PROM1 p.Pro152=
c.456C>G · rs377209685 · VCV811186
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.068%, 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 0.14 | GERP -0.17 |
| Overall | ||
| CADD | 5.443 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.068%
African / African-American · 51/75,000 alleles
Filtering AF
0.0531%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0478%
Overall
0.00335%
54/1,613,862 alleles · ultra-rare
exomes 27/1,461,652 · genomes 27/152,210 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.068% | 1,471 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,828 |
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.Pro152=
- Coding
- c.456C>G
- MANE Select
- NM_006017
- dbSNP
- rs377209685
- Type
- single nucleotide variant
- Location
- chr4:16033357 (GRCh38)
- Gene constraint
- LOEUF 1.104 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 85.68
Similar variants
- 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
- PROM1 c.1984-1G>T Pathogenic ★★ same type
- PROM1 c.2131-1G>A 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-pro152 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown