STEAP3 p.Ala8Val
c.23C>T · VCV3963201
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0258%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.04 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP 0.075 | GERP 0.18, phastCons 0.002 |
| Regional constraint | o/e 0.98 | unconstrained · MANE · 32 kb · p 0.55 · regional, not allelic |
| Overall | ||
| CADD | 13.37 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0258%
Admixed American · 15/58,130 alleles
Filtering AF
0.0158%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0128%
Overall
0.00108%
17/1,575,384 alleles · ultra-rare
exomes 10/1,423,164 · genomes 7/152,220 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0258% | 3,875 |
| Remaining individualsnot grpmax-eligible | 0.0033% | 30,343 |
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.Ala8Val
- Coding
- c.23C>T
- MANE Select
- NM_182915
- Type
- single nucleotide variant
- Location
- chr2:119245489 (GRCh38)
- Gene constraint
- LOEUF 1.27 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 89.24 · 2 PDB
Similar variants
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- 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-ala8val (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown