NCOR1 p.Arg856=
c.2568A>G · rs201420293 · VCV2647505
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0656%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.02 | GERP -2, phastCons 0.009 |
| Overall | ||
| CADD | 4.748 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0656%
European (non-Finnish) · 774/1,180,054 alleles
Filtering AF
0.0618%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0602%
Overall
0.0495%
799/1,614,126 alleles · ultra-rare
exomes 769/1,461,894 · genomes 30/152,232 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0656% | 1,525 |
| Remaining individualsnot grpmax-eligible | 0.0256% | 3,906 |
| African / African-American | 0.0107% | 9,367 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,608 |
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
- NCOR1
- Protein
- p.Arg856=
- Coding
- c.2568A>G
- MANE Select
- NM_006311
- dbSNP
- rs201420293
- Type
- single nucleotide variant
- Location
- chr17:16101372 (GRCh38)
- Gene constraint
- LOEUF 0.292 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 41.40 · 27 PDB
- Residue 856
- the 'disordered' region
Similar variants
- NCOR1 p.Pro613Leu Uncertain significance ★★ ⚠ same type
- NCOR1 p.Ala2182Thr Benign ★★ same type
- NCOR1 p.Arg2132= Benign ★★ same type
- NCOR1 p.Gln1621= Benign ★★ same type
- NCOR1 p.Gly1348= Benign ★★ same type
- NCOR1 p.Gly838Ala Benign/Likely benign ★★ same type
- NCOR1 p.Ile2055= Benign/Likely benign ★★ same type
- NCOR1 p.Leu1406Phe Benign ★★ ⚠ 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/ncor1-p-arg856 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown