rs1060501008

Variant names:

• chr12-51706506-A-C
• rs1060501008
• NM_001330260.2:c.1426A>C

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2 PP2

The NM_001330260.2(SCN8A):​c.1426A>C​(p.Ser476Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000206 in 1,452,946 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000021 (0 hom.)
• Consequence: SCN8A NM_001330260.2 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 9.32

Genes affected

SCN8A (HGNC:10596): (sodium voltage-gated channel alpha subunit 8) This gene encodes a member of the sodium channel alpha subunit gene family. The encoded protein forms the ion pore region of the voltage-gated sodium channel. This protein is essential for the rapid membrane depolarization that occurs during the formation of the action potential in excitable neurons. Mutations in this gene are associated with cognitive disability, pancerebellar atrophy and ataxia. Alternate splicing results in multiple transcript variants.[provided by RefSeq, May 2010]

ACMG classification

Verdict is Uncertain_significance. Variant got 3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP2: Missense variant in the SCN8A gene, where missense mutations are typically associated with disease (based on misZ statistic). The gene has 213 curated pathogenic missense variants (we use a threshold of 10). The gene has 45 curated benign missense variants. Gene score misZ: 0.78755 (below the threshold of 3.09). Trascript score misZ: 10.436 (above the threshold of 3.09). GenCC associations: The gene is linked to myoclonus, familial, 2, infantile convulsions and choreoathetosis, cognitive impairment with or without cerebellar ataxia, undetermined early-onset epileptic encephalopathy, complex neurodevelopmental disorder, developmental and epileptic encephalopathy, 13, benign familial infantile epilepsy, seizures, benign familial infantile, 5.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SCN8A	NM_001330260.2	c.1426A>C	p.Ser476Arg	missense_variant	Exon 11 of 27	ENST00000627620.5	NP_001317189.1
SCN8A	NM_014191.4	c.1426A>C	p.Ser476Arg	missense_variant	Exon 11 of 27	ENST00000354534.11	NP_055006.1
SCN8A	NM_001177984.3	c.1426A>C	p.Ser476Arg	missense_variant	Exon 11 of 26		NP_001171455.1
SCN8A	NM_001369788.1	c.1426A>C	p.Ser476Arg	missense_variant	Exon 11 of 26		NP_001356717.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SCN8A	ENST00000354534.11	c.1426A>C	p.Ser476Arg	missense_variant	Exon 11 of 27	1	NM_014191.4	ENSP00000346534.4
SCN8A	ENST00000627620.5	c.1426A>C	p.Ser476Arg	missense_variant	Exon 11 of 27	5	NM_001330260.2	ENSP00000487583.2
SCN8A	ENST00000599343.5	c.1426A>C	p.Ser476Arg	missense_variant	Exon 10 of 26	5		ENSP00000476447.3
SCN8A	ENST00000355133.7	c.1426A>C	p.Ser476Arg	missense_variant	Exon 10 of 25	1		ENSP00000347255.4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000206 AC: 3 AN: 1452946 Hom.: 0 Cov.: 31 AF XY: 0.00000139 AC XY: 1 AN XY: 721828

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000181

Gnomad4 OTH exome AF: 0.0000166

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

Early infantile epileptic encephalopathy with suppression bursts Uncertain:1

Aug 16, 2016

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

In summary, this variant is a novel missense change with uncertain impact on protein function. It has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0"). This variant is not present in population databases (ExAC no frequency) and has not been reported in the literature in individuals with a SCN8A-related disease. This sequence change replaces serine with arginine at codon 476 of the SCN8A protein (p.Ser476Arg). The serine residue is highly conserved and there is a moderate physicochemical difference between serine and arginine. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.91
BayesDel_addAF	Pathogenic	0.31	D
BayesDel_noAF	Pathogenic	0.21
CADD	Uncertain	24
DANN	Uncertain	1.0
DEOGEN2	Uncertain	0.72	.;D;.;.;.;.;.
Eigen	Uncertain	0.45
Eigen_PC	Uncertain	0.48
FATHMM_MKL	Pathogenic	1.0	D
LIST_S2	Benign	0.82	T;T;T;.;T;T;T
M_CAP	Pathogenic	0.52	D
MetaRNN	Uncertain	0.72	D;D;D;D;D;D;D
MetaSVM	Pathogenic	0.93	D
MutationAssessor	Uncertain	2.2	.;M;M;M;M;M;.
PrimateAI	Uncertain	0.69	T
PROVEAN	Uncertain	-3.6	.;D;D;D;.;.;.
REVEL	Pathogenic	0.80
Sift	Uncertain	0.0020	.;D;D;D;.;.;.
Sift4G	Uncertain	0.037	.;D;D;D;T;D;D
Polyphen		0.99, 0.88	.;D;.;.;P;.;.
Vest4		0.52, 0.51, 0.49, 0.57, 0.45
MutPred		0.30		Loss of phosphorylation at S476 (P = 7e-04);Loss of phosphorylation at S476 (P = 7e-04);Loss of phosphorylation at S476 (P = 7e-04);Loss of phosphorylation at S476 (P = 7e-04);Loss of phosphorylation at S476 (P = 7e-04);Loss of phosphorylation at S476 (P = 7e-04);.;
MVP		0.91
MPC		1.5
ClinPred		0.98	D
GERP RS		4.4
Varity_R		0.76
gMVP		0.79

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1060501008; hg19: chr12-52100290;