rs879255704

chr12-51786578-A-G

Variant summary

Our verdict is Pathogenic. Variant got 15 ACMG points: 15P and 0B. PM1 PM2 PP2 PP3_Moderate PP5_Very_Strong

The NM_014191.4(SCN8A):c.3979A>G(p.Ile1327Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: SCN8A NM_014191.4 missense
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:4 O:2
• 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 Pathogenic. Variant got 15 ACMG points.

• PM1: In a hotspot region, there are 6 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 4 uncertain in NM_014191.4
• PM2: Very rare variant in population databases, with high coverage
• PP2: Missense variant where missense usually causes diseases, SCN8A
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.939
• PP5: Variant 12-51786578-A-G is Pathogenic according to our data. Variant chr12-51786578-A-G is described in ClinVar as [Likely_pathogenic]. Clinvar id is 253288.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SCN8A	NM_001330260.2	c.3979A>G	p.Ile1327Val	missense_variant	22/27	ENST00000627620.5
SCN8A	NM_014191.4	c.3979A>G	p.Ile1327Val	missense_variant	22/27	ENST00000354534.11
SCN8A	NM_001177984.3	c.3856A>G	p.Ile1286Val	missense_variant	21/26
SCN8A	NM_001369788.1	c.3856A>G	p.Ile1286Val	missense_variant	21/26

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SCN8A	ENST00000354534.11	c.3979A>G	p.Ile1327Val	missense_variant	22/27	1	NM_014191.4	P4
SCN8A	ENST00000627620.5	c.3979A>G	p.Ile1327Val	missense_variant	22/27	5	NM_001330260.2	A1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:4 Other:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Athena Diagnostics	Oct 01, 2020	This variant occurs de novo in an individual tested at Athena Diagnostics and in published literature (PMID: 26993267, 24352161, 25799905). This variant has not been reported in large, multi-ethnic general populations (http://gnomad.broadinstitute.org). Assessment of experimental evidence suggests that this variant alters the voltage-gated sodium channel (PMID: 27375106).This observation is not an independent occurrence and has been identified in the same individual by RCIGM, the other laboratory participating in the GEMINI study. -
Likely pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Oct 29, 2015	The I1327V variant in the SCN8A gene has been reported previously in the heterozygous state in an individual with neonatal epileptic encephalopathy, multiple congenital anomalies, and movement disorders (Vaher et al., 2014). The I1327 variant has also been reported in the heterozygous state in an unrelated individual with in utero onset movement disorder, epileptic encephalopahy, and developmental delay (Singh et al., 2015). The I1327V variant was not observed in approximately 6,400 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. This substitution occurs at a position within the predicted S5 transmembrane segment of third homologous domain that is conserved across species. In silico analysis predicts this variant is probably damaging to the protein structure/function. However, the I1327V variant is a conservative amino acid substitution, which is not likely to impact secondary protein structure as these residues share similar properties. The I1327V variant is a strong candidate for a pathogenic variant. However, the possibility it may be a rare benign variant cannot be excluded. -

Early infantile epileptic encephalopathy with suppression bursts Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Invitae

Oct 05, 2022

Experimental studies have shown that this missense change affects SCN8A function (PMID: 27375106). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt SCN8A protein function. ClinVar contains an entry for this variant (Variation ID: 253288). This missense change has been observed in individual(s) with epileptic encephalopathy (PMID: 24352161, 25799905, 26993267). In at least one individual the variant was observed to be de novo. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces isoleucine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 1327 of the SCN8A protein (p.Ile1327Val). For these reasons, this variant has been classified as Pathogenic. -

SCN8A-related disorder Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego

-

This variant has been previously reported as a de novo heterozygous change and as a heterozygous change of unknown inheritance in several individuals with SCN8A-related early-infantile epileptic encephalopathy (PMID: 24352161, 25799905, 31010614, 30078772, 26993267, 33915942). In-vitro functional studies showed that the p.Ile1327Val variant leads to an impaired channel inactivation suggesting a gain-of-function effect (PMID: 24352161, 27375106). The p.Ile1327Val variant is absent from the gnomAD population database and thus is presumed to be rare. The c.3979A>G (p.Ile1327Val) variant affects a highly conserved amino acid and is predicted by multiple in silico tools to have a deleterious effect on protein function. Based on the available evidence, the c.3979A>G (p.Ile1327Val) variant is classified as Pathogenic. -

Developmental and epileptic encephalopathy, 13 Other:1

not provided, no classification provided

literature only

GeneReviews

-

- -

Complex neurodevelopmental disorder Other:1

not provided, no classification provided

literature only

Channelopathy-Associated Epilepsy Research Center

-

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.52
BayesDel_addAF	Pathogenic	0.40	D
BayesDel_noAF	Pathogenic	0.34
Cadd	Uncertain	25
Dann	Pathogenic	1.0
DEOGEN2	Uncertain	0.76	D;.;.;.;.
Eigen	Pathogenic	0.86
Eigen_PC	Pathogenic	0.83
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Uncertain	0.97	D;D;.;D;D
M_CAP	Pathogenic	0.91	D
MetaRNN	Pathogenic	0.94	D;D;D;D;D
MetaSVM	Pathogenic	1.1	D
MutationAssessor	Pathogenic	2.9	M;.;.;.;M
MutationTaster	Benign	1.0	D;D
PrimateAI	Pathogenic	0.89	D
PROVEAN	Benign	-0.95	N;N;N;.;.
REVEL	Pathogenic	0.94
Sift	Pathogenic	0.0	D;D;D;.;.
Sift4G	Uncertain	0.014	D;D;D;D;D
Polyphen		1.0	D;.;.;.;.
Vest4		0.83
MutPred		0.87		Gain of catalytic residue at I1327 (P = 0.0235);.;.;.;Gain of catalytic residue at I1327 (P = 0.0235);
MVP		0.99
MPC		2.1
ClinPred		0.97	D
GERP RS		5.3
Varity_R		0.68
gMVP		0.92

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: rs879255704; hg19: chr12-52180362;