SCN2A p.Ile1663=
c.4989C>T · rs373347369 · VCV331736
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Rare
rare (popmax 0.153%, amr)
Conditions
3
Inborn genetic diseases
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 -11 | GERP -3.5 |
| Overall | ||
| CADD | 2.026 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.153%
Admixed American · 92/59,998 alleles
Filtering AF
0.128%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.119%
Overall
0.00644%
104/1,614,102 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.153% | 652 |
| East Asian | 0.00669% | 14,955 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,253 |
| African / African-American | 0.00267% | 37,521 |
| South Asian | 0.0011% | 91,088 |
| European (non-Finnish) | 0.000339% | 294,997 |
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
- SCN2A
- Protein
- p.Ile1663=
- Coding
- c.4989C>T
- MANE Select
- NM_001040142
- dbSNP
- rs373347369
- Type
- single nucleotide variant
- Location
- chr2:165388795 (GRCh38)
- Gene constraint
- LOEUF 0.161 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 69.28 · 5 PDB
- Residue 1663
- a UniProt-annotated variant site (found in a patient with intractable epilepsy and severe mental decline; likely pathogenic; non-conducting; loss of voltage-gated sodium channel activity; dominant-negative); a UniProt-annotated variant site (found in a patient with schizofrenia; uncertain significance); a UniProt-annotated variant site (found in a patient with autism spectrum disorder; likely pathogenic); a UniProt-annotated variant site (found in a patient with autism spectrum disorder; likely pathogenic; loss of voltage-gated sodium channel activity; non-conducting); a UniProt-annotated variant site (in dee11); an α-helix
Similar variants
- SCN2A p.Ile1663fs Likely pathogenic ★ same residue
- SCN2A p.Ile1663Thr Uncertain significance ★ ⚠ same residue
- SCN2A p.Ile1663Leu Uncertain significance ⚠ same residue
- SCN2A p.Ala1773Thr Pathogenic ★★★ same condition
- SCN2A p.Arg220Gly Likely pathogenic ★★★ same condition
- SCN2A p.Arg853Gln Pathogenic ★★★ same condition
- SCN2A p.Gly899Asp Likely pathogenic ★★★ same condition
- SCN2A p.Leu1611Pro 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/scn2a-p-ile1663 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown