RERE p.Pro1015=
c.3045G>C · rs1052664473 · VCV3250579
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.64%, nfe)
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 -1.2 | GERP -3.5 |
| Overall | ||
| CADD | 0.116 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.64%
European (non-Finnish) · 411/64,212 alleles
Filtering AF
0.589%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.569%
Overall
0.513%
548/106,918 alleles · rare
exomes 518/72,200 · genomes 30/34,718 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.64% | 156 |
| Finnishnot grpmax-eligible | 0.608% | 164 |
| Middle Eastern | 0.588% | 170 |
| South Asian | 0.482% | 207 |
| Remaining individualsnot grpmax-eligible | 0.478% | 209 |
| Ashkenazi Jewishnot grpmax-eligible | 0.319% | 314 |
| African / African-American | 0.136% | 736 |
| East Asian | 0.127% | 786 |
| Admixed American | 0.103% | 975 |
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.Pro1015=
- Coding
- c.3045G>C
- MANE Select
- NM_001042681
- dbSNP
- rs1052664473
- Type
- single nucleotide variant
- Location
- chr1:8360462 (GRCh38)
- Gene constraint
- LOEUF 0.459 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 54.51 · 1 PDB
- Residue 1015
- the 'disordered' region
Similar variants
- RERE p.Pro1015Leu Uncertain significance ★ ⚠ same residue
- RERE p.Pro1015Ser Uncertain significance ★ ⚠ same residue
- 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
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-pro1015 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown