RCOR1 p.Pro288=
c.864C>T · rs753884913 · VCV2865306
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.418%, 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 -0.47 | GERP -3, phastCons 0.025 |
| Overall | ||
| CADD | 3.714 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.418%
Middle Eastern · 25/5,988 alleles
Filtering AF
0.29%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.248%
Overall
0.00537%
86/1,601,568 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.418% | 240 |
| Remaining individualsnot grpmax-eligible | 0.0178% | 5,626 |
| Admixed American | 0.00856% | 11,689 |
| European (non-Finnish) | 0.0035% | 28,600 |
| African / African-American | 0.00269% | 37,200 |
| East Asian | 0.00224% | 44,736 |
| South Asian | 0.00111% | 89,758 |
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
- RCOR1
- Protein
- p.Pro288=
- Coding
- c.864C>T
- MANE Select
- NM_015156
- dbSNP
- rs753884913
- Type
- single nucleotide variant
- Location
- chr14:102714428 (GRCh38)
- Gene constraint
- LOEUF 0.674 · pLI 0.47 (gnomAD)
- Structure
- AlphaFold pLDDT 70.32 · 103 PDB
- Residue 288
- the 'disordered' region
Similar variants
- RCOR1 c.498+9A>G Benign ★★ same type
- RCOR1 p.Ile355= Benign ★★ same type
- RCOR1 p.Ser31= Likely benign ★★ same type
- RCOR1 p.Thr189= Benign ★★ same type
- RCOR1 c.1189+6G>C Uncertain significance ★ same type
- RCOR1 p.Ala147Thr Uncertain significance ★ ⚠ same type
- RCOR1 p.Ala21Val Uncertain significance ★ ⚠ same type
- RCOR1 p.Ala22Thr Uncertain significance ★ ⚠ 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/rcor1-p-pro288 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown