 (GRCm39) M1L probably benign Het
P4hb A C 11: 120,453,235 (GRCm39) H440Q probably benign Het
Pbsn T C X: 76,891,702 (GRCm39) T32A probably damaging Het
Rptn A C 3: 93,302,883 (GRCm39) H72P possibly damaging Het
Sf3a1 T A 11: 4,130,024 (GRCm39) probably null Het
Slc35f1 C T 10: 52,984,314 (GRCm39) T358I probably damaging Het
Slc9c1 A G 16: 45,427,193 (GRCm39) probably benign Het
Sorcs3 T A 19: 48,701,943 (GRCm39) V608D probably damaging Het
Sult2b1 C T 7: 45,391,640 (GRCm39) V49M probably benign Het
Tlr11 A G 14: 50,600,192 (GRCm39) E726G possibly damaging Het
Treh C T 9: 44,595,840 (GRCm39) R342W probably benign Het
Other mutations in Scn1a
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00513:Scn1a APN 2 66,165,875 (GRCm39) critical splice acceptor site probably null
IGL00650:Scn1a APN 2 66,111,137 (GRCm39) missense probably damaging 1.00
IGL00658:Scn1a APN 2 66,116,382 (GRCm39) missense probably damaging 1.00
IGL00823:Scn1a APN 2 66,155,279 (GRCm39) missense probably benign 0.04
IGL00907:Scn1a APN 2 66,158,141 (GRCm39) missense probably damaging 1.00
IGL01339:Scn1a APN 2 66,156,304 (GRCm39) missense probably benign 0.09
IGL01401:Scn1a APN 2 66,119,455 (GRCm39) missense probably damaging 1.00
IGL01503:Scn1a APN 2 66,152,687 (GRCm39) missense probably damaging 1.00
IGL01575:Scn1a APN 2 66,103,580 (GRCm39) missense probably damaging 1.00
IGL01598:Scn1a APN 2 66,132,829 (GRCm39) missense possibly damaging 0.63
IGL01613:Scn1a APN 2 66,116,281 (GRCm39) missense probably damaging 1.00
IGL01796:Scn1a APN 2 66,162,645 (GRCm39) splice site probably benign
IGL02079:Scn1a APN 2 66,153,704 (GRCm39) missense probably benign 0.14
IGL02171:Scn1a APN 2 66,103,543 (GRCm39) missense probably damaging 1.00
IGL02335:Scn1a APN 2 66,108,005 (GRCm39) missense possibly damaging 0.93
IGL02406:Scn1a APN 2 66,156,380 (GRCm39) missense possibly damaging 0.88
IGL02436:Scn1a APN 2 66,181,497 (GRCm39) missense probably benign 0.01
IGL02507:Scn1a APN 2 66,108,157 (GRCm39) missense probably damaging 1.00
IGL02646:Scn1a APN 2 66,129,962 (GRCm39) splice site probably null
IGL02729:Scn1a APN 2 66,129,994 (GRCm39) missense probably damaging 1.00
IGL02740:Scn1a APN 2 66,148,421 (GRCm39) missense probably benign 0.00
IGL02740:Scn1a APN 2 66,155,106 (GRCm39) missense probably damaging 1.00
IGL02752:Scn1a APN 2 66,161,756 (GRCm39) missense probably damaging 1.00
IGL02815:Scn1a APN 2 66,155,202 (GRCm39) missense probably damaging 1.00
IGL03163:Scn1a APN 2 66,148,418 (GRCm39) missense probably benign 0.00
IGL03229:Scn1a APN 2 66,130,057 (GRCm39) missense probably damaging 1.00
IGL03286:Scn1a APN 2 66,107,920 (GRCm39) missense probably damaging 0.99
IGL03393:Scn1a APN 2 66,148,362 (GRCm39) missense probably benign 0.19
BB008:Scn1a UTSW 2 66,148,156 (GRCm39) missense probably damaging 0.99
BB018:Scn1a UTSW 2 66,148,156 (GRCm39) missense probably damaging 0.99
PIT4791001:Scn1a UTSW 2 66,103,626 (GRCm39) missense probably benign 0.18
R0053:Scn1a UTSW 2 66,130,119 (GRCm39) missense probably benign 0.05
R0053:Scn1a UTSW 2 66,130,119 (GRCm39) missense probably benign 0.05
R0107:Scn1a UTSW 2 66,154,977 (GRCm39) missense probably benign 0.07
R0141:Scn1a UTSW 2 66,119,406 (GRCm39) missense probably damaging 1.00
R0485:Scn1a UTSW 2 66,104,269 (GRCm39) missense probably damaging 0.98
R0517:Scn1a UTSW 2 66,132,751 (GRCm39) missense possibly damaging 0.88
R0532:Scn1a UTSW 2 66,148,167 (GRCm39) missense probably damaging 1.00
R0746:Scn1a UTSW 2 66,181,470 (GRCm39) missense probably benign 0.25
R0755:Scn1a UTSW 2 66,151,379 (GRCm39) missense probably damaging 1.00
R0830:Scn1a UTSW 2 66,130,128 (GRCm39) missense probably damaging 1.00
R0846:Scn1a UTSW 2 66,155,099 (GRCm39) missense probably benign 0.43
R0918:Scn1a UTSW 2 66,153,651 (GRCm39) splice site probably null
R1055:Scn1a UTSW 2 66,168,340 (GRCm39) missense probably benign 0.08
R1432:Scn1a UTSW 2 66,152,773 (GRCm39) missense probably damaging 1.00
R1497:Scn1a UTSW 2 66,162,631 (GRCm39) missense probably damaging 1.00
R1512:Scn1a UTSW 2 66,161,629 (GRCm39) missense possibly damaging 0.82
R1525:Scn1a UTSW 2 66,149,806 (GRCm39) nonsense probably null
R1567:Scn1a UTSW 2 66,103,675 (GRCm39) missense probably damaging 1.00
R1702:Scn1a UTSW 2 66,148,567 (GRCm39) missense probably damaging 1.00
R1744:Scn1a UTSW 2 66,152,620 (GRCm39) missense probably benign 0.06
R1834:Scn1a UTSW 2 66,154,961 (GRCm39) missense probably benign 0.00
R1834:Scn1a UTSW 2 66,154,960 (GRCm39) missense probably benign 0.04
R1860:Scn1a UTSW 2 66,148,326 (GRCm39) missense probably damaging 0.99
R1871:Scn1a UTSW 2 66,148,369 (GRCm39) missense probably damaging 0.98
R1909:Scn1a UTSW 2 66,161,696 (GRCm39) missense possibly damaging 0.58
R1967:Scn1a UTSW 2 66,158,769 (GRCm39) missense probably damaging 1.00
R1976:Scn1a UTSW 2 66,161,615 (GRCm39) missense probably benign 0.02
R2291:Scn1a UTSW 2 66,119,312 (GRCm39) missense probably benign 0.44
R2302:Scn1a UTSW 2 66,108,089 (GRCm39) missense probably damaging 1.00
R2367:Scn1a UTSW 2 66,158,023 (GRCm39) missense probably damaging 1.00
R2418:Scn1a UTSW 2 66,104,187 (GRCm39) missense probably damaging 0.98
R2517:Scn1a UTSW 2 66,104,176 (GRCm39) missense probably damaging 1.00
R2568:Scn1a UTSW 2 66,103,813 (GRCm39) missense probably damaging 1.00
R3083:Scn1a UTSW 2 66,129,981 (GRCm39) missense probably damaging 1.00
R3903:Scn1a UTSW 2 66,148,476 (GRCm39) missense probably benign 0.08
R3909:Scn1a UTSW 2 66,104,332 (GRCm39) missense probably damaging 1.00
R3916:Scn1a UTSW 2 66,107,957 (GRCm39) missense probably damaging 1.00
R3935:Scn1a UTSW 2 66,158,120 (GRCm39) missense probably damaging 0.99
R4043:Scn1a UTSW 2 66,156,380 (GRCm39) missense possibly damaging 0.60
R4429:Scn1a UTSW 2 66,181,329 (GRCm39) missense possibly damaging 0.77
R4495:Scn1a UTSW 2 66,111,146 (GRCm39) critical splice acceptor site probably null
R4662:Scn1a UTSW 2 66,181,332 (GRCm39) missense probably benign 0.23
R4834:Scn1a UTSW 2 66,158,866 (GRCm39) nonsense probably null
R4873:Scn1a UTSW 2 66,158,820 (GRCm39) missense possibly damaging 0.92
R4875:Scn1a UTSW 2 66,158,820 (GRCm39) missense possibly damaging 0.92
R5099:Scn1a UTSW 2 66,108,145 (GRCm39) missense probably damaging 1.00
R5255:Scn1a UTSW 2 66,108,013 (GRCm39) missense probably damaging 0.99
R5435:Scn1a UTSW 2 66,103,878 (GRCm39) missense probably damaging 1.00
R5449:Scn1a UTSW 2 66,151,346 (GRCm39) missense probably damaging 0.96
R5519:Scn1a UTSW 2 66,162,557 (GRCm39) missense probably damaging 1.00
R5541:Scn1a UTSW 2 66,154,977 (GRCm39) missense probably benign 0.07
R5556:Scn1a UTSW 2 66,155,141 (GRCm39) missense probably benign 0.00
R5587:Scn1a UTSW 2 66,103,425 (GRCm39) missense probably benign 0.01
R5972:Scn1a UTSW 2 66,181,454 (GRCm39) missense possibly damaging 0.65
R5992:Scn1a UTSW 2 66,165,800 (GRCm39) missense probably damaging 1.00
R6195:Scn1a UTSW 2 66,107,962 (GRCm39) missense possibly damaging 0.59
R6233:Scn1a UTSW 2 66,107,962 (GRCm39) missense possibly damaging 0.59
R6328:Scn1a UTSW 2 66,103,660 (GRCm39) missense probably damaging 1.00
R6417:Scn1a UTSW 2 66,103,542 (GRCm39) missense probably damaging 1.00
R6420:Scn1a UTSW 2 66,103,542 (GRCm39) missense probably damaging 1.00
R6421:Scn1a UTSW 2 66,103,271 (GRCm39) missense probably damaging 1.00
R6461:Scn1a UTSW 2 66,156,466 (GRCm39) missense probably null 0.01
R6701:Scn1a UTSW 2 66,168,304 (GRCm39) missense probably damaging 0.99
R6717:Scn1a UTSW 2 66,162,631 (GRCm39) missense probably damaging 1.00
R6834:Scn1a UTSW 2 66,158,086 (GRCm39) missense probably damaging 1.00
R6918:Scn1a UTSW 2 66,162,557 (GRCm39) missense probably damaging 1.00
R6953:Scn1a UTSW 2 66,149,813 (GRCm39) missense probably damaging 1.00
R6996:Scn1a UTSW 2 66,118,075 (GRCm39) missense probably damaging 1.00
R7022:Scn1a UTSW 2 66,148,243 (GRCm39) missense probably damaging 1.00
R7109:Scn1a UTSW 2 66,181,286 (GRCm39) missense possibly damaging 0.62
R7115:Scn1a UTSW 2 66,154,962 (GRCm39) nonsense probably null
R7239:Scn1a UTSW 2 66,108,000 (GRCm39) splice site probably null
R7434:Scn1a UTSW 2 66,103,389 (GRCm39) missense probably benign
R7646:Scn1a UTSW 2 66,118,102 (GRCm39) missense possibly damaging 0.93
R7711:Scn1a UTSW 2 66,134,004 (GRCm39) missense probably benign
R7879:Scn1a UTSW 2 66,116,349 (GRCm39) nonsense probably null
R7931:Scn1a UTSW 2 66,148,156 (GRCm39) missense probably damaging 0.99
R7962:Scn1a UTSW 2 66,158,786 (GRCm39) missense probably damaging 1.00
R8025:Scn1a UTSW 2 66,148,557 (GRCm39) missense probably benign 0.02
R8055:Scn1a UTSW 2 66,149,845 (GRCm39) missense probably damaging 1.00
R8095:Scn1a UTSW 2 66,132,809 (GRCm39) missense possibly damaging 0.93
R8167:Scn1a UTSW 2 66,155,182 (GRCm39) missense probably damaging 0.98
R8339:Scn1a UTSW 2 66,116,373 (GRCm39) missense probably damaging 1.00
R8363:Scn1a UTSW 2 66,152,601 (GRCm39) missense probably damaging 1.00
R8516:Scn1a UTSW 2 66,156,478 (GRCm39) missense possibly damaging 0.79
R8559:Scn1a UTSW 2 66,118,077 (GRCm39) missense probably damaging 1.00
R8726:Scn1a UTSW 2 66,133,983 (GRCm39) missense probably benign
R8733:Scn1a UTSW 2 66,154,944 (GRCm39) missense probably benign
R8779:Scn1a UTSW 2 66,181,257 (GRCm39) critical splice donor site probably benign
R8841:Scn1a UTSW 2 66,156,466 (GRCm39) missense probably benign 0.09
R8916:Scn1a UTSW 2 66,108,127 (GRCm39) missense probably damaging 1.00
R8919:Scn1a UTSW 2 66,168,330 (GRCm39) missense probably benign 0.16
R9040:Scn1a UTSW 2 66,148,245 (GRCm39) missense probably damaging 0.99
R9086:Scn1a UTSW 2 66,181,358 (GRCm39) missense probably benign 0.01
R9176:Scn1a UTSW 2 66,103,689 (GRCm39) missense probably damaging 1.00
R9228:Scn1a UTSW 2 66,130,099 (GRCm39) missense probably benign 0.10
R9275:Scn1a UTSW 2 66,130,026 (GRCm39) missense probably damaging 1.00
R9365:Scn1a UTSW 2 66,148,465 (GRCm39) missense probably benign 0.10
R9478:Scn1a UTSW 2 66,156,493 (GRCm39) missense probably benign 0.01
R9560:Scn1a UTSW 2 66,158,131 (GRCm39) missense probably damaging 1.00
R9608:Scn1a UTSW 2 66,152,687 (GRCm39) missense probably benign 0.02
R9624:Scn1a UTSW 2 66,153,766 (GRCm39) missense probably benign
Z1176:Scn1a UTSW 2 66,156,472 (GRCm39) missense possibly damaging 0.92
Z1177:Scn1a UTSW 2 66,155,296 (GRCm39) critical splice acceptor site probably null
Predicted Primers PCR Primer
(F):5'- AGCTCTTTGTAACATGGCAGTG -3'
(R):5'- GTTAATTTTGTCAGAGTTCTGCCAC -3'

Sequencing Primer
(F):5'- CTCTTTGTAACATGGCAGTGAAAGAG -3'
(R):5'- TGTCAGAGTTCTGCCACATACAC -3'
Posted On 2015-04-17