rs794726775
Positions:
Variant summary
Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PM2PP3_StrongPP5_Very_Strong
The NM_001165963.4(SCN1A):c.2589+3A>T variant causes a splice donor region, intron change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★).
Frequency
Genomes: not found (cov: 30)
Consequence
SCN1A
NM_001165963.4 splice_donor_region, intron
NM_001165963.4 splice_donor_region, intron
Scores
2
Splicing: ADA: 1.000
2
Clinical Significance
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]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 14 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
PP3
?
Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: dbscSNV1_ADA, dbscSNV1_RF, max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.
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 | UniProt |
---|---|---|---|---|---|---|---|
SCN1A | NM_001165963.4 | c.2589+3A>T | splice_donor_region_variant, intron_variant | ENST00000674923.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCN1A | ENST00000674923.1 | c.2589+3A>T | splice_donor_region_variant, intron_variant | NM_001165963.4 | P4 | ||||
SCN1A-AS1 | ENST00000651574.1 | n.487+3290T>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? Cov.: 30
GnomAD3 genomes
?
Cov.:
30
GnomAD4 exome Cov.: 36
GnomAD4 exome
Cov.:
36
GnomAD4 genome ? Cov.: 30
GnomAD4 genome
?
Cov.:
30
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:13
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Severe myoclonic epilepsy in infancy Pathogenic:6
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 | research | Center for Bioinformatics, Peking University | Dec 20, 2014 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | MGZ Medical Genetics Center | Jan 31, 2022 | - - |
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 | 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. - |
not provided Pathogenic:5
Pathogenic, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
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) - |
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, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
Early infantile epileptic encephalopathy with suppression bursts Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | 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:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Pathogenic
dbscSNV1_RF
Pathogenic
SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_DL_spliceai
Position offset: 3
Find out detailed SpliceAI scores and Pangolin per-transcript scores at