Mutagenetix > Incidental Mutation

Incidental Mutation 'R5888:Scnm1'

457775

Institutional Source

Beutler Lab

Gene Symbol

Scnm1

Ensembl Gene

ENSMUSG00000092607

Gene Name

sodium channel modifier 1

Synonyms

3110001I17Rik, Scnm1-ps

MMRRC Submission

044089-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.188) question?

Stock #

R5888 (G1)

Quality Score

225

Status

Validated

Chromosome

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

Domain	Start	End	E-Value	Type
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

Domain	Start	End	E-Value	Type
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

Domain	Start	End	E-Value	Type
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

Domain	Start	End	E-Value	Type
Pfam:Tropomodulin	1	144	1.5e-72	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000135867

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000149898

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

Domain	Start	End	E-Value	Type
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: ENSMUST00000196728

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000173527

Predicted Effect

probably benign
Transcript: ENSMUST00000173462

SMART Domains

Protein: ENSMUSP00000133769
Gene: ENSMUSG00000092607

Domain	Start	End	E-Value	Type
Blast:ZnF_C2H2	42	68	2e-7	BLAST

Meta Mutation Damage Score

0.0663

Coding Region Coverage

1x: 99.9%
3x: 99.6%
10x: 98.2%
20x: 94.9%

Validation Efficiency

94% (96/102)

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 Scn8a^med-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: 92 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adcy1	T	A	11: 7,089,095 (GRCm39)	V503E	possibly damaging	Het
Alk	C	A	17: 72,181,938 (GRCm39)	V1362L	probably damaging	Het
Ankrd55	T	A	13: 112,492,453 (GRCm39)	I208N	possibly damaging	Het
Asap2	T	A	12: 21,268,191 (GRCm39)	I319N	probably damaging	Het
Atp11b	T	C	3: 35,891,696 (GRCm39)	I1036T	probably benign	Het
B4gat1	T	C	19: 5,089,560 (GRCm39)	F186L	probably benign	Het
C3	T	A	17: 57,521,831 (GRCm39)	T1079S	probably damaging	Het
Cacul1	G	T	19: 60,525,902 (GRCm39)	T287K	possibly damaging	Het
Cbr3	G	C	16: 93,487,614 (GRCm39)	G266R	probably damaging	Het
Cd63	T	A	10: 128,748,160 (GRCm39)		probably null	Het
Chd7	G	A	4: 8,866,382 (GRCm39)	M851I	probably damaging	Het
Chst13	T	A	6: 90,286,554 (GRCm39)	H136L	probably benign	Het
Cyp2d22	T	C	15: 82,258,014 (GRCm39)	T179A	probably benign	Het
Dclre1b	A	T	3: 103,711,053 (GRCm39)	V286E	probably damaging	Het
Defb45	G	A	2: 152,435,154 (GRCm39)		probably benign	Het
Dlg1	T	C	16: 31,610,704 (GRCm39)		probably null	Het
Dock3	A	G	9: 106,901,002 (GRCm39)	V321A	probably benign	Het
Dytn	A	T	1: 63,716,396 (GRCm39)	V59E	possibly damaging	Het
Efcab3	T	C	11: 104,612,227 (GRCm39)		probably benign	Het
Eif2ak1	A	G	5: 143,823,733 (GRCm39)	I393M	probably damaging	Het
Fam83g	A	T	11: 61,593,420 (GRCm39)	E318V	probably benign	Het
Fbxo34	T	A	14: 47,767,176 (GRCm39)	F179I	probably damaging	Het
Fmo5	T	A	3: 97,549,041 (GRCm39)	Y230N	probably benign	Het
Fzd9	T	G	5: 135,278,317 (GRCm39)		probably null	Het
Gata2	T	C	6: 88,177,722 (GRCm39)	S251P	probably benign	Het
Gigyf1	A	G	5: 137,523,959 (GRCm39)	D1043G	probably damaging	Het
Gm10322	T	A	10: 59,452,125 (GRCm39)	S81T	probably benign	Het
Gm15517	A	T	7: 43,910,066 (GRCm39)		probably benign	Het
Haus4	T	C	14: 54,781,676 (GRCm39)	T232A	probably benign	Het
Hgfac	A	T	5: 35,202,751 (GRCm39)	H417L	probably damaging	Het
Iqgap2	T	C	13: 95,772,118 (GRCm39)	K1354E	possibly damaging	Het
Kcnk12	C	A	17: 88,054,077 (GRCm39)	R195L	probably benign	Het
Kcnn2	A	T	18: 45,725,412 (GRCm39)	I303F	probably damaging	Het
Kcnt1	T	C	2: 25,798,122 (GRCm39)	F879S	probably damaging	Het
Kndc1	T	C	7: 139,475,133 (GRCm39)	F11L	probably benign	Het
Kpna7	A	G	5: 144,926,605 (GRCm39)	F449S	probably damaging	Het
Krt77	G	T	15: 101,773,888 (GRCm39)	N255K	probably benign	Het
Lair1	A	T	7: 4,013,844 (GRCm39)	D134E	probably damaging	Het
Loxhd1	T	C	18: 77,490,211 (GRCm39)	V1318A	probably damaging	Het
Marchf10	A	T	11: 105,292,972 (GRCm39)	V145D	possibly damaging	Het
Mcpt1	T	A	14: 56,256,969 (GRCm39)	M169K	probably benign	Het
Mdc1	T	A	17: 36,158,712 (GRCm39)	V364E	probably benign	Het
Mfsd11	T	C	11: 116,762,210 (GRCm39)	F270S	probably damaging	Het
Mfsd4b2	T	G	10: 39,798,031 (GRCm39)	D108A	probably benign	Het
Mink1	A	T	11: 70,500,885 (GRCm39)		probably benign	Het
Mmp25	T	C	17: 23,850,048 (GRCm39)	Y504C	probably damaging	Het
Ms4a13	C	T	19: 11,168,870 (GRCm39)	V52I	probably benign	Het
Msh4	C	T	3: 153,573,360 (GRCm39)		probably null	Het
Muc5b	T	G	7: 141,412,158 (GRCm39)	S1701R	unknown	Het
Naalad2	A	T	9: 18,241,937 (GRCm39)	S656T	probably benign	Het
Ncapd2	T	C	6: 125,164,052 (GRCm39)	Y64C	probably damaging	Het
Ncapg2	T	A	12: 116,389,420 (GRCm39)	S347T	possibly damaging	Het
Ndufb11b	T	C	15: 81,864,872 (GRCm39)	S38P	probably benign	Het
Nipal4	T	C	11: 46,042,166 (GRCm39)	T172A	probably damaging	Het
Nrros	T	C	16: 31,961,905 (GRCm39)	K652R	probably benign	Het
Nrxn3	G	T	12: 89,478,855 (GRCm39)	A983S	possibly damaging	Het
Or4a76	T	A	2: 89,461,143 (GRCm39)	Y33F	probably damaging	Het
Or4ac1-ps1	T	C	2: 88,370,588 (GRCm39)		noncoding transcript	Het
Or4c115	T	A	2: 88,928,269 (GRCm39)	M1L	probably damaging	Het
Or4k77	T	C	2: 111,199,088 (GRCm39)	M37T	probably benign	Het
Or51m1	A	G	7: 103,578,239 (GRCm39)	T70A	possibly damaging	Het
Or8g24	A	T	9: 38,989,263 (GRCm39)	Y259*	probably null	Het
Or8k37	A	C	2: 86,469,488 (GRCm39)	L188R	probably damaging	Het
P2rx4	T	A	5: 122,857,228 (GRCm39)	S155T	probably benign	Het
P2rx4	T	G	5: 122,865,271 (GRCm39)	Y299D	probably damaging	Het
Pcsk6	A	T	7: 65,693,372 (GRCm39)	L7F	probably null	Het
Pdss2	T	C	10: 43,097,793 (GRCm39)		silent	Het
Pfkl	A	G	10: 77,827,204 (GRCm39)	V494A	possibly damaging	Het
Prep	G	T	10: 44,943,460 (GRCm39)	D12Y	possibly damaging	Het
Prg4	A	G	1: 150,328,101 (GRCm39)	F188S	probably damaging	Het
Ripor3	T	C	2: 167,839,207 (GRCm39)	Y98C	probably damaging	Het
Rnf216	T	A	5: 143,054,069 (GRCm39)		probably null	Het
Rnf24	A	G	2: 131,164,165 (GRCm39)		probably benign	Het
Rps18-ps6	G	A	13: 97,896,901 (GRCm39)	R66*	probably null	Het
Scn3a	A	G	2: 65,327,742 (GRCm39)	M916T	probably benign	Het
Sh2b3	C	G	5: 121,967,084 (GRCm39)	R10P	possibly damaging	Het
Slc25a27	T	C	17: 43,960,585 (GRCm39)	D211G	probably damaging	Het
Slc36a4	A	T	9: 15,638,324 (GRCm39)	Y250F	probably damaging	Het
Slc4a1	T	A	11: 102,247,351 (GRCm39)	E448V	probably damaging	Het
Slit1	C	A	19: 41,731,735 (GRCm39)	C38F	probably damaging	Het
Spock3	T	A	8: 63,808,334 (GRCm39)	N410K	unknown	Het
Supt20	G	T	3: 54,619,628 (GRCm39)	W370L	probably benign	Het
Tas2r139	T	A	6: 42,118,430 (GRCm39)	N187K	probably damaging	Het
Tbc1d9b	G	A	11: 50,031,311 (GRCm39)	V111I	probably benign	Het
Thsd7b	T	A	1: 130,138,057 (GRCm39)	Y1578*	probably null	Het
Tln2	T	A	9: 67,136,685 (GRCm39)	I1267F	probably damaging	Het
Tnk2	G	A	16: 32,490,185 (GRCm39)	V363I	probably damaging	Het
Ttc32	A	G	12: 9,085,870 (GRCm39)	K139R	possibly damaging	Het
Vmn1r30	G	C	6: 58,412,550 (GRCm39)	T94S	possibly damaging	Het
Vmn1r90	G	A	7: 14,295,780 (GRCm39)	T106I	probably damaging	Het
Zfp677	T	A	17: 21,618,520 (GRCm39)	C526S	probably damaging	Het
Zfp831	T	G	2: 174,485,420 (GRCm39)	S32A	probably benign	Het

Other mutations in Scnm1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH 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
R5955:Scnm1	UTSW	3	95,037,596 (GRCm39)	missense	probably benign	0.06
R5956: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'- ACAGAAGTGTGCCCCTATAAAG -3'
(R):5'- AAATCAGTTTCAAGCGCTGCTC -3'

Sequencing Primer
(F):5'- GTCTGAAAACAGGCAGGTCCC -3'
(R):5'- AAGCGCTGCTCTTCTGG -3'

Posted On

2017-02-15