SCN8A p.Ala413=
c.1239T>C · rs2138748288 · VCV1259325
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.14 | GERP -2.9, phastCons 0.98 |
| Overall | ||
| CADD | 9.261 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- SCN8A
- Protein
- p.Ala413=
- Coding
- c.1239T>C
- MANE Select
- NM_001330260
- dbSNP
- rs2138748288
- Type
- single nucleotide variant
- Location
- chr12:51705521 (GRCh38)
- Gene constraint
- LOEUF 0.189 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 68.90 · 7 PDB
- Residue 413
- an α-helix
Similar variants
- SCN8A p.Ala413Asp Likely pathogenic ★ same residue
- SCN8A c.615-1G>A Pathogenic ★★★ same type
- SCN8A p.Arg1872Gln Pathogenic ★★★ ⚠ same type
- SCN8A p.Asn1318Ser Likely pathogenic ★★★ same type
- SCN8A p.Asn418Asp Likely pathogenic ★★★ same type
- SCN8A p.Glu1218Lys Pathogenic ★★★ same type
- SCN8A p.Ile1631Thr Likely pathogenic ★★★ same type
- SCN8A p.Ser845Cys Likely pathogenic ★★★ ⚠ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/scn8a-p-ala413 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown