SCN3A p.Val899=
c.2697C>T · rs571183520 · VCV1106024
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0593%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>T here scores Δ0.50 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -8.2 | GERP -5 |
| Overall | ||
| CADD | 6.132 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0593%
South Asian · 54/91,080 alleles
Filtering AF
0.0466%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0421%
Overall
0.00409%
66/1,614,048 alleles · ultra-rare
exomes 64/1,461,878 · genomes 2/152,170 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0593% | 1,687 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,626 |
| African / African-American | 0.00267% | 37,489 |
| East Asian | 0.00223% | 44,884 |
| European (non-Finnish) | 0.000424% | 236,004 |
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
- SCN3A
- Protein
- p.Val899=
- Coding
- c.2697C>T
- MANE Select
- NM_006922
- dbSNP
- rs571183520
- Type
- single nucleotide variant
- Location
- chr2:165130165 (GRCh38)
- Gene constraint
- LOEUF 0.348 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 68.76 · 2 PDB
- Residue 899
- an α-helix
Similar variants
- SCN3A p.Ile875Thr Pathogenic ★★★ same type
- SCN3A p.Gly876Ser Uncertain significance ★★★ ⚠ same type
- SCN3A p.Asp1803Asn Benign ★★★ same type
- SCN3A p.Asp815Asn Benign ★★★ same type
- SCN3A p.Gly1862Cys Benign ★★★ same type
- SCN3A p.Gly900Ser Likely benign ★★★ same type
- SCN3A p.Val1084Ile Benign ★★★ same type
- SCN3A p.Arg1621Gln Pathogenic/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/scn3a-p-val899 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown