NCOR2 p.Pro66=
c.198C>T · rs186081475 · VCV2643565
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.771%, 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 -2.5 | GERP -1.2 |
| Overall | ||
| CADD | 5.722 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.771%
Admixed American · 461/59,828 alleles
Filtering AF
0.712%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.689%
Overall
0.619%
9,973/1,612,312 alleles · rare
exomes 9,082/1,459,936 · genomes 891/152,376 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.771% | 130 |
| European (non-Finnish) | 0.688% | 145 |
| Ashkenazi Jewishnot grpmax-eligible | 0.643% | 155 |
| Remaining individualsnot grpmax-eligible | 0.59% | 170 |
| Middle Eastern | 0.579% | 173 |
| South Asian | 0.539% | 185 |
| Finnishnot grpmax-eligible | 0.352% | 284 |
| African / African-American | 0.121% | 824 |
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
- NCOR2
- Protein
- p.Pro66=
- Coding
- c.198C>T
- MANE Select
- NM_006312
- dbSNP
- rs186081475
- Type
- single nucleotide variant
- Location
- chr12:124486476 (GRCh38)
- Gene constraint
- LOEUF 0.448 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 41.00 · 36 PDB
Similar variants
- NCOR2 p.Ala1526Thr Uncertain significance ★★ ⚠ same type
- NCOR2 p.Arg2174Cys Uncertain significance ★★ ⚠ same type
- NCOR2 p.Arg2467Gln Uncertain significance ★★ ⚠ same type
- NCOR2 p.Gly1520Ser Uncertain significance ★★ ⚠ same type
- NCOR2 c.3986-17C>T Benign ★★ same type
- NCOR2 c.6265+16T>C Benign ★★ same type
- NCOR2 c.-36G>C Benign ★★ same type
- NCOR2 p.Ala1699Thr 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/ncor2-p-pro66 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown