Incidental Mutation 'R5898:Scn3a'
ID 457632
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 044097-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R5898 (G1)
Quality Score 225
Status Validated
Chromosome 2
Chromosomal Location 65287462-65397935 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 65345039 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Glutamic Acid to Glycine at position 483 (E483G)
Ref Sequence ENSEMBL: ENSMUSP00000097647 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000066432] [ENSMUST00000100069]
AlphaFold A2ASI5
Predicted Effect probably damaging
Transcript: ENSMUST00000066432
AA Change: E483G

PolyPhen 2 Score 0.959 (Sensitivity: 0.78; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000065023
Gene: ENSMUSG00000057182
AA Change: E483G

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 damaging
Transcript: ENSMUST00000100069
AA Change: E483G

PolyPhen 2 Score 0.959 (Sensitivity: 0.78; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000097647
Gene: ENSMUSG00000057182
AA Change: E483G

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 noncoding transcript
Transcript: ENSMUST00000145994
Meta Mutation Damage Score 0.0664 question?
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.5%
  • 10x: 97.9%
  • 20x: 93.8%
Validation Efficiency 96% (86/90)
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: 83 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700017N19Rik G T 10: 100,448,762 (GRCm39) R158L possibly damaging Het
1700017N19Rik G A 10: 100,451,070 (GRCm39) M179I probably benign Het
Abhd12 T C 2: 150,681,698 (GRCm39) I231V possibly damaging Het
Adsl A G 15: 80,845,554 (GRCm39) probably null Het
Ahnak C A 19: 8,991,131 (GRCm39) N4138K possibly damaging Het
Ahnak T C 19: 8,995,575 (GRCm39) S5620P probably damaging Het
Akap13 C T 7: 75,378,894 (GRCm39) T2145I probably damaging Het
Alpk2 T A 18: 65,440,694 (GRCm39) Q700L probably damaging Het
Apobec1 T C 6: 122,557,732 (GRCm39) Y159C probably damaging Het
Atg9a T C 1: 75,162,916 (GRCm39) T395A probably damaging Het
Atp6v1f A G 6: 29,467,957 (GRCm39) I48V probably benign Het
BC051665 A C 13: 60,930,518 (GRCm39) V278G probably damaging Het
Bicd1 A T 6: 149,415,201 (GRCm39) H638L probably damaging Het
Cacna2d4 A G 6: 119,251,192 (GRCm39) Y460C probably damaging Het
Ccdc157 C A 11: 4,094,538 (GRCm39) R496L probably benign Het
Cdcp3 T G 7: 130,843,696 (GRCm39) probably null Het
Cep44 C G 8: 56,994,056 (GRCm39) V174L probably damaging Het
Clca3a1 G T 3: 144,722,522 (GRCm39) F283L possibly damaging Het
Csk T C 9: 57,537,585 (GRCm39) T110A probably benign Het
Cspg4 T A 9: 56,792,506 (GRCm39) probably null Het
Cutc A G 19: 43,748,468 (GRCm39) I124V probably benign Het
Cyp2d9 A G 15: 82,339,725 (GRCm39) T104A probably benign Het
Cyp2j9 G T 4: 96,465,951 (GRCm39) T294K probably benign Het
D630003M21Rik T A 2: 158,046,577 (GRCm39) probably null Het
Dcaf15 G T 8: 84,825,081 (GRCm39) F450L probably damaging Het
Ddhd1 A T 14: 45,840,125 (GRCm39) I723K probably damaging Het
Dnah17 C T 11: 118,005,039 (GRCm39) A782T probably benign Het
Dnah3 T C 7: 119,677,724 (GRCm39) D399G probably benign Het
Dync2h1 T C 9: 7,148,717 (GRCm39) N909S probably benign Het
Erbin A G 13: 103,975,813 (GRCm39) probably null Het
Fanci G A 7: 79,083,069 (GRCm39) V682I probably benign Het
Fap A T 2: 62,403,847 (GRCm39) F9L probably benign Het
Fat3 T C 9: 15,849,757 (GRCm39) I3882V probably benign Het
Fkbp15 A T 4: 62,244,294 (GRCm39) probably null Het
Fsd2 T C 7: 81,186,975 (GRCm39) Y601C probably damaging Het
Gm5900 T C 7: 104,599,468 (GRCm39) noncoding transcript Het
Gramd4 G T 15: 85,984,985 (GRCm39) G82V probably damaging Het
Hc C T 2: 34,887,449 (GRCm39) V1352I probably benign Het
Hsph1 A T 5: 149,548,623 (GRCm39) N466K probably damaging Het
Ice2 T A 9: 69,315,544 (GRCm39) D133E probably benign Het
Ifi213 T C 1: 173,396,545 (GRCm39) M510V probably benign Het
Itpkb T G 1: 180,248,880 (GRCm39) L861R probably damaging Het
Kbtbd3 T A 9: 4,330,476 (GRCm39) D283E probably damaging Het
Man2a1 A G 17: 64,932,375 (GRCm39) K154R probably benign Het
Masp1 T A 16: 23,310,677 (GRCm39) I252F probably damaging Het
Megf11 G T 9: 64,593,246 (GRCm39) C586F probably damaging Het
Myh2 C A 11: 67,083,545 (GRCm39) A1476E possibly damaging Het
Myo18b A T 5: 112,950,196 (GRCm39) probably null Het
Naip6 A T 13: 100,435,829 (GRCm39) V898E possibly damaging Het
Nav1 T C 1: 135,512,884 (GRCm39) M59V probably benign Het
Nlrp3 A T 11: 59,437,678 (GRCm39) Y119F probably benign Het
Oxa1l T A 14: 54,600,758 (GRCm39) I77N possibly damaging Het
Pcdhb8 T A 18: 37,490,537 (GRCm39) D738E possibly damaging Het
Pdia5 A T 16: 35,243,335 (GRCm39) W269R probably damaging Het
Peak1 T A 9: 56,114,622 (GRCm39) T1440S probably benign Het
Piezo1 A G 8: 123,214,682 (GRCm39) V1547A probably benign Het
Pkp1 T C 1: 135,810,259 (GRCm39) Y437C probably damaging Het
Pla2r1 T C 2: 60,253,104 (GRCm39) D1329G probably damaging Het
Ppip5k2 T C 1: 97,671,887 (GRCm39) probably benign Het
Prrg4 C T 2: 104,675,378 (GRCm39) S75N probably benign Het
Psmb9 T A 17: 34,401,266 (GRCm39) I198F probably damaging Het
Rcbtb2 T A 14: 73,399,405 (GRCm39) L23* probably null Het
Sbno1 A T 5: 124,524,854 (GRCm39) probably benign Het
Sdccag8 T A 1: 176,652,388 (GRCm39) D46E probably benign Het
Selenov A G 7: 27,987,579 (GRCm39) F293L probably damaging Het
Septin2 A C 1: 93,407,023 (GRCm39) D20A probably benign Het
Shc1 T A 3: 89,334,274 (GRCm39) Y313* probably null Het
Siglec1 T A 2: 130,915,553 (GRCm39) Y1346F probably damaging Het
Slc22a5 T A 11: 53,764,559 (GRCm39) I296F probably damaging Het
Slc9c1 A G 16: 45,365,123 (GRCm39) N152S probably damaging Het
Smoc1 C T 12: 81,151,531 (GRCm39) R83* probably null Het
Ssx2ip A G 3: 146,133,586 (GRCm39) D227G possibly damaging Het
Tbrg4 T C 11: 6,567,372 (GRCm39) D576G probably damaging Het
Tbx20 T A 9: 24,670,155 (GRCm39) Y226F probably damaging Het
Trav10d G T 14: 53,048,929 (GRCm39) A107S probably damaging Het
Trim60 A T 8: 65,453,016 (GRCm39) L411* probably null Het
Ttbk2 A T 2: 120,575,521 (GRCm39) V1083D probably benign Het
Unc93a T A 17: 13,344,464 (GRCm39) Q26L probably damaging Het
Usp14 T A 18: 10,022,819 (GRCm39) N65I possibly damaging Het
Vip A T 10: 5,593,988 (GRCm39) S114C probably damaging Het
Vmn1r237 A T 17: 21,534,813 (GRCm39) I179F probably damaging Het
Wdr47 T A 3: 108,545,201 (GRCm39) probably null Het
Zfp975 A T 7: 42,311,963 (GRCm39) C217S 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
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
R7733:Scn3a UTSW 2 65,338,994 (GRCm39) missense probably benign 0.08
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'- AGAGCACAGCTTCTTGTCGC -3'
(R):5'- AATGCACATTGTGTTATGCCC -3'

Sequencing Primer
(F):5'- TCAGCGGGTTCCCATCCAG -3'
(R):5'- CACATTGTGTTATGCCCTTTAAAAAG -3'
Posted On 2017-02-15