PROP1 p.Phe167=
c.501C>T · rs2113059884 · VCV1114057
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0166%, 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 0.73 | phastCons 1 |
| Overall | ||
| CADD | 3.589 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0166%
Middle Eastern · 1/6,010 alleles
Overall
0.000124%
2/1,613,832 alleles · ultra-rare
exomes 2/1,461,684 · genomes 0/152,148 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0166% | 6,010 |
| European (non-Finnish) | 8.47e-05% | 1,179,954 |
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.Phe167=
- Coding
- c.501C>T
- MANE Select
- NM_006261
- dbSNP
- rs2113059884
- Type
- single nucleotide variant
- Location
- chr5:177992889 (GRCh38)
- Gene constraint
- LOEUF 0.87 · pLI 0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 70.74
Similar variants
- PROP1 p.Phe167Ile Likely pathogenic ⚠ same residue
- 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
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-phe167 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown