SCN7A

sodium voltage-gated channel alpha subunit 7

Basic information

Region (hg38): 2:166403572-166611482

Previous symbols: [ "SCN6A" ]

Links

ENSG00000136546 ∙ NCBI:6332 ∙ OMIM:182392 ∙ HGNC:10594 ∙ Uniprot:Q01118 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

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	5	21
missense			60	17	9	86
nonsense			2	1		3
start loss						0
frameshift			1		1	2
inframe indel						0
splice donor/acceptor (+/-2bp)					1	1
splice region					1	1
non coding					1	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 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)
2-166405843-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)
2-166406082-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)
2-166406295-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)
2-166406373-G-C		not specified	Uncertain significance (Apr 22, 2022)
2-166406387-C-T		SCN7A-related disorder	Benign (Dec 31, 2019)
2-166406420-G-A			Likely benign (Nov 03, 2017)
2-166406429-A-G		SCN7A-related disorder	Benign (Nov 26, 2019)

GnomAD

Source: gnomAD

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: 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

	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