Is STEAP3 p.Pro334= (c.1002G>A) pathogenic?

STEAP3 p.Pro334= (c.1002G>A) is classified Likely benign in STEAP3 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-07-01). Ultra-rare (popmax 0.0251%, amr).

How common is STEAP3 p.Pro334= (c.1002G>A) in the general population?

STEAP3 p.Pro334= (c.1002G>A) is ultra-rare (popmax 0.0251%, amr) (gnomAD).

STEAP3 p.Pro334=

c.1002G>A · rs568494916 · VCV1671561

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0251%, amr)

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -20	GERP -3.9
Overall
CADD	0.007	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0251% Admixed American · 15/59,848 alleles

Filtering AF 0.0154% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0125%

Overall 0.0033% 53/1,604,706 alleles · ultra-rare exomes 47/1,452,678 · genomes 6/152,028 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0251%	3,990
East Asian	0.0112%	8,946
Remaining individualsnot grpmax-eligible	0.00642%	15,565
South Asian	0.0044%	22,705
European (non-Finnish)	0.00212%	47,100

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.Pro334=
Coding: c.1002G>A
MANE Select: NM_182915
dbSNP: rs568494916
Type: single nucleotide variant
Location: chr2:119248158 (GRCh38)

Full STEAP3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

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-pro334 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown