Is BCOR p.Ser209= (c.627G>A) pathogenic?

BCOR p.Ser209= (c.627G>A) is classified Likely benign in BCOR (ClinVar, Single submitter, 1 submitter; last evaluated 2021-04-16). Very rare (popmax 0.00887%, eas); Associated with microphthalmia, syndromic 2.

What condition is associated with BCOR p.Ser209= (c.627G>A)?

BCOR p.Ser209= (c.627G>A) is associated with microphthalmia, syndromic 2 (ClinVar).

How common is BCOR p.Ser209= (c.627G>A) in the general population?

BCOR p.Ser209= (c.627G>A) is very rare (popmax 0.00887%, eas) (gnomAD).

BCOR p.Ser209=

c.627G>A · rs1366096747 · VCV1572187

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00887%, eas)

Conditions

microphthalmia, syndromic 2

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 -0.49	GERP -0.83, phastCons 0.032
Overall
CADD	7.539	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00887% East Asian · 3/33,823 alleles

Filtering AF 0.0034% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00216%

Overall 0.000728% 8/1,098,151 alleles · very rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00887%	11,274
South Asian	0.00878%	11,390

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.Ser209=
Coding: c.627G>A
MANE Select: NM_001123385
dbSNP: rs1366096747
Type: single nucleotide variant
Location: chrX:40074719 (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-ser209 (accessed [today's date]).

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