Is BCOR p.Asp1668del (c.5003_5005del) pathogenic?

BCOR p.Asp1668del (c.50035005del) is classified Uncertain significance in BCOR (ClinVar, Single submitter, 1 submitter; last evaluated 2021-11-25). Absent from gnomAD; Associated with microphthalmia, syndromic 2.

What condition is associated with BCOR p.Asp1668del (c.5003_5005del)?

BCOR p.Asp1668del (c.5003_5005del) is associated with microphthalmia, syndromic 2 (ClinVar).

How common is BCOR p.Asp1668del (c.5003_5005del) in the general population?

BCOR p.Asp1668del (c.5003_5005del) is absent from gnomAD (gnomAD).

BCOR p.Asp1668del

c.5003_5005del · rs2146829974 · VCV1394962

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

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 · substitutions only
Constraint at this position
Conservation	phyloP 8.1	GERP 1.4, phastCons 1

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: BCOR
Protein: p.Asp1668del
Coding: c.5003_5005del
MANE Select: NM_001123385
dbSNP: rs2146829974
Type: Deletion
Location: chrX:40052372 (GRCh38)
Structure: AlphaFold pLDDT 39.82 · 5 PDB
Residue 1668: the 'necessary and sufficient for interaction with pcgf1' region; an α-helix

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.Asp1668Glu Uncertain significance ★ ⚠ same residue
BCOR p.Val379fs Pathogenic ★★ same condition
BCOR p.Val797fs Pathogenic/Likely pathogenic ★★ same condition
BCOR c.2997+1_2997+25del Likely pathogenic ★ same condition
BCOR p.Arg1469fs Pathogenic ★ same condition
BCOR p.Asp1006fs Likely pathogenic ★ same condition
BCOR p.Asp1155fs Pathogenic ★ same condition
BCOR p.Asp328fs Pathogenic ★ 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-asp1668del (accessed [today's date]).

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