Incidental Mutation 'R4856:Scn3a'
ID 373931
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 042467-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R4856 (G1)
Quality Score 225
Status Not validated
Chromosome 2
Chromosomal Location 65287462-65397935 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 65291376 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Aspartic acid to Glycine at position 1790 (D1790G)
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: D1790G

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000065023
Gene: ENSMUSG00000057182
AA Change: D1790G

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: D1790G

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000097647
Gene: ENSMUSG00000057182
AA Change: D1790G

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
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.4%
  • 10x: 96.4%
  • 20x: 92.8%
Validation Efficiency
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: 85 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Aebp2 G A 6: 140,589,799 (GRCm39) probably null Het
Arsi G A 18: 61,049,723 (GRCm39) G202E probably benign Het
Atp2b4 T A 1: 133,634,518 (GRCm39) I1177L probably benign Het
Bub3 A T 7: 131,163,297 (GRCm39) D76V probably damaging Het
Cacna2d4 G A 6: 119,255,217 (GRCm39) R578Q possibly damaging Het
Caprin2 A C 6: 148,774,509 (GRCm39) S268A probably benign Het
Card6 T C 15: 5,134,623 (GRCm39) probably null Het
Cdk13 A G 13: 17,894,319 (GRCm39) S1103P probably benign Het
Cfap221 T C 1: 119,861,934 (GRCm39) T614A probably damaging Het
Cfap221 T A 1: 119,912,488 (GRCm39) Y133F probably damaging Het
Clcc1 A G 3: 108,584,154 (GRCm39) T513A probably benign Het
Clec4g T A 8: 3,766,419 (GRCm39) probably benign Het
Cntln A C 4: 84,889,466 (GRCm39) E316D probably benign Het
Cpne2 T A 8: 95,290,592 (GRCm39) D392E probably benign Het
Cry1 G T 10: 84,984,634 (GRCm39) P147T probably damaging Het
Cyp4a29 T C 4: 115,110,078 (GRCm39) V440A probably benign Het
Ddx46 A G 13: 55,786,012 (GRCm39) D64G unknown Het
Dhx34 A G 7: 15,949,367 (GRCm39) S354P possibly damaging Het
Ecm2 A T 13: 49,676,263 (GRCm39) I327F possibly damaging Het
Elavl3 T C 9: 21,937,614 (GRCm39) K189E possibly damaging Het
Enam A T 5: 88,636,593 (GRCm39) R82* probably null Het
Erf A G 7: 24,945,636 (GRCm39) V45A probably damaging Het
Fat3 T A 9: 15,932,626 (GRCm39) I1436F probably benign Het
Flnc T C 6: 29,447,889 (GRCm39) Y1231H probably damaging Het
Ggta1 T A 2: 35,292,803 (GRCm39) H180L possibly damaging Het
Grin2c T C 11: 115,151,616 (GRCm39) T115A probably damaging Het
H6pd C T 4: 150,067,235 (GRCm39) V384M possibly damaging Het
Hba-x A G 11: 32,227,008 (GRCm39) E39G probably benign Het
Hnrnpul2 C T 19: 8,807,191 (GRCm39) P618S probably benign Het
Hpse2 C T 19: 42,777,396 (GRCm39) R590H probably damaging Het
Ighv1-54 C A 12: 115,157,423 (GRCm39) G75C probably damaging Het
Ighv8-11 C A 12: 115,530,774 (GRCm39) R118L possibly damaging Het
Iqcm A T 8: 76,615,228 (GRCm39) R436S possibly damaging Het
Islr T C 9: 58,064,889 (GRCm39) D206G probably damaging Het
Itih1 A G 14: 30,658,658 (GRCm39) probably null Het
Jam2 G A 16: 84,598,490 (GRCm39) D34N probably benign Het
Klhl14 A T 18: 21,691,029 (GRCm39) probably null Het
Lama2 TTTGCGCATT TTT 10: 26,919,639 (GRCm39) probably null Het
Lrrc66 A G 5: 73,765,910 (GRCm39) F378L probably benign Het
Map10 T A 8: 126,397,431 (GRCm39) Y275N probably damaging Het
Mpi T C 9: 57,452,590 (GRCm39) Y314C probably damaging Het
Mpp3 A G 11: 101,915,962 (GRCm39) Y55H probably benign Het
Nectin4 T C 1: 171,212,383 (GRCm39) V327A possibly damaging Het
Nlrp12 T A 7: 3,289,072 (GRCm39) D480V probably damaging Het
Nolc1 GAGCAGCAGCAGCAGCAGCAGCAGCAGC GAGCAGCAGCAGCAGCAGCAGCAGC 19: 46,071,594 (GRCm39) probably benign Het
Notch2 A T 3: 98,009,735 (GRCm39) Y554F probably damaging Het
Nrsn2 T C 2: 152,211,531 (GRCm39) K167E probably benign Het
Olr1 T A 6: 129,470,559 (GRCm39) K203* probably null Het
Or14j8 A T 17: 38,262,962 (GRCm39) S318T probably benign Het
Or2ag13 T A 7: 106,473,177 (GRCm39) I92F probably damaging Het
Or5b117 T C 19: 13,431,885 (GRCm39) probably null Het
Or8b3 A T 9: 38,314,764 (GRCm39) N195I probably damaging Het
Or9i2 T A 19: 13,815,643 (GRCm39) E298V probably damaging Het
Osbpl9 T C 4: 108,925,564 (GRCm39) N485S probably benign Het
Pbk T A 14: 66,052,650 (GRCm39) H164Q probably damaging Het
Pfn2 G T 3: 57,754,874 (GRCm39) N10K probably damaging Het
Pik3ca A G 3: 32,491,312 (GRCm39) D133G probably damaging Het
Pramel27 G T 4: 143,579,873 (GRCm39) R486L probably benign Het
Prl6a1 A T 13: 27,502,983 (GRCm39) D193V probably damaging Het
Rad21 G T 15: 51,831,896 (GRCm39) P395Q probably damaging Het
Reps1 T A 10: 17,999,373 (GRCm39) I720N probably damaging Het
Rpn2 T C 2: 157,159,964 (GRCm39) probably null Het
Rreb1 G A 13: 38,115,034 (GRCm39) V798M possibly damaging Het
Sardh C T 2: 27,134,489 (GRCm39) R9H probably benign Het
Scgb3a2 C T 18: 43,899,819 (GRCm39) P36S probably damaging Het
Scn10a C A 9: 119,523,375 (GRCm39) G6V possibly damaging Het
Scn10a C T 9: 119,523,376 (GRCm39) G6R possibly damaging Het
Sec24b A T 3: 129,777,619 (GRCm39) H1226Q probably benign Het
Shroom3 G T 5: 93,090,945 (GRCm39) V1151F probably damaging Het
Slc12a3 G A 8: 95,078,438 (GRCm39) probably null Het
Slitrk6 T C 14: 110,989,315 (GRCm39) T131A probably damaging Het
Spata1 C G 3: 146,175,529 (GRCm39) D326H probably damaging Het
Tex52 A T 6: 128,361,951 (GRCm39) probably null Het
Tma16 A C 8: 66,934,129 (GRCm39) C75W probably damaging Het
Tmem67 G A 4: 12,089,416 (GRCm39) probably benign Het
Trgv4 T C 13: 19,369,236 (GRCm39) V29A probably benign Het
Trmt10a A T 3: 137,854,146 (GRCm39) K75* probably null Het
Ttc3 T C 16: 94,191,142 (GRCm39) V228A probably benign Het
Ttn T C 2: 76,561,644 (GRCm39) D28954G probably damaging Het
Uggt2 A G 14: 119,273,376 (GRCm39) probably null Het
Vars1 T A 17: 35,234,702 (GRCm39) V1177E probably benign Het
Vmn1r59 T C 7: 5,457,532 (GRCm39) D76G possibly damaging Het
Vmn2r114 G T 17: 23,527,008 (GRCm39) A508E probably benign Het
Vps41 G A 13: 19,013,425 (GRCm39) V348M probably damaging Het
Zbtb43 T C 2: 33,343,944 (GRCm39) H427R 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
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
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'- TGATAGCAGCAGACACCTCC -3'
(R):5'- TTCAGCGTTGCCACAGAAG -3'

Sequencing Primer
(F):5'- GATAGCAGCAGACACCTCCTCTTG -3'
(R):5'- GAAAGTGCAGAGCCCCTG -3'
Posted On 2016-03-01