PROM1 p.Ser293=
c.879C>T · rs148242593 · VCV198838
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
rare (popmax 0.321%, 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 -9.5 | GERP -3.5 |
| Overall | ||
| CADD | 0.05 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.321%
African / African-American · 241/75,026 alleles
Filtering AF
0.288%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.275%
Overall
0.0177%
285/1,613,728 alleles · rare
exomes 143/1,461,452 · genomes 142/152,276 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.321% | 311 |
| Remaining individualsnot grpmax-eligible | 0.0272% | 3,675 |
| Admixed American | 0.0217% | 4,617 |
| Middle Eastern | 0.0171% | 5,864 |
| South Asian | 0.00439% | 22,766 |
| European (non-Finnish) | 0.000763% | 131,098 |
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
- PROM1
- Protein
- p.Ser293=
- Coding
- c.879C>T
- MANE Select
- NM_006017
- dbSNP
- rs148242593
- Type
- single nucleotide variant
- Location
- chr4:16018446 (GRCh38)
- Gene constraint
- LOEUF 1.104 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 85.68
Similar variants
- PROM1 p.Ser293Arg Uncertain significance ★★ ⚠ same residue
- PROM1 p.Ser293Gly Uncertain significance ★ ⚠ same residue
- PROM1 c.1142-1G>A Pathogenic/Likely pathogenic ★★ same type
- PROM1 c.1301+1G>A Pathogenic/Likely pathogenic ★★ same type
- PROM1 c.1301+2T>C Pathogenic/Likely pathogenic ★★ same type
- PROM1 c.1578+1G>A Pathogenic/Likely pathogenic ★★ same type
- PROM1 c.1579-1G>C Pathogenic ★★ same type
- PROM1 c.1579-2A>C 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/prom1-p-ser293 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown