SCN1A p.Pro660=
c.1980T>G · rs1379958414 · VCV1641629
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.000763%, nfe)
Conditions
1
early-infantile DEE
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 2.7 | GERP -2.9, phastCons 1 |
| Overall | ||
| CADD | 10.64 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000763%
European (non-Finnish) · 9/1,180,006 alleles
Filtering AF
0.000359%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00026%
Overall
0.000558%
9/1,614,040 alleles · very rare
exomes 6/1,461,860 · genomes 3/152,180 · joint denominator
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- SCN1A
- Protein
- p.Pro660=
- Coding
- c.1980T>G
- MANE Select
- NM_001165963
- dbSNP
- rs1379958414
- Type
- single nucleotide variant
- Location
- chr2:166043732 (GRCh38)
- Gene constraint
- LOEUF 0.098 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 68.97 · 1 PDB
- Residue 660
- a UniProt-annotated variant site (in drvt)
Similar variants
- SCN1A p.Pro660Thr Uncertain significance ★ ⚠ same residue
- SCN1A p.Ala420Val Likely pathogenic ★★★ same condition
- SCN1A p.Arg1639Pro Pathogenic ★★★ same condition
- SCN1A p.Arg219Gly Likely pathogenic ★★★ same condition
- SCN1A p.Arg219Thr Likely pathogenic ★★★ same condition
- SCN1A p.Arg931His Pathogenic ★★★ same condition
- SCN1A p.Pro768Leu Likely pathogenic ★★★ same condition
- SCN1A p.Ser570Asn Likely pathogenic ★★★ same condition
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/scn1a-p-pro660 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown