PROP1 p.Pro94=
c.282C>T · rs776294029 · VCV1154353
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0534%, afr)
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 -5.7 | |
| Overall | ||
| CADD | 0.837 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0534%
African / African-American · 40/74,902 alleles
Filtering AF
0.0402%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0357%
Overall
0.00713%
115/1,614,006 alleles · ultra-rare
exomes 87/1,461,884 · genomes 28/152,122 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0534% | 1,873 |
| Remaining individualsnot grpmax-eligible | 0.0096% | 10,413 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00675% | 14,804 |
| Admixed American | 0.00667% | 15,002 |
| European (non-Finnish) | 0.00517% | 19,345 |
| East Asian | 0.00223% | 44,882 |
| South Asian | 0.0011% | 91,080 |
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
- PROP1
- Protein
- p.Pro94=
- Coding
- c.282C>T
- MANE Select
- NM_006261
- dbSNP
- rs776294029
- Type
- single nucleotide variant
- Location
- chr5:177994166 (GRCh38)
- Gene constraint
- LOEUF 0.87 · pLI 0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 70.74
- Residue 94
- a DNA-binding region
Similar variants
- PROP1 c.109+1G>A Pathogenic ★★ same type
- PROP1 c.110-2A>G Likely pathogenic ★★ same type
- PROP1 c.343-1G>A Likely pathogenic ★★ same type
- PROP1 p.Arg112Ter Pathogenic/Likely pathogenic ★★ same type
- PROP1 p.Arg120Cys Pathogenic/Likely pathogenic ★★ same type
- PROP1 p.Arg125Gln Likely pathogenic ★★ same type
- PROP1 p.Arg125Trp Pathogenic ★★ same type
- PROP1 p.Arg16Ter 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/prop1-p-pro94 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown