rs121917912
Positions:
Variant summary
Our verdict is Pathogenic. Variant got 13 ACMG points: 13P and 0B. PM1PP2PP3_ModeratePP5_Very_Strong
The NM_001165963.4(SCN1A):c.3734G>A(p.Arg1245Gln) variant causes a missense change. The variant allele was found at a frequency of 0.00000435 in 1,609,000 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000041 ( 0 hom. )
Consequence
SCN1A
NM_001165963.4 missense
NM_001165963.4 missense
Scores
12
5
2
Clinical Significance
Conservation
PhyloP100: 6.12
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)
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 13 ACMG points.
PM1
In a topological_domain Extracellular (size 12) in uniprot entity SCN1A_HUMAN there are 4 pathogenic changes around while only 0 benign (100%) in NM_001165963.4
PP2
Missense variant in gene, where missense usually causes diseases (based on misZ statistic), SCN1A. . Gene score misZ 5.2206 (greater than the threshold 3.09). Trascript score misZ 7.6022 (greater than threshold 3.09). GenCC has associacion of gene with migraine, familial hemiplegic, 3, familial hemiplegic migraine, Dravet syndrome, malignant migrating partial seizures of infancy, generalized epilepsy with febrile seizures plus, myoclonic-astatic epilepsy, developmental and epileptic encephalopathy, developmental and epileptic encephalopathy, 6, familial or sporadic hemiplegic migraine, arthrogryposis, Lennox-Gastaut syndrome, generalized epilepsy with febrile seizures plus, type 2.
PP3
MetaRNN computational evidence supports a deleterious effect, 0.886
PP5
Variant 2-166012254-C-T is Pathogenic according to our data. Variant chr2-166012254-C-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 68533.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SCN1A | NM_001165963.4 | c.3734G>A | p.Arg1245Gln | missense_variant | 22/29 | ENST00000674923.1 | NP_001159435.1 | |
LOC102724058 | NR_110598.1 | n.176-3359C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SCN1A | ENST00000674923.1 | c.3734G>A | p.Arg1245Gln | missense_variant | 22/29 | NM_001165963.4 | ENSP00000501589 | P4 | ||
SCN1A-AS1 | ENST00000651574.1 | n.193-3359C>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.00000662 AC: 1AN: 151126Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 0.00000412 AC: 6AN: 1457874Hom.: 0 Cov.: 30 AF XY: 0.00000689 AC XY: 5AN XY: 725290
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GnomAD4 genome AF: 0.00000662 AC: 1AN: 151126Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 73814
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ClinVar
Significance: Pathogenic/Likely pathogenic
Submissions summary: Pathogenic:4Other:1
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Generalized epilepsy with febrile seizures plus, type 2 Pathogenic:2
Likely pathogenic, criteria provided, single submitter | clinical testing | New York Genome Center | Jan 29, 2021 | The inherited c.3734G>A (p.Arg1245Gln) variant identified in the SCN1A gene substitutes a very well conserved Arginine for Glutamine at amino acid 1245/2010(exon 22/29). This variant is found with low frequency in gnomAD(v3.0) (1 heterozygote, 0 homozygotes; allele frequency: 6.62e-6) suggesting it is not a common benign variant in the populations represented in that database. In silico algorithms predict this variant to be Damaging (SIFT; score:0.001) and Pathogenic (REVEL; score: 0.808) to the function of the canonical transcript. This variant is reported as Pathogenic / Likely Pathogenic in ClinVar (VarID: 68533). The c.3734G>A (p.Arg1245Gln) variant identified here has been previously reported in several individuals in the literature with SCN1A associated epilepsy syndromes [PMID:17054684; PMID: 21906962; PMID: 28202706]. Given its low frequency in population databases, observation in several affected individuals in the literature, and in silico predictions of pathogenicity, the inherited c.3734G>A (p.Arg1245Gln) variant identified in the SCN1A gene is reported as Likely Pathogenic. - |
Likely pathogenic, criteria provided, single submitter | clinical testing | MGZ Medical Genetics Center | Aug 19, 2022 | - - |
Early infantile epileptic encephalopathy with suppression bursts Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Oct 16, 2023 | This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 1245 of the SCN1A protein (p.Arg1245Gln). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with severe myoclonic epilepsy of infancy (PMID: 17054684, 21906962, 28202706). In at least one individual the variant was observed to be de novo. ClinVar contains an entry for this variant (Variation ID: 68533). 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 SCN1A protein function. For these reasons, this variant has been classified as Pathogenic. - |
not provided Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Apr 02, 2024 | Identified in multiple patients with Dravet syndrome or other SCN1A-related epilepsy referred for genetic testing at GeneDx and in published literature (PMID: 28202706, 21906962, 36993157); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This substitution is predicted to be within the extracellular loop between the S1 and S2 transmembrane segments of the third homologous domain; This variant is associated with the following publications: (PMID: 18804930, 21906962, 17054684, 24331359, 32347949, 24136861, 17381446, 31440721, 36993157, 35074891, 28202706) - |
Severe myoclonic epilepsy in infancy Other:1
not provided, no classification provided | literature only | UniProtKB/Swiss-Prot | - | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Pathogenic
DEOGEN2
Pathogenic
.;.;.;D;.;.;D;.;.;.
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D;D;D;.;D;.;.;D;D
M_CAP
Pathogenic
D
MetaRNN
Pathogenic
D;D;D;D;D;D;D;D;D;D
MetaSVM
Pathogenic
D
MutationAssessor
Pathogenic
.;.;.;M;.;.;M;.;.;.
MutationTaster
Benign
D;D;D;D
PrimateAI
Pathogenic
D
PROVEAN
Uncertain
.;.;.;D;.;.;D;.;D;D
REVEL
Pathogenic
Sift
Uncertain
.;.;.;D;.;.;D;.;D;D
Sift4G
Uncertain
.;.;.;D;.;.;D;.;D;D
Polyphen
1.0, 1.0
.;.;.;D;D;.;D;D;D;.
Vest4
0.84, 0.89, 0.87, 0.85
MutPred
0.40
.;Gain of ubiquitination at K1246 (P = 0.1278);.;Gain of ubiquitination at K1246 (P = 0.1278);.;.;Gain of ubiquitination at K1246 (P = 0.1278);.;.;.;
MVP
1.0
MPC
1.1
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at