Is NCOR2 p.Pro2225= (c.6675G>A) pathogenic?

NCOR2 p.Pro2225= (c.6675G>A) is classified Likely benign in NCOR2 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-02-22). Low-frequency (popmax 3.43%, eas); Associated with NCOR2-related disorder.

What condition is associated with NCOR2 p.Pro2225= (c.6675G>A)?

NCOR2 p.Pro2225= (c.6675G>A) is associated with NCOR2-related disorder (ClinVar).

How common is NCOR2 p.Pro2225= (c.6675G>A) in the general population?

NCOR2 p.Pro2225= (c.6675G>A) is low-frequency (popmax 3.43%, eas) (gnomAD).

NCOR2 p.Pro2225=

c.6675G>A · rs75362677 · VCV3041930

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

low-frequency (popmax 3.43%, eas)

Conditions

NCOR2-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.008	strongly benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -20	GERP -3.2
Overall
CADD	0.125	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 3.43% East Asian · 1,539/44,844 alleles

Filtering AF 3.29% ClinGen BA1/BS1 input FAF95, joint · FAF99 3.23%

Overall 0.108% 1,746/1,613,186 alleles · low-frequency exomes 1,564/1,460,914 · genomes 182/152,272 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	3.43%	29
Remaining individualsnot grpmax-eligible	0.219%	456
South Asian	0.0318%	3,140
Middle Eastern	0.0165%	6,056
Admixed American	0.015%	6,666
Ashkenazi Jewishnot grpmax-eligible	0.00338%	29,594
European (non-Finnish)	0.00237%	42,138
Finnishnot grpmax-eligible	0.00158%	63,330
African / African-American	0.00133%	75,030

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.Pro2225=
Coding: c.6675G>A
MANE Select: NM_006312
dbSNP: rs75362677
Type: single nucleotide variant
Location: chr12:124333210 (GRCh38)
Gene constraint: LOEUF 0.448 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 41.00 · 36 PDB
Residue 2225: 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.Pro2225Leu 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-pro2225 (accessed [today's date]).

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