Mutagenetix > Incidental Mutation

Incidental Mutation 'R1917:Scnm1'

212590

Institutional Source

Beutler Lab

Gene Symbol

Scnm1

Ensembl Gene

ENSMUSG00000092607

Gene Name

sodium channel modifier 1

Synonyms

3110001I17Rik, Scnm1-ps

MMRRC Submission

039935-MU

Accession Numbers

Essential gene?

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

Stock #

R1917 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

95037030-95041285 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to T at 95037584 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Proline to Threonine at position 161 (P161T)

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

possibly damaging
Transcript: ENSMUST00000172572
AA Change: P161T

PolyPhen 2 Score 0.587 (Sensitivity: 0.87; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000134337
Gene: ENSMUSG00000092607
AA Change: P161T

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: ENSMUST00000174859

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000174835

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000196728

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000173527

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000199730

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000174508

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

0.0975

Coding Region Coverage

1x: 97.5%
3x: 97.0%
10x: 95.8%
20x: 93.6%

Validation Efficiency

100% (83/83)

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: 81 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca8a	A	G	11: 109,982,341 (GRCm39)		probably benign	Het
Adgre5	A	G	8: 84,455,738 (GRCm39)	V190A	probably damaging	Het
Akap6	A	G	12: 53,151,395 (GRCm39)	N1153S	probably benign	Het
Aldh1a7	G	A	19: 20,704,819 (GRCm39)	H20Y	probably benign	Het
B430306N03Rik	A	G	17: 48,631,176 (GRCm39)	E278G	probably benign	Het
Cacna1b	C	A	2: 24,506,891 (GRCm39)	R72L	probably null	Het
Cc2d2a	C	G	5: 43,863,564 (GRCm39)	S675R	probably damaging	Het
Ccdc88b	T	A	19: 6,826,594 (GRCm39)	E1040D	probably damaging	Het
Cmtm7	A	G	9: 114,592,432 (GRCm39)	V55A	probably damaging	Het
Coq4	A	C	2: 29,679,938 (GRCm39)	T77P	probably damaging	Het
Cyp2j11	C	A	4: 96,228,211 (GRCm39)	W136L	probably damaging	Het
Dctn2	T	A	10: 127,110,918 (GRCm39)	Y86*	probably null	Het
Ddx56	A	G	11: 6,213,937 (GRCm39)		probably null	Het
Dop1b	T	C	16: 93,513,150 (GRCm39)	S30P	probably damaging	Het
Ep400	T	C	5: 110,851,441 (GRCm39)	K1347R	unknown	Het
Fat3	T	A	9: 15,908,353 (GRCm39)	T2550S	possibly damaging	Het
Fcrla	G	T	1: 170,755,095 (GRCm39)	C5*	probably null	Het
Fem1al	A	G	11: 29,774,039 (GRCm39)	S473P	probably benign	Het
Fermt1	T	A	2: 132,764,762 (GRCm39)	D365V	probably damaging	Het
Fhod3	A	G	18: 25,123,022 (GRCm39)		probably benign	Het
Fhod3	A	G	18: 25,218,658 (GRCm39)	D807G	probably benign	Het
Fnip1	C	T	11: 54,371,510 (GRCm39)	T177I	probably damaging	Het
Gart	T	C	16: 91,425,037 (GRCm39)	Y662C	probably damaging	Het
Gda	A	T	19: 21,375,004 (GRCm39)		probably benign	Het
Gk	A	G	X: 84,804,186 (GRCm39)	I85T	probably damaging	Het
Gm3476	A	G	14: 6,118,358 (GRCm38)	L255P	possibly damaging	Het
Gm9966	T	C	7: 95,607,684 (GRCm39)	C2R	unknown	Het
Gnpda1	T	C	18: 38,466,243 (GRCm39)		probably null	Het
Gtf2h4	G	A	17: 35,981,090 (GRCm39)	L246F	possibly damaging	Het
Hao1	A	T	2: 134,364,980 (GRCm39)	S216T	probably benign	Het
Hnrnpr	C	A	4: 136,059,799 (GRCm39)	S301*	probably null	Het
Hsd3b2	A	G	3: 98,619,342 (GRCm39)	I201T	probably benign	Het
Jade2	T	C	11: 51,709,365 (GRCm39)	E548G	possibly damaging	Het
Katnbl1	T	C	2: 112,239,524 (GRCm39)	I241T	probably benign	Het
Keap1	G	T	9: 21,145,102 (GRCm39)	Q299K	probably benign	Het
Kif1a	T	C	1: 92,946,753 (GRCm39)	I1650V	possibly damaging	Het
Lrba	G	A	3: 86,571,808 (GRCm39)	G275R	probably damaging	Het
Map3k9	C	A	12: 81,827,564 (GRCm39)	E29*	probably null	Het
Mat1a	G	A	14: 40,843,394 (GRCm39)	V307I	probably damaging	Het
Mcm2	A	T	6: 88,868,785 (GRCm39)	M324K	possibly damaging	Het
Metap1d	T	C	2: 71,341,871 (GRCm39)	V155A	probably damaging	Het
Mtbp	A	G	15: 55,428,073 (GRCm39)		probably benign	Het
Myh14	T	C	7: 44,307,349 (GRCm39)	T231A	probably benign	Het
Mylk4	A	T	13: 32,908,836 (GRCm39)	D90E	probably benign	Het
Myo15b	T	A	11: 115,773,080 (GRCm39)	I1837K	possibly damaging	Het
Myo3a	T	A	2: 22,296,733 (GRCm39)	H242Q	probably damaging	Het
Nxn	A	G	11: 76,152,498 (GRCm39)		probably benign	Het
Or6c2	T	A	10: 129,362,918 (GRCm39)	V274D	probably damaging	Het
Pak3	C	A	X: 142,574,298 (GRCm39)	A553E	possibly damaging	Het
Pdia2	T	A	17: 26,417,079 (GRCm39)	T122S	possibly damaging	Het
Pira12	C	T	7: 3,900,637 (GRCm39)	V38M	probably damaging	Het
Plod2	A	G	9: 92,463,310 (GRCm39)	T132A	probably benign	Het
Ptprz1	T	A	6: 23,035,039 (GRCm39)		probably benign	Het
Rad54b	A	C	4: 11,601,693 (GRCm39)	N416T	probably damaging	Het
Recql4	A	T	15: 76,588,037 (GRCm39)	Y1142*	probably null	Het
Rnf216	A	G	5: 142,978,561 (GRCm39)	V859A	probably benign	Het
Serpinb6b	A	G	13: 33,162,223 (GRCm39)	I222V	probably benign	Het
Serpinf1	A	G	11: 75,301,833 (GRCm39)	I274T	possibly damaging	Het
Slc28a1	T	C	7: 80,819,334 (GRCm39)	F641L	probably benign	Het
Slc8a2	A	G	7: 15,886,845 (GRCm39)	I657V	probably benign	Het
Smchd1	A	G	17: 71,714,232 (GRCm39)	I877T	possibly damaging	Het
Spata31	T	C	13: 65,068,679 (GRCm39)	Y276H	possibly damaging	Het
Spire2	A	G	8: 124,089,810 (GRCm39)	D447G	probably benign	Het
Stk3	G	A	15: 35,073,363 (GRCm39)	T119I	probably damaging	Het
Stxbp5	C	A	10: 9,688,042 (GRCm39)	V420F	possibly damaging	Het
Sult2a5	T	C	7: 13,404,609 (GRCm39)	F282S	probably damaging	Het
Syk	A	T	13: 52,776,744 (GRCm39)	D248V	probably damaging	Het
Thoc6	C	T	17: 23,888,364 (GRCm39)		probably benign	Het
Timd5	A	G	11: 46,419,358 (GRCm39)	D58G	possibly damaging	Het
Tll2	T	A	19: 41,116,936 (GRCm39)	D293V	possibly damaging	Het
Umodl1	G	A	17: 31,203,017 (GRCm39)	V457M	probably damaging	Het
Usp19	T	A	9: 108,376,524 (GRCm39)	C689*	probably null	Het
Usp24	T	G	4: 106,267,483 (GRCm39)	V1955G	probably damaging	Het
Vmn1r226	T	C	17: 20,907,842 (GRCm39)	S25P	probably damaging	Het
Vmn2r69	C	T	7: 85,060,891 (GRCm39)	C231Y	probably damaging	Het
Wdr73	C	T	7: 80,543,081 (GRCm39)	D176N	probably benign	Het
Wnt7b	T	A	15: 85,443,281 (GRCm39)	I41F	probably damaging	Het
Zfhx3	T	C	8: 109,682,880 (GRCm39)	S3440P	unknown	Het
Zfp52	T	G	17: 21,780,426 (GRCm39)	N91K	probably benign	Het
Zfp930	C	A	8: 69,681,357 (GRCm39)	Q350K	probably benign	Het
Zfp949	T	C	9: 88,452,115 (GRCm39)	S562P	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
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
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'- GACTTACAGAAGTGTGCCCC -3'
(R):5'- TTCAAGCGCTGCTCTTCTGG -3'

Sequencing Primer
(F):5'- CTTACAGAAGTGTGCCCCTATAAAG -3'
(R):5'- CGCTGCTCTTCTGGCTTGG -3'

Posted On

2014-07-14