Incidental Mutation 'R2180:Scn5a'
ID 237135
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 040182-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R2180 (G1)
Quality Score 220
Status Not validated
Chromosome 9
Chromosomal Location 119312474-119408082 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 119345117 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Alanine at position 1083 (V1083A)
Ref Sequence ENSEMBL: ENSMUSP00000113272 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000065196] [ENSMUST00000117911] [ENSMUST00000120420]
AlphaFold Q9JJV9
Predicted Effect probably benign
Transcript: ENSMUST00000065196
AA Change: V1084A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000066228
Gene: ENSMUSG00000032511
AA Change: V1084A

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 probably benign
Transcript: ENSMUST00000117911
AA Change: V1084A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000112838
Gene: ENSMUSG00000032511
AA Change: V1084A

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 benign
Transcript: ENSMUST00000120420
AA Change: V1083A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000113272
Gene: ENSMUSG00000032511
AA Change: V1083A

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
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.7%
  • 10x: 97.4%
  • 20x: 95.1%
Validation Efficiency
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: 60 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adamts5 T C 16: 85,684,812 (GRCm39) D377G probably damaging Het
Adgrl4 A T 3: 151,205,779 (GRCm39) I164F probably damaging Het
Anxa9 T C 3: 95,213,735 (GRCm39) probably null Het
Aox4 A T 1: 58,252,226 (GRCm39) T34S probably benign Het
Asic1 G T 15: 99,569,846 (GRCm39) V56F probably benign Het
Atpaf1 T C 4: 115,645,557 (GRCm39) M1T probably null Het
Axin1 A G 17: 26,362,309 (GRCm39) T218A probably benign Het
Bdp1 ATTCTTCTTCTTCTTCTTC ATTCTTCTTCTTCTTCTTCTTC 13: 100,197,913 (GRCm39) probably benign Het
Birc6 T C 17: 74,919,146 (GRCm39) I1988T probably benign Het
Btbd7 A T 12: 102,752,156 (GRCm39) D869E probably damaging Het
Caln1 T C 5: 130,868,249 (GRCm39) *220Q probably null Het
Ccdc150 G A 1: 54,311,706 (GRCm39) probably null Het
Ccnt1 A T 15: 98,441,481 (GRCm39) S596T possibly damaging Het
Cd44 C T 2: 102,658,955 (GRCm39) G640E possibly damaging Het
Cep192 A G 18: 67,957,813 (GRCm39) E582G possibly damaging Het
Clcnkb G T 4: 141,136,819 (GRCm39) probably null Het
Dhx29 T C 13: 113,099,406 (GRCm39) probably null Het
Dnah8 T C 17: 31,059,621 (GRCm39) F4407S probably benign Het
Enah A T 1: 181,746,024 (GRCm39) M419K probably damaging Het
Fancd2 A T 6: 113,551,598 (GRCm39) T1055S probably benign Het
Gigyf2 G A 1: 87,344,642 (GRCm39) G525D probably damaging Het
Gm5800 T A 14: 51,953,451 (GRCm39) K55* probably null Het
Gpr149 A G 3: 62,511,489 (GRCm39) L170P probably damaging Het
Grik4 A T 9: 42,453,301 (GRCm39) Y695N probably benign Het
Gsg1 A T 6: 135,217,143 (GRCm39) V228D probably damaging Het
Helb G A 10: 119,941,353 (GRCm39) T445M probably benign Het
Helz2 A T 2: 180,875,525 (GRCm39) D1656E probably damaging Het
Hyou1 A T 9: 44,299,316 (GRCm39) K669M probably benign Het
Itga2 T C 13: 114,985,917 (GRCm39) N953D possibly damaging Het
Ldhd T C 8: 112,356,018 (GRCm39) I122V probably benign Het
Lrrtm1 A G 6: 77,221,329 (GRCm39) D262G probably damaging Het
Mapkapk5 T C 5: 121,673,927 (GRCm39) probably null Het
Msantd5l C A 11: 51,145,437 (GRCm39) W50L probably damaging Het
Niban1 A T 1: 151,593,829 (GRCm39) H838L probably benign Het
Numa1 T C 7: 101,649,197 (GRCm39) I976T probably benign Het
Or10x1 A G 1: 174,196,967 (GRCm39) I161M probably damaging Het
Or2a12 C T 6: 42,904,459 (GRCm39) T98I probably benign Het
Or4f14b A G 2: 111,775,348 (GRCm39) V151A probably benign Het
Or52e4 T C 7: 104,706,092 (GRCm39) I213T probably benign Het
Patj G A 4: 98,411,739 (GRCm39) probably null Het
Pfas T C 11: 68,883,013 (GRCm39) D757G possibly damaging Het
Pom121l2 A G 13: 22,166,145 (GRCm39) N139D probably benign Het
Ppp2r3d A T 9: 101,004,214 (GRCm39) Y994* probably null Het
Ppp6c T C 2: 39,087,525 (GRCm39) D227G probably benign Het
Ptpn13 T G 5: 103,717,424 (GRCm39) H1855Q probably damaging Het
Ptprh T A 7: 4,604,867 (GRCm39) Q59L probably benign Het
Rap1gap2 T C 11: 74,283,972 (GRCm39) K669E probably benign Het
Rbl2 T C 8: 91,816,683 (GRCm39) S348P possibly damaging Het
Rptor T A 11: 119,615,970 (GRCm39) N161K probably damaging Het
Satb1 C T 17: 52,110,524 (GRCm39) A192T probably damaging Het
Sec14l2 C T 11: 4,058,964 (GRCm39) A194T probably damaging Het
Sema4b A G 7: 79,862,583 (GRCm39) N53S probably benign Het
Sin3b T A 8: 73,479,923 (GRCm39) Y876* probably null Het
Smchd1 C A 17: 71,770,794 (GRCm39) M129I probably benign Het
Spmip6 T A 4: 41,507,170 (GRCm39) M209L probably benign Het
Tmc1 T C 19: 20,801,448 (GRCm39) Y484C probably damaging Het
Utp20 A G 10: 88,656,801 (GRCm39) S135P probably damaging Het
Zfp266 A T 9: 20,410,975 (GRCm39) C401S probably damaging Het
Zfp738 G A 13: 67,819,313 (GRCm39) T226I probably damaging Het
Zfp871 G A 17: 32,994,275 (GRCm39) T300M probably damaging 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
R1597:Scn5a UTSW 9 119,391,563 (GRCm39) missense probably damaging 0.99
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
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'- TCCCTTGGTAAACGTAGCCAG -3'
(R):5'- GGAACCTCTCACTTACTGACCC -3'

Sequencing Primer
(F):5'- TCACAGCCTGACCCTGG -3'
(R):5'- CCCAAGTCAGCAGAGGATG -3'
Posted On 2014-10-02