Incidental Mutation 'R1595:Scn3a'
ID 175703
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 039632-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R1595 (G1)
Quality Score 225
Status Validated
Chromosome 2
Chromosomal Location 65287462-65397935 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 65329323 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Tyrosine to Phenylalanine at position 769 (Y769F)
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: Y769F

PolyPhen 2 Score 0.993 (Sensitivity: 0.70; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000065023
Gene: ENSMUSG00000057182
AA Change: Y769F

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: Y769F

PolyPhen 2 Score 0.993 (Sensitivity: 0.70; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000097647
Gene: ENSMUSG00000057182
AA Change: Y769F

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: ENSMUST00000155838
Meta Mutation Damage Score 0.3578 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.3%
  • 10x: 96.1%
  • 20x: 92.1%
Validation Efficiency 97% (77/79)
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: 72 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcb6 C T 1: 75,153,944 (GRCm39) probably null Het
Abcc10 G T 17: 46,633,164 (GRCm39) P556H probably damaging Het
Abcc9 A T 6: 142,578,821 (GRCm39) D914E probably benign Het
Adgrf4 A G 17: 42,978,764 (GRCm39) V193A probably benign Het
Adm A T 7: 110,228,298 (GRCm39) T160S probably damaging Het
Ammecr1l T C 18: 31,905,173 (GRCm39) probably null Het
Angpt2 T C 8: 18,748,129 (GRCm39) D377G probably damaging Het
Ankfn1 A G 11: 89,313,593 (GRCm39) probably null Het
Arhgap30 T G 1: 171,235,909 (GRCm39) M761R probably benign Het
Asb4 T G 6: 5,390,692 (GRCm39) N28K probably damaging Het
Cd177 A T 7: 24,444,389 (GRCm39) D696E probably benign Het
Cd200 G A 16: 45,215,214 (GRCm39) T123I probably benign Het
Cfap70 A G 14: 20,497,604 (GRCm39) V50A probably benign Het
Chaf1b T C 16: 93,701,987 (GRCm39) probably null Het
Chgb A C 2: 132,635,657 (GRCm39) D533A probably benign Het
Col12a1 A G 9: 79,509,536 (GRCm39) Y3041H probably damaging Het
Crot T C 5: 9,024,186 (GRCm39) N337D probably benign Het
Csad G A 15: 102,086,217 (GRCm39) A51V probably damaging Het
Cstdc7 T C 18: 42,306,454 (GRCm39) M7T probably benign Het
Cyp2b9 A G 7: 25,900,332 (GRCm39) Y380C possibly damaging Het
Dpysl2 G T 14: 67,052,952 (GRCm39) A299E probably damaging Het
Efcc1 A G 6: 87,708,440 (GRCm39) E189G probably damaging Het
Egfr T C 11: 16,856,847 (GRCm39) I940T probably damaging Het
Etnk2 T G 1: 133,300,917 (GRCm39) L228R possibly damaging Het
Fitm2 A G 2: 163,311,610 (GRCm39) I201T probably benign Het
Foxo1 A T 3: 52,253,375 (GRCm39) M513L probably benign Het
Galnt16 A T 12: 80,637,410 (GRCm39) K379I probably damaging Het
Gm57858 C T 3: 36,073,146 (GRCm39) A379T probably damaging Het
Gtf2a1 T A 12: 91,556,323 (GRCm39) N6Y probably damaging Het
Kcnc1 G A 7: 46,077,010 (GRCm39) V271M probably benign Het
Klhdc8b T A 9: 108,328,362 (GRCm39) D30V probably damaging Het
Lrrc7 G A 3: 157,882,914 (GRCm39) Q448* probably null Het
Med29 T C 7: 28,091,928 (GRCm39) D54G probably damaging Het
Mfn2 T C 4: 147,979,153 (GRCm39) T60A probably benign Het
Mroh1 T C 15: 76,317,730 (GRCm39) probably benign Het
Mxd1 A T 6: 86,628,453 (GRCm39) V149E possibly damaging Het
Naip6 A T 13: 100,435,602 (GRCm39) Y974N probably damaging Het
Ndn C T 7: 61,998,256 (GRCm39) P34L probably benign Het
Nhsl1 G T 10: 18,402,096 (GRCm39) K1107N probably damaging Het
Nlrc3 T C 16: 3,783,166 (GRCm39) E81G probably benign Het
Or10al3 G T 17: 38,012,004 (GRCm39) A148S probably benign Het
Or9e1 G T 11: 58,732,478 (GRCm39) M179I probably benign Het
Osbpl5 C T 7: 143,256,955 (GRCm39) V392M possibly damaging Het
Pcdhb22 T A 18: 37,653,506 (GRCm39) V401E probably damaging Het
Pcm1 T A 8: 41,762,672 (GRCm39) H1444Q probably damaging Het
Pdlim2 A G 14: 70,402,193 (GRCm39) Y308H probably damaging Het
Phf14 T G 6: 11,988,752 (GRCm39) L664R possibly damaging Het
Phkb T C 8: 86,753,182 (GRCm39) probably benign Het
Ptchd3 T A 11: 121,721,420 (GRCm39) F98I probably damaging Het
Ptprt C T 2: 161,652,469 (GRCm39) probably null Het
Rbp3 A T 14: 33,678,155 (GRCm39) H701L possibly damaging Het
Rgl1 T C 1: 152,550,774 (GRCm39) probably benign Het
Satb1 A T 17: 52,089,729 (GRCm39) S373T possibly damaging Het
Senp7 A G 16: 56,005,131 (GRCm39) I922V probably damaging Het
Serpina3g A G 12: 104,205,531 (GRCm39) E90G probably benign Het
Sh3rf2 C T 18: 42,244,353 (GRCm39) T273I probably damaging Het
Slc15a3 A G 19: 10,831,675 (GRCm39) T350A probably benign Het
Socs5 T C 17: 87,441,623 (GRCm39) C188R probably damaging Het
Tacr1 A G 6: 82,380,723 (GRCm39) T45A probably benign Het
Th A G 7: 142,450,745 (GRCm39) V117A probably benign Het
Thpo C A 16: 20,547,206 (GRCm39) D81Y probably damaging Het
Tmem229b-ps A G 10: 53,351,385 (GRCm39) noncoding transcript Het
Trpc4 A G 3: 54,223,236 (GRCm39) E724G probably benign Het
Ttn T C 2: 76,576,977 (GRCm39) T24639A probably damaging Het
Ulk4 A G 9: 120,873,904 (GRCm39) S1176P probably damaging Het
Urgcp T C 11: 5,667,447 (GRCm39) D297G probably damaging Het
Vmn1r168 G A 7: 23,240,620 (GRCm39) G159D probably damaging Het
Vmn1r67 A T 7: 10,181,597 (GRCm39) N226I probably benign Het
Vmn2r27 T C 6: 124,208,574 (GRCm39) E57G probably benign Het
Zdhhc14 G T 17: 5,543,831 (GRCm39) R37L probably benign Het
Zfp512b G A 2: 181,230,229 (GRCm39) T499I probably damaging Het
Zmym2 A T 14: 57,158,187 (GRCm39) K575N probably benign 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
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
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'- AATCCTGACATTAACTGGGGCTCAAC -3'
(R):5'- CAATGCCAGCTTGTGGGGAAAATC -3'

Sequencing Primer
(F):5'- GAGTATAAACCCATTTTAGAAGGAGC -3'
(R):5'- AGCTTGTGGGGAAAATCTCTAAGTC -3'
Posted On 2014-04-24