Incidental Mutation 'IGL02335:Scn1a'
ID 289681
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 # IGL02335
Quality Score
Status
Chromosome 2
Chromosomal Location 66101125-66271181 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 66108005 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Serine at position 1557 (T1557S)
Ref Sequence ENSEMBL: ENSMUSP00000092558 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000077489] [ENSMUST00000094951] [ENSMUST00000112366] [ENSMUST00000112371] [ENSMUST00000156865]
AlphaFold A2APX8
Predicted Effect probably benign
Transcript: ENSMUST00000077489
AA Change: T1574S

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)
SMART Domains Protein: ENSMUSP00000076697
Gene: ENSMUSG00000064329
AA Change: T1574S

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 possibly damaging
Transcript: ENSMUST00000094951
AA Change: T1557S

PolyPhen 2 Score 0.926 (Sensitivity: 0.81; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000092558
Gene: ENSMUSG00000064329
AA Change: T1557S

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 benign
Transcript: ENSMUST00000112366
AA Change: T1585S

PolyPhen 2 Score 0.187 (Sensitivity: 0.92; Specificity: 0.87)
SMART Domains Protein: ENSMUSP00000107985
Gene: ENSMUSG00000064329
AA Change: T1585S

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 benign
Transcript: ENSMUST00000112371
AA Change: T1574S

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)
SMART Domains Protein: ENSMUSP00000107990
Gene: ENSMUSG00000064329
AA Change: T1574S

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 benign
Transcript: ENSMUST00000156865
SMART Domains Protein: ENSMUSP00000144633
Gene: ENSMUSG00000064329

DomainStartEndE-ValueType
Pfam:Na_trans_assoc 1 182 2.2e-44 PFAM
Pfam:Ion_trans 186 462 1.3e-66 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000200839
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: 45 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
A4gnt C T 9: 99,502,266 (GRCm39) T142I probably benign Het
Aadacl2fm2 G A 3: 59,651,026 (GRCm39) M49I probably benign Het
Acaca A G 11: 84,105,084 (GRCm39) T147A possibly damaging Het
Agbl3 A G 6: 34,776,685 (GRCm39) D397G probably damaging Het
Ank1 C T 8: 23,625,654 (GRCm39) T1597M possibly damaging Het
Arl4d A G 11: 101,557,755 (GRCm39) T94A possibly damaging Het
Cd22 A G 7: 30,575,559 (GRCm39) I161T probably damaging Het
Clcn7 C T 17: 25,365,821 (GRCm39) L166F probably benign Het
Cnbd1 G T 4: 19,055,095 (GRCm39) N110K possibly damaging Het
Col14a1 A T 15: 55,327,165 (GRCm39) probably benign Het
Col6a6 C T 9: 105,661,300 (GRCm39) V270M probably damaging Het
Cox8b C A 7: 140,478,990 (GRCm39) G42W probably damaging Het
Csn1s1 A T 5: 87,828,704 (GRCm39) D275V probably benign Het
Cubn T A 2: 13,432,645 (GRCm39) probably null Het
Dctn2 T C 10: 127,111,690 (GRCm39) probably benign Het
Dnm1l A G 16: 16,160,604 (GRCm39) probably benign Het
Dpp4 T C 2: 62,164,988 (GRCm39) E687G probably benign Het
Fbxw20 T C 9: 109,052,377 (GRCm39) K249E possibly damaging Het
Fhl2 C T 1: 43,167,550 (GRCm39) W181* probably null Het
G2e3 T A 12: 51,415,941 (GRCm39) M559K probably benign Het
Gdap1l1 A T 2: 163,289,515 (GRCm39) Y160F possibly damaging Het
Gm1110 T C 9: 26,793,059 (GRCm39) I572M probably benign Het
Gpatch2l T A 12: 86,303,711 (GRCm39) probably benign Het
Kcnq4 A G 4: 120,573,051 (GRCm39) L250P probably damaging Het
Lamc2 A T 1: 153,041,962 (GRCm39) N57K probably benign Het
Lingo1 A G 9: 56,527,365 (GRCm39) L408P probably damaging Het
Mmrn1 A T 6: 60,954,131 (GRCm39) N804I possibly damaging Het
Mroh7 A G 4: 106,564,979 (GRCm39) L545S probably damaging Het
Nup188 T A 2: 30,213,648 (GRCm39) probably null Het
Or10q1 A G 19: 13,727,298 (GRCm39) D276G probably benign Het
Or11a4 A G 17: 37,536,217 (GRCm39) N67S probably damaging Het
Or5b94 T C 19: 12,651,602 (GRCm39) I11T probably damaging Het
Pls1 A T 9: 95,666,236 (GRCm39) N138K probably benign Het
Prkch C A 12: 73,749,286 (GRCm39) N345K probably benign Het
Reps1 T C 10: 17,931,865 (GRCm39) probably null Het
Rrp7a T C 15: 83,006,892 (GRCm39) E15G probably benign Het
Scart2 A T 7: 139,876,453 (GRCm39) N526Y probably damaging Het
Smtn T C 11: 3,476,215 (GRCm39) E602G probably damaging Het
Syvn1 T C 19: 6,100,123 (GRCm39) probably null Het
Tbxas1 A G 6: 39,000,014 (GRCm39) D267G probably damaging Het
Topbp1 A G 9: 103,205,722 (GRCm39) N787D probably damaging Het
Vmn2r22 T G 6: 123,615,051 (GRCm39) S180R probably damaging Het
Zfp345 T A 2: 150,316,463 (GRCm39) E48D possibly damaging Het
Zfp608 G A 18: 55,030,509 (GRCm39) Q1144* probably null Het
Zfp936 T A 7: 42,836,691 (GRCm39) L34Q probably damaging 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
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 2015-04-16