Is NCOR2 p.Ser1964= (c.5892C>T) pathogenic?

NCOR2 p.Ser1964= (c.5892C>T) is classified Likely benign in NCOR2 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-08-30). Rare (popmax 0.342%, eas); Associated with NCOR2-related disorder.

What condition is associated with NCOR2 p.Ser1964= (c.5892C>T)?

NCOR2 p.Ser1964= (c.5892C>T) is associated with NCOR2-related disorder (ClinVar).

How common is NCOR2 p.Ser1964= (c.5892C>T) in the general population?

NCOR2 p.Ser1964= (c.5892C>T) is rare (popmax 0.342%, eas) (gnomAD).

NCOR2 p.Ser1964=

c.5892C>T · rs376833353 · VCV3034760

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.342%, eas)

Conditions

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 -14	GERP -1.8
Overall
CADD	0.518	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.342% East Asian · 148/43,294 alleles

Filtering AF 0.297% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.28%

Overall 0.0286% 434/1,518,100 alleles · rare exomes 405/1,365,810 · genomes 29/152,290 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.342%	293
European (non-Finnish)	0.0234%	4,272
Remaining individualsnot grpmax-eligible	0.0189%	5,288
South Asian	0.00528%	18,929
Finnishnot grpmax-eligible	0.00525%	19,055
Admixed American	0.0022%	45,440
African / African-American	0.00139%	72,070

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.Ser1964=
Coding: c.5892C>T
MANE Select: NM_006312
dbSNP: rs376833353
Type: single nucleotide variant
Location: chr12:124336976 (GRCh38)
Gene constraint: LOEUF 0.448 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 41.00 · 36 PDB
Residue 1964: 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-ser1964 (accessed [today's date]).

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