STEAP3 p.Pro220=
c.660G>T · VCV4956604
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0022%, sas)
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 -20 | GERP -3.9 |
| Overall | ||
| CADD | 0.003 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0022%
South Asian · 2/91,078 alleles
Filtering AF
0.000365%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000137%
Overall
0.000124%
2/1,612,486 alleles · very rare
exomes 2/1,460,212 · genomes 0/152,274 · 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
- STEAP3
- Protein
- p.Pro220=
- Coding
- c.660G>T
- MANE Select
- NM_182915
- Type
- single nucleotide variant
- Location
- chr2:119247816 (GRCh38)
- Gene constraint
- LOEUF 1.27 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 89.24 · 2 PDB
Similar variants
- 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
- STEAP3 p.Gly379Cys 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-pro220 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown