Is BCOR p.Ala564= (c.1692A>G) pathogenic?

BCOR p.Ala564= (c.1692A>G) is classified Benign in BCOR (ClinVar, Multiple submitters, 11 submitters; last evaluated 2026-02-03). Common (popmax 80.9%, afr) — too common for a highly-penetrant pathogenic allele; Associated with Inborn genetic diseases.

What condition is associated with BCOR p.Ala564= (c.1692A>G)?

BCOR p.Ala564= (c.1692A>G) is associated with Inborn genetic diseases, microphthalmia, syndromic 2 (ClinVar).

BCOR p.Ala564=

Q: How common is BCOR p.Ala564= (c.1692A>G) in the general population?

BCOR p.Ala564= (c.1692A>G) is common (popmax 80.9%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.1692A>G · rs6520618 · VCV95766

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 11 submitters

gnomAD v4.1

Common

common (popmax 80.9%, afr) — too common for a highly-penetrant pathogenic allele

Conditions

Inborn genetic diseases

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 -13	GERP -3.2
Overall
CADD	0.012	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 80.9% African / African-American · 46,346/57,254 alleles

Filtering AF 80.3% ClinGen BA1/BS1 input FAF95, joint · FAF99 80.1%

Overall 17.4% 211,023/1,210,479 alleles · common exomes 172,780/1,098,058 · genomes 38,243/112,421 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	80.9%	1
East Asian	65.7%	2
South Asian	40%	2
Amishnot grpmax-eligible	32.7%	3
Remaining individualsnot grpmax-eligible	22.4%	4
Middle Eastern	21.8%	5
Admixed American	20.9%	5
Ashkenazi Jewishnot grpmax-eligible	20.1%	5
Finnishnot grpmax-eligible	11.5%	9
European (non-Finnish)	9.89%	10

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.Ala564=
Coding: c.1692A>G
MANE Select: NM_001123385
dbSNP: rs6520618
Type: single nucleotide variant
Location: chrX:40073654 (GRCh38)
Structure: AlphaFold pLDDT 39.82 · 5 PDB
Residue 564: the 'disordered' region

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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: microphthalmia, syndromic 2

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.Arg810Ter Pathogenic ★★ same condition
BCOR p.Arg976Ter Pathogenic ★★ same condition
BCOR p.Ala1262Ser Uncertain significance ★★ ⚠ same condition
BCOR p.Ala1307Pro 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-ala564 (accessed [today's date]).

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