NCOR2 p.Ala130=
c.390G>C · rs577563958 · VCV3052008
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.237%, afr)
Conditions
1
NCOR2-related disorder
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 -4.9 | GERP -12 |
| Overall | ||
| CADD | 0.141 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.237%
African / African-American · 177/74,778 alleles
Filtering AF
0.208%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.197%
Overall
0.0122%
196/1,606,378 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.237% | 422 |
| Admixed American | 0.017% | 5,883 |
| Remaining individualsnot grpmax-eligible | 0.0129% | 7,763 |
| European (non-Finnish) | 8.5e-05% | 1,176,777 |
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.Ala130=
- Coding
- c.390G>C
- MANE Select
- NM_006312
- dbSNP
- rs577563958
- Type
- single nucleotide variant
- Location
- chr12:124483617 (GRCh38)
- Gene constraint
- LOEUF 0.448 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 41.00 · 36 PDB
- Residue 130
- the 'disordered' region
Disease context
NCOR2-related disorder
Similar variants
- NCOR2 p.Ala130Val Uncertain significance ★ ⚠ same residue
- NCOR2 p.Ala1526Thr Uncertain significance ★★ ⚠ same condition
- NCOR2 p.Arg2467Gln Uncertain significance ★★ ⚠ same condition
- NCOR2 c.1329-4G>A Benign same condition
- NCOR2 c.3242-9G>A Benign same condition
- NCOR2 c.6411+8C>T Likely benign same condition
- NCOR2 c.7364-5C>T Likely benign same condition
- NCOR2 c.-6A>C Likely benign same condition
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-ala130 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown