Is NCOR2 p.Pro1567= (c.4701G>A) pathogenic?

NCOR2 p.Pro1567= (c.4701G>A) is classified Likely benign in NCOR2 (ClinVar, Single submitter, 2 submitters; last evaluated 2023-03-01). Rare (popmax 0.831%, nfe).

How common is NCOR2 p.Pro1567= (c.4701G>A) in the general population?

NCOR2 p.Pro1567= (c.4701G>A) is rare (popmax 0.831%, nfe) (gnomAD).

NCOR2 p.Pro1567=

c.4701G>A · rs193097789 · VCV2643552

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

rare (popmax 0.831%, nfe)

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 -3
Overall
CADD	0.091	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.831% European (non-Finnish) · 9,112/1,097,116 alleles

Filtering AF 0.816% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.81%

Overall 0.713% 10,360/1,452,766 alleles · rare exomes 9,594/1,300,446 · genomes 766/152,320 · joint denominator

Ancestry group	Frequency	1 in
Finnishnot grpmax-eligible	1.08%	93
European (non-Finnish)grpmax	0.831%	120
Remaining individualsnot grpmax-eligible	0.556%	180
Amishnot grpmax-eligible	0.44%	228
Admixed American	0.339%	295
South Asian	0.172%	581
Middle Eastern	0.145%	689
African / African-American	0.128%	780
Ashkenazi Jewishnot grpmax-eligible	0.0132%	7,555
East Asian	0.00503%	19,895

Finnish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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.Pro1567=
Coding: c.4701G>A
MANE Select: NM_006312
dbSNP: rs193097789
Type: single nucleotide variant
Location: chr12:124344610 (GRCh38)
Gene constraint: LOEUF 0.448 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 41.00 · 36 PDB
Residue 1567: the 'disordered' region

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

Similar variants

NCOR2 p.Pro1567Gln Uncertain significance ★ ⚠ same residue
NCOR2 p.Pro1567Leu Uncertain significance ★ ⚠ 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

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-pro1567 (accessed [today's date]).

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