ClinVar Genomic variation as it relates to human health
NM_000334.4(SCN4A):c.3917G>T (p.Gly1306Val)
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.
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
-
NM_000334.4(SCN4A):c.3917G>T (p.Gly1306Val)
Variation ID: 5903 Accession: VCV000005903.48
- Type and length
-
single nucleotide variant, 1 bp
- Location
-
Cytogenetic: 17q23.3 17: 63943846 (GRCh38) [ NCBI UCSC ] 17: 62021206 (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 Feb 13, 2015 Oct 20, 2024 Aug 11, 2023 - HGVS
-
Nucleotide Protein Molecular
consequenceNM_000334.4:c.3917G>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000325.4:p.Gly1306Val missense NC_000017.11:g.63943846C>A NC_000017.10:g.62021206C>A NG_011699.1:g.34073G>T NG_042788.1:g.26754C>A P35499:p.Gly1306Val - Protein change
- G1306V
- Other names
- -
- Canonical SPDI
- NC_000017.11:63943845:C:A
-
Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
- -
-
Global minor allele
frequency (GMAF) HelpThe 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.
-
Trans-Omics for Precision Medicine (TOPMed) 0.00000
- Links
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 | ||
---|---|---|---|---|---|---|
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. |
|||
GH-LCR | - | - | - | GRCh38 | - | 1626 |
SCN4A | - | - |
GRCh38 GRCh37 |
736 | 2045 |
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. |
---|---|---|---|---|
Pathogenic (3) |
criteria provided, multiple submitters, no conflicts
|
Feb 23, 2023 | RCV000006264.13 | |
Pathogenic (1) |
no assertion criteria provided
|
May 1, 2009 | RCV000006265.10 | |
Pathogenic (3) |
criteria provided, multiple submitters, no conflicts
|
Jul 1, 2023 | RCV000479620.35 | |
Pathogenic (2) |
criteria provided, multiple submitters, no conflicts
|
Aug 11, 2023 | RCV000690377.12 | |
SCN4A-related non-dystrophic myotonia
|
Pathogenic (1) |
no assertion criteria provided
|
Apr 6, 2022 | RCV002267601.3 |
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
(Jan 01, 2016)
|
criteria provided, single submitter
Method: clinical testing
|
Familial hyperkalemic periodic paralysis
Affected status: yes
Allele origin:
unknown
|
Centre for Mendelian Genomics, University Medical Centre Ljubljana
Accession: SCV001370154.2
First in ClinVar: Jul 04, 2020 Last updated: Dec 12, 2020 |
Comment:
This variant was classified as: Pathogenic. The following ACMG criteria were applied in classifying this variant: PS1,PS3,PM2,PP2,PP3.
|
|
Pathogenic
(Oct 25, 2021)
|
criteria provided, single submitter
Method: clinical testing
|
Paramyotonia congenita of Von Eulenburg
Affected status: yes
Allele origin:
germline
|
MGZ Medical Genetics Center
Accession: SCV002581212.1
First in ClinVar: Oct 15, 2022 Last updated: Oct 15, 2022
Comment:
ACMG criteria applied: PS3, PS2_MOD, PS4_MOD, PM1, PM5, PM2_SUP, PP1, PP3
|
Number of individuals with the variant: 1
Sex: male
|
|
Pathogenic
(May 13, 2021)
|
criteria provided, single submitter
Method: clinical testing
|
Not Provided
Affected status: yes
Allele origin:
germline
|
GeneDx
Accession: SCV000567468.4
First in ClinVar: Apr 27, 2017 Last updated: Apr 17, 2019 |
Comment:
Reported previously as a heterozygous variant in two unrelated families with paramyotonia congenita (McClatchey et al., 1992); Functional studies suggest that G1306V results in slower … (more)
Reported previously as a heterozygous variant in two unrelated families with paramyotonia congenita (McClatchey et al., 1992); Functional studies suggest that G1306V results in slower inactivation of the SCN4A sodium channel (Lerche et al., 1993); Not observed at a significant frequency in large population cohorts (Lek et al., 2016); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 25525159, 8308722, 1310898, 27415035, 26944947, 18337100, 18337730, 28150151, 26885337, 26080010, 22094069, 20445432, 17823953, 16832098, 8044656, 16392038, 7473241, 32849172, 32660787) (less)
|
|
Pathogenic
(Feb 23, 2023)
|
criteria provided, single submitter
Method: clinical testing
|
Paramyotonia congenita of Von Eulenburg
Affected status: yes
Allele origin:
unknown
|
3billion
Accession: SCV003841909.1
First in ClinVar: Mar 18, 2023 Last updated: Mar 18, 2023 |
Comment:
The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: <0.001%). Missense changes are a common disease-causing mechanism. … (more)
The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: <0.001%). Missense changes are a common disease-causing mechanism. In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.92; 3Cnet: 0.91). Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000005903). The variant has been reported to co-segregate with the disease in at least 3 similarly affected relatives/individuals in the same family or similarly affected unrelated families (PMID: 27415035). Different missense changes at the same codon (p.Gly1306Ala, p.Gly1306Glu) have been reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000005908, VCV000005920). Therefore, this variant is classified as Pathogenic according to the recommendation of ACMG/AMP guideline. (less)
Clinical Features:
Myalgia (present) , Fasciculations (present) , Limb fasciculations (present) , Elevated circulating creatine kinase concentration (present) , Fatigue (present) , Somatic sensory dysfunction (present) , … (more)
Myalgia (present) , Fasciculations (present) , Limb fasciculations (present) , Elevated circulating creatine kinase concentration (present) , Fatigue (present) , Somatic sensory dysfunction (present) , EMG: myotonic runs (present) , Hand tremor (present) , Esodeviation (present) , Weakness of facial musculature (present) , Calf muscle hypertrophy (present) , Proximal muscle weakness (present) (less)
|
|
Pathogenic
(May 03, 2023)
|
criteria provided, single submitter
Method: clinical testing
|
not provided
Affected status: unknown
Allele origin:
unknown
|
Athena Diagnostics
Accession: SCV000615092.4
First in ClinVar: Apr 27, 2017 Last updated: Jan 26, 2024 |
Comment:
The frequency of this variant in the general population is consistent with pathogenicity (http://gnomad.broadinstitute.org). This variant associates with paramyotonia congenita in multiple families, and is … (more)
The frequency of this variant in the general population is consistent with pathogenicity (http://gnomad.broadinstitute.org). This variant associates with paramyotonia congenita in multiple families, and is reported in multiple other unrelated individuals with non-dystrophic myotonia. At least one other missense variant at this codon is considered to be pathogenic or likely pathogenic. Assessment of experimental evidence suggests this variant results in abnormal protein function. Multiple studies indicate that this variant disrupts normal ion channel properties, resulting in aberrant channel regulation of current and signaling (PMID: 7473241, 16392038). (less)
|
|
Pathogenic
(Aug 11, 2023)
|
criteria provided, single submitter
Method: clinical testing
|
Familial hyperkalemic periodic paralysis
Affected status: unknown
Allele origin:
germline
|
Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV000818060.7
First in ClinVar: Oct 10, 2018 Last updated: Feb 14, 2024 |
Comment:
This sequence change replaces glycine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 1306 of the SCN4A protein (p.Gly1306Val). … (more)
This sequence change replaces glycine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 1306 of the SCN4A protein (p.Gly1306Val). This variant is present in population databases (rs80338792, gnomAD 0.0009%). This missense change has been observed in individuals with paramyotonia congenita (PMID: 1310898, 8044656, 8308722, 17823953, 18337100, 18337730, 20445432, 22094069, 27415035). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 5903). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on SCN4A protein function. Experimental studies have shown that this missense change affects SCN4A function (PMID: 7473241, 16392038). This variant disrupts the p.Gly1306 amino acid residue in SCN4A. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 7980103, 16832098, 20713951, 25088311, 25311598, 26080010, 26885337, 26944947). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic. (less)
|
|
Pathogenic
(Jul 01, 2023)
|
criteria provided, single submitter
Method: clinical testing
|
not provided
Affected status: yes
Allele origin:
germline
|
CeGaT Center for Human Genetics Tuebingen
Accession: SCV001249362.26
First in ClinVar: May 09, 2020 Last updated: Oct 20, 2024 |
Comment:
SCN4A: PM2, PM5, PP1:Moderate, PS4:Moderate, PP3, PS3:Supporting
Number of individuals with the variant: 5
|
|
Pathogenic
(Apr 06, 2022)
|
no assertion criteria provided
Method: research
|
SCN4A-related non-dystrophic myotonia
Affected status: yes
Allele origin:
germline
|
Department of Neurology and Geriatrics, Kagoshima University Graduate School of Medical and Dental Sciences
Accession: SCV002549812.1
First in ClinVar: Jul 23, 2022 Last updated: Jul 23, 2022 |
|
|
Pathogenic
(May 01, 2009)
|
no assertion criteria provided
Method: literature only
|
PARAMYOTONIA CONGENITA
Affected status: not provided
Allele origin:
germline
|
OMIM
Accession: SCV000026446.5
First in ClinVar: Apr 04, 2013 Last updated: Jul 23, 2024 |
Comment on evidence:
In a Belgian family with paramyotonia congenita (PMC; 168300), McClatchey et al. (1992) identified a heterozygous c.3917G-T transversion in the SCN4A gene, resulting in a … (more)
In a Belgian family with paramyotonia congenita (PMC; 168300), McClatchey et al. (1992) identified a heterozygous c.3917G-T transversion in the SCN4A gene, resulting in a gly1306-to-val (G1306V) substitution. The mutation affected a highly conserved residue in the III-IV cytoplasmic loop, a portion of the sodium channel thought to pivot in response to membrane depolarization, thereby blocking and inactivating the channel. Muscle weakness was not reported. The authors suggested that this is a temperature-sensitive mutation. Lerche et al. (1993) identified a heterozygous G1306V substitution in a mother and son with potassium-aggravated myotonia (608390). Muscle stiffness in these individuals was also aggravated by exercise, but not by cold. Muscle weakness was not reported. Patch-clamp recordings on patient muscle samples showed slower sodium fast channel inactivation and an increase in late channel opening, resulting in a steady-state inward current, sustained muscle depolarization, and muscle fiber hyperexcitability. Lerche et al. (1993) identified different pathogenic mutations in the same codon (G1306A; 603967.0012 and G1306E; 603967.0025) in other families with similar disorders, indicating that residue 1306 is important for sodium channel inactivation. Dupre et al. (2009) reported French Canadian patients with myotonia associated with the G1306V mutation. They had moderate myotonia with mild muscle hypertrophy. They noted exacerbation of symptoms with cold temperatures but no paradoxical myotonia. Female patients showed dramatic symptom improvement after menopause. (less)
|
|
Pathogenic
(May 01, 2009)
|
no assertion criteria provided
Method: literature only
|
MYOTONIA, POTASSIUM-AGGRAVATED
Affected status: not provided
Allele origin:
germline
|
OMIM
Accession: SCV000026447.5
First in ClinVar: Apr 04, 2013 Last updated: Jul 23, 2024 |
Comment on evidence:
In a Belgian family with paramyotonia congenita (PMC; 168300), McClatchey et al. (1992) identified a heterozygous c.3917G-T transversion in the SCN4A gene, resulting in a … (more)
In a Belgian family with paramyotonia congenita (PMC; 168300), McClatchey et al. (1992) identified a heterozygous c.3917G-T transversion in the SCN4A gene, resulting in a gly1306-to-val (G1306V) substitution. The mutation affected a highly conserved residue in the III-IV cytoplasmic loop, a portion of the sodium channel thought to pivot in response to membrane depolarization, thereby blocking and inactivating the channel. Muscle weakness was not reported. The authors suggested that this is a temperature-sensitive mutation. Lerche et al. (1993) identified a heterozygous G1306V substitution in a mother and son with potassium-aggravated myotonia (608390). Muscle stiffness in these individuals was also aggravated by exercise, but not by cold. Muscle weakness was not reported. Patch-clamp recordings on patient muscle samples showed slower sodium fast channel inactivation and an increase in late channel opening, resulting in a steady-state inward current, sustained muscle depolarization, and muscle fiber hyperexcitability. Lerche et al. (1993) identified different pathogenic mutations in the same codon (G1306A; 603967.0012 and G1306E; 603967.0025) in other families with similar disorders, indicating that residue 1306 is important for sodium channel inactivation. Dupre et al. (2009) reported French Canadian patients with myotonia associated with the G1306V mutation. They had moderate myotonia with mild muscle hypertrophy. They noted exacerbation of symptoms with cold temperatures but no paradoxical myotonia. Female patients showed dramatic symptom improvement after menopause. (less)
|
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. |
Citations for germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
---|---|---|---|---|
Non-dystrophic myotonias: clinical and mutation spectrum of 70 German patients. | Vereb N | Journal of neurology | 2021 | PMID: 33263785 |
Clinical and Molecular Spectrum of Myotonia and Periodic Paralyses Associated With Mutations in SCN4A in a Large Cohort of Italian Patients. | Maggi L | Frontiers in neurology | 2020 | PMID: 32849172 |
Mutation spectrum and health status in skeletal muscle channelopathies in Japan. | Sasaki R | Neuromuscular disorders : NMD | 2020 | PMID: 32660787 |
Structure-based assessment of disease-related mutations in human voltage-gated sodium channels. | Huang W | Protein & cell | 2017 | PMID: 28150151 |
Sequence CLCN1 and SCN4A in patients with Nondystrophic myotonias in Chinese populations: Genetic and pedigree analysis of 10 families and review of the literature. | Yang X | Channels (Austin, Tex.) | 2017 | PMID: 27415035 |
Flecainide-Responsive Myotonia Permanens With SNEL Onset: A New Case and Literature Review. | Portaro S | Pediatrics | 2016 | PMID: 26944947 |
Mutation analysis in exons 22 and 24 of SCN4A gene in Iranian patients with non-dystrophic myotonia. | Heidari MM | Iranian journal of neurology | 2015 | PMID: 26885337 |
Painful cramps and giant myotonic discharges in a family with the Nav1.4-G1306A mutation. | Torbergsen T | Muscle & nerve | 2015 | PMID: 26080010 |
Mutations in SCN4A: a rare but treatable cause of recurrent life-threatening laryngospasm. | Singh RR | Pediatrics | 2014 | PMID: 25311598 |
Heterozygous CLCN1 mutations can modulate phenotype in sodium channel myotonia. | Furby A | Neuromuscular disorders : NMD | 2014 | PMID: 25088311 |
Screening for mutations in Spanish families with myotonia. Functional analysis of novel mutations in CLCN1 gene. | Mazón MJ | Neuromuscular disorders : NMD | 2012 | PMID: 22094069 |
Severe neonatal episodic laryngospasm due to de novo SCN4A mutations: a new treatable disorder. | Lion-Francois L | Neurology | 2010 | PMID: 20713951 |
A case of paramyotonia congenita without periodic paralysis: electrophysiological and molecular genetic studies. | Park JH | The neurologist | 2010 | PMID: 20445432 |
Clinical, electrophysiologic, and genetic study of non-dystrophic myotonia in French-Canadians. | Dupré N | Neuromuscular disorders : NMD | 2009 | PMID: 18337100 |
In tandem analysis of CLCN1 and SCN4A greatly enhances mutation detection in families with non-dystrophic myotonia. | Trip J | European journal of human genetics : EJHG | 2008 | PMID: 18337730 |
Reduced muscle-fiber conduction but normal slowing after cold exposure in paramyotonia congenita. | Blijham PJ | Muscle & nerve | 2008 | PMID: 17823953 |
Autosomal dominant monosymptomatic myotonia permanens. | Colding-Jørgensen E | Neurology | 2006 | PMID: 16832098 |
Cold extends electromyography distinction between ion channel mutations causing myotonia. | Fournier E | Annals of neurology | 2006 | PMID: 16786525 |
K-aggravated myotonia mutations at residue G1306 differentially alter deactivation gating of human skeletal muscle sodium channels. | Groome JR | Cellular and molecular neurobiology | 2005 | PMID: 16392038 |
Different effects on gating of three myotonia-causing mutations in the inactivation gate of the human muscle sodium channel. | Mitrović N | The Journal of physiology | 1995 | PMID: 7473241 |
Mutations in the muscle sodium channel gene (SCN4A) in 13 French families with hyperkalemic periodic paralysis and paramyotonia congenita: phenotype to genotype correlations and demonstration of the predominance of two mutations. | Plassart E | European journal of human genetics : EJHG | 1994 | PMID: 8044656 |
Myotonia fluctuans. A third type of muscle sodium channel disease. | Ricker K | Archives of neurology | 1994 | PMID: 7980103 |
Human sodium channel myotonia: slowed channel inactivation due to substitutions for a glycine within the III-IV linker. | Lerche H | The Journal of physiology | 1993 | PMID: 8308722 |
Temperature-sensitive mutations in the III-IV cytoplasmic loop region of the skeletal muscle sodium channel gene in paramyotonia congenita. | McClatchey AI | Cell | 1992 | PMID: 1310898 |
click to load more click to collapse |
Text-mined citations for rs80338792 ...
HelpRecord last updated Oct 20, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.