Incidental Mutation 'R1597:Scn5a'
ID 175877
Institutional Source Beutler Lab
Gene Symbol Scn5a
Ensembl Gene ENSMUSG00000032511
Gene Name sodium channel, voltage-gated, type V, alpha
Synonyms Nav1.5c, mH1, Nav1.5, SkM2
MMRRC Submission 039634-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R1597 (G1)
Quality Score 225
Status Validated
Chromosome 9
Chromosomal Location 119312474-119408082 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to A at 119391563 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Arginine to Leucine at position 43 (R43L)
Ref Sequence ENSEMBL: ENSMUSP00000113272 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000065196] [ENSMUST00000117911] [ENSMUST00000120420] [ENSMUST00000138934]
AlphaFold Q9JJV9
Predicted Effect probably damaging
Transcript: ENSMUST00000065196
AA Change: R43L

PolyPhen 2 Score 0.990 (Sensitivity: 0.72; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000066228
Gene: ENSMUSG00000032511
AA Change: R43L

DomainStartEndE-ValueType
Pfam:Ion_trans 130 423 2.4e-82 PFAM
Pfam:Na_trans_cytopl 478 667 5.2e-49 PFAM
Pfam:Ion_trans 716 950 1.1e-54 PFAM
Pfam:Na_trans_assoc 955 1203 2.9e-57 PFAM
Pfam:Ion_trans 1207 1484 2e-66 PFAM
Pfam:Ion_trans 1530 1786 7.2e-55 PFAM
Pfam:PKD_channel 1627 1780 3.5e-7 PFAM
IQ 1903 1925 5e-2 SMART
low complexity region 1961 1983 N/A INTRINSIC
Predicted Effect possibly damaging
Transcript: ENSMUST00000117911
AA Change: R43L

PolyPhen 2 Score 0.745 (Sensitivity: 0.85; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000112838
Gene: ENSMUSG00000032511
AA Change: R43L

DomainStartEndE-ValueType
Pfam:Ion_trans 159 412 9.6e-76 PFAM
coiled coil region 413 451 N/A INTRINSIC
Pfam:DUF3451 461 668 4.9e-44 PFAM
Pfam:Ion_trans 751 940 2.3e-46 PFAM
Pfam:Na_trans_assoc 955 1218 1.2e-73 PFAM
Pfam:Ion_trans 1244 1472 2e-56 PFAM
PDB:1BYY|A 1474 1526 5e-29 PDB
Pfam:Ion_trans 1565 1774 1.5e-49 PFAM
Pfam:PKD_channel 1627 1781 2.6e-10 PFAM
IQ 1903 1925 5e-2 SMART
low complexity region 1961 1983 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000120420
AA Change: R43L

PolyPhen 2 Score 0.990 (Sensitivity: 0.72; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000113272
Gene: ENSMUSG00000032511
AA Change: R43L

DomainStartEndE-ValueType
Pfam:Ion_trans 159 412 4.5e-75 PFAM
coiled coil region 413 451 N/A INTRINSIC
Pfam:DUF3451 461 668 7.4e-43 PFAM
Pfam:Ion_trans 751 940 1.2e-45 PFAM
Pfam:Na_trans_assoc 955 1217 1.6e-72 PFAM
Pfam:Ion_trans 1243 1471 1.1e-55 PFAM
PDB:1BYY|A 1473 1525 5e-29 PDB
Pfam:Ion_trans 1564 1773 8.2e-49 PFAM
Pfam:PKD_channel 1626 1780 2.6e-9 PFAM
IQ 1902 1924 5e-2 SMART
low complexity region 1960 1982 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000138934
Meta Mutation Damage Score 0.1857 question?
Coding Region Coverage
  • 1x: 99.0%
  • 3x: 98.2%
  • 10x: 95.8%
  • 20x: 91.1%
Validation Efficiency 100% (77/77)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is an integral membrane protein and tetrodotoxin-resistant voltage-gated sodium channel subunit. This protein is found primarily in cardiac muscle and is responsible for the initial upstroke of the action potential in an electrocardiogram. Defects in this gene are a cause of long QT syndrome type 3 (LQT3), an autosomal dominant cardiac disease. Alternative splicing results in several transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for mutations in this gene die prenatally usually during organogenesis and may display decreased embryo size and abnormal cardiovascular system physiology. Heterozygous mice typically display abnormal heartbeats and defects in the function of the impulse conduction system. [provided by MGI curators]
Allele List at MGI

All alleles(11) : Targeted(9) Gene trapped(2)

Other mutations in this stock
Total: 70 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Acta2 A T 19: 34,229,983 (GRCm39) probably benign Het
Afap1l2 T C 19: 56,902,881 (GRCm39) N748S probably benign Het
Aox1 T A 1: 58,086,326 (GRCm39) I77N probably damaging Het
Ap1s1 A T 5: 137,072,095 (GRCm39) M20K probably damaging Het
Atad3a A T 4: 155,835,892 (GRCm39) probably null Het
Atp1b1 G T 1: 164,265,889 (GRCm39) R291S probably damaging Het
Birc7 T C 2: 180,570,974 (GRCm39) V12A possibly damaging Het
Btnl2 T C 17: 34,582,211 (GRCm39) V259A probably damaging Het
Cdh11 A T 8: 103,377,343 (GRCm39) N434K probably benign Het
Cel G T 2: 28,450,479 (GRCm39) probably benign Het
Col10a1 A G 10: 34,271,074 (GRCm39) K349E probably damaging Het
Ddhd2 A G 8: 26,239,768 (GRCm39) V315A probably benign Het
Dnah17 C A 11: 117,994,324 (GRCm39) probably benign Het
Dock2 T C 11: 34,595,474 (GRCm39) T441A probably benign Het
Ermap A T 4: 119,041,152 (GRCm39) I286N probably damaging Het
Fbxl17 T C 17: 63,794,813 (GRCm39) K423R probably damaging Het
Frem2 T C 3: 53,561,940 (GRCm39) T856A probably benign Het
Gas6 T C 8: 13,543,901 (GRCm39) E64G probably damaging Het
Gzma T A 13: 113,232,331 (GRCm39) N190I probably damaging Het
Ifngr1 C T 10: 19,485,090 (GRCm39) T363M probably damaging Het
Itga7 A G 10: 128,782,732 (GRCm39) T690A probably benign Het
Kif15 A G 9: 122,823,074 (GRCm39) E485G probably benign Het
Kif18a A G 2: 109,123,336 (GRCm39) I203M probably damaging Het
Klhl1 A T 14: 96,438,647 (GRCm39) probably null Het
Lrch3 C T 16: 32,770,781 (GRCm39) Q128* probably null Het
Lrriq4 C G 3: 30,705,037 (GRCm39) P355R probably damaging Het
Mcm10 A T 2: 5,003,563 (GRCm39) H551Q probably damaging Het
Mcm3ap T C 10: 76,319,060 (GRCm39) F763L probably damaging Het
Mdc1 T A 17: 36,156,758 (GRCm39) V55E probably damaging Het
Me2 A T 18: 73,931,016 (GRCm39) N92K probably damaging Het
Mtss1 A G 15: 58,815,560 (GRCm39) S667P probably damaging Het
Mup5 A T 4: 61,753,317 (GRCm39) Y15N possibly damaging Het
Mx1 T A 16: 97,256,329 (GRCm39) M197L probably damaging Het
N4bp2 C T 5: 65,964,483 (GRCm39) T844I probably benign Het
Nlrc3 T A 16: 3,781,859 (GRCm39) R517W probably damaging Het
Nos3 A T 5: 24,573,995 (GRCm39) I227F probably damaging Het
Or52a5 A G 7: 103,427,267 (GRCm39) F95S probably benign Het
Pabpc2 A G 18: 39,906,953 (GRCm39) N73D probably damaging Het
Pcdhb18 A G 18: 37,624,820 (GRCm39) R717G probably benign Het
Pcsk5 T A 19: 17,413,964 (GRCm39) M1702L probably benign Het
Plxna2 A C 1: 194,431,614 (GRCm39) probably benign Het
Polr2a A G 11: 69,630,755 (GRCm39) M1221T possibly damaging Het
Polr2b A G 5: 77,473,948 (GRCm39) D384G probably damaging Het
Ppl T A 16: 4,925,438 (GRCm39) H67L probably benign Het
Psmd5 A G 2: 34,757,035 (GRCm39) L63S probably damaging Het
Psme1 A G 14: 55,818,222 (GRCm39) T150A probably damaging Het
Rapgef5 C T 12: 117,621,940 (GRCm39) R33C probably damaging Het
Rela G A 19: 5,695,359 (GRCm39) R295H probably damaging Het
Rpe65 T A 3: 159,320,421 (GRCm39) V326E probably damaging Het
Skida1 T C 2: 18,051,143 (GRCm39) probably benign Het
Slc4a4 G A 5: 89,283,587 (GRCm39) A469T probably benign Het
Spaca7 G T 8: 12,630,991 (GRCm39) E48* probably null Het
Syn3 G T 10: 85,970,908 (GRCm39) T238K probably benign Het
Taok1 A G 11: 77,470,626 (GRCm39) S60P probably benign Het
Tecpr1 A G 5: 144,151,128 (GRCm39) I256T probably benign Het
Tenm4 T A 7: 96,552,196 (GRCm39) probably null Het
Tex15 A G 8: 34,061,511 (GRCm39) T588A probably damaging Het
Tgfbi T A 13: 56,780,004 (GRCm39) probably benign Het
Tmem62 G A 2: 120,814,843 (GRCm39) A169T probably benign Het
Tnc A G 4: 63,924,621 (GRCm39) S1026P probably benign Het
Tnik T C 3: 28,658,418 (GRCm39) S568P probably damaging Het
Trpm6 A T 19: 18,804,888 (GRCm39) I947F probably damaging Het
Ttc27 T A 17: 75,170,402 (GRCm39) L832Q possibly damaging Het
U2surp C T 9: 95,363,793 (GRCm39) probably benign Het
Ube4a A T 9: 44,841,064 (GRCm39) D1009E possibly damaging Het
Unc13d T C 11: 115,965,262 (GRCm39) E192G probably benign Het
Vmn2r71 T C 7: 85,273,352 (GRCm39) V722A possibly damaging Het
Zfp386 T C 12: 116,023,709 (GRCm39) S476P probably damaging Het
Zfp644 A T 5: 106,786,199 (GRCm39) V116D probably damaging Het
Zfyve16 T A 13: 92,644,755 (GRCm39) N1149I probably benign Het
Other mutations in Scn5a
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00336:Scn5a APN 9 119,315,290 (GRCm39) missense probably damaging 1.00
IGL00480:Scn5a APN 9 119,346,604 (GRCm39) missense possibly damaging 0.73
IGL00542:Scn5a APN 9 119,321,192 (GRCm39) missense probably damaging 1.00
IGL00852:Scn5a APN 9 119,366,748 (GRCm39) missense probably benign 0.26
IGL00895:Scn5a APN 9 119,342,170 (GRCm39) splice site probably null
IGL00905:Scn5a APN 9 119,365,567 (GRCm39) missense probably damaging 1.00
IGL01347:Scn5a APN 9 119,391,507 (GRCm39) nonsense probably null
IGL01396:Scn5a APN 9 119,363,770 (GRCm39) missense probably damaging 0.98
IGL01402:Scn5a APN 9 119,315,536 (GRCm39) missense probably damaging 1.00
IGL01404:Scn5a APN 9 119,315,536 (GRCm39) missense probably damaging 1.00
IGL01487:Scn5a APN 9 119,391,689 (GRCm39) start codon destroyed probably null 0.90
IGL01612:Scn5a APN 9 119,315,091 (GRCm39) missense possibly damaging 0.86
IGL02134:Scn5a APN 9 119,314,958 (GRCm39) missense probably damaging 0.98
IGL02434:Scn5a APN 9 119,362,859 (GRCm39) missense possibly damaging 0.83
IGL02698:Scn5a APN 9 119,350,163 (GRCm39) missense probably damaging 1.00
IGL02717:Scn5a APN 9 119,358,076 (GRCm39) missense probably benign 0.12
IGL02746:Scn5a APN 9 119,379,703 (GRCm39) missense probably damaging 1.00
IGL02951:Scn5a APN 9 119,324,751 (GRCm39) missense probably damaging 1.00
IGL03155:Scn5a APN 9 119,341,248 (GRCm39) missense possibly damaging 0.74
IGL03188:Scn5a APN 9 119,351,632 (GRCm39) missense probably damaging 1.00
IGL03268:Scn5a APN 9 119,350,297 (GRCm39) missense probably damaging 1.00
IGL03287:Scn5a APN 9 119,318,844 (GRCm39) missense probably damaging 1.00
IGL03328:Scn5a APN 9 119,366,702 (GRCm39) missense probably benign 0.12
PIT4142001:Scn5a UTSW 9 119,315,324 (GRCm39) missense probably damaging 1.00
PIT4520001:Scn5a UTSW 9 119,363,636 (GRCm39) missense possibly damaging 0.56
R0026:Scn5a UTSW 9 119,351,632 (GRCm39) missense probably damaging 1.00
R0044:Scn5a UTSW 9 119,321,113 (GRCm39) critical splice donor site probably null
R0044:Scn5a UTSW 9 119,321,113 (GRCm39) critical splice donor site probably null
R0267:Scn5a UTSW 9 119,372,201 (GRCm39) missense probably damaging 0.98
R0313:Scn5a UTSW 9 119,363,637 (GRCm39) missense probably damaging 1.00
R0360:Scn5a UTSW 9 119,351,665 (GRCm39) missense probably damaging 0.99
R0364:Scn5a UTSW 9 119,351,665 (GRCm39) missense probably damaging 0.99
R0369:Scn5a UTSW 9 119,362,838 (GRCm39) missense probably damaging 0.99
R0512:Scn5a UTSW 9 119,379,724 (GRCm39) missense probably damaging 1.00
R0681:Scn5a UTSW 9 119,368,706 (GRCm39) missense probably damaging 0.96
R1163:Scn5a UTSW 9 119,362,993 (GRCm39) missense probably damaging 1.00
R1469:Scn5a UTSW 9 119,362,727 (GRCm39) critical splice donor site probably null
R1469:Scn5a UTSW 9 119,362,727 (GRCm39) critical splice donor site probably null
R1470:Scn5a UTSW 9 119,365,541 (GRCm39) missense possibly damaging 0.82
R1470:Scn5a UTSW 9 119,365,541 (GRCm39) missense possibly damaging 0.82
R1530:Scn5a UTSW 9 119,324,628 (GRCm39) missense probably damaging 1.00
R1532:Scn5a UTSW 9 119,362,913 (GRCm39) missense probably damaging 1.00
R1544:Scn5a UTSW 9 119,315,699 (GRCm39) missense probably damaging 1.00
R1588:Scn5a UTSW 9 119,350,367 (GRCm39) missense probably damaging 1.00
R1607:Scn5a UTSW 9 119,315,158 (GRCm39) missense probably damaging 1.00
R1657:Scn5a UTSW 9 119,391,446 (GRCm39) missense probably damaging 1.00
R1664:Scn5a UTSW 9 119,350,243 (GRCm39) missense possibly damaging 0.84
R1785:Scn5a UTSW 9 119,350,195 (GRCm39) missense probably damaging 1.00
R1925:Scn5a UTSW 9 119,358,085 (GRCm39) missense probably benign
R1956:Scn5a UTSW 9 119,346,479 (GRCm39) missense possibly damaging 0.82
R2006:Scn5a UTSW 9 119,365,546 (GRCm39) missense probably damaging 1.00
R2061:Scn5a UTSW 9 119,314,717 (GRCm39) missense probably damaging 0.98
R2083:Scn5a UTSW 9 119,321,189 (GRCm39) missense probably benign 0.45
R2180:Scn5a UTSW 9 119,345,117 (GRCm39) missense probably benign
R2216:Scn5a UTSW 9 119,342,151 (GRCm39) missense probably benign
R2216:Scn5a UTSW 9 119,314,678 (GRCm39) missense probably benign 0.37
R2320:Scn5a UTSW 9 119,359,022 (GRCm39) critical splice donor site probably null
R2377:Scn5a UTSW 9 119,368,793 (GRCm39) missense probably damaging 1.00
R2510:Scn5a UTSW 9 119,362,751 (GRCm39) missense probably benign 0.05
R3113:Scn5a UTSW 9 119,314,738 (GRCm39) missense probably damaging 1.00
R3769:Scn5a UTSW 9 119,381,142 (GRCm39) critical splice acceptor site probably benign
R4133:Scn5a UTSW 9 119,315,438 (GRCm39) missense probably damaging 1.00
R4164:Scn5a UTSW 9 119,324,844 (GRCm39) missense probably damaging 1.00
R4447:Scn5a UTSW 9 119,379,693 (GRCm39) missense probably damaging 1.00
R4635:Scn5a UTSW 9 119,358,051 (GRCm39) missense possibly damaging 0.47
R4734:Scn5a UTSW 9 119,368,604 (GRCm39) missense probably damaging 0.98
R4829:Scn5a UTSW 9 119,363,773 (GRCm39) missense probably benign 0.00
R4867:Scn5a UTSW 9 119,379,737 (GRCm39) nonsense probably null
R5055:Scn5a UTSW 9 119,351,632 (GRCm39) missense probably damaging 1.00
R5229:Scn5a UTSW 9 119,365,042 (GRCm39) missense probably damaging 1.00
R5344:Scn5a UTSW 9 119,363,073 (GRCm39) missense probably benign 0.25
R5424:Scn5a UTSW 9 119,330,800 (GRCm39) missense probably damaging 1.00
R5517:Scn5a UTSW 9 119,324,779 (GRCm39) missense probably damaging 1.00
R5526:Scn5a UTSW 9 119,350,237 (GRCm39) missense probably damaging 1.00
R5560:Scn5a UTSW 9 119,389,352 (GRCm39) missense probably damaging 1.00
R5719:Scn5a UTSW 9 119,359,118 (GRCm39) missense possibly damaging 0.91
R5726:Scn5a UTSW 9 119,362,913 (GRCm39) missense probably damaging 1.00
R5800:Scn5a UTSW 9 119,330,732 (GRCm39) missense probably damaging 1.00
R5826:Scn5a UTSW 9 119,350,399 (GRCm39) missense probably damaging 1.00
R6046:Scn5a UTSW 9 119,391,440 (GRCm39) missense probably damaging 1.00
R6101:Scn5a UTSW 9 119,351,716 (GRCm39) missense probably damaging 0.98
R6162:Scn5a UTSW 9 119,351,621 (GRCm39) missense probably damaging 0.98
R6375:Scn5a UTSW 9 119,372,422 (GRCm39) missense probably damaging 1.00
R6378:Scn5a UTSW 9 119,315,102 (GRCm39) missense probably damaging 1.00
R6464:Scn5a UTSW 9 119,363,646 (GRCm39) missense probably damaging 1.00
R6794:Scn5a UTSW 9 119,364,955 (GRCm39) missense probably damaging 0.98
R6799:Scn5a UTSW 9 119,324,688 (GRCm39) missense possibly damaging 0.62
R6850:Scn5a UTSW 9 119,330,815 (GRCm39) missense possibly damaging 0.92
R6858:Scn5a UTSW 9 119,321,156 (GRCm39) missense probably benign 0.11
R6861:Scn5a UTSW 9 119,359,089 (GRCm39) missense probably damaging 1.00
R6875:Scn5a UTSW 9 119,315,710 (GRCm39) missense probably damaging 1.00
R6989:Scn5a UTSW 9 119,315,395 (GRCm39) missense probably damaging 1.00
R7009:Scn5a UTSW 9 119,314,996 (GRCm39) missense probably damaging 1.00
R7064:Scn5a UTSW 9 119,318,977 (GRCm39) missense probably damaging 0.99
R7145:Scn5a UTSW 9 119,315,437 (GRCm39) missense probably damaging 1.00
R7212:Scn5a UTSW 9 119,372,451 (GRCm39) missense possibly damaging 0.94
R7238:Scn5a UTSW 9 119,320,610 (GRCm39) missense possibly damaging 0.73
R7266:Scn5a UTSW 9 119,391,626 (GRCm39) missense probably benign 0.37
R7348:Scn5a UTSW 9 119,364,899 (GRCm39) missense probably benign 0.00
R7399:Scn5a UTSW 9 119,315,596 (GRCm39) missense probably damaging 1.00
R7453:Scn5a UTSW 9 119,351,656 (GRCm39) missense possibly damaging 0.82
R7495:Scn5a UTSW 9 119,372,200 (GRCm39) missense probably damaging 0.99
R7681:Scn5a UTSW 9 119,359,043 (GRCm39) missense probably benign 0.01
R7729:Scn5a UTSW 9 119,324,606 (GRCm39) missense probably damaging 1.00
R7791:Scn5a UTSW 9 119,372,402 (GRCm39) missense possibly damaging 0.47
R7794:Scn5a UTSW 9 119,358,153 (GRCm39) missense probably damaging 0.99
R7873:Scn5a UTSW 9 119,327,193 (GRCm39) missense probably damaging 1.00
R7951:Scn5a UTSW 9 119,358,145 (GRCm39) missense probably damaging 1.00
R8154:Scn5a UTSW 9 119,391,611 (GRCm39) missense possibly damaging 0.48
R8306:Scn5a UTSW 9 119,350,357 (GRCm39) missense probably damaging 1.00
R8329:Scn5a UTSW 9 119,365,030 (GRCm39) missense probably damaging 0.96
R8390:Scn5a UTSW 9 119,368,604 (GRCm39) missense possibly damaging 0.59
R8536:Scn5a UTSW 9 119,368,811 (GRCm39) missense probably damaging 1.00
R8922:Scn5a UTSW 9 119,363,766 (GRCm39) missense probably benign
R9000:Scn5a UTSW 9 119,321,171 (GRCm39) missense possibly damaging 0.95
R9015:Scn5a UTSW 9 119,381,142 (GRCm39) critical splice acceptor site probably benign
R9272:Scn5a UTSW 9 119,315,717 (GRCm39) missense probably damaging 1.00
R9394:Scn5a UTSW 9 119,324,682 (GRCm39) missense probably damaging 1.00
R9448:Scn5a UTSW 9 119,381,127 (GRCm39) missense probably damaging 0.99
R9511:Scn5a UTSW 9 119,351,611 (GRCm39) missense probably benign 0.00
R9563:Scn5a UTSW 9 119,315,803 (GRCm39) missense probably damaging 1.00
R9593:Scn5a UTSW 9 119,315,839 (GRCm39) missense probably damaging 1.00
X0023:Scn5a UTSW 9 119,346,835 (GRCm39) missense probably damaging 1.00
X0065:Scn5a UTSW 9 119,314,735 (GRCm39) missense probably damaging 1.00
Z1177:Scn5a UTSW 9 119,362,997 (GRCm39) missense probably benign 0.04
Z1177:Scn5a UTSW 9 119,351,584 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- AAAGCTCCATCTGTCTGCTGCC -3'
(R):5'- TTTACCCGAGCCGCTGTCAATC -3'

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