NM_001330260.2(SCN8A):c.5157del (p.Asp1720fs) AND not provided

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Dec 27, 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:: RCV001590452.3

Allele description [Variation Report for NM_001330260.2(SCN8A):c.5157del (p.Asp1720fs)]

NM_001330260.2(SCN8A):c.5157del (p.Asp1720fs)

Gene:

SCN8A:sodium voltage-gated channel alpha subunit 8 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

12q13.13

Genomic location:

Preferred name:

NM_001330260.2(SCN8A):c.5157del (p.Asp1720fs)

HGVS:

NC_000012.12:g.51806643del
NG_021180.3:g.221686del
NM_001177984.3:c.5034del
NM_001330260.2:c.5157delMANE SELECT
NM_001369788.1:c.5034del
NM_014191.4:c.5157del
NP_001171455.1:p.Asp1679fs
NP_001317189.1:p.Asp1720fs
NP_001356717.1:p.Asp1679fs
NP_055006.1:p.Asp1720fs
LRG_1389t1:c.5157del
LRG_1389t2:c.5157del
LRG_1389:g.221686del
LRG_1389p1:p.Asp1720fs
LRG_1389p2:p.Asp1720fs
NC_000012.11:g.52200427del
NM_014191.3:c.5157del

Protein change:

D1679fs

Links:

dbSNP: rs2138943001

NCBI 1000 Genomes Browser:

rs2138943001

Molecular consequence:

NM_001177984.3:c.5034del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001330260.2:c.5157del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001369788.1:c.5034del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_014191.4:c.5157del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001825516	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Likely pathogenic (Dec 27, 2019)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001825516

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Likely pathogenic
(Dec 27, 2019)

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, SCV001825516.1

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

Description

Frameshift variant in the C-terminus predicted to result in protein truncation, as the last 261 amino acids are lost and replaced with 3 incorrect amino acids; Not observed in large population cohorts (Lek et al., 2016); Has not been previously published as pathogenic or benign to our knowledge

#	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: Dec 24, 2023

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Relating variation to medicine