Is NCOR2 p.Ser2432= (c.7296G>A) pathogenic?

NCOR2 p.Ser2432= (c.7296G>A) is classified Benign in NCOR2 (ClinVar, No assertion criteria, 2 submitters; last evaluated 2019-04-02). Low-frequency (popmax 1.31%, afr); Associated with NCOR2-related disorder.

What condition is associated with NCOR2 p.Ser2432= (c.7296G>A)?

NCOR2 p.Ser2432= (c.7296G>A) is associated with NCOR2-related disorder (ClinVar).

How common is NCOR2 p.Ser2432= (c.7296G>A) in the general population?

NCOR2 p.Ser2432= (c.7296G>A) is low-frequency (popmax 1.31%, afr) (gnomAD).

NCOR2 p.Ser2432=

c.7296G>A · rs187350105 · VCV3050430

Benign No assertion criteria

Classification

Benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

low-frequency (popmax 1.31%, afr)

Conditions

NCOR2-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.353	indeterminate
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -7	GERP -3.8
Overall
CADD	8.128	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 1.31% African / African-American · 962/73,300 alleles

Filtering AF 1.24% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.22%

Overall 0.0766% 1,194/1,559,662 alleles · low-frequency exomes 620/1,407,322 · genomes 574/152,340 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	1.31%	76
Admixed American	0.0902%	1,109
Remaining individualsnot grpmax-eligible	0.0893%	1,120
Middle Eastern	0.0507%	1,971
European (non-Finnish)	0.0109%	9,160
East Asian	0.0024%	41,714
South Asian	0.00117%	85,262

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.Ser2432=
Coding: c.7296G>A
MANE Select: NM_006312
dbSNP: rs187350105
Type: single nucleotide variant
Location: chr12:124326258 (GRCh38)
Gene constraint: LOEUF 0.448 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 41.00 · 36 PDB
Residue 2432: the 'disordered' region

Full NCOR2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

NCOR2-related disorder

Similar variants

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
NCOR2 p.Ala1037= 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-ser2432 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown