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NM_000334.4(SCN4A):c.2717G>C (p.Ser906Thr)

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
13 (Most recent: Oct 4, 2021)
Last evaluated:
Apr 12, 2021
Accession:
VCV000021154.8
Variation ID:
21154
Description:
single nucleotide variant
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NM_000334.4(SCN4A):c.2717G>C (p.Ser906Thr)

Allele ID
34006
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
17q23.3
Genomic location
17: 63951560 (GRCh38) GRCh38 UCSC
17: 62028920 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000017.10:g.62028920C>G
NC_000017.11:g.63951560C>G
NG_011699.1:g.26359G>C
... more HGVS
Protein change
S906T
Other names
-
Canonical SPDI
NC_000017.11:63951559:C:G
Functional consequence
-
Global minor allele frequency (GMAF)
0.00499 (G)

Allele frequency
Exome Aggregation Consortium (ExAC) 0.00946
1000 Genomes Project 0.00499
Trans-Omics for Precision Medicine (TOPMed) 0.01075
Trans-Omics for Precision Medicine (TOPMed) 0.01087
The Genome Aggregation Database (gnomAD) 0.00784
The Genome Aggregation Database (gnomAD) 0.01003
The Genome Aggregation Database (gnomAD), exomes 0.00990
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.01170
Links
ClinGen: CA146047
dbSNP: rs41280102
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign/Likely benign 3 criteria provided, multiple submitters, no conflicts Dec 8, 2020 RCV000020269.9
Benign 6 criteria provided, multiple submitters, no conflicts Apr 12, 2021 RCV000078659.12
Likely benign 1 criteria provided, single submitter Apr 27, 2017 RCV000288548.2
Likely benign 1 criteria provided, single submitter Apr 27, 2017 RCV000348143.2
Likely benign 1 criteria provided, single submitter Apr 27, 2017 RCV000342369.2
Likely benign 1 criteria provided, single submitter Apr 27, 2017 RCV000398742.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
GH-LCR - - - GRCh38 - 875
SCN4A - - GRCh38
GRCh37
354 1081

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(-)
criteria provided, single submitter
Method: clinical testing
NOT SPECIFIED
Allele origin: germline
PreventionGenetics,PreventionGenetics
Accession: SCV000303640.1
Submitted: (Apr 28, 2016)
Evidence details
Benign
(Oct 19, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000520902.4
Submitted: (Mar 26, 2018)
Evidence details
Comment:
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at … (more)
Benign
(Aug 12, 2013)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000110515.8
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Likely benign
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Familial hyperkalemic periodic paralysis
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000405172.3
Submitted: (Feb 20, 2020)
Evidence details
Publications
PubMed (1)
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
Likely benign
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Potassium-aggravated myotonia
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000405173.3
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
Likely benign
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Congenital myasthenic syndrome, acetazolamide-responsive
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000405174.3
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
Likely benign
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Paramyotonia congenita of von Eulenburg
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000405171.3
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
Likely benign
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Hypokalemic periodic paralysis, type 2
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000405175.3
Submitted: (Feb 20, 2020)
Evidence details
Publications
PubMed (1)
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
Benign
(Dec 08, 2020)
criteria provided, single submitter
Method: clinical testing
Familial hyperkalemic periodic paralysis
Allele origin: germline
Invitae
Accession: SCV000658540.5
Submitted: (Jan 07, 2021)
Evidence details
Benign
(Apr 12, 2021)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: unknown
Athena Diagnostics Inc
Accession: SCV000615073.2
Submitted: (Sep 13, 2021)
Evidence details
Publications
PubMed (5)
Benign
(Jan 08, 2020)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Al Jalila Children's Genomics Center,Al Jalila Childrens Speciality Hospital
Accession: SCV001984711.1
Submitted: (Oct 04, 2021)
Evidence details
Benign
(Jan 28, 2016)
no assertion criteria provided
Method: literature only
Familial hyperkalemic periodic paralysis
Allele origin: germline
GeneReviews
Accession: SCV000040623.2
Submitted: (Jan 28, 2016)
Evidence details
Publications
PubMed (1)
Other databases
http://www.ncbi.nlm.nih.gov/book…
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
AllHighlyPenetrant
(Autosomal recessive inheritance)
Allele origin: germline
Genetic Services Laboratory,University of Chicago
Accession: SCV000152635.2
Submitted: (Jun 27, 2014)
Evidence details
Comment:
Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated … (more)

Functional evidence

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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.

Citations for this variant

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Title Author Journal Year Link
Hyperkalemic Periodic Paralysis Weber F - 2021 PMID: 20301669
SCN4A as modifier gene in patients with myotonic dystrophy type 2. Binda A Scientific reports 2018 PMID: 30038349
Effects of S906T polymorphism on the severity of a novel borderline mutation I692M in Na<sub>v</sub> 1.4 cause periodic paralysis. Fan C Clinical genetics 2017 PMID: 27714768
Myotonic Dystrophy Type 2: An Update on Clinical Aspects, Genetic and Pathomolecular Mechanism. Meola G Journal of neuromuscular diseases 2015 PMID: 27858759
Correlating phenotype and genotype in the periodic paralyses. Miller TM Neurology 2004 PMID: 15534250
Impaired slow inactivation due to a polymorphism and substitutions of Ser-906 in the II-III loop of the human Nav1.4 channel. Kuzmenkin A Pflugers Archiv : European journal of physiology 2003 PMID: 12898257
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=SCN4A - - - -
http://www.ncbi.nlm.nih.gov/books/NBK1496/ - - - -

Text-mined citations for rs41280102...

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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 Nov 27, 2021