RERE p.Pro558=
c.1674C>T · rs372438002 · VCV2081503
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0483%, 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 -3.8 | GERP -4.2 |
| Overall | ||
| CADD | 1.638 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0483%
Admixed American · 29/60,016 alleles
Filtering AF
0.0345%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0299%
Overall
0.00279%
45/1,614,146 alleles · ultra-rare
exomes 39/1,461,888 · genomes 6/152,258 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0483% | 2,070 |
| African / African-American | 0.00666% | 15,006 |
| South Asian | 0.00549% | 18,217 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,508 |
| European (non-Finnish) | 0.000424% | 236,006 |
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
- RERE
- Protein
- p.Pro558=
- Coding
- c.1674C>T
- MANE Select
- NM_001042681
- dbSNP
- rs372438002
- Type
- single nucleotide variant
- Location
- chr1:8364122 (GRCh38)
- Gene constraint
- LOEUF 0.459 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 54.51 · 1 PDB
- Residue 558
- the 'disordered' region
Similar variants
- RERE p.Gln858Ter Pathogenic/Likely pathogenic ★★ same type
- RERE p.His1429Arg Likely pathogenic ★★ same type
- RERE p.His1431Gln Pathogenic/Likely pathogenic ★★ ⚠ same type
- RERE p.His1433Pro Likely pathogenic ★★ ⚠ same type
- RERE p.His1435Arg Pathogenic/Likely pathogenic ★★ same type
- RERE p.His1435Leu Likely pathogenic ★★ same type
- RERE p.Pro1049Leu Pathogenic/Likely pathogenic ★★ ⚠ same type
- RERE p.Pro1424Leu 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/rere-p-pro558 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown