Mutagenetix > Incidental Mutation

Incidental Mutation 'R5538:Scnm1'

434907

Institutional Source

Beutler Lab

Gene Symbol

Scnm1

Ensembl Gene

ENSMUSG00000092607

Gene Name

sodium channel modifier 1

Synonyms

3110001I17Rik, Scnm1-ps

MMRRC Submission

043096-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.152) question?

Stock #

R5538 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

95037030-95041285 bp(-) (GRCm39)

Type of Mutation

utr 3 prime

DNA Base Change (assembly)

A to G at 95037066 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000133769 (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: ENSMUST00000174835

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000174508

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000174859

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000196728

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000173527

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000199730

Predicted Effect

probably benign
Transcript: ENSMUST00000172572

SMART Domains

Protein: ENSMUSP00000134337
Gene: ENSMUSG00000092607

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

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

0.0898

Coding Region Coverage

1x: 99.9%
3x: 99.7%
10x: 98.3%
20x: 95.1%

Validation Efficiency

94% (73/78)

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: 69 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adgrv1	C	A	13: 81,581,808 (GRCm39)	R4745S	probably benign	Het
Ank3	A	G	10: 69,823,257 (GRCm39)	E642G	probably damaging	Het
Arhgap11a	G	T	2: 113,667,875 (GRCm39)	D375E	probably benign	Het
Arl8b	C	A	6: 108,760,297 (GRCm39)	L28M	probably damaging	Het
Bbs2	G	A	8: 94,816,391 (GRCm39)	T157M	probably damaging	Het
C2cd3	T	A	7: 100,104,700 (GRCm39)		probably null	Het
C6	T	A	15: 4,844,311 (GRCm39)	I911N	possibly damaging	Het
Cc2d2a	T	C	5: 43,852,518 (GRCm39)	I365T	possibly damaging	Het
Cd46	T	G	1: 194,750,478 (GRCm39)		probably null	Het
Ceacam3	A	T	7: 16,892,346 (GRCm39)	D363V	probably damaging	Het
Cep63	A	T	9: 102,465,992 (GRCm39)	L678*	probably null	Het
Clasrp	A	C	7: 19,318,707 (GRCm39)		probably benign	Het
Clk2	T	A	3: 89,082,962 (GRCm39)	Y412N	probably damaging	Het
Col24a1	C	T	3: 144,998,882 (GRCm39)	A5V	probably damaging	Het
Cox16	T	C	12: 81,531,703 (GRCm39)	N13D	possibly damaging	Het
Cybb	C	G	X: 9,316,989 (GRCm39)	D246H	probably benign	Het
Dhx32	A	T	7: 133,324,946 (GRCm39)	M437K	probably benign	Het
Dnm2	T	C	9: 21,416,923 (GRCm39)	F819L	probably benign	Het
Dpysl4	A	G	7: 138,671,906 (GRCm39)	T85A	probably benign	Het
Dspp	A	T	5: 104,323,096 (GRCm39)	K80*	probably null	Het
Dync2h1	T	C	9: 7,168,630 (GRCm39)		probably benign	Het
Ern1	A	G	11: 106,312,727 (GRCm39)	V218A	possibly damaging	Het
Fbn2	G	A	18: 58,204,973 (GRCm39)	R1157C	probably benign	Het
Fez1	T	A	9: 36,780,172 (GRCm39)	I323N	probably damaging	Het
Fmo9	T	A	1: 166,501,198 (GRCm39)	T199S	probably benign	Het
Fry	T	A	5: 150,419,313 (GRCm39)	L915Q	probably damaging	Het
Gatd1	A	G	7: 140,986,758 (GRCm39)		probably benign	Het
Gm10719	T	C	9: 3,018,962 (GRCm39)	L69S	probably benign	Het
Gnpda2	A	T	5: 69,735,394 (GRCm39)	H230Q	probably damaging	Het
Gramd1c	T	A	16: 43,802,455 (GRCm39)	N652I	probably damaging	Het
H2-T13	T	A	17: 36,392,178 (GRCm39)	H178L	probably benign	Het
Hells	T	A	19: 38,942,096 (GRCm39)	F462Y	probably benign	Het
Htr7	A	G	19: 35,947,235 (GRCm39)	F260L	probably benign	Het
Itsn1	C	A	16: 91,580,990 (GRCm39)	A23D	probably damaging	Het
Jak3	A	G	8: 72,131,417 (GRCm39)	D94G	probably benign	Het
Kctd16	T	A	18: 40,390,319 (GRCm39)	Y97*	probably null	Het
Kif20b	A	T	19: 34,930,364 (GRCm39)	K25*	probably null	Het
Klf2	T	C	8: 73,073,316 (GRCm39)	L40P	probably damaging	Het
Kmt2a	A	G	9: 44,731,639 (GRCm39)		probably benign	Het
Kmt2d	G	A	15: 98,749,990 (GRCm39)		probably benign	Het
Lonrf1	T	A	8: 36,690,178 (GRCm39)		probably null	Het
Lrp1b	A	T	2: 40,587,486 (GRCm39)	I154K	unknown	Het
Mybpc1	T	A	10: 88,381,891 (GRCm39)	I600L	possibly damaging	Het
Npnt	T	C	3: 132,610,724 (GRCm39)	N285S	probably damaging	Het
Or4c12b	T	A	2: 89,646,964 (GRCm39)	F92Y	probably damaging	Het
Or51h5	A	G	7: 102,577,728 (GRCm39)	T298A	probably damaging	Het
Or6c69	T	A	10: 129,747,871 (GRCm39)	Y92F	probably benign	Het
Or6n1	T	C	1: 173,917,544 (GRCm39)	*313R	probably null	Het
Pcnx1	T	C	12: 81,907,183 (GRCm39)	V13A	probably damaging	Het
Phkb	G	A	8: 86,648,756 (GRCm39)	V191I	possibly damaging	Het
Pnpla6	A	G	8: 3,581,508 (GRCm39)	M594V	probably benign	Het
Potefam3e	A	C	8: 19,799,430 (GRCm39)		probably null	Het
Prkdc	A	G	16: 15,469,333 (GRCm39)	E146G	probably damaging	Het
Ror1	T	C	4: 100,298,208 (GRCm39)	M527T	probably benign	Het
Skint11	A	T	4: 114,088,959 (GRCm39)	N251I	probably damaging	Het
Slc19a3	T	A	1: 83,000,282 (GRCm39)	N245I	possibly damaging	Het
Slc1a3	A	T	15: 8,675,188 (GRCm39)	D272E	probably damaging	Het
Smok2b	T	A	17: 13,454,440 (GRCm39)	V200D	possibly damaging	Het
Sspo	T	C	6: 48,429,112 (GRCm39)	Y417H	probably damaging	Het
Stk11ip	C	A	1: 75,504,979 (GRCm39)	S388R	probably damaging	Het
Svep1	T	C	4: 58,049,282 (GRCm39)		probably null	Het
Sytl2	A	G	7: 90,038,114 (GRCm39)	I525V	probably benign	Het
Tie1	T	C	4: 118,343,390 (GRCm39)	N158D	probably benign	Het
Tle2	T	C	10: 81,416,418 (GRCm39)	L180P	probably damaging	Het
Txlnb	T	C	10: 17,714,657 (GRCm39)	L363P	probably damaging	Het
Upk3b	C	G	5: 136,072,890 (GRCm39)	A258G	probably benign	Het
Usp32	A	T	11: 84,908,612 (GRCm39)	D1031E	possibly damaging	Het
Vmn2r116	C	T	17: 23,620,041 (GRCm39)	L592F	probably benign	Het
Zfp607b	A	G	7: 27,402,294 (GRCm39)	H250R	probably damaging	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
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
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'- CTGAAAGCAGCTGACGCTTG -3'
(R):5'- TGTAGGTTCCTGGGATGCAAC -3'

Sequencing Primer
(F):5'- AGCTGACGCTTGGCAAG -3'
(R):5'- GCAGCACAGGAAGCCTTTC -3'

Posted On

2016-10-24