VCV000068673.4 - ClinVar

NM_001165963.4(SCN1A):c.777C>A (p.Ser259Arg)

Germline

Classification

criteria provided, multiple submitters, no conflicts. Learn more about how ClinVar calculates review status.

Pathogenic/Likely pathogenic

2 out of 4 submissions contributed to this classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_001165963.4(SCN1A):c.777C>A (p.Ser259Arg)

Variation ID: 68673 Accession: VCV000068673.4

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 2q24.3 2: 166051906 (GRCh38) [ NCBI UCSC ] 2: 166908416 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Oct 31, 2013	Apr 13, 2025	Jun 10, 2022

HGVS

Nucleotide	Protein	Molecular consequence
NM_001165963.4:c.777C>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_001159435.1:p.Ser259Arg	missense
NM_001165964.3:c.777C>A	NP_001159436.1:p.Ser259Arg	missense
NM_001202435.3:c.777C>A	NP_001189364.1:p.Ser259Arg	missense
NM_001353948.2:c.777C>A	NP_001340877.1:p.Ser259Arg	missense
NM_001353949.2:c.777C>A	NP_001340878.1:p.Ser259Arg	missense
NM_001353950.2:c.777C>A	NP_001340879.1:p.Ser259Arg	missense
NM_001353951.2:c.777C>A	NP_001340880.1:p.Ser259Arg	missense
NM_001353952.2:c.777C>A	NP_001340881.1:p.Ser259Arg	missense
NM_001353954.2:c.777C>A	NP_001340883.1:p.Ser259Arg	missense
NM_001353955.2:c.777C>A	NP_001340884.1:p.Ser259Arg	missense
NM_001353957.2:c.777C>A	NP_001340886.1:p.Ser259Arg	missense
NM_001353958.2:c.777C>A	NP_001340887.1:p.Ser259Arg	missense
NM_001353960.2:c.777C>A	NP_001340889.1:p.Ser259Arg	missense
NM_001353961.2:c.-1649C>A		5 prime UTR
NM_006920.6:c.777C>A	NP_008851.3:p.Ser259Arg	missense
NR_148667.2:n.1163C>A		non-coding transcript variant
NC_000002.12:g.166051906G>T
NC_000002.11:g.166908416G>T
NG_011906.1:g.26734C>A
LRG_8:g.26734C>A
LRG_8t1:c.777C>A
	P35498:p.Ser259Arg

... more HGVS ... less HGVS

Protein change

S259R

Other names

Canonical SPDI

NC_000002.12:166051905:G:T

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

Allele frequency Help The frequency of the allele represented by this VCV record.

Links

ClinGen: CA285258 UniProtKB: P35498#VAR_064240 UniProtKB/Swiss-Prot: VAR_064240 dbSNP: rs121918735 VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
SCN1A		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	2411	4994

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
Severe myoclonic epilepsy in infancy	Pathogenic/Likely pathogenic (3)	criteria provided, multiple submitters, no conflicts	Jun 10, 2022	RCV000059553.7
Seizure	Pathogenic (1)	no assertion criteria provided	Aug 14, 2017	RCV000678837.2

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Pathogenic (Dec 20, 2014) C Contributing to aggregate classification	criteria provided, single submitter (Xu et al. (Hum Mutat. 2015)) Method: research	Dravet syndrome Affected status: yes Allele origin: de novo	Center for Bioinformatics, Peking University Additional submitter: Pediatric Department, Peking University First Hospital Study: University Clinical Cooperation “985 Project” PKU-2014-1-1 Accession: SCV000221859.1 First in ClinVar: Jul 02, 2015 Last updated: Jul 02, 2015 Comment: Dravet syndrome (DS) probands were recruited from the outpatient and inpatient child neurology units of Peking University First Hospital from 2005 till present. The study … (more) Dravet syndrome (DS) probands were recruited from the outpatient and inpatient child neurology units of Peking University First Hospital from 2005 till present. The study was approved by the Ethics Committee of Peking University First Hospital and the Institutional Review Board at Peking University. Participants or their parents provided written informed consent before enrollment. We collected a total of 267 mutations from 255 families with probands diagnosed with DS in China. All probands fulfilled the clinical diagnostic criteria. (less)	Publications: PubMed (1) PubMed: 26096185 Other databases http://www.openbioinformatics.or… http://www.openbioinformatics.org/annovar/annovar_startup.html Number of individuals with the variant: 1 Ethnicity/Population group: Chinese

Likely pathogenic (Jun 10, 2022) C Contributing to aggregate classification	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Severe myoclonic epilepsy in infancy Affected status: yes Allele origin: germline	DASA Accession: SCV002526397.2 First in ClinVar: Jun 18, 2022 Last updated: Apr 13, 2025	Publications: PubMed (2) PubMed: 30735520‚ 20431604 Comment: The c.777C>A;p.(Ser259Arg) missense change has been observed in affected individual(s) and ClinVar contains an entry for this variant (Clinvar ID: 68673; PMID: 20431604; 30735520) - … (more) The c.777C>A;p.(Ser259Arg) missense change has been observed in affected individual(s) and ClinVar contains an entry for this variant (Clinvar ID: 68673; PMID: 20431604; 30735520) - PS4.Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product (PMID: 30735520) - PS3_supporting. This variant is not present in population databases:rs121918735 , gnomAD; ABraOM no frequency - http://abraom.ib.usp.br/) - PM2. The variant was assumed de novo, but without confirmation of paternity and maternity (PMID: 20431604; 30735520)PM6. In summary, the currently available evidence indicates that the variant is Likely Pathogenic (less) Number of individuals with the variant: 1 Sex: female Geographic origin: Brazil

Pathogenic (Aug 14, 2017) N Not contributing to aggregate classification	no assertion criteria provided Method: clinical testing	seizures Affected status: yes Allele origin: germline	Clinical Molecular Genetics Laboratory, Johns Hopkins All Children's Hospital Accession: SCV000805026.1 First in ClinVar: Sep 14, 2018 Last updated: Sep 14, 2018

not provided (-) N Not contributing to aggregate classification	no classification provided Method: not provided	Severe myoclonic epilepsy in infancy Affected status: not provided Allele origin: germline	UniProtKB/Swiss-Prot Accession: SCV000091085.1 First in ClinVar: Oct 31, 2013 Last updated: Oct 31, 2013

Comment:

The c.777C>A;p.(Ser259Arg) missense change has been observed in affected individual(s) and ClinVar contains an entry for this variant (Clinvar ID: 68673; PMID: 20431604; 30735520) - PS4.Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product (PMID: 30735520) - PS3_supporting. This variant is not present in population databases:rs121918735 , gnomAD; ABraOM no frequency - http://abraom.ib.usp.br/) - PM2. The variant was assumed de novo, but without confirmation of paternity and maternity (PMID: 20431604; 30735520)PM6. In summary, the currently available evidence indicates that the variant is Likely Pathogenic

Germline Functional Evidence

There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Comment:

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
In vivo, in vitro and in silico correlations of four de novo SCN1A missense mutations.	Nissenkorn A	PloS one	2019	PMID: 30735520
Amplicon Resequencing Identified Parental Mosaicism for Approximately 10% of "de novo" SCN1A Mutations in Children with Dravet Syndrome.	Xu X	Human mutation	2015	PMID: 26096185
Analysis of SCN1A mutation and parental origin in patients with Dravet syndrome.	Sun H	Journal of human genetics	2010	PMID: 20431604
http://www.openbioinformatics.org/annovar/annovar_startup.html	-	-	-	-

Text-mined citations for rs121918735 ...

These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Apr 13, 2025

ClinVar Genomic variation as it relates to human health

NM_001165963.4(SCN1A):c.777C>A (p.Ser259Arg)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for rs121918735 ...