Is NCOR1 p.Pro815= (c.2445C>T) pathogenic?

NCOR1 p.Pro815= (c.2445C>T) is classified Benign in NCOR1 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-04-02). Low-frequency (popmax 1.49%, afr); Associated with NCOR1-related disorder.

What condition is associated with NCOR1 p.Pro815= (c.2445C>T)?

NCOR1 p.Pro815= (c.2445C>T) is associated with NCOR1-related disorder (ClinVar).

How common is NCOR1 p.Pro815= (c.2445C>T) in the general population?

NCOR1 p.Pro815= (c.2445C>T) is low-frequency (popmax 1.49%, afr) (gnomAD).

NCOR1 p.Pro815=

c.2445C>T · rs139942816 · VCV3055775

Benign No assertion criteria

Classification

Benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

low-frequency (popmax 1.49%, afr)

Conditions

NCOR1-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP -3.8	GERP -3.6
Overall
CADD	0.42	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 1.49% African / African-American · 1,116/75,026 alleles

Filtering AF 1.41% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.39%

Overall 0.0789% 1,274/1,614,144 alleles · low-frequency exomes 631/1,461,866 · genomes 643/152,278 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	1.49%	67
Admixed American	0.0983%	1,017
Remaining individualsnot grpmax-eligible	0.0944%	1,059
Middle Eastern	0.033%	3,031
East Asian	0.029%	3,453
South Asian	0.00769%	13,010
European (non-Finnish)	0.00153%	65,557

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: NCOR1
Protein: p.Pro815=
Coding: c.2445C>T
MANE Select: NM_006311
dbSNP: rs139942816
Type: single nucleotide variant
Location: chr17:16101495 (GRCh38)
Gene constraint: LOEUF 0.292 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 41.40 · 27 PDB
Residue 815: the 'disordered' region

Full NCOR1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

NCOR1-related disorder

Similar variants

NCOR1 p.Arg1561Trp Uncertain significance ★ same condition
NCOR1 p.Arg1876Thr Uncertain significance ★ ⚠ same condition
NCOR1 p.Asp1944Val Uncertain significance ★ ⚠ same condition
NCOR1 p.Thr2243Met Uncertain significance ★ ⚠ same condition
NCOR1 p.Arg33Cys Likely pathogenic ⚠ same condition
NCOR1 p.Gly1634Arg Uncertain significance ⚠ same condition
NCOR1 p.Thr1027Ala Uncertain significance ⚠ same condition
NCOR1 p.Thr1502Ile Uncertain significance ⚠ 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/ncor1-p-pro815 (accessed [today's date]).

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