NCOR1 p.Pro2156=
c.6468G>A · rs147734590 · VCV722887
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.428%, afr)
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 -0.23 | GERP -0.96, phastCons 0.004 |
| Overall | ||
| CADD | 9.722 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.428%
African / African-American · 321/75,034 alleles
Filtering AF
0.389%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.374%
Overall
0.0266%
429/1,613,960 alleles · rare
exomes 216/1,461,692 · genomes 213/152,268 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.428% | 234 |
| East Asian | 0.0914% | 1,094 |
| Admixed American | 0.04% | 2,500 |
| Remaining individualsnot grpmax-eligible | 0.0288% | 3,472 |
| South Asian | 0.00329% | 30,349 |
| European (non-Finnish) | 0.00186% | 53,632 |
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.Pro2156=
- Coding
- c.6468G>A
- MANE Select
- NM_006311
- dbSNP
- rs147734590
- Type
- single nucleotide variant
- Location
- chr17:16048913 (GRCh38)
- Gene constraint
- LOEUF 0.292 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 41.40 · 27 PDB
- Residue 2156
- the 'interaction with c1d' region
Similar variants
- NCOR1 p.Pro613Leu Uncertain significance ★★ ⚠ same type
- NCOR1 p.Ala2182Thr Benign ★★ same type
- NCOR1 p.Arg2132= Benign ★★ same type
- NCOR1 p.Arg856= Likely 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
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-pro2156 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown