Is BCOR p.Thr1560= (c.4680G>A) pathogenic?

BCOR p.Thr1560= (c.4680G>A) is classified Benign/Likely benign in BCOR (ClinVar, Multiple submitters, 4 submitters; last evaluated 2025-08-10). Rare (popmax 0.426%, afr); Associated with microphthalmia, syndromic 1.

What condition is associated with BCOR p.Thr1560= (c.4680G>A)?

BCOR p.Thr1560= (c.4680G>A) is associated with microphthalmia, syndromic 1, microphthalmia, syndromic 2 (ClinVar).

How common is BCOR p.Thr1560= (c.4680G>A) in the general population?

BCOR p.Thr1560= (c.4680G>A) is rare (popmax 0.426%, afr) (gnomAD).

BCOR p.Thr1560=

c.4680G>A · rs146007249 · VCV434506

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

rare (popmax 0.426%, afr)

Conditions

microphthalmia, syndromic 1

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.025	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -13	GERP -3.5
Overall
CADD	2.601	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.426% African / African-American · 244/57,312 alleles

Filtering AF 0.382% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.365%

Overall 0.028% 338/1,208,856 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.426%	235
Remaining individualsnot grpmax-eligible	0.0357%	2,798
Admixed American	0.0262%	3,816
European (non-Finnish)	0.00682%	14,655
South Asian	0.00528%	18,934
East Asian	0.00296%	33,771

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.Thr1560=
Coding: c.4680G>A
MANE Select: NM_001123385
dbSNP: rs146007249
Type: single nucleotide variant
Location: chrX:40055429 (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 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: microphthalmia, syndromic 2

Similar variants

BCOR p.Thr1560Met Uncertain significance ★ ⚠ same residue
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

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-thr1560 (accessed [today's date]).

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