Is BCOR p.Val237= (c.711C>T) pathogenic?

BCOR p.Val237= (c.711C>T) is classified Conflicting classifications of pathogenicity in BCOR (ClinVar, Conflicting submitters, 2 submitters; last evaluated 2019-07-14). Rare (popmax 0.545%, eas); Associated with microphthalmia, syndromic 2.

What condition is associated with BCOR p.Val237= (c.711C>T)?

BCOR p.Val237= (c.711C>T) is associated with microphthalmia, syndromic 2 (ClinVar).

How common is BCOR p.Val237= (c.711C>T) in the general population?

BCOR p.Val237= (c.711C>T) is rare (popmax 0.545%, eas) (gnomAD).

BCOR p.Val237=

c.711C>T · rs727503827 · VCV166751

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

rare (popmax 0.545%, 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 5.1	GERP 0.36, phastCons 1
Overall
CADD	9.019	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.545% East Asian · 184/33,767 alleles

Filtering AF 0.481% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.456%

Overall 0.0153% 185/1,210,826 alleles · rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.545%	184
Remaining individualsnot grpmax-eligible	0.0021%	47,620

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.Val237=
Coding: c.711C>T
MANE Select: NM_001123385
dbSNP: rs727503827
Type: single nucleotide variant
Location: chrX:40074635 (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-val237 (accessed [today's date]).

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