Is BCOR p.Asn1461= (c.4383C>T) pathogenic?

BCOR p.Asn1461= (c.4383C>T) is classified Benign/Likely benign in BCOR (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-08-18). Ultra-rare (popmax 0.0463%, mid); Associated with microphthalmia, syndromic 2.

What condition is associated with BCOR p.Asn1461= (c.4383C>T)?

BCOR p.Asn1461= (c.4383C>T) is associated with microphthalmia, syndromic 2 (ClinVar).

How common is BCOR p.Asn1461= (c.4383C>T) in the general population?

BCOR p.Asn1461= (c.4383C>T) is ultra-rare (popmax 0.0463%, mid) (gnomAD).

BCOR p.Asn1461=

c.4383C>T · rs189731022 · VCV696948

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0463%, mid)

Conditions

microphthalmia, syndromic 2

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.382	indeterminate
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -4.6	GERP -3.5
Overall
CADD	0.138	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0463% Middle Eastern · 2/4,324 alleles

Filtering AF 0.0198% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0188%

Overall 0.0184% 222/1,205,230 alleles · ultra-rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0463%	2,162
European (non-Finnish)	0.0224%	4,465
African / African-American	0.0176%	5,698
Remaining individualsnot grpmax-eligible	0.0148%	6,776
South Asian	0.00359%	27,882
Admixed American	0.0022%	45,373

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: BCOR
Protein: p.Asn1461=
Coding: c.4383C>T
MANE Select: NM_001123385
dbSNP: rs189731022
Type: single nucleotide variant
Location: chrX:40062184 (GRCh38)
Structure: AlphaFold pLDDT 39.82 · 5 PDB

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

Disease context

microphthalmia, syndromic 2 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

BCOR p.Arg1163Ter Pathogenic ★★ same condition
BCOR p.Arg1217Ter Pathogenic ★★ same condition
BCOR p.Arg1514Ter Pathogenic ★★ same condition
BCOR p.Arg342Ter Pathogenic ★★ same condition
BCOR p.Arg976Ter Pathogenic ★★ same condition
BCOR p.Ala1262Ser Uncertain significance ★★ ⚠ same condition
BCOR p.Ala1307Pro Uncertain significance ★★ ⚠ same condition
BCOR p.Ala165Pro 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/bcor-p-asn1461 (accessed [today's date]).

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