PROP1 p.Cys153=
c.459C>T · rs2480284690 · VCV2031366
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00167%, amr)
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 -0.76 | |
| Overall | ||
| CADD | 0.862 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00167%
Admixed American · 1/59,988 alleles
Filtering AF
0.000183%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00012%
Overall
0.000434%
7/1,613,954 alleles · very rare
exomes 7/1,461,748 · genomes 0/152,206 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00167% | 59,988 |
| European (non-Finnish) | 0.000508% | 196,665 |
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.Cys153=
- Coding
- c.459C>T
- MANE Select
- NM_006261
- dbSNP
- rs2480284690
- Type
- single nucleotide variant
- Location
- chr5:177992931 (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 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-cys153 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown