Incidental Mutation 'R5956:Scnm1'
ID 471168
Institutional Source Beutler Lab
Gene Symbol Scnm1
Ensembl Gene ENSMUSG00000092607
Gene Name sodium channel modifier 1
Synonyms 3110001I17Rik, Scnm1-ps
MMRRC Submission 044144-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.152) question?
Stock # R5956 (G1)
Quality Score 225
Status Validated
Chromosome 3
Chromosomal Location 95037030-95041285 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 95037596 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Valine at position 157 (I157V)
Ref Sequence ENSEMBL: ENSMUSP00000134337 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000005769] [ENSMUST00000066386] [ENSMUST00000107227] [ENSMUST00000131597] [ENSMUST00000172572] [ENSMUST00000173462]
AlphaFold no structure available at present
Predicted Effect probably benign
Transcript: ENSMUST00000005769
SMART Domains Protein: ENSMUSP00000005769
Gene: ENSMUSG00000005628

DomainStartEndE-ValueType
Pfam:Tropomodulin 4 143 2.7e-62 PFAM
PDB:1IO0|A 160 343 6e-77 PDB
SCOP:d1a4ya_ 184 289 4e-4 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000066386
SMART Domains Protein: ENSMUSP00000067811
Gene: ENSMUSG00000053769

DomainStartEndE-ValueType
low complexity region 10 19 N/A INTRINSIC
LysM 41 85 2.58e-7 SMART
low complexity region 100 108 N/A INTRINSIC
low complexity region 117 132 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000107227
SMART Domains Protein: ENSMUSP00000102846
Gene: ENSMUSG00000005628

DomainStartEndE-ValueType
Pfam:Tropomodulin 1 144 4.4e-72 PFAM
PDB:1IO0|A 160 343 6e-77 PDB
SCOP:d1a4ya_ 184 289 4e-4 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000130545
Predicted Effect probably benign
Transcript: ENSMUST00000131597
SMART Domains Protein: ENSMUSP00000116341
Gene: ENSMUSG00000005628

DomainStartEndE-ValueType
Pfam:Tropomodulin 1 144 1.5e-72 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000135867
Predicted Effect noncoding transcript
Transcript: ENSMUST00000199730
Predicted Effect probably benign
Transcript: ENSMUST00000172572
AA Change: I157V

PolyPhen 2 Score 0.063 (Sensitivity: 0.94; Specificity: 0.84)
SMART Domains Protein: ENSMUSP00000134337
Gene: ENSMUSG00000092607
AA Change: I157V

DomainStartEndE-ValueType
Pfam:zf-SCNM1 44 70 7.6e-19 PFAM
low complexity region 133 148 N/A INTRINSIC
low complexity region 172 179 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000174508
Predicted Effect noncoding transcript
Transcript: ENSMUST00000174835
Predicted Effect noncoding transcript
Transcript: ENSMUST00000174859
Predicted Effect noncoding transcript
Transcript: ENSMUST00000149898
Predicted Effect noncoding transcript
Transcript: ENSMUST00000196728
Predicted Effect noncoding transcript
Transcript: ENSMUST00000173527
Predicted Effect probably benign
Transcript: ENSMUST00000173462
SMART Domains Protein: ENSMUSP00000133769
Gene: ENSMUSG00000092607

DomainStartEndE-ValueType
Blast:ZnF_C2H2 42 68 2e-7 BLAST
Meta Mutation Damage Score 0.0663 question?
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.6%
  • 10x: 97.9%
  • 20x: 93.5%
Validation Efficiency 98% (63/64)
MGI Phenotype FUNCTION: Mutations in the voltage-gated sodium channel gene Scn8a lead to neurological problems in mice. For one particular mutation, Scn8amedJ, mice live to adulthood but have tremors and muscle weakness, among other problems, in all strains except those derived from C57BL6 mice. In these strains, the product of the Scnm1 gene (229 aa) partially overcomes the effects of the Scn8amedJ mutation. However, in C57BL6-derived mice, a one nt change in the penultimate exon creates a premature stop codon, truncating the Scnm1 protein at 186 aa. This truncated protein lacks the ability to overcome the effects of the Scn8amedJ mutation, and these mice suffer paralysis and juvenile death. [provided by RefSeq, Jul 2009]
PHENOTYPE: The Scnm1 locus influences the severity of the Scn8amed-J phenotype. Mice carrying the recesive susceptibility allele of the modifier are paralyzed and do not survive beyond 1 month. Mice carryimg the resistant allele display progressive dystonia with ataxia and live more than 1.5 years. [provided by MGI curators]
Allele List at MGI

All alleles(10) : Targeted, knock-out(1) Targeted, other(1) Gene trapped(6) Spontaneous(1) Chemically induced(1)

Other mutations in this stock
Total: 58 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2700049A03Rik T A 12: 71,203,893 (GRCm39) I398K possibly damaging Het
Acad9 A G 3: 36,129,323 (GRCm39) probably benign Het
Acsm2 T C 7: 119,153,704 (GRCm39) S5P unknown Het
Akp3 T C 1: 87,054,667 (GRCm39) I334T probably damaging Het
Amy1 C T 3: 113,357,311 (GRCm39) R176H probably benign Het
Ank2 A T 3: 126,736,337 (GRCm39) probably benign Het
Cav1 C A 6: 17,307,918 (GRCm39) N23K probably damaging Het
Cep126 A G 9: 8,112,120 (GRCm39) V151A probably benign Het
Cnot1 A G 8: 96,481,606 (GRCm39) probably null Het
Crim1 T A 17: 78,623,146 (GRCm39) V448E probably damaging Het
Csmd3 T C 15: 48,655,278 (GRCm39) E8G possibly damaging Het
Ddx31 A T 2: 28,764,185 (GRCm39) I464F probably damaging Het
Ddx54 A G 5: 120,764,432 (GRCm39) probably benign Het
Dhx16 A G 17: 36,193,762 (GRCm39) E319G probably damaging Het
Efl1 A G 7: 82,301,107 (GRCm39) D37G probably damaging Het
Epha5 T C 5: 84,298,228 (GRCm39) R444G probably damaging Het
Exoc2 C A 13: 31,004,606 (GRCm39) C859F probably benign Het
Gbx2 T C 1: 89,860,908 (GRCm39) probably benign Het
Gm12258 G A 11: 58,750,285 (GRCm39) A9T probably benign Het
Gpr141b T G 13: 19,913,300 (GRCm39) noncoding transcript Het
Grm4 A G 17: 27,654,129 (GRCm39) V607A probably benign Het
Gvin3 T C 7: 106,200,677 (GRCm39) noncoding transcript Het
Ighv1-74 C A 12: 115,766,455 (GRCm39) W55L probably damaging Het
Irx4 C A 13: 73,415,626 (GRCm39) Y138* probably null Het
Itpr1 C A 6: 108,482,988 (GRCm39) T2352K probably benign Het
Kcnk3 T G 5: 30,745,854 (GRCm39) V65G probably damaging Het
Mctp2 T C 7: 71,908,923 (GRCm39) E130G probably benign Het
Mgat5 C A 1: 127,310,676 (GRCm39) R197S probably benign Het
Mpg T C 11: 32,177,951 (GRCm39) probably null Het
Muc5b T C 7: 141,417,910 (GRCm39) C3619R probably damaging Het
Myo15b G A 11: 115,764,583 (GRCm39) V1321I probably benign Het
Myo1b T C 1: 51,815,391 (GRCm39) T658A probably damaging Het
Nomo1 T C 7: 45,692,037 (GRCm39) S154P possibly damaging Het
Nsd1 T A 13: 55,411,217 (GRCm39) F1423I probably damaging Het
Or1e16 AGCGGTCGTAGGC AGC 11: 73,286,480 (GRCm39) probably null Het
Or9g3 A G 2: 85,584,183 (GRCm39) probably benign Het
Osbpl6 A G 2: 76,379,856 (GRCm39) R149G probably damaging Het
Pacc1 A G 1: 191,080,568 (GRCm39) S263G probably damaging Het
Papola T A 12: 105,777,300 (GRCm39) W281R probably damaging Het
Pole C T 5: 110,485,153 (GRCm39) probably benign Het
Rptn A G 3: 93,305,334 (GRCm39) N889S possibly damaging Het
Scn10a A G 9: 119,460,626 (GRCm39) S1084P probably damaging Het
Sertad2 G A 11: 20,597,884 (GRCm39) G27S probably benign Het
Siglece T C 7: 43,308,760 (GRCm39) T198A probably damaging Het
Sptb T A 12: 76,650,942 (GRCm39) M1678L probably benign Het
Taf8 A T 17: 47,809,467 (GRCm39) M98K probably damaging Het
Tead2 T A 7: 44,870,138 (GRCm39) probably benign Het
Trrap C T 5: 144,744,201 (GRCm39) silent Het
Ttn G T 2: 76,775,914 (GRCm39) N1709K probably damaging Het
Ube3a T C 7: 58,926,768 (GRCm39) probably benign Het
Ube3c T C 5: 29,804,054 (GRCm39) probably benign Het
Unc80 T C 1: 66,567,123 (GRCm39) S910P probably damaging Het
Usp30 G A 5: 114,257,682 (GRCm39) R280Q possibly damaging Het
Vsx1 T C 2: 150,530,457 (GRCm39) S142G possibly damaging Het
Wdr95 T G 5: 149,517,947 (GRCm39) C360G probably benign Het
Zbtb4 A G 11: 69,669,040 (GRCm39) I588V probably benign Het
Zdhhc4 A T 5: 143,310,604 (GRCm39) probably benign Het
Zfp568 C A 7: 29,697,288 (GRCm39) N69K probably damaging Het
Other mutations in Scnm1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL02964:Scnm1 APN 3 95,040,348 (GRCm39) missense probably benign 0.07
R1917:Scnm1 UTSW 3 95,037,584 (GRCm39) missense possibly damaging 0.59
R5538:Scnm1 UTSW 3 95,037,066 (GRCm39) utr 3 prime probably benign
R5888:Scnm1 UTSW 3 95,037,596 (GRCm39) missense probably benign 0.06
R5955:Scnm1 UTSW 3 95,037,596 (GRCm39) missense probably benign 0.06
R6082:Scnm1 UTSW 3 95,037,596 (GRCm39) missense probably benign 0.06
R6086:Scnm1 UTSW 3 95,037,596 (GRCm39) missense probably benign 0.06
R7182:Scnm1 UTSW 3 95,041,165 (GRCm39) missense possibly damaging 0.60
R7206:Scnm1 UTSW 3 95,041,205 (GRCm39) start codon destroyed probably null 1.00
R7605:Scnm1 UTSW 3 95,040,186 (GRCm39) missense probably benign 0.03
R8517:Scnm1 UTSW 3 95,040,134 (GRCm39) critical splice donor site probably null
Z1176:Scnm1 UTSW 3 95,037,652 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- AGACTTACAGAAGTGTGCCCC -3'
(R):5'- AGTTTCAAGCGCTGCTCTTC -3'

Sequencing Primer
(F):5'- CTTACAGAAGTGTGCCCCTATAAAG -3'
(R):5'- CGCTGCTCTTCTGGCTTGG -3'
Posted On 2017-03-31