Incidental Mutation 'IGL01401:Scn1a'
ID 79647
Institutional Source Australian Phenomics Network (link to record)
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 # IGL01401
Quality Score
Status
Chromosome 2
Chromosomal Location 66101125-66271181 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 66119455 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Asparagine to Lysine at position 1349 (N1349K)
Ref Sequence ENSEMBL: ENSMUSP00000107985 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000077489] [ENSMUST00000094951] [ENSMUST00000112366] [ENSMUST00000112371] [ENSMUST00000156865]
AlphaFold A2APX8
Predicted Effect probably damaging
Transcript: ENSMUST00000077489
AA Change: N1338K

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000076697
Gene: ENSMUSG00000064329
AA Change: N1338K

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: N1321K

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000092558
Gene: ENSMUSG00000064329
AA Change: N1321K

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: N1349K

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000107985
Gene: ENSMUSG00000064329
AA Change: N1349K

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: N1338K

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000107990
Gene: ENSMUSG00000064329
AA Change: N1338K

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: ENSMUST00000156865
AA Change: N318K

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000144633
Gene: ENSMUSG00000064329
AA Change: N318K

DomainStartEndE-ValueType
Pfam:Na_trans_assoc 1 182 2.2e-44 PFAM
Pfam:Ion_trans 186 462 1.3e-66 PFAM
Predicted Effect unknown
Transcript: ENSMUST00000200839
AA Change: C275S
Coding Region Coverage
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: 38 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adgrl3 T C 5: 81,836,516 (GRCm39) V758A possibly damaging Het
Arf4 T C 14: 26,359,609 (GRCm39) L12P probably damaging Het
Bltp1 A G 3: 36,996,441 (GRCm39) N1051S probably benign Het
C4bp A T 1: 130,575,801 (GRCm39) V230E possibly damaging Het
Carm1 T A 9: 21,480,878 (GRCm39) probably null Het
Cd4 G A 6: 124,856,341 (GRCm39) T50I probably benign Het
Ceacam16 T C 7: 19,595,054 (GRCm39) Y8C probably benign Het
Ckap2l A T 2: 129,111,136 (GRCm39) V687E probably damaging Het
Dcaf4 A G 12: 83,588,148 (GRCm39) D449G probably damaging Het
Dhx38 T C 8: 110,278,746 (GRCm39) Y1113C probably benign Het
Fry A G 5: 150,362,253 (GRCm39) I161V probably benign Het
Gm17093 A C 14: 44,758,984 (GRCm39) M169L unknown Het
Gm20721 A G 2: 174,187,295 (GRCm39) D999G probably damaging Het
Grin2b T C 6: 135,713,361 (GRCm39) H840R probably damaging Het
Hoxc12 C A 15: 102,845,755 (GRCm39) H156Q probably benign Het
Htr3b T C 9: 48,858,934 (GRCm39) D68G probably damaging Het
Inpp5b T C 4: 124,639,880 (GRCm39) V99A probably damaging Het
Klhl42 C T 6: 147,009,241 (GRCm39) T360M probably benign Het
Lmo7 C T 14: 102,031,713 (GRCm39) R36* probably null Het
Lmod3 T G 6: 97,229,513 (GRCm39) N7T probably damaging Het
Malrd1 G A 2: 16,106,768 (GRCm39) probably null Het
Mthfd2l T A 5: 91,148,425 (GRCm39) I284K possibly damaging Het
Myo1e T A 9: 70,234,448 (GRCm39) I267N probably damaging Het
Or13c7d T C 4: 43,770,112 (GRCm39) R300G probably damaging Het
Or2y1g T A 11: 49,171,314 (GRCm39) V113E possibly damaging Het
Prkce T C 17: 86,476,268 (GRCm39) V83A probably damaging Het
Pxdn G T 12: 30,051,983 (GRCm39) C540F probably damaging Het
Resf1 A G 6: 149,228,394 (GRCm39) E480G probably damaging Het
Ryr2 T A 13: 11,606,238 (GRCm39) E4448V possibly damaging Het
Smarcc1 T C 9: 109,979,033 (GRCm39) I172T possibly damaging Het
Syt16 T C 12: 74,269,437 (GRCm39) V92A possibly damaging Het
Tenm4 A G 7: 96,523,474 (GRCm39) Y1672C probably damaging Het
Tmem131 A G 1: 36,838,468 (GRCm39) Y1486H probably damaging Het
Tmem132a A G 19: 10,838,888 (GRCm39) probably benign Het
Usp40 A T 1: 87,921,920 (GRCm39) D314E probably damaging Het
Vmn2r79 G A 7: 86,686,481 (GRCm39) V621I probably benign Het
Wnk4 A G 11: 101,167,509 (GRCm39) probably benign Het
Wwc1 C A 11: 35,789,445 (GRCm39) probably null 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
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
R3936: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
Posted On 2013-11-05