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NM_001330260.2(SCN8A):c.3148G>A (p.Gly1050Ser) AND Seizures, benign familial infantile, 5

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Mar 5, 2021
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:
RCV001838987.3

Allele description [Variation Report for NM_001330260.2(SCN8A):c.3148G>A (p.Gly1050Ser)]

NM_001330260.2(SCN8A):c.3148G>A (p.Gly1050Ser)

Gene:
SCN8A:sodium voltage-gated channel alpha subunit 8 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
12q13.13
Genomic location:
Preferred name:
NM_001330260.2(SCN8A):c.3148G>A (p.Gly1050Ser)
Other names:
p.G1050S:GGT>AGT
HGVS:
  • NC_000012.12:g.51769111G>A
  • NG_021180.3:g.184154G>A
  • NM_001177984.3:c.3148G>A
  • NM_001330260.2:c.3148G>AMANE SELECT
  • NM_001369788.1:c.3148G>A
  • NM_014191.4:c.3148G>A
  • NP_001171455.1:p.Gly1050Ser
  • NP_001317189.1:p.Gly1050Ser
  • NP_001356717.1:p.Gly1050Ser
  • NP_055006.1:p.Gly1050Ser
  • LRG_1389t1:c.3148G>A
  • LRG_1389t2:c.3148G>A
  • LRG_1389:g.184154G>A
  • LRG_1389p1:p.Gly1050Ser
  • LRG_1389p2:p.Gly1050Ser
  • NC_000012.11:g.52162895G>A
  • NM_001330260.1:c.3148G>A
  • NM_014191.2:c.3148G>A
  • NM_014191.3:c.3148G>A
Protein change:
G1050S
Links:
dbSNP: rs202006479
NCBI 1000 Genomes Browser:
rs202006479
Molecular consequence:
  • NM_001177984.3:c.3148G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001330260.2:c.3148G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001369788.1:c.3148G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_014191.4:c.3148G>A - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Name:
Seizures, benign familial infantile, 5 (BFIS5)
Synonyms:
CONVULSIONS, BENIGN FAMILIAL INFANTILE, 5
Identifiers:
MONDO: MONDO:0014903; MedGen: C4310728; Orphanet: 306; OMIM: 617080

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002099095New York Genome Center - CSER-NYCKidSeq
criteria provided, single submitter

(NYGC Assertion Criteria 2020)		Uncertain significance
(Mar 5, 2021) 		inheritedclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedinheritedunknown1not providednot provided1not providedclinical testing

Details of each submission

From New York Genome Center - CSER-NYCKidSeq, SCV002099095.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided

Description

The inherited heterozygous c.3148G>A (p.Gly1050Ser) variant identified in the SCN8A gene has been reported in the literature as de novo in a patient affected with hemiplegic cerebral palsy and intellectual disability [2]. The variant has been reported in ClinVar database with conflicting interpretations of pathogenicity [benign (1), likely benign (1), uncertain significance (2). Variation ID:207142]. The variant has 0.0001709 allele frequency in the gnomAD(v3) database (26 out of 152168 heterozygous alleles, no homozygotes) suggesting it is not a common benign variant in the populations represented in that database. The affected residue is evolutionarily conserved and is predicted deleterious by in silico predictiontools [CADD score= 22.5, REVEL score = 0.828]. Based on the available evidence, the inherited heterozygous c.3148G>A (p.Gly1050Ser) variant identified in the SCN8A gene is reported as a variant of uncertainsignificance.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1inheritedunknown1not providednot provided1not providednot providednot provided

Last Updated: Oct 26, 2024