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GeneBe

SCN7A

sodium voltage-gated channel alpha subunit 7

Basic information

Region (hg38): 2:166403572-166611482

Previous symbols: [ "SCN6A" ]

Links

ENSG00000136546NCBI:6332OMIM:182392HGNC:10594Uniprot:Q01118AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SCN7A gene.

  • Inborn genetic diseases (63 variants)
  • not provided (53 variants)
  • not specified (1 variants)

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
clinvar
5
clinvar
21
missense
60
clinvar
17
clinvar
9
clinvar
86
nonsense
2
clinvar
1
clinvar
3
start loss
0
frameshift
1
clinvar
1
clinvar
2
inframe indel
0
splice donor/acceptor (+/-2bp)
1
clinvar
1
splice region
1
1
non coding
1
clinvar
1
Total 0 0 63 34 17

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 condition Benign (Oct 21, 2019)3056929
2-166405659-T-C SCN7A-related condition Benign (Nov 26, 2019)3055990
2-166405696-C-A Likely benign (Dec 07, 2019)1148518
2-166405701-C-T Likely benign (Dec 31, 2019)713051
2-166405739-G-A Benign (Nov 08, 2017)731320
2-166405764-C-T SCN7A-related condition Likely benign (Sep 28, 2023)1136974
2-166405765-G-A Likely benign (Oct 31, 2018)747563
2-166405773-G-A Inborn genetic diseases Uncertain significance (Jun 18, 2021)2380808
2-166405843-C-G SCN7A-related condition Benign (Oct 21, 2019)3057148
2-166405877-T-A Inborn genetic diseases Uncertain significance (May 10, 2022)2350365
2-166405893-A-G Inborn genetic diseases Uncertain significance (Mar 23, 2023)2528649
2-166406082-C-T SCN7A-related condition Likely benign (Dec 31, 2019)709139
2-166406105-C-T Likely benign (Jun 08, 2018)750467
2-166406121-G-A SCN7A-related condition Likely benign (Apr 08, 2023)3055155
2-166406236-C-T Inborn genetic diseases Uncertain significance (Sep 15, 2021)2224354
2-166406367-C-T Uncertain significance (Jan 01, 2023)2651508
2-166406387-C-T SCN7A-related condition Benign (Dec 31, 2019)737372
2-166406420-G-A Likely benign (Nov 03, 2017)732457
2-166406429-A-G SCN7A-related condition Benign (Nov 26, 2019)3055922
2-166406507-C-T Inborn genetic diseases Uncertain significance (Apr 13, 2023)2536774
2-166406537-C-T Likely benign (Jun 08, 2018)749292
2-166406547-T-C Inborn genetic diseases Uncertain significance (Jun 07, 2023)2558785
2-166406556-C-T Inborn genetic diseases Uncertain significance (Dec 03, 2021)2356232
2-166406557-G-A SCN7A-related condition Likely benign (Mar 21, 2022)3057552
2-166409706-C-G Inborn genetic diseases Uncertain significance (Apr 11, 2023)2515492

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SCN7Aprotein_codingprotein_codingENST00000409855 2490675
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
2.16e-170.99712547112711257430.00108
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.4077617930.9590.000037511092
Missense in Polyphen245273.650.895324079
Synonymous-0.5902812691.050.00001293017
Loss of Function2.953762.10.5960.00000300903

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.001340.00131
Ashkenazi Jewish0.001940.00189
East Asian0.001780.00174
Finnish0.000.00
European (Non-Finnish)0.0005750.000545
Middle Eastern0.001780.00174
South Asian0.004070.00396
Other0.0008560.000815

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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