NM_001165963.4(SCN1A):c.4255G>T (p.Gly1419Ter) AND not provided

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Jun 23, 2016
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:: RCV000489767.1

Allele description [Variation Report for NM_001165963.4(SCN1A):c.4255G>T (p.Gly1419Ter)]

NM_001165963.4(SCN1A):c.4255G>T (p.Gly1419Ter)

Genes:

SCN1A:sodium voltage-gated channel alpha subunit 1 [Gene - OMIM - HGNC]
LOC102724058:uncharacterized LOC102724058 [Gene]

Variant type:

single nucleotide variant

Cytogenetic location:

2q24.3

Genomic location:

Preferred name:

NM_001165963.4(SCN1A):c.4255G>T (p.Gly1419Ter)

HGVS:

NC_000002.12:g.166002501C>A
NG_011906.1:g.76139G>T
NM_001165963.4:c.4255G>TMANE SELECT
NM_001165964.3:c.4171G>T
NM_001202435.3:c.4255G>T
NM_001353948.2:c.4255G>T
NM_001353949.2:c.4222G>T
NM_001353950.2:c.4222G>T
NM_001353951.2:c.4222G>T
NM_001353952.2:c.4222G>T
NM_001353954.2:c.4219G>T
NM_001353955.2:c.4219G>T
NM_001353957.2:c.4171G>T
NM_001353958.2:c.4171G>T
NM_001353960.2:c.4168G>T
NM_001353961.2:c.1813G>T
NM_006920.6:c.4222G>T
NP_001159435.1:p.Gly1419Ter
NP_001159436.1:p.Gly1391Ter
NP_001189364.1:p.Gly1419Ter
NP_001340877.1:p.Gly1419Ter
NP_001340878.1:p.Gly1408Ter
NP_001340879.1:p.Gly1408Ter
NP_001340880.1:p.Gly1408Ter
NP_001340881.1:p.Gly1408Ter
NP_001340883.1:p.Gly1407Ter
NP_001340884.1:p.Gly1407Ter
NP_001340886.1:p.Gly1391Ter
NP_001340887.1:p.Gly1391Ter
NP_001340889.1:p.Gly1390Ter
NP_001340890.1:p.Gly605Ter
NP_008851.3:p.Gly1408Ter
LRG_8:g.76139G>T
NC_000002.11:g.166859011C>A
NM_001165963.1:c.4255G>T
NR_148667.2:n.4672G>T

Protein change:

G1390*

Links:

dbSNP: rs1085307893

NCBI 1000 Genomes Browser:

rs1085307893

Molecular consequence:

NR_148667.2:n.4672G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_001165963.4:c.4255G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001165964.3:c.4171G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001202435.3:c.4255G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001353948.2:c.4255G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001353949.2:c.4222G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001353950.2:c.4222G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001353951.2:c.4222G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001353952.2:c.4222G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001353954.2:c.4219G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001353955.2:c.4219G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001353957.2:c.4171G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001353958.2:c.4171G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001353960.2:c.4168G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001353961.2:c.1813G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_006920.6:c.4222G>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: CN517202

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000577612	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Likely pathogenic (Jun 23, 2016)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000577612

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Likely pathogenic
(Jun 23, 2016)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV000577612.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

The G1419X variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. It was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. The G1419X nonsense variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. Therefore, this variant is likely pathogenic; however, the possibility that it is benign cannot be excluded.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Apr 23, 2022

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