PROM1 p.Pro68=
c.204G>A · rs775249686 · VCV1958834
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0164%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1.7 | GERP -4.4 |
| Overall | ||
| CADD | 1.594 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0164%
Middle Eastern · 1/6,082 alleles
Filtering AF
0.00437%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00309%
Overall
0.000992%
16/1,612,548 alleles · ultra-rare
exomes 11/1,460,418 · genomes 5/152,130 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0164% | 6,082 |
| African / African-American | 0.00935% | 10,699 |
| East Asian | 0.00446% | 22,433 |
| Finnishnot grpmax-eligible | 0.00156% | 63,970 |
| European (non-Finnish) | 0.000424% | 235,866 |
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.Pro68=
- Coding
- c.204G>A
- MANE Select
- NM_006017
- dbSNP
- rs775249686
- Type
- single nucleotide variant
- Location
- chr4:16075703 (GRCh38)
- Gene constraint
- LOEUF 1.104 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 85.68
Similar variants
- PROM1 p.Pro68Leu 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
- PROM1 c.1984-1G>T 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-pro68 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown