Is BCOR p.Thr708= (c.2124C>T) pathogenic?

BCOR p.Thr708= (c.2124C>T) is classified Benign/Likely benign in BCOR (ClinVar, Multiple submitters, 2 submitters; last evaluated 2023-08-25). Ultra-rare (popmax 0.0686%, mid); Associated with Inborn genetic diseases.

What condition is associated with BCOR p.Thr708= (c.2124C>T)?

BCOR p.Thr708= (c.2124C>T) is associated with Inborn genetic diseases, microphthalmia, syndromic 2 (ClinVar).

How common is BCOR p.Thr708= (c.2124C>T) in the general population?

BCOR p.Thr708= (c.2124C>T) is ultra-rare (popmax 0.0686%, mid) (gnomAD).

BCOR p.Thr708=

c.2124C>T · rs749386912 · VCV695595

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0686%, mid)

Conditions

Inborn genetic diseases

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 -15	GERP -3.1
Overall
CADD	0.029	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0686% Middle Eastern · 3/4,373 alleles

Filtering AF 0.044% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0385%

Overall 0.00586% 71/1,210,787 alleles · ultra-rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0686%	1,458
South Asian	0.0598%	1,673
Admixed American	0.024%	4,175
Remaining individualsnot grpmax-eligible	0.0084%	11,902
European (non-Finnish)	0.00201%	49,744
African / African-American	0.00174%	57,369

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.Thr708=
Coding: c.2124C>T
MANE Select: NM_001123385
dbSNP: rs749386912
Type: single nucleotide variant
Location: chrX:40073222 (GRCh38)
Structure: AlphaFold pLDDT 39.82 · 5 PDB

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-thr708 (accessed [today's date]).

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