SCN7A
Basic information
Region (hg38): 2:166403573-166611482
Previous symbols: [ "SCN6A" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCN7A gene is commonly pathogenic or not.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
---|---|---|---|---|---|---|
synonymous | 16 | 23 | ||||
missense | 84 | 21 | 15 | 120 | ||
nonsense | 3 | |||||
start loss | 0 | |||||
frameshift | 2 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 1 | |||||
splice region | 2 | 2 | ||||
non coding | 2 | |||||
Total | 0 | 0 | 87 | 38 | 26 |
Variants in SCN7A
This is a list of pathogenic ClinVar variants found in the SCN7A region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
2-166405578-T-G | SCN7A-related disorder | Benign (Oct 21, 2019) | ||
2-166405659-T-C | SCN7A-related disorder | Benign (Nov 26, 2019) | ||
2-166405696-C-A | Likely benign (Dec 07, 2019) | |||
2-166405701-C-T | Likely benign (Dec 31, 2019) | |||
2-166405739-G-A | Benign (Nov 08, 2017) | |||
2-166405764-C-T | SCN7A-related disorder | Likely benign (Sep 28, 2023) | ||
2-166405765-G-A | Likely benign (Oct 31, 2018) | |||
2-166405767-T-A | not specified | Uncertain significance (Jan 24, 2024) | ||
2-166405773-G-A | not specified | Uncertain significance (Jun 18, 2021) | ||
2-166405777-T-A | not specified | Uncertain significance (Mar 31, 2024) | ||
2-166405843-C-G | SCN7A-related disorder | Benign (Oct 21, 2019) | ||
2-166405877-T-A | not specified | Uncertain significance (May 10, 2022) | ||
2-166405893-A-G | not specified | Uncertain significance (Mar 23, 2023) | ||
2-166405894-G-A | not specified | Uncertain significance (Feb 16, 2023) | ||
2-166406011-C-A | not specified | Uncertain significance (May 14, 2024) | ||
2-166406062-T-C | not specified | Uncertain significance (Apr 23, 2024) | ||
2-166406082-C-T | SCN7A-related disorder | Likely benign (Dec 31, 2019) | ||
2-166406104-T-C | not specified | Uncertain significance (Jan 09, 2024) | ||
2-166406105-C-T | Likely benign (Jun 08, 2018) | |||
2-166406121-G-A | SCN7A-related disorder | Likely benign (Apr 08, 2023) | ||
2-166406236-C-T | not specified | Uncertain significance (Sep 15, 2021) | ||
2-166406258-G-T | not specified | Uncertain significance (Mar 15, 2024) | ||
2-166406295-T-C | not specified | Uncertain significance (Nov 10, 2023) | ||
2-166406313-A-G | not specified | Uncertain significance (Dec 22, 2023) | ||
2-166406367-C-T | Uncertain significance (Jan 01, 2023) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
SCN7A | protein_coding | protein_coding | ENST00000409855 | 24 | 90675 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
2.16e-17 | 0.997 | 125471 | 1 | 271 | 125743 | 0.00108 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.407 | 761 | 793 | 0.959 | 0.0000375 | 11092 |
Missense in Polyphen | 245 | 273.65 | 0.89532 | 4079 | ||
Synonymous | -0.590 | 281 | 269 | 1.05 | 0.0000129 | 3017 |
Loss of Function | 2.95 | 37 | 62.1 | 0.596 | 0.00000300 | 903 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00134 | 0.00131 |
Ashkenazi Jewish | 0.00194 | 0.00189 |
East Asian | 0.00178 | 0.00174 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.000575 | 0.000545 |
Middle Eastern | 0.00178 | 0.00174 |
South Asian | 0.00407 | 0.00396 |
Other | 0.000856 | 0.000815 |
dbNSFP
Source:
- Function
- FUNCTION: Mediates the voltage-dependent sodium ion permeability of excitable membranes. Assuming opened or closed conformations in response to the voltage difference across the membrane, the protein forms a sodium-selective channel through which Na(+) ions may pass in accordance with their electrochemical gradient. {ECO:0000305}.;
- Pathway
- Adrenergic signaling in cardiomyocytes - Homo sapiens (human);Developmental Biology;Phase 0 - rapid depolarisation;Cardiac conduction;Muscle contraction;Interaction between L1 and Ankyrins;L1CAM interactions;Axon guidance
(Consensus)
Recessive Scores
- pRec
- 0.0940
Intolerance Scores
- loftool
- 0.115
- rvis_EVS
- 0.86
- rvis_percentile_EVS
- 88.57
Haploinsufficiency Scores
- pHI
- 0.0777
- hipred
- N
- hipred_score
- 0.146
- ghis
- 0.448
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.189
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Scn7a
- Phenotype
- taste/olfaction phenotype;
Gene ontology
- Biological process
- sodium ion transport;muscle contraction;response to bacterium;neuronal action potential;regulation of ion transmembrane transport;sodium ion transmembrane transport;sodium ion homeostasis;membrane depolarization during action potential
- Cellular component
- voltage-gated sodium channel complex;plasma membrane;axon;glial cell projection
- Molecular function
- voltage-gated ion channel activity;voltage-gated sodium channel activity