Incidental Mutation 'R7733:Scn3a'
ID 595959
Institutional Source Beutler Lab
Gene Symbol Scn3a
Ensembl Gene ENSMUSG00000057182
Gene Name sodium channel, voltage-gated, type III, alpha
Synonyms Nav1.3, LOC381367
MMRRC Submission 045789-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R7733 (G1)
Quality Score 225.009
Status Validated
Chromosome 2
Chromosomal Location 65287462-65397935 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 65338994 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Phenylalanine at position 562 (I562F)
Ref Sequence ENSEMBL: ENSMUSP00000065023 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000066432] [ENSMUST00000100069]
AlphaFold A2ASI5
Predicted Effect probably benign
Transcript: ENSMUST00000066432
AA Change: I562F

PolyPhen 2 Score 0.081 (Sensitivity: 0.93; Specificity: 0.85)
SMART Domains Protein: ENSMUSP00000065023
Gene: ENSMUSG00000057182
AA Change: I562F

DomainStartEndE-ValueType
low complexity region 23 40 N/A INTRINSIC
Pfam:Ion_trans 127 435 5.2e-83 PFAM
low complexity region 473 498 N/A INTRINSIC
Pfam:Na_trans_cytopl 504 626 2e-42 PFAM
Pfam:Ion_trans 710 945 1.4e-58 PFAM
Pfam:Na_trans_assoc 949 1153 2.7e-58 PFAM
Pfam:Ion_trans 1157 1430 3e-67 PFAM
Pfam:Ion_trans 1477 1734 6.3e-55 PFAM
Pfam:PKD_channel 1573 1728 8e-7 PFAM
IQ 1851 1873 5.75e-2 SMART
low complexity region 1913 1921 N/A INTRINSIC
low complexity region 1927 1943 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000100069
AA Change: I562F

PolyPhen 2 Score 0.081 (Sensitivity: 0.93; Specificity: 0.85)
SMART Domains Protein: ENSMUSP00000097647
Gene: ENSMUSG00000057182
AA Change: I562F

DomainStartEndE-ValueType
low complexity region 23 40 N/A INTRINSIC
Pfam:Ion_trans 127 435 5.2e-83 PFAM
low complexity region 473 498 N/A INTRINSIC
Pfam:Na_trans_cytopl 504 626 2e-42 PFAM
Pfam:Ion_trans 710 945 1.4e-58 PFAM
Pfam:Na_trans_assoc 949 1153 2.7e-58 PFAM
Pfam:Ion_trans 1157 1430 3e-67 PFAM
Pfam:Ion_trans 1477 1734 6.3e-55 PFAM
Pfam:PKD_channel 1573 1728 8e-7 PFAM
IQ 1851 1873 5.75e-2 SMART
low complexity region 1913 1921 N/A INTRINSIC
low complexity region 1927 1943 N/A INTRINSIC
Meta Mutation Damage Score 0.0600 question?
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.7%
  • 20x: 99.3%
Validation Efficiency 100% (83/83)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] Voltage-gated sodium channels are transmembrane glycoprotein complexes composed of a large alpha subunit with 24 transmembrane domains and one or more regulatory beta subunits. They are responsible for the generation and propagation of action potentials in neurons and muscle. This gene encodes one member of the sodium channel alpha subunit gene family, and is found in a cluster of five alpha subunit genes on chromosome 2. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygous mutation of this gene results in lethality of most mutants by weaning. Heterozygous mice exhibit improved glucose tolerance. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 82 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
5530400C23Rik T A 6: 133,271,240 (GRCm39) S95T probably benign Het
Abca8a A G 11: 109,945,413 (GRCm39) F1070L probably benign Het
Acsl3 G C 1: 78,665,953 (GRCm39) probably null Het
Adarb2 T A 13: 8,802,644 (GRCm39) S640T possibly damaging Het
Adgre5 T C 8: 84,456,025 (GRCm39) D257G probably benign Het
Adora2b A T 11: 62,156,165 (GRCm39) I205F possibly damaging Het
Asb14 A G 14: 26,634,309 (GRCm39) M505V probably benign Het
Atrnl1 T C 19: 57,690,420 (GRCm39) V876A probably benign Het
AU040320 A G 4: 126,729,322 (GRCm39) N495D possibly damaging Het
Bcam A T 7: 19,494,313 (GRCm39) V361E probably benign Het
Ccdc7a T A 8: 129,719,533 (GRCm39) E247V probably damaging Het
Cd84 T A 1: 171,668,226 (GRCm39) M1K probably null Het
Cfap43 C T 19: 47,886,432 (GRCm39) R61H possibly damaging Het
Clec4a1 A G 6: 122,909,109 (GRCm39) D159G possibly damaging Het
Ctcfl C T 2: 172,958,985 (GRCm39) R247Q probably benign Het
Ctdnep1 G A 11: 69,880,835 (GRCm39) R236Q probably damaging Het
Cwf19l2 A T 9: 3,450,066 (GRCm39) H589L probably benign Het
Cyp2u1 G T 3: 131,096,676 (GRCm39) A34E probably benign Het
Cyp4x1 A G 4: 114,977,391 (GRCm39) S281P possibly damaging Het
Dag1 T C 9: 108,086,047 (GRCm39) T365A probably benign Het
Dhx57 A T 17: 80,572,503 (GRCm39) probably null Het
Dnajb1 T G 8: 84,335,006 (GRCm39) S16A probably benign Het
Dsc2 A T 18: 20,181,372 (GRCm39) L145Q probably benign Het
Dsc2 G C 18: 20,181,373 (GRCm39) L145V probably benign Het
Eefsec T C 6: 88,353,202 (GRCm39) T156A possibly damaging Het
Eif6 T A 2: 155,665,152 (GRCm39) D169V probably benign Het
Ell3 C A 2: 121,273,001 (GRCm39) G3V possibly damaging Het
Eprs1 A T 1: 185,129,358 (GRCm39) H615L probably benign Het
Fbxw10 A G 11: 62,764,223 (GRCm39) Y630C unknown Het
Fcgbpl1 A T 7: 27,839,390 (GRCm39) D401V probably damaging Het
G6pc2 C T 2: 69,050,527 (GRCm39) Q51* probably null Het
Glt8d1 C T 14: 30,723,935 (GRCm39) probably benign Het
Gpr4 T C 7: 18,956,635 (GRCm39) Y186H probably damaging Het
Grhpr T C 4: 44,981,494 (GRCm39) probably benign Het
Gsdma3 A G 11: 98,526,041 (GRCm39) H264R probably damaging Het
Hcfc2 A G 10: 82,575,013 (GRCm39) Y224C probably benign Het
Helz2 A G 2: 180,872,148 (GRCm39) F2608S possibly damaging Het
Herc2 C T 7: 55,838,412 (GRCm39) T3313M probably damaging Het
Hmgcl A T 4: 135,687,394 (GRCm39) H223L probably benign Het
Igf2r A G 17: 12,958,256 (GRCm39) V139A possibly damaging Het
Iqcn A G 8: 71,170,100 (GRCm39) T1397A possibly damaging Het
Kif5a T A 10: 127,072,609 (GRCm39) T727S probably benign Het
Kifc1 G A 17: 34,102,543 (GRCm39) R357W probably damaging Het
Krt81 T A 15: 101,361,395 (GRCm39) S62C probably damaging Het
Lgi2 T C 5: 52,695,873 (GRCm39) N362S probably benign Het
Lig1 G T 7: 13,030,157 (GRCm39) R378L possibly damaging Het
Map3k13 C T 16: 21,740,436 (GRCm39) R588C probably damaging Het
Mov10l1 T A 15: 88,909,004 (GRCm39) F1008L probably damaging Het
Nr4a2 A G 2: 57,002,333 (GRCm39) V40A probably benign Het
Nrde2 A T 12: 100,110,399 (GRCm39) C206S possibly damaging Het
Or4f14d C T 2: 111,960,386 (GRCm39) V257I probably benign Het
Parp1 T C 1: 180,427,777 (GRCm39) probably null Het
Pcdhb12 A G 18: 37,570,089 (GRCm39) T412A probably damaging Het
Plekhh2 T A 17: 84,890,952 (GRCm39) Y839* probably null Het
Pnpla6 T A 8: 3,572,660 (GRCm39) F316I probably benign Het
Prcp C T 7: 92,550,506 (GRCm39) T101M probably damaging Het
Prex2 G T 1: 11,252,183 (GRCm39) R1076L probably benign Het
Prpf40b T C 15: 99,206,224 (GRCm39) probably null Het
Psd3 T G 8: 68,573,568 (GRCm39) K204N possibly damaging Het
Ptpro C A 6: 137,391,284 (GRCm39) C801* probably null Het
Ptprt A G 2: 161,417,707 (GRCm39) V923A probably damaging Het
Ptprz1 T A 6: 23,000,383 (GRCm39) D824E probably benign Het
Rasgrf1 A G 9: 89,863,780 (GRCm39) D582G probably benign Het
Rfc2 T C 5: 134,622,070 (GRCm39) L183P probably damaging Het
Rnf114 T C 2: 167,354,438 (GRCm39) V173A probably damaging Het
Setmar T C 6: 108,053,088 (GRCm39) I194T probably damaging Het
Sptb A T 12: 76,644,695 (GRCm39) probably null Het
Sptbn2 C G 19: 4,799,040 (GRCm39) R2037G probably benign Het
Sptlc3 G T 2: 139,473,288 (GRCm39) M512I possibly damaging Het
Svep1 C A 4: 58,049,239 (GRCm39) A3423S probably benign Het
Sycp1 T C 3: 102,803,278 (GRCm39) T511A probably benign Het
Synm T A 7: 67,385,693 (GRCm39) probably null Het
Tada1 C T 1: 166,217,511 (GRCm39) P216L probably damaging Het
Tas2r117 T A 6: 132,780,138 (GRCm39) M92K probably benign Het
Thoc2l T C 5: 104,667,826 (GRCm39) F783L possibly damaging Het
Thsd1 T C 8: 22,748,737 (GRCm39) L536P probably damaging Het
Timp2 T G 11: 118,208,355 (GRCm39) probably null Het
Trak1 T A 9: 121,196,291 (GRCm39) V41D possibly damaging Het
Ubqln3 T A 7: 103,790,283 (GRCm39) L602F probably damaging Het
Vmn2r59 A G 7: 41,661,443 (GRCm39) F791L probably benign Het
Wbp4 A G 14: 79,714,480 (GRCm39) probably null Het
Zng1 T C 19: 24,918,158 (GRCm39) D204G probably damaging Het
Other mutations in Scn3a
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00953:Scn3a APN 2 65,327,736 (GRCm39) missense probably benign 0.05
IGL01086:Scn3a APN 2 65,300,503 (GRCm39) missense probably benign 0.27
IGL01141:Scn3a APN 2 65,325,457 (GRCm39) missense possibly damaging 0.73
IGL01150:Scn3a APN 2 65,327,709 (GRCm39) splice site probably null
IGL01564:Scn3a APN 2 65,291,790 (GRCm39) missense probably damaging 1.00
IGL01594:Scn3a APN 2 65,291,775 (GRCm39) missense probably damaging 1.00
IGL01751:Scn3a APN 2 65,291,596 (GRCm39) missense possibly damaging 0.87
IGL01803:Scn3a APN 2 65,352,127 (GRCm39) unclassified probably benign
IGL01822:Scn3a APN 2 65,325,608 (GRCm39) missense probably damaging 1.00
IGL02063:Scn3a APN 2 65,291,854 (GRCm39) missense probably damaging 1.00
IGL02142:Scn3a APN 2 65,356,965 (GRCm39) missense possibly damaging 0.95
IGL02198:Scn3a APN 2 65,338,833 (GRCm39) missense probably benign 0.12
IGL02501:Scn3a APN 2 65,356,899 (GRCm39) missense possibly damaging 0.82
IGL02608:Scn3a APN 2 65,354,510 (GRCm39) nonsense probably null
IGL02645:Scn3a APN 2 65,344,871 (GRCm39) missense probably benign 0.12
IGL02653:Scn3a APN 2 65,291,531 (GRCm39) missense probably damaging 1.00
IGL03077:Scn3a APN 2 65,367,016 (GRCm39) missense probably damaging 0.99
IGL03099:Scn3a APN 2 65,367,016 (GRCm39) missense probably damaging 0.99
IGL03299:Scn3a APN 2 65,327,860 (GRCm39) missense probably benign 0.01
IGL03327:Scn3a APN 2 65,367,016 (GRCm39) missense probably damaging 0.99
IGL03346:Scn3a APN 2 65,367,016 (GRCm39) missense probably damaging 0.99
IGL03355:Scn3a APN 2 65,290,912 (GRCm39) missense possibly damaging 0.91
curtsey UTSW 2 65,295,180 (GRCm39) missense probably damaging 1.00
dip UTSW 2 65,354,523 (GRCm39) missense probably benign 0.01
Regime UTSW 2 65,355,194 (GRCm39) missense possibly damaging 0.93
Willpower UTSW 2 65,356,098 (GRCm39) missense possibly damaging 0.92
R0019:Scn3a UTSW 2 65,292,045 (GRCm39) missense probably damaging 1.00
R0316:Scn3a UTSW 2 65,291,173 (GRCm39) missense probably damaging 1.00
R0374:Scn3a UTSW 2 65,338,918 (GRCm39) missense probably damaging 0.97
R0414:Scn3a UTSW 2 65,356,326 (GRCm39) splice site probably benign
R0609:Scn3a UTSW 2 65,366,854 (GRCm39) missense probably damaging 0.96
R0613:Scn3a UTSW 2 65,302,628 (GRCm39) missense possibly damaging 0.92
R0645:Scn3a UTSW 2 65,355,194 (GRCm39) missense possibly damaging 0.93
R0665:Scn3a UTSW 2 65,314,755 (GRCm39) missense probably null 0.00
R0667:Scn3a UTSW 2 65,314,755 (GRCm39) missense probably null 0.00
R0710:Scn3a UTSW 2 65,299,390 (GRCm39) missense probably damaging 0.99
R1202:Scn3a UTSW 2 65,336,491 (GRCm39) missense probably benign 0.07
R1440:Scn3a UTSW 2 65,359,785 (GRCm39) missense possibly damaging 0.95
R1447:Scn3a UTSW 2 65,300,324 (GRCm39) missense probably damaging 1.00
R1564:Scn3a UTSW 2 65,344,979 (GRCm39) missense probably damaging 0.98
R1595:Scn3a UTSW 2 65,329,323 (GRCm39) missense probably damaging 0.99
R1775:Scn3a UTSW 2 65,302,686 (GRCm39) missense probably damaging 1.00
R1781:Scn3a UTSW 2 65,302,729 (GRCm39) missense probably damaging 1.00
R1822:Scn3a UTSW 2 65,314,716 (GRCm39) missense probably damaging 1.00
R1924:Scn3a UTSW 2 65,291,878 (GRCm39) missense probably damaging 1.00
R2061:Scn3a UTSW 2 65,291,652 (GRCm39) missense probably damaging 1.00
R2070:Scn3a UTSW 2 65,351,210 (GRCm39) missense possibly damaging 0.72
R2174:Scn3a UTSW 2 65,337,550 (GRCm39) missense probably damaging 0.99
R2656:Scn3a UTSW 2 65,356,862 (GRCm39) missense probably damaging 0.99
R2680:Scn3a UTSW 2 65,366,880 (GRCm39) missense probably benign 0.04
R3882:Scn3a UTSW 2 65,312,623 (GRCm39) missense probably benign 0.03
R4019:Scn3a UTSW 2 65,356,295 (GRCm39) intron probably benign
R4106:Scn3a UTSW 2 65,325,379 (GRCm39) missense probably benign 0.07
R4108:Scn3a UTSW 2 65,325,379 (GRCm39) missense probably benign 0.07
R4109:Scn3a UTSW 2 65,325,379 (GRCm39) missense probably benign 0.07
R4225:Scn3a UTSW 2 65,366,771 (GRCm39) missense probably damaging 0.99
R4419:Scn3a UTSW 2 65,297,304 (GRCm39) missense probably damaging 1.00
R4552:Scn3a UTSW 2 65,354,523 (GRCm39) missense probably benign 0.01
R4687:Scn3a UTSW 2 65,295,074 (GRCm39) missense possibly damaging 0.65
R4780:Scn3a UTSW 2 65,336,537 (GRCm39) missense probably damaging 1.00
R4820:Scn3a UTSW 2 65,291,622 (GRCm39) missense probably damaging 1.00
R4856:Scn3a UTSW 2 65,291,376 (GRCm39) missense probably damaging 1.00
R4886:Scn3a UTSW 2 65,291,376 (GRCm39) missense probably damaging 1.00
R4914:Scn3a UTSW 2 65,291,799 (GRCm39) missense probably damaging 1.00
R4915:Scn3a UTSW 2 65,291,799 (GRCm39) missense probably damaging 1.00
R4918:Scn3a UTSW 2 65,291,799 (GRCm39) missense probably damaging 1.00
R5088:Scn3a UTSW 2 65,302,643 (GRCm39) missense probably damaging 1.00
R5101:Scn3a UTSW 2 65,291,850 (GRCm39) missense probably damaging 1.00
R5128:Scn3a UTSW 2 65,338,862 (GRCm39) missense probably benign 0.08
R5132:Scn3a UTSW 2 65,298,548 (GRCm39) missense probably benign 0.09
R5297:Scn3a UTSW 2 65,299,378 (GRCm39) missense possibly damaging 0.83
R5595:Scn3a UTSW 2 65,291,057 (GRCm39) missense probably benign
R5699:Scn3a UTSW 2 65,337,608 (GRCm39) missense possibly damaging 0.54
R5730:Scn3a UTSW 2 65,325,604 (GRCm39) missense probably benign 0.00
R5735:Scn3a UTSW 2 65,314,803 (GRCm39) missense probably benign 0.09
R5735:Scn3a UTSW 2 65,312,622 (GRCm39) missense probably damaging 0.98
R5855:Scn3a UTSW 2 65,295,074 (GRCm39) missense possibly damaging 0.65
R5888:Scn3a UTSW 2 65,327,742 (GRCm39) missense probably benign 0.06
R5898:Scn3a UTSW 2 65,345,039 (GRCm39) missense probably damaging 0.96
R5935:Scn3a UTSW 2 65,295,180 (GRCm39) missense probably damaging 1.00
R5970:Scn3a UTSW 2 65,325,125 (GRCm39) intron probably benign
R6214:Scn3a UTSW 2 65,325,380 (GRCm39) missense probably benign 0.29
R6215:Scn3a UTSW 2 65,325,380 (GRCm39) missense probably benign 0.29
R6235:Scn3a UTSW 2 65,291,679 (GRCm39) missense probably damaging 0.97
R6307:Scn3a UTSW 2 65,302,685 (GRCm39) missense probably damaging 1.00
R6355:Scn3a UTSW 2 65,291,643 (GRCm39) missense probably damaging 0.99
R6376:Scn3a UTSW 2 65,291,843 (GRCm39) missense possibly damaging 0.88
R6517:Scn3a UTSW 2 65,327,907 (GRCm39) missense possibly damaging 0.73
R6775:Scn3a UTSW 2 65,352,159 (GRCm39) missense possibly damaging 0.82
R6893:Scn3a UTSW 2 65,356,098 (GRCm39) missense possibly damaging 0.92
R6986:Scn3a UTSW 2 65,338,962 (GRCm39) missense probably damaging 0.97
R7065:Scn3a UTSW 2 65,295,199 (GRCm39) missense probably benign
R7078:Scn3a UTSW 2 65,327,944 (GRCm39) missense probably damaging 1.00
R7146:Scn3a UTSW 2 65,313,486 (GRCm39) missense probably damaging 1.00
R7240:Scn3a UTSW 2 65,299,386 (GRCm39) missense possibly damaging 0.77
R7294:Scn3a UTSW 2 65,302,685 (GRCm39) missense probably damaging 1.00
R7352:Scn3a UTSW 2 65,356,045 (GRCm39) missense possibly damaging 0.51
R7636:Scn3a UTSW 2 65,328,033 (GRCm39) missense probably damaging 1.00
R7708:Scn3a UTSW 2 65,313,512 (GRCm39) missense possibly damaging 0.47
R7761:Scn3a UTSW 2 65,359,798 (GRCm39) missense possibly damaging 0.95
R7792:Scn3a UTSW 2 65,297,334 (GRCm39) nonsense probably null
R7828:Scn3a UTSW 2 65,338,918 (GRCm39) missense probably damaging 0.97
R7875:Scn3a UTSW 2 65,327,826 (GRCm39) missense probably damaging 1.00
R7884:Scn3a UTSW 2 65,366,859 (GRCm39) missense probably damaging 0.96
R7958:Scn3a UTSW 2 65,336,537 (GRCm39) missense probably damaging 1.00
R7965:Scn3a UTSW 2 65,336,555 (GRCm39) missense probably damaging 1.00
R8171:Scn3a UTSW 2 65,361,154 (GRCm39) missense possibly damaging 0.85
R8345:Scn3a UTSW 2 65,329,335 (GRCm39) missense possibly damaging 0.86
R8356:Scn3a UTSW 2 65,291,017 (GRCm39) missense probably benign 0.08
R8456:Scn3a UTSW 2 65,291,017 (GRCm39) missense probably benign 0.08
R8527:Scn3a UTSW 2 65,327,863 (GRCm39) missense probably damaging 0.99
R8688:Scn3a UTSW 2 65,356,047 (GRCm39) missense possibly damaging 0.92
R8731:Scn3a UTSW 2 65,298,507 (GRCm39) nonsense probably null
R8901:Scn3a UTSW 2 65,352,252 (GRCm39) missense probably benign 0.00
R8910:Scn3a UTSW 2 65,338,883 (GRCm39) missense probably damaging 1.00
R9011:Scn3a UTSW 2 65,352,170 (GRCm39) missense possibly damaging 0.71
R9364:Scn3a UTSW 2 65,291,596 (GRCm39) missense possibly damaging 0.87
R9460:Scn3a UTSW 2 65,300,535 (GRCm39) missense probably damaging 1.00
R9496:Scn3a UTSW 2 65,312,493 (GRCm39) critical splice donor site probably null
R9542:Scn3a UTSW 2 65,366,860 (GRCm39) missense probably damaging 0.99
R9563:Scn3a UTSW 2 65,291,595 (GRCm39) missense probably damaging 1.00
X0062:Scn3a UTSW 2 65,355,191 (GRCm39) nonsense probably null
X0062:Scn3a UTSW 2 65,297,345 (GRCm39) missense probably damaging 0.98
Z1177:Scn3a UTSW 2 65,329,236 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- CTAACGTTACTGTTGCGTCG -3'
(R):5'- TCCTGACATTTGCACTGTGG -3'

Sequencing Primer
(F):5'- GTCGCTCTCCAGGTCTGTG -3'
(R):5'- GCACTGTGGCCTTCAATATATAAAAG -3'
Posted On 2019-11-12