rs794726775

Positions:

• chr2-166039420-T-A
• chr2-166039420-T-C

Variant summary

Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PM2 PP5_Very_Strong

The NM_001165963.4(SCN1A):​c.2589+3A>T variant causes a splice region, intron change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (★★).

• Frequency: Genomes: not found (cov: 30)
• Consequence: SCN1A NM_001165963.4 splice_region, intron
• Scores: Splicing: ADA: 1.000
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:14
• Conservation: PhyloP100: 6.07

Genes affected

SCN1A (HGNC:10585): (sodium voltage-gated channel alpha subunit 1) Voltage-dependent sodium channels are heteromeric complexes that regulate sodium exchange between intracellular and extracellular spaces and are essential for the generation and propagation of action potentials in muscle cells and neurons. Each sodium channel is composed of a large pore-forming, glycosylated alpha subunit and two smaller beta subunits. This gene encodes a sodium channel alpha subunit, which has four homologous domains, each of which contains six transmembrane regions. Allelic variants of this gene are associated with generalized epilepsy with febrile seizures and epileptic encephalopathy. Alternative splicing results in multiple transcript variants. The RefSeq Project has decided to create four representative RefSeq records. Three of the transcript variants are supported by experimental evidence and the fourth contains alternate 5' untranslated exons, the exact combination of which have not been experimentally confirmed for the full-length transcript. [provided by RefSeq, Oct 2015]

SCN1A-AS1 (HGNC:54069): (SCN1A and SCN9A antisense RNA 1)

ACMG classification

Verdict is Pathogenic. Variant got 10 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 2-166039420-T-A is Pathogenic according to our data. Variant chr2-166039420-T-A is described in ClinVar as [Pathogenic]. Clinvar id is 189938.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-166039420-T-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SCN1A	NM_001165963.4	c.2589+3A>T		splice_region_variant, intron_variant		ENST00000674923.1	NP_001159435.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SCN1A	ENST00000674923.1	c.2589+3A>T		splice_region_variant, intron_variant			NM_001165963.4	ENSP00000501589.1
SCN1A	ENST00000303395.9	c.2589+3A>T		splice_region_variant, intron_variant		5		ENSP00000303540.4
SCN1A	ENST00000375405.7	c.2556+3A>T		splice_region_variant, intron_variant		5		ENSP00000364554.3
SCN1A	ENST00000409050.1	c.2505+3A>T		splice_region_variant, intron_variant		5		ENSP00000386312.1

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome Cov.: 36

GnomAD4 genome Cov.: 30

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:14

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Pathogenic:6

Likely pathogenic, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Mar 01, 2024	SCN1A: PS2:Very Strong, PM2, PS4:Moderate, PS3:Supporting -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Mar 10, 2023	Published RNA and protein studies have shown that this variant leads to the skipping of exon 14, and results in greatly reduced protein levels in heterologous expression systems. In addition, functional studies using induced neurons derived from patient cells, indicated that this variant caused hyperexcitability, a result consistent with an in vitro epileptic-like phenotype (Liu et al., 2013); In silico analysis supports a deleterious effect on splicing; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 27465585, 27790834, 33067208, 32090326, 17347258, 26373465, 29408779, 30619928, 31864146, 31139143, 23821540, 32613771, 35072530, 31440721, 31069529, 33278787) -
Pathogenic, criteria provided, single submitter	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	Feb 01, 2024	PP3, PM2, PM5, PM6, PS3, PS4 -
Pathogenic, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, University Medical Center Utrecht	-	- -
Pathogenic, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -

Severe myoclonic epilepsy in infancy Pathogenic:6

Pathogenic, criteria provided, single submitter	clinical testing	MGZ Medical Genetics Center	Jan 31, 2022	- -
Pathogenic, criteria provided, single submitter	research	Center for Bioinformatics, Peking University	Dec 20, 2014	- -
Pathogenic, criteria provided, single submitter	clinical testing	Athena Diagnostics	Dec 26, 2014	- -
Pathogenic, criteria provided, single submitter	research	HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology	Nov 09, 2017	- -
Pathogenic, criteria provided, single submitter	clinical testing	Institute of Human Genetics, University of Leipzig Medical Center	Mar 22, 2021	This variant was identified as de novo (maternity and paternity confirmed). -
Pathogenic, criteria provided, single submitter	clinical testing	Lifecell International Pvt. Ltd	-	A heterozygous 5’ splice site variation in intron 17 of the SCN1A gene (c.2589+3A>T) that affects the position 3 bases downstream of exon 17 was detected. The observed variant is not present in both the 1000 Genomes and gnomAD databases. The reference base is conserved across the species and in-silico predictions by Mutation taster, NNSplice and PWM are damaging. This variant (also known as IVS14+3A>T) has previously been reported for Dravet syndrome by Xu X. et al., 2015. This variant has been shown to result in skipping of exon 17 during splicing of the SCN1A gene, which correlates with a little to no SCN1A protein expression and no sodium current in a heterologous system by Liu Y. et al., 2013. The variant c.2589+3A>T has been previously classified as Pathogenic in ClinVar (Variation ID 189938 as of 2020-09-03) with respect to Severe myoclonic epilepsy in infancy and 2 other conditions with a status of (2 stars) criteria provided, multiple submitters, no conflicts. Based on the above evidence this variant has been classified as Pathogenic according to the ACMG guidelines. -

Early infantile epileptic encephalopathy with suppression bursts Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Dec 07, 2023

This sequence change falls in intron 14 of the SCN1A gene. It does not directly change the encoded amino acid sequence of the SCN1A protein. It affects a nucleotide within the consensus splice site. This variant is not present in population databases (gnomAD no frequency). This variant has been observed in individual(s) with severe myoclonic epilepsy of infancy (SMEI) or intractable seizures (PMID: 17347258, 23195492, 23821540). In at least one individual the variant was observed to be de novo. ClinVar contains an entry for this variant (Variation ID: 189938). Algorithms developed to predict the effect of variants on protein structure and function are not available or were not evaluated for this variant. Experimental studies have shown that this variant affects SCN1A function (PMID: 23821540). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic. -

Severe myoclonic epilepsy in infancy;C1858673:Generalized epilepsy with febrile seizures plus, type 2;C1864987:Migraine, familial hemiplegic, 3;C5543353:Developmental and epileptic encephalopathy 6B Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago

Oct 21, 2022

This variant has been reported in the literature in several individuals with epileptic encephalopathy/Dravet syndrome including numerous de novo incidences (Harkin 2007 PMID:17347258, Liu 2013 PMID:23821540, Mahdieh 2018 PMID:29408779, Kong 2019 PMID:30619928, Long 2019 PMID:31139143, Brunklaus 2020 PMID:3209326, Gertler 2020 PMID:31864146, Lee 2020 32613771, Wang 2021 PMID:33278787). This variant is not present in large control databases. Evolutionary conservation and computational predictive tools for this variant are limited or unavailable. This variant is present in ClinVar, with several labs classifying this variant as pathogenic (Variation ID:189938).In vitro functional studies predict that this variant will impact the protein (Liu 2013 PMID:23821540). Of note, although this variant occurs in the splice region, computational prediction tools do not suggest that it alters splicing. In summary, this variant is classified as pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.20
CADD	Benign	22
DANN	Benign	0.96

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.97
SpliceAI score (max)		0.95		Details are displayed if max score is > 0.2
DS_DL_spliceai		0.95		Position offset: 3

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

Publications

LitVar

Other links and lift over

dbSNP: rs794726775; hg19: chr2-166895930;