NCOR2 p.Ser1518=
c.4554G>A · rs551690182 · VCV2643553
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.113%, sas)
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 -20 | GERP -2.8 |
| Overall | ||
| CADD | 0.141 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.113%
South Asian · 95/84,060 alleles
Filtering AF
0.0946%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0878%
Overall
0.00859%
133/1,548,740 alleles · rare
exomes 117/1,396,384 · genomes 16/152,356 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.113% | 885 |
| Middle Eastern | 0.0335% | 2,985 |
| Remaining individualsnot grpmax-eligible | 0.02% | 5,003 |
| African / African-American | 0.00683% | 14,636 |
| Admixed American | 0.00391% | 25,588 |
| Finnishnot grpmax-eligible | 0.00347% | 28,830 |
| European (non-Finnish) | 0.00131% | 76,416 |
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.Ser1518=
- Coding
- c.4554G>A
- MANE Select
- NM_006312
- dbSNP
- rs551690182
- Type
- single nucleotide variant
- Location
- chr12:124344757 (GRCh38)
- Gene constraint
- LOEUF 0.448 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 41.00 · 36 PDB
- Residue 1518
- the 'disordered' region
Similar variants
- NCOR2 p.Ser1518Thr Benign same residue
- 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
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-ser1518 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown