Incidental Mutation 'R6235:Scn3a'
ID 504847
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 044433-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R6235 (G1)
Quality Score 225.009
Status Validated
Chromosome 2
Chromosomal Location 65287462-65397935 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to C at 65291679 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Glycine at position 1689 (V1689G)
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: V1689G

PolyPhen 2 Score 0.967 (Sensitivity: 0.77; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000065023
Gene: ENSMUSG00000057182
AA Change: V1689G

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: V1689G

PolyPhen 2 Score 0.967 (Sensitivity: 0.77; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000097647
Gene: ENSMUSG00000057182
AA Change: V1689G

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 0.2889 question?
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.7%
  • 10x: 98.4%
  • 20x: 95.4%
Validation Efficiency 95% (73/77)
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: 77 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adam34l T G 8: 44,078,949 (GRCm39) N425T probably benign Het
Adam6b T C 12: 113,455,330 (GRCm39) F716L probably benign Het
Akip1 A G 7: 109,306,620 (GRCm39) M106V probably benign Het
Aldh1l1 A T 6: 90,541,439 (GRCm39) I278F probably benign Het
Aplnr A G 2: 84,967,970 (GRCm39) T332A probably benign Het
Aqp4 A G 18: 15,531,170 (GRCm39) V197A probably damaging Het
Arid4a A T 12: 71,116,546 (GRCm39) probably null Het
Baiap2 A T 11: 119,872,234 (GRCm39) N99Y probably damaging Het
Ceacam1 A T 7: 25,171,217 (GRCm39) probably null Het
Cep78 T C 19: 15,953,850 (GRCm39) probably null Het
Cldn3 T C 5: 135,015,573 (GRCm39) F92S possibly damaging Het
Clec16a C A 16: 10,512,499 (GRCm39) P812Q probably damaging Het
Cnga4 T G 7: 105,056,906 (GRCm39) Y336* probably null Het
Copg2 A G 6: 30,793,006 (GRCm39) I443T probably damaging Het
Crhbp C A 13: 95,580,358 (GRCm39) A81S probably damaging Het
Csad A T 15: 102,087,041 (GRCm39) V410D probably damaging Het
Ctps1 G A 4: 120,416,003 (GRCm39) L207F probably benign Het
Dab2ip A G 2: 35,613,099 (GRCm39) E1003G probably damaging Het
Ddx31 C G 2: 28,734,854 (GRCm39) A5G probably benign Het
Dnah12 A T 14: 26,576,761 (GRCm39) I3004F probably damaging Het
Fbxo15 A G 18: 84,999,029 (GRCm39) probably benign Het
Fbxw28 C A 9: 109,155,258 (GRCm39) W356C probably damaging Het
Gimap6 G T 6: 48,679,391 (GRCm39) T215K probably benign Het
Hspa4 C T 11: 53,153,766 (GRCm39) E702K probably benign Het
Hunk A G 16: 90,229,594 (GRCm39) I152V probably damaging Het
Itk T C 11: 46,227,255 (GRCm39) E456G probably benign Het
Krt40 G A 11: 99,433,920 (GRCm39) A22V possibly damaging Het
Lars2 T C 9: 123,240,945 (GRCm39) V204A probably damaging Het
Lipo3 A G 19: 33,760,963 (GRCm39) Y140H probably damaging Het
Lrp1 G A 10: 127,424,046 (GRCm39) R809W probably damaging Het
Magi3 C T 3: 103,923,384 (GRCm39) G1111D probably damaging Het
Mis18bp1 A T 12: 65,205,182 (GRCm39) V47E probably damaging Het
Mpdz T C 4: 81,303,518 (GRCm39) E140G probably damaging Het
Myo1d T C 11: 80,583,770 (GRCm39) I81V probably benign Het
Nek10 T A 14: 14,821,113 (GRCm38) Y26* probably null Het
Ntng2 C A 2: 29,117,991 (GRCm39) E152D probably damaging Het
Or10w1 C A 19: 13,632,145 (GRCm39) C117* probably null Het
Or5m9b T C 2: 85,905,510 (GRCm39) L142P possibly damaging Het
Otud3 A T 4: 138,629,212 (GRCm39) V185D probably damaging Het
Parp6 C T 9: 59,538,098 (GRCm39) R248W probably benign Het
Pcdhga7 A G 18: 37,849,483 (GRCm39) T497A probably benign Het
Ppp1r18 A G 17: 36,184,769 (GRCm39) E140G probably damaging Het
Prl3b1 T C 13: 27,431,928 (GRCm39) L151P probably damaging Het
Pth1r C T 9: 110,551,384 (GRCm39) E572K possibly damaging Het
Ptprq T A 10: 107,471,199 (GRCm39) T1401S possibly damaging Het
Rad51ap2 A G 12: 11,507,517 (GRCm39) T480A possibly damaging Het
Rax T A 18: 66,068,232 (GRCm39) Q291L unknown Het
Reck T C 4: 43,937,450 (GRCm39) L734P probably damaging Het
Rgmb A G 17: 16,041,081 (GRCm39) F169L probably damaging Het
Rhobtb3 T C 13: 76,041,029 (GRCm39) I426M probably damaging Het
Ring1 C A 17: 34,242,280 (GRCm39) A76S probably damaging Het
Robo3 T G 9: 37,332,225 (GRCm39) Y891S probably damaging Het
Rpusd2 A G 2: 118,865,338 (GRCm39) I12V probably benign Het
Rragd T C 4: 32,995,985 (GRCm39) V165A possibly damaging Het
Rsf1 G GACGGCGGCT 7: 97,229,116 (GRCm39) probably benign Homo
Ryr1 G T 7: 28,815,606 (GRCm39) Q95K probably benign Het
S1pr4 T A 10: 81,334,716 (GRCm39) N253Y possibly damaging Het
Sdhb A G 4: 140,700,984 (GRCm39) N147D probably damaging Het
Sdk1 A T 5: 142,020,181 (GRCm39) H913L possibly damaging Het
Serpina3i T A 12: 104,232,791 (GRCm39) M232K probably damaging Het
Sipa1l2 A T 8: 126,201,610 (GRCm39) V646E probably damaging Het
Slc38a1 A T 15: 96,476,673 (GRCm39) I396N probably benign Het
Slc6a13 A T 6: 121,279,753 (GRCm39) E42D probably benign Het
Stard9 G A 2: 120,544,027 (GRCm39) V4442M probably damaging Het
Sumo3 T A 10: 77,452,071 (GRCm39) probably benign Het
Syngap1 A G 17: 27,177,104 (GRCm39) I356V probably benign Het
Tcam1 C T 11: 106,174,880 (GRCm39) Q112* probably null Het
Tdp2 T A 13: 25,024,378 (GRCm39) L225* probably null Het
Tmprss7 A G 16: 45,478,485 (GRCm39) V747A probably benign Het
Ugt2b34 T A 5: 87,054,223 (GRCm39) Y186F probably benign Het
Usp37 G T 1: 74,514,292 (GRCm39) S293* probably null Het
Vmn1r36 A G 6: 66,693,230 (GRCm39) I109T probably benign Het
Vsig10l T A 7: 43,118,396 (GRCm39) V798E probably benign Het
Zfp36l1 G T 12: 80,159,596 (GRCm39) C18* probably null Het
Zfp959 T C 17: 56,204,427 (GRCm39) Y152H probably damaging Het
Zfyve26 A T 12: 79,296,373 (GRCm39) C1949S probably damaging Het
Zswim9 T A 7: 12,995,529 (GRCm39) E209V 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
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'- TCTATGAACTGGGTGGCGTC -3'
(R):5'- GGGATGTCCAACTTTGCCTATG -3'

Sequencing Primer
(F):5'- TCAGGGTCGAACTTCTCCCAG -3'
(R):5'- CTGCCTGTTCCAAATCAC -3'
Posted On 2018-02-28