Is BCOR p.Asp37= (c.111C>T) pathogenic?

BCOR p.Asp37= (c.111C>T) is classified Benign in BCOR (ClinVar, Single submitter, 1 submitter; last evaluated 2023-05-02). Very rare (popmax 0.00526%, afr); Associated with microphthalmia, syndromic 2.

What condition is associated with BCOR p.Asp37= (c.111C>T)?

BCOR p.Asp37= (c.111C>T) is associated with microphthalmia, syndromic 2 (ClinVar).

How common is BCOR p.Asp37= (c.111C>T) in the general population?

BCOR p.Asp37= (c.111C>T) is very rare (popmax 0.00526%, afr) (gnomAD).

BCOR p.Asp37=

c.111C>T · rs142207652 · VCV2748790

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00526%, afr)

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 -0.72	GERP -0.44
Overall
CADD	4.248	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00526% African / African-American · 3/57,067 alleles

Filtering AF 0.00139% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000687%

Overall 0.00108% 13/1,203,028 alleles · very rare exomes 8/1,090,728 · genomes 5/112,300 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00526%	19,022
Finnishnot grpmax-eligible	0.00215%	46,424
Remaining individualsnot grpmax-eligible	0.00211%	47,324
European (non-Finnish)	0.0009%	111,137

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.Asp37=
Coding: c.111C>T
MANE Select: NM_001123385
dbSNP: rs142207652
Type: single nucleotide variant
Location: chrX:40076508 (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-asp37 (accessed [today's date]).

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