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NM_001165963.4(SCN1A):c.319G>T (p.Ala107Ser) AND Early infantile epileptic encephalopathy with suppression bursts

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Sep 20, 2019
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV001213403.8

Allele description [Variation Report for NM_001165963.4(SCN1A):c.319G>T (p.Ala107Ser)]

NM_001165963.4(SCN1A):c.319G>T (p.Ala107Ser)

Gene:
SCN1A:sodium voltage-gated channel alpha subunit 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
2q24.3
Genomic location:
Preferred name:
NM_001165963.4(SCN1A):c.319G>T (p.Ala107Ser)
HGVS:
  • NC_000002.12:g.166058634C>A
  • NG_011906.1:g.20006G>T
  • NM_001165963.4:c.319G>TMANE SELECT
  • NM_001165964.3:c.319G>T
  • NM_001202435.3:c.319G>T
  • NM_001353948.2:c.319G>T
  • NM_001353949.2:c.319G>T
  • NM_001353950.2:c.319G>T
  • NM_001353951.2:c.319G>T
  • NM_001353952.2:c.319G>T
  • NM_001353954.2:c.319G>T
  • NM_001353955.2:c.319G>T
  • NM_001353957.2:c.319G>T
  • NM_001353958.2:c.319G>T
  • NM_001353960.2:c.319G>T
  • NM_001353961.2:c.-2107G>T
  • NM_006920.6:c.319G>T
  • NP_001159435.1:p.Ala107Ser
  • NP_001159436.1:p.Ala107Ser
  • NP_001189364.1:p.Ala107Ser
  • NP_001340877.1:p.Ala107Ser
  • NP_001340878.1:p.Ala107Ser
  • NP_001340879.1:p.Ala107Ser
  • NP_001340880.1:p.Ala107Ser
  • NP_001340881.1:p.Ala107Ser
  • NP_001340883.1:p.Ala107Ser
  • NP_001340884.1:p.Ala107Ser
  • NP_001340886.1:p.Ala107Ser
  • NP_001340887.1:p.Ala107Ser
  • NP_001340889.1:p.Ala107Ser
  • NP_008851.3:p.Ala107Ser
  • LRG_8:g.20006G>T
  • NC_000002.11:g.166915144C>A
  • NM_001165963.1:c.319G>T
  • NR_148667.2:n.705G>T
Protein change:
A107S
Links:
dbSNP: rs745404213
NCBI 1000 Genomes Browser:
rs745404213
Molecular consequence:
  • NM_001353961.2:c.-2107G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001165963.4:c.319G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001165964.3:c.319G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001202435.3:c.319G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353948.2:c.319G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353949.2:c.319G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353950.2:c.319G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353951.2:c.319G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353952.2:c.319G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353954.2:c.319G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353955.2:c.319G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353957.2:c.319G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353958.2:c.319G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353960.2:c.319G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_006920.6:c.319G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_148667.2:n.705G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
Early infantile epileptic encephalopathy with suppression bursts (EIEE)
Synonyms:
Early infantile epileptic encephalopathy; Ohtahara syndrome; Developmental and epileptic encephalopathy
Identifiers:
MONDO: MONDO:0100062; MedGen: C0393706; Orphanet: 1934; OMIM: PS308350

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001385032Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Sep 20, 2019) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV001385032.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C65"). This variant has not been reported in the literature in individuals with SCN1A-related conditions. This variant is present in population databases (rs745404213, ExAC 0.006%). This sequence change replaces alanine with serine at codon 107 of the SCN1A protein (p.Ala107Ser). The alanine residue is highly conserved and there is a moderate physicochemical difference between alanine and serine.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Feb 28, 2024