STEAP3 p.Ser406=
c.1218C>T · rs11885203 · VCV788511
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.51%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.23 | GERP 0.22, phastCons 0.97 |
| Overall | ||
| CADD | 9.563 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.51%
African / African-American · 1,885/74,998 alleles
Filtering AF
2.42%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.38%
Overall
0.132%
2,115/1,604,280 alleles · low-frequency
exomes 1,005/1,451,948 · genomes 1,110/152,332 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.51% | 40 |
| Remaining individualsnot grpmax-eligible | 0.172% | 582 |
| Admixed American | 0.165% | 606 |
| Middle Eastern | 0.0407% | 2,458 |
| South Asian | 0.00549% | 18,202 |
| European (non-Finnish) | 0.00144% | 69,381 |
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
- STEAP3
- Protein
- p.Ser406=
- Coding
- c.1218C>T
- MANE Select
- NM_182915
- dbSNP
- rs11885203
- Type
- single nucleotide variant
- Location
- chr2:119263059 (GRCh38)
- Gene constraint
- LOEUF 1.27 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 89.24 · 2 PDB
- Residue 406
- the ferric oxidoreductase domain
Similar variants
- STEAP3 p.Ser406Phe Uncertain significance ★ ⚠ same residue
- STEAP3 p.Ala490Thr Uncertain significance ★★ ⚠ same type
- STEAP3 p.Arg217Ser Uncertain significance ★★ ⚠ same type
- STEAP3 p.Arg293Trp Uncertain significance ★★ ⚠ same type
- STEAP3 p.Arg336His Uncertain significance ★★ ⚠ same type
- STEAP3 p.Arg466Cys Uncertain significance ★★ ⚠ same type
- STEAP3 p.Gln87Arg Uncertain significance ★★ ⚠ same type
- STEAP3 p.Glu141Lys Uncertain significance ★★ ⚠ 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/steap3-p-ser406 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown